text:
Quantitative analysis permits the isolation of invariant relations in the study of behavior. The parameters of these relations can serve as higher-order dependent variables in more extensive analyses. These points are illustrated by reference to quantitative descriptions of performance maintained by concurrent schedules, multiple schedules, and signal-detection procedures. Such quantitative descriptions of empirical data may be derived from mathematical theories, which in turn can lead to novel empirical analyses so long as their terms refer to behavioral and environmental events. Thus, quantitative analysis is an integral aspect of the experimental analysis of behavior.
Nevin, John A.
Increasing the Accuracy of MODIS Snow Product using Quantitative Restoration for MODIS Band 6 on Aqua
NASA Astrophysics Data System (ADS)
A common problem in satellite imagery is striping and scan line dropout. While transmission errors are sometimes the cause of this problem, a more frequent source is damage to individual detectors, or to the electronics that record the response of the detectors. Launch, deployment into the harsh environment of space, particle bombardment, radiation, and space dust can result in detector damage at any point of an imager's life cycle. There are many examples of imagers which suffer from periodic line drop. Classical examples include Landsat 4 and 5. More recent examples include the 1.6 micron (Band 6) in MODIS on Aqua and WV 6.2 band on SEVIRI. To use standard image processing operations and off the shelf software, the missing data must be first estimated in some principled way. End users may have little or no knowledge of how to do that. It is important to note that many end users will often work with partial data, selected bands or regions of interest. The damaged bands create uncertainty in the reliability of the results of prediction algorithms that rely on that band. For example, the calculation of the NASA snow mask relies prominently on the Band 6 measurement in determining the likelihood of snow cover on the ground at the location of each pixel in the image. The current NASA-utilized solution to this problem is to use 2.1 micron (Band 7) measurements from MODIS on Aqua with an appropriately-adjusted algorithm. In response to the Band 6 problem, our group has developed an algorithm to recreate the missing Band 6 data from reliable data in the other 500m bands using quantitative restoration techniques. Our algorithm uses values in a spectral/spatial neighborhood of the pixel to be estimated, and proposes a value based on training data from the uncorrupted pixels. Due to the non-parametric nature of the estimator, we avoid the blurring inherent spatial interpolation, which has implicit smoothness priors. Our preliminary work shows this approach not only reduces the RMSE but restores the correct gradient information as well. We have shown that using all the neighboring channels we are able to quantitatively estimate the value at dead or noisy detectors applied to the MODIS band 6 case. We have performed an initial evaluation using MODIS Terra data, to estimate the potential benefit to the Aqua snow product. Since the corresponding band 6 of the MODIS/Terra has no such problem, it makes it possible to evaluate the algorithm by simulating the band 6 MODIS/Aqua damage on MODIS/Terra. Our tests demonstrate that NASA's snow product applied to our restored band 6, better matches the true band 6 snow product than the currently used band 7 proxy. We will present the evaluations based on several standard performance metrics that demonstrate that the use of the original NASA algorithm with the restored Band 6 data generates a more reliable snow mask than the modified algorithm with Band 7 data. In particular, the restored Band 6 data is much more reliable under certain conditions where the Band 7 algorithm tends to run into problems, including the very important border areas between snowy regions and snow-free regions, and areas where tree cover makes determinations of snow on the ground difficult.
Bonev, G.; Gladkova, I.; Grossberg, M.
Terra and Aqua MODIS calibration algorithms and uncertainty analysis
NASA Astrophysics Data System (ADS)
NASA's Earth Observing System (EOS) Terra spacecraft was launched in December 1999 and the Aqua spacecraft in May 2002. The Moderate Resolution Imaging Spectroradiometer (MODIS) is one of the key instruments for NASA's EOS missions, currently operated on both the Terra and Aqua spacecrafts. Together they have made continuous global observations for more than 8 years and led to many applications and studies for the Earth's system of land, oceans, and atmosphere. Compared to its heritage sensors, the MODIS was designed with more stringent requirements on the sensor's calibration accuracy and data product quality. Because of this it is equipped with a set of on-board calibrators (OBCs), including a solar diffuser (SD) and a solar diffuser stability monitor (SDSM) for the reflective solar bands (RSB) calibration and a blackbody (BB) for the thermal emissive bands (TEB) calibration. In addition to the sensor's intrinsic design characteristics, the quality of MODIS data products depends on the quality of its on-orbit calibration and characterization and on its on-orbit performance. The primary objective of this paper is to provide an overview of MODIS on-orbit radiometric calibration approaches and a summary of the calibration uncertainties for both RSB and TEB (Terra and Aqua). This paper provides an update to our previous reports with considerations based on each sensor's characteristics identified pre-launch, measured and validated on-orbit. It also serves as a useful reference for the users of MODIS data products.
Xiong, Xiaoxiong; Sun, Junqiang; Wu, Aisheng; Chiang, Kwo-Fu; Esposito, Joe; Barnes, William
Quantitative analysis of estrogen receptor heterogeneity in breast cancer.
Immunohistochemical analyses (IHC) of biomarkers are extensively used for tumor characterization and as prognostic and predictive measures. The current standard of single slide analysis assumes that one 5 microM section is representative of the entire tumor. We used our automated image analysis technology (AQUA) using a modified IHC technique with fluorophores to compare estrogen receptor (ER) expression in multiple blocks/slides from cases of primary breast cancer with the objective of quantifying tumor heterogeneity within sections and between blocks. To normalize our ER scores and allow slide-to-slide comparisons, 0.6 microm histospots of representative breast cancer cases with known ER scores were assembled into a 'gold standard array' (GSA) and placed adjacently to each whole section. Overall, there was excellent correlation between AQUA scores and the pathologist's scores and reproducibility of GSA scores (mean linear regression R value 0.8903). Twenty-nine slides from 11 surgical cases were then analyzed totaling over 2000 AQUA images. Using standard binary assignments of AQUA (>10) and pathologist's (>10%) scores as being positive, there was fair concordancy between AQUA and pathologist scores (73%) and between slides from different blocks from the same cases (75%). However using continuous AQUA scores, agreement between AQUA and pathologist was far lower and between slides from different blocks from the same cases only 19%. Within individual slides there was also significant heterogeneity in a scattered pattern, most notably for slides with the highest AQUA scores. In sum, using a quantitative measure of ER expression, significant block-to-block heterogeneity was found in 81% of cases. These results most likely reflect both laboratory-based variability due to lack of standardization of immunohistochemistry and true biological heterogeneity. It is also likely to be dependent on the biomarker analyzed and suggests further studies should be carried out to determine how these findings may affect clinical decision-making processes. PMID:17334408
Chung, Gina G; Zerkowski, Maciej P; Ghosh, Sriparna; Camp, Robert L; Rimm, David L
Analysis of leaf area index products from combination of MODIS Terra and Aqua data
A prototype product suite, containing the Terra 8-day, Aqua 8-day, Terra�Aqua combined 8- and 4-day products, was generated as part of testing for the next version (Collection 5) of the MODerate resolution Imaging Spectroradiometer (MODIS) leaf area index (LAI) products. These products were analyzed for consistency between Terra and Aqua retrievals over the following data subsets in North America: single
W. Yang; N. V. Shabanov; D. Huang; W. Wanga; R. E. Dickinson; R. R. Nemani; Y. Knyazikhin; R. B. Myneni
Multivariate Quantitative Chemical Analysis
NASA Technical Reports Server (NTRS)
Technique of multivariate quantitative chemical analysis devised for use in determining relative proportions of two components mixed and sprayed together onto object to form thermally insulating foam. Potentially adaptable to other materials, especially in process-monitoring applications in which necessary to know and control critical properties of products via quantitative chemical analyses of products. In addition to chemical composition, also used to determine such physical properties as densities and strengths.
Kinchen, David G.; Capezza, Mary
Quantitative Hydrocarbon Surface Analysis
NASA Technical Reports Server (NTRS)
The elimination of ozone depleting substances, such as carbon tetrachloride, has resulted in the use of new analytical techniques for cleanliness verification and contamination sampling. The last remaining application at Rocketdyne which required a replacement technique was the quantitative analysis of hydrocarbons by infrared spectrometry. This application, which previously utilized carbon tetrachloride, was successfully modified using the SOC-400, a compact portable FTIR manufactured by Surface Optics Corporation. This instrument can quantitatively measure and identify hydrocarbons from solvent flush of hardware as well as directly analyze the surface of metallic components without the use of ozone depleting chemicals. Several sampling accessories are utilized to perform analysis for various applications.
Douglas, Vonnie M.
Analysis of the tropical tropopause layer using the Nonhydrostatic Icosahedral Atmospheric Model (NICAM): Aqua planet experiments
The dynamical characteristics of the tropical tropopause layer (TTL) are investigated using the Nonhydrostatic Icosahedral Atmospheric Model (NICAM) run on the Earth Simulator under an aqua planet condition. Two experiments are performed: one with a 3.5 km horizontal spacing and a three-dimensional snapshot output and another with a 7 km horizontal spacing and 3-hourly averages for 1 month. The number
H. Kubokawa; M. Fujiwara; T. Nasuno; M. Satoh
Quantitative cytokinetic analysis reviewed
The importance of mathematical analysis in the field of cell kinetics is increasing as new experimental tools make apparent the complexity of the cytokinetic behavior of all populations. Intuitive or casual interpretation of such complex behavior is becoming increasingly difficult. Thus future cytokinetic understanding will almost certainly come from mathematical analysis of careful experiments and will depend heavily on the degree to which biologists and biomathematicians can work together to develop mathematical analysis that are biologically reasonable.
Gray, J.W.
Quantitative intracerebral brain hemorrhage analysis
NASA Astrophysics Data System (ADS)
In this paper a system for 3-D quantitative analysis of human spontaneous intracerebral brain hemorrhage (ICH) is described. The purpose of the developed system is to perform quantitative 3-D measurements of the parameters of ICH region and from computed tomography (CT) images. The measured parameter in this phase of the system development is volume of the hemorrhage region. The goal of the project is to measure parameters for a large number of patients having ICH and to correlate measured parameters to patient morbidity and mortality.
Loncaric, Sven; Dhawan, Atam P.; Cosic, Dubravko; Kovacevic, Domagoj; Broderick, Joseph; Brott, Thomas
Quantitative analysis using chromatographic techniques
The book is divided into nine contributed chapters. Chapter 1 is an elementary introduction to the concepts of the chromatographic process. Chapter 2 is a brief discussion of the detectors used in liquid chromatography; many similar and more comprehensive reviews exist. Quantitative measurements in liquid chromatography are discussed in Chapter 3 with examples taken from the author's work. The most popular detectors used in gas chromatography are reviewed in Chapter 4, which is followed by a treatment of quantitative analysis with gas chromatography (Chapter 5). A good portion of Chapter 6 dealing with quantitative thin-layer chromatography is taken from an earlier book by one of the authors, but the discussion of errors is new and more complete than those in Chapter 3 and 5. Chapter 7 deals with the application of quantitative chromatographic methods to the analysis of pharmaceuticals. The desiderata of automated analytical methods are discussed in Chapter 8; it concludes with a discussion of the use of robots for the preparation of samples and the loading of them into otherwise fully automated chromatographic systems. In Chapter 9 an introduction is given to the complex matter of extracting information from the shapes of peaks generated by liquid chromatography.
Katz, E.
Improved centroid moment tensor analyses in the NIED AQUA (Accurate and QUick Analysis system for source parameters)
NASA Astrophysics Data System (ADS)
The rapid determination of hypocentral parameters and their transmission to the public are valuable components of disaster mitigation. We have operated an automatic system for this purpose�termed the Accurate and QUick Analysis system for source parameters (AQUA)�since 2005 (Matsumura et al., 2006). In this system, the initial hypocenter, the moment tensor (MT), and the centroid moment tensor (CMT) solutions are automatically determined and posted on the NIED Hi-net Web site (www.hinet.bosai.go.jp). This paper describes improvements made to the AQUA to overcome limitations that became apparent after the 2011 Tohoku Earthquake (05:46:17, March 11, 2011 in UTC). The improvements included the processing of NIED F-net velocity-type strong motion records, because NIED F-net broadband seismographs are saturated for great earthquakes such as the 2011 Tohoku Earthquake. These velocity-type strong motion seismographs provide unsaturated records not only for the 2011 Tohoku Earthquake, but also for recording stations located close to the epicenters of M>7 earthquakes. We used 0.005-0.020 Hz records for M>7.5 earthquakes, in contrast to the 0.01-0.05 Hz records employed in the original system. The initial hypocenters determined based on arrival times picked by using seismograms recorded by NIED Hi-net stations can have large errors in terms of magnitude and hypocenter location, especially for great earthquakes or earthquakes located far from the onland Hi-net network. The size of the 2011 Tohoku Earthquake was initially underestimated in the AQUA to be around M5 at the initial stage of rupture. Numerous aftershocks occurred at the outer rise east of the Japan trench, where a great earthquake is anticipated to occur. Hence, we modified the system to repeat the MT analyses assuming a larger size, for all earthquakes for which the magnitude was initially underestimated. We also broadened the search range of centroid depth for earthquakes located far from the onland Hi-net network. After implementing the above improvements, the CMT solution for the 2011 Tohoku Earthquake was successfully determined with a moment magnitude (Mw) of 8.6 (9.04 � 10^21 Nm). The focal mechanisms and centroid depths of the 2011 Tohoku Earthquake and M>7 aftershocks, as obtained using the improved system, are in agreement with those from the GlobalCMT. The sizes of these earthquakes are also consistent with those of GlobalCMT, with differences of less than Mw 0.1 except for the mainshock (Mw9.1, 5.31 � 10^22 Nm, GlobalCMT). This discrepancy may indicate that the bandwidth used in the analysis is insufficient for an earthquake of this size. To address this shortcoming, we used 0.0025-0.0100 Hz records and obtained a magnitude of Mw8.9 (3.35 � 10^22 Nm). This result is consistent with the GlobalCMT and other results (e.g., Mw 9.0, 3.43 � 10^22 Nm reported by Ozawa et al., 2011; Mw9.0, 4.42 � 10^22 Nm reported by Suzuki et al., 2011). Using the improved system, the CMT analysis for the 2011 Tohoku Earthquake is estimated to be completed within 12 minutes of the origin time.
Kimura, H.; Asano, Y.; Matsumoto, T.
Validity in quantitative content analysis
Over the past 15 years, educational technologists have been dabbling with a research technique known as quantitative content\\u000a analysis (QCA). Although it is characterized as a systematic and objective procedure for describing communication, readers\\u000a find insufficient evidence of either quality in published reports. In this paper, it is argued that QCA should be conceived\\u000a of as a form of testing
Liam Rourke; Terry Anderson
A quantitative fitness analysis workflow.
Quantitative Fitness Analysis (QFA) is an experimental and computational workflow for comparing fitnesses of microbial cultures grown in parallel(1,2,3,4). QFA can be applied to focused observations of single cultures but is most useful for genome-wide genetic interaction or drug screens investigating up to thousands of independent cultures. The central experimental method is the inoculation of independent, dilute liquid microbial cultures onto solid agar plates which are incubated and regularly photographed. Photographs from each time-point are analyzed, producing quantitative cell density estimates, which are used to construct growth curves, allowing quantitative fitness measures to be derived. Culture fitnesses can be compared to quantify and rank genetic interaction strengths or drug sensitivities. The effect on culture fitness of any treatments added into substrate agar (e.g. small molecules, antibiotics or nutrients) or applied to plates externally (e.g. UV irradiation, temperature) can be quantified by QFA. The QFA workflow produces growth rate estimates analogous to those obtained by spectrophotometric measurement of parallel liquid cultures in 96-well or 200-well plate readers. Importantly, QFA has significantly higher throughput compared with such methods. QFA cultures grow on a solid agar surface and are therefore well aerated during growth without the need for stirring or shaking. QFA throughput is not as high as that of some Synthetic Genetic Array (SGA) screening methods(5,6). However, since QFA cultures are heavily diluted before being inoculated onto agar, QFA can capture more complete growth curves, including exponential and saturation phases(3). For example, growth curve observations allow culture doubling times to be estimated directly with high precision, as discussed previously(1). Here we present a specific QFA protocol applied to thousands of S. cerevisiae cultures which are automatically handled by robots during inoculation, incubation and imaging. Any of these automated steps can be replaced by an equivalent, manual procedure, with an associated reduction in throughput, and we also present a lower throughput manual protocol. The same QFA software tools can be applied to images captured in either workflow. We have extensive experience applying QFA to cultures of the budding yeast S. cerevisiae but we expect that QFA will prove equally useful for examining cultures of the fission yeast S. pombe and bacterial cultures. PMID:22907268
Banks, A P; Lawless, C; Lydall, D A
Quantitative Analysis of Glaciated Landscapes
NASA Astrophysics Data System (ADS)
The evolution of glaciated mountains is at the heart of the debate over Late Cenozoic linkages between climate and tectonics. Traditionally, the development of high summit elevations is attributed to tectonic processes. However, much of the high elevation of the Transantarctic Mountains can be attributed solely to uplift in response to glacial erosion (Stern et al., 2005). The Transantarctic Mountains (TAM) provide an unparalleled opportunity to study glacial erosion. The mountain range has experienced glacial conditions since Oligocene time. In the higher and dryer regions of the TAM there is only a thin veneer of ice and snow draping the topography. In these regions landforms that were shaped during earlier climatic conditions are preserved. In fact, both glacial and fluvial landforms dating as far back as 18 Ma are preserved locally. In addition, the TAM are ideal for studying glacial erosion since the range has experienced minimal tectonic uplift since late Oligocene time, thus isolating the erosion signal from any tectonic signal. With the advent of digital data sets and GIS methodologies, quantitative analysis can identify key aspects of glaciated landscape morphology, and thus develop powerful analytical techniques for objective study of glaciation. Inspection of USGS topographic maps of the TAM reveals that mountain tops display an extreme range of glacial modification. For example, in the Mt. Rabot region (83�-84� S), mountain peaks are strongly affected by glaciation; cirque development is advanced with cirque diameters on the range of several kilometers, and cirque confluence has resulted in the formation of ``knife-edge'' ar�tes up to 10 km long. In contrast, in the Mt. Murchison area (73�-74� S) cirque development is youthful, and there is minimal development of ar�tes. Preliminary work indicates that analysis of DEM's and contour lines can be used to distinguish degree of glaciation. In particular, slope, curvature, and power spectrum analysis reveal characteristics that capture the development of cirques and ar�tes.
Huerta, A. D.
Aqua Education and Public Outreach
NASA Astrophysics Data System (ADS)
NASA's Aqua satellite was launched on May 4, 2002, with six instruments designed to collect data about the Earth's atmosphere, biosphere, hydrosphere, and cryosphere. Since the late 1990s, the Aqua mission has involved considerable education and public outreach (EPO) activities, including printed products, formal education, an engineering competition, webcasts, and high-profile multimedia efforts. The printed products include Aqua and instrument brochures, an Aqua lithograph, Aqua trading cards, NASA Fact Sheets on Aqua, the water cycle, and weather forecasting, and an Aqua science writers' guide. On-going formal education efforts include the Students' Cloud Observations On-Line (S'COOL) Project, the MY NASA DATA Project, the Earth System Science Education Alliance, and, in partnership with university professors, undergraduate student research modules. Each of these projects incorporates Aqua data into its inquiry-based framework. Additionally, high school and undergraduate students have participated in summer internship programs. An earlier formal education activity was the Aqua Engineering Competition, which was a high school program sponsored by the NASA Goddard Space Flight Center, Morgan State University, and the Baltimore Museum of Industry. The competition began with the posting of a Round 1 Aqua-related engineering problem in December 2002 and concluded in April 2003 with a final round of competition among the five finalist teams. The Aqua EPO efforts have also included a wide range of multimedia products. Prior to launch, the Aqua team worked closely with the Special Projects Initiative (SPI) Office to produce a series of live webcasts on Aqua science and the Cool Science website aqua.nasa.gov/coolscience, which displays short video clips of Aqua scientists and engineers explaining the many aspects of the Aqua mission. These video clips, the Aqua website, and numerous presentations have benefited from dynamic visualizations showing the Aqua launch, instrument deployments, instrument sensing, and the Aqua orbit. More recently, in 2008 the Aqua team worked with the ViewSpace production team from the Space Telescope Science Institute to create an 18-minute ViewSpace feature showcasing the science and applications of the Aqua mission. Then in 2010 and 2011, Aqua and other NASA Earth-observing missions partnered with National CineMedia on the "Know Your Earth" (KYE) project. During January and July 2010 and 2011, KYE ran 2-minute segments highlighting questions that promoted global climate literacy on lobby LCD screens in movie theaters throughout the U.S. Among the ongoing Aqua EPO efforts is the incorporation of Aqua data sets onto the Dynamic Planet, a large digital video globe that projects a wide variety of spherical data sets. Aqua also has a highly successful collaboration with EarthSky communications on the production of an Aqua/EarthSky radio show and podcast series. To date, eleven productions have been completed and distributed via the EarthSky network. In addition, a series of eight video podcasts (i.e., vodcasts) are under production by NASA Goddard TV in conjunction with Aqua personnel, highlighting various aspects of the Aqua mission.
Graham, S. M.; Parkinson, C. L.; Chambers, L. H.; Ray, S. E.
Analysis of Raman Lidar and radiosonde measurements from the AWEX-G field campaign and its relation to Aqua validation
NASA Technical Reports Server (NTRS)
Early work within the Aqua validation activity revealed there to be large differences in water vapor measurement accuracy among the various technologies in use for providing validation data. The validation measurements were made at globally distributed sites making it difficult to isolate the sources of the apparent measurement differences among the various sensors, which included both Raman lidar and radiosonde. Because of this, the AIRS Water Vapor Experiment-Ground (AWEX-G) was held in October - November, 2003 with the goal of bringing validation technologies to a common site for intercomparison and resolution of the measurement discrepancies. Using the University of Colorado Cryogenic Frostpoint Hygrometer (CFH) as the water vapor reference, the AWEX-G field campaign resulted in new correction techniques for both Raman lidar, Vaisala RS80-H and RS90/92 measurements that significantly improve the absolute accuracy of those measurement systems particularly in the upper troposphere. Mean comparisons of radiosondes and lidar are performed demonstrating agreement between corrected sensors and the CFH to generally within 5% thereby providing data of sufficient accuracy for Aqua validation purposes. Examples of the use of the correction techniques in radiance and retrieval comparisons are provided and discussed.
Whiteman, D. N.; Russo, F.; Demoz, B.; Miloshevich, L. M.; Veselovskii, I.; Hannon, S.; Wang, Z.; Vomel, H.; Schmidlin, F.; Lesht, B.
Analysis of Raman Lidar and Radiosonde Measurements from the AWEX-G Field Campaign and Its Relation to Aqua Validation
NASA Technical Reports Server (NTRS)
Early work within the Aqua validation activity revealed there to be large differences in water vapor measurement accuracy among the various technologies in use for providing validation data. The validation measurements were made at globally distributed sites making it difficult to isolate the sources of the apparent measurement differences among the various sensors, which included both Raman lidar and radiosonde. Because of this, the AIRS Water Vapor Experiment-Ground (AWEX-G) was held in October-November 2003 with the goal of bringing validation technologies to a common site for intercomparison and resolving the measurement discrepancies. Using the University of Colorado Cryogenic Frostpoint Hygrometer (CFH) as the water vapor reference, the AWEX-G field campaign permitted correction techniques to be validated for Raman lidar, Vaisala RS80-H and RS90/92 that significantly improve the absolute accuracy of water vapor measurements from these systems particularly in the upper troposphere. Mean comparisons of radiosondes and lidar are performed demonstrating agreement between corrected sensors and the CFH to generally within 5% thereby providing data of sufficient accuracy for Aqua validation purposes. Examples of the use of the correction techniques in radiance and retrieval comparisons are provided and discussed.
Whiteman, D. N.; Russo, F.; Demoz, B.; Miloshevich, L. M.; Veselovskii, I.; Hannon, S.; Wang, Z.; Vomel, H.; Schmidlin, F.; Lesht, B.; Moore, P. J.; Beebe, A. S.; Gambacorta, A.; Barnet, C.
Google My Maps: Simple Quantitative Analysis
NSDL National Science Digital Library
Carsten Braun, Westfield State College Summary This activity shows how to use Google My Maps for simple quantitative analysis, for example to find the latitude and longitude of a location or the length and area of ...
Braun, Carsten
Plural analysis: Multiple approaches to quantitative research
The dominant approach to decision analysis in particular, and quantitative research in general, issingular, i.e., all conclusions are based on a single preferred model or approach. Inplural analysis, several singular analyses are pursued in parallel, the typically conflicting results are merged. Although it is a central feature of intelligent everyday thinking, plural analysis has largely been ignored by the research
Rex V. Brown; Dennis V. Lindley
Methods in quantitative image analysis
The main steps of image analysis are image capturing, image storage (compression), correcting imaging defects (e.g. non-uniform illumination, electronic noise, glare effect), image enhancement, segmentation of objects in the image and image measurements. Digitisation is made by a camera. The most modern types include a frame-grabber, converting the analog-to-digital signal into digital (numerical) information. The numerical information consists of the
Martin Oberholzer; Marc �streicher; Heinz Christen; Marcel Br�hlmann
Quantitative histogram analysis of images
NASA Astrophysics Data System (ADS)
A routine for histogram analysis of images has been written in the object-oriented, graphical development environment LabVIEW. The program converts an RGB bitmap image into an intensity-linear greyscale image according to selectable conversion coefficients. This greyscale image is subsequently analysed by plots of the intensity histogram and probability distribution of brightness, and by calculation of various parameters, including average brightness, standard deviation, variance, minimal and maximal brightness, mode, skewness and kurtosis of the histogram and the median of the probability distribution. The program allows interactive selection of specific regions of interest (ROI) in the image and definition of lower and upper threshold levels (e.g., to permit the removal of a constant background signal). The results of the analysis of multiple images can be conveniently saved and exported for plotting in other programs, which allows fast analysis of relatively large sets of image data. The program file accompanies this manuscript together with a detailed description of two application examples: The analysis of fluorescence microscopy images, specifically of tau-immunofluorescence in primary cultures of rat cortical and hippocampal neurons, and the quantification of protein bands by Western-blot. The possibilities and limitations of this kind of analysis are discussed. Program summaryTitle of program: HAWGC Catalogue identifier: ADXG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXG_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computers: Mobile Intel Pentium III, AMD Duron Installations: No installation necessary�Executable file together with necessary files for LabVIEW Run-time engine Operating systems or monitors under which the program has been tested: WindowsME/2000/XP Programming language used: LabVIEW 7.0 Memory required to execute with typical data:�16MB for starting and �160MB used for loading of an image No. of bits in a word: 32 No. of processors used: 1 Has the code been vectorized or parallelized?: No No of lines in distributed program, including test data, etc.:138 946 No. of bytes in distributed program, including test data, etc.:15 166 675 Distribution format: tar.gz Nature of physical problem: Quantification of image data (e.g., for discrimination of molecular species in gels or fluorescent molecular probes in cell cultures) requires proprietary or complex software packages, which might not include the relevant statistical parameters or make the analysis of multiple images a tedious procedure for the general user. Method of solution: Tool for conversion of RGB bitmap image into luminance-linear image and extraction of luminance histogram, probability distribution, and statistical parameters (average brightness, standard deviation, variance, minimal and maximal brightness, mode, skewness and kurtosis of histogram and median of probability distribution) with possible selection of region of interest (ROI) and lower and upper threshold levels. Restrictions on the complexity of the problem: Does not incorporate application-specific functions (e.g., morphometric analysis) Typical running time: Seconds (depending on image size and processor speed) Unusual features of the program: None
Holub, Oliver; Ferreira, S�rgio T.
Basics of quantitative image analysis
Increasing demands for quality in a highly competitive marketplace are driving industry to seek out statistical methods of quantifying the results of materials analyses. Automated image analysis or computer-aided microscopy is a particularly useful tool for analyzing metallographic specimens. It is a more accurate and repeatable alternative to manual specimen characterization techniques. In computer-aided microscopy, the large amount of information contained in a microscopic image is collected and computer-enhanced. Features of interest are then statistically analyzed. Typical applications include rating inclusions, determining ASTM grain size, measuring porosity and coating thickness, and characterizing phases. The results of image analyses are used in research, product development, process control, quality assurance, and customer technical service.
Leithner, K.A. (Buehler Ltd., Lake Bluff, IL (United States))
Methods in quantitative image analysis.
The main steps of image analysis are image capturing, image storage (compression), correcting imaging defects (e.g. non-uniform illumination, electronic-noise, glare effect), image enhancement, segmentation of objects in the image and image measurements. Digitisation is made by a camera. The most modern types include a frame-grabber, converting the analog-to-digital signal into digital (numerical) information. The numerical information consists of the grey values describing the brightness of every point within the image, named a pixel. The information is stored in bits. Eight bits are summarised in one byte. Therefore, grey values can have a value between 0 and 256 (2(8)). The human eye seems to be quite content with a display of 5-bit images (corresponding to 64 different grey values). In a digitised image, the pixel grey values can vary within regions that are uniform in the original scene: the image is noisy. The noise is mainly manifested in the background of the image. For an optimal discrimination between different objects or features in an image, uniformity of illumination in the whole image is required. These defects can be minimised by shading correction [subtraction of a background (white) image from the original image, pixel per pixel, or division of the original image by the background image]. The brightness of an image represented by its grey values can be analysed for every single pixel or for a group of pixels. The most frequently used pixel-based image descriptors are optical density, integrated optical density, the histogram of the grey values, mean grey value and entropy. The distribution of the grey values existing within an image is one of the most important characteristics of the image. However, the histogram gives no information about the texture of the image. The simplest way to improve the contrast of an image is to expand the brightness scale by spreading the histogram out to the full available range. Rules for transforming the grey value histogram of an existing image (input image) into a new grey value histogram (output image) are most quickly handled by a look-up table (LUT). The histogram of an image can be influenced by gain, offset and gamma of the camera. Gain defines the voltage range, offset defines the reference voltage and gamma the slope of the regression line between the light intensity and the voltage of the camera. A very important descriptor of neighbourhood relations in an image is the co-occurrence matrix. The distance between the pixels (original pixel and its neighbouring pixel) can influence the various parameters calculated from the co-occurrence matrix. The main goals of image enhancement are elimination of surface roughness in an image (smoothing), correction of defects (e.g. noise), extraction of edges, identification of points, strengthening texture elements and improving contrast. In enhancement, two types of operations can be distinguished: pixel-based (point operations) and neighbourhood-based (matrix operations). The most important pixel-based operations are linear stretching of grey values, application of pre-stored LUTs and histogram equalisation. The neighbourhood-based operations work with so-called filters. These are organising elements with an original or initial point in their centre. Filters can be used to accentuate or to suppress specific structures within the image. Filters can work either in the spatial or in the frequency domain. The method used for analysing alterations of grey value intensities in the frequency domain is the Hartley transform. Filter operations in the spatial domain can be based on averaging or ranking the grey values occurring in the organising element. The most important filters, which are usually applied, are the Gaussian filter and the Laplace filter (both averaging filters), and the median filter, the top hat filter and the range operator (all ranking filters). Segmentation of objects is traditionally based on threshold grey values. (AB PMID:8781988
Oberholzer, M; Ostreicher, M; Christen, H; Br�hlmann, M
Quantitative WDS analysis using electron probe microanalyzer
In this paper, the procedure for conducting quantitative elemental analysis by ZAF correction method using wavelength dispersive X-ray spectroscopy (WDS) in an electron probe microanalyzer (EPMA) is elaborated. Analysis of a thermal barrier coating (TBC) system formed on a Ni-based single crystal superalloy is presented as an example to illustrate the analysis of samples consisting of a large number of major and minor elements. The analysis was performed by known standards and measured peak-to-background intensity ratios. The procedure for using separate set of acquisition conditions for major and minor element analysis is explained and its importance is stressed.
Ul-Hamid, Anwar [Research Institute, King Fahd University of Petroleum and Minerals, P.O. Box 1073, Dhahran 31261 (Saudi Arabia)]. E-mail: email@example.com; Tawancy, Hani M. [Research Institute, King Fahd University of Petroleum and Minerals, P.O. Box 1073, Dhahran 31261 (Saudi Arabia); Mohammed, Abdul-Rashid I. [Research Institute, King Fahd University of Petroleum and Minerals, P.O. Box 1073, Dhahran 31261 (Saudi Arabia); Al-Jaroudi, Said S. [Saudi Aramco, P.O. Box 65, Tanajib 31311 (Saudi Arabia); Abbas, Nureddin M. [Research Institute, King Fahd University of Petroleum and Minerals, P.O. Box 1073, Dhahran 31261 (Saudi Arabia)
Quantitative resilience analysis through control design
Critical infrastructure resilience has become a national priority for the U. S. Department of Homeland Security. System resilience has been studied for several decades in many different disciplines, but no standards or unifying methods exist for critical infrastructure resilience analysis. Few quantitative resilience methods exist, and those existing approaches tend to be rather simplistic and, hence, not capable of sufficiently
Daniel Sunderland; Eric D. Vugrin; Russell Chris Camphouse
Seniors' Online Communities: A Quantitative Content Analysis
ERIC Educational Resources Information Center
Purpose: To examine the contents and characteristics of seniors' online communities and to explore their potential benefits to older adults. Design and Methods: Quantitative content analysis of a full year's data from 14 leading online communities using a novel computerized system. The overall database included 686,283 messages. Results: There was�
Nimrod, Galit
Quantitative Phase Analysis in Textured Materials.
National Technical Information Service (NTIS)
The problem of preferred orientation was considered in quantitative phase analysis by X-ray diffraction techniques. The average intensity of a diffraction peak can be obtained by integration over the whole pole figure, or by random rotation of the specime...
S. L. Lopata E. B. Kula
Quantitative methods for ecological network analysi
The analysis of networks of ecological trophic transfers is a useful complement to simulation modeling in the quest for understanding whole-ecosystem dynamics. Trophic networks can be studied in quantitative and systematic fashion at several levels. Indirect relationships between any two individual taxa in an ecosystem, which often differ in either nature or magnitude from their direct influences, can be assayed
Robert E. Ulanowicz
Aqua Satellite Mission Educational Outreach
NASA Astrophysics Data System (ADS)
An important component of the Aqua mission, launched into space on May 4, 2002 with a suite of six instruments from the U.S., Japan, and Brazil, is the effort to educate the public about the mission and the science topics that it addresses. This educational outreach includes printed products, web casts, other web-based materials, animations, presentations, and a student contest. The printed products include brochures for the mission as a whole and for the instruments, NASA Fact Sheets on the mission, the water cycle, and weather forecasting, an Aqua Science Writers' Guide, an Aqua lithograph, posters, and trading cards. Animations include animations of the launch, the orbit, instrument deployments, instrument sensing, and several of the data products. Each of these materials is available on the Aqua web site at http://aqua.nasa.gov, as are archived versions of the eight Aqua web casts. The web casts were done live on the internet and focused on the spacecraft, the science, the launch, and the validation efforts. All web casts had key Aqua personnel as live guests and had a web-based chat session allowing viewers to ask questions. Other web-based materials include a "Cool Science" section of the aqua.nasa.gov website, with videos of Aqua scientists and engineers speaking about Aqua and the science and engineering behind it, arranged in a framework organized for the convenience of teachers dealing with core curriculum requirements. The web casts and "Cool Science" site were produced by the Special Project Initiatives Office at NASA's Goddard Space Flight Center. Outreach presentations about Aqua have been given at schools, universities, and public forums at many locations around the world, especially in the U.S. A competition was held for high school students during the 2002-03 school year, culminating in April 2003, with five finalist teams competing for the top slots, followed by an awards ceremony. The competition had all the student teams analyzing an anomalous situation encountered by Aqua shortly after launch and the five finalist teams determining how best to handle a hypothetical degradation of the solid state recorder.
Parkinson, C. L.; Graham, S. M.
Method and apparatus for chromatographic quantitative analysis
An improved apparatus and method for the quantitative analysis of a solution containing a plurality of anion species by ion exchange chromatography which utilizes a single eluent and a single ion exchange bed which does not require periodic regeneration. The solution containing the anions is added to an anion exchange resin bed which is a low capacity macroreticular polystyrene-divinylbenzene resin containing quarternary ammonium functional groups, and is eluted therefrom with a dilute solution of a low electrical conductance organic acid salt. As each anion species is eluted from the bed, it is quantitatively sensed by conventional detection means such as a conductivity cell.
Fritz, James S. (Ames, IA) [Ames, IA; Gjerde, Douglas T. (Ames, IA) [Ames, IA; Schmuckler, Gabriella (Haifa, IL) [Haifa, IL
Quantitative analysis of colony morphology in yeast
Microorganisms often form multicellular structures such as biofilms and structured colonies that can influence the organism�s virulence, drug resistance, and adherence to medical devices. Phenotypic classification of these structures has traditionally relied on qualitative scoring systems that limit detailed phenotypic comparisons between strains. Automated imaging and quantitative analysis have the potential to improve the speed and accuracy of experiments designed to study the genetic and molecular networks underlying different morphological traits. For this reason, we have developed a platform that uses automated image analysis and pattern recognition to quantify phenotypic signatures of yeast colonies. Our strategy enables quantitative analysis of individual colonies, measured at a single time point or over a series of time-lapse images, as well as the classification of distinct colony shapes based on image-derived features. Phenotypic changes in colony morphology can be expressed as changes in feature space trajectories over time, thereby enabling the visualization and quantitative analysis of morphological development. To facilitate data exploration, results are plotted dynamically through an interactive Yeast Image Analysis web application (YIMAA; http://yimaa.cs.tut.fi) that integrates the raw and processed images across all time points, allowing exploration of the image-based features and principal components associated with morphological development.
Ruusuvuori, Pekka; Lin, Jake; Scott, Adrian C.; Tan, Zhihao; Sorsa, Saija; Kallio, Aleksi; Nykter, Matti; Yli-Harja, Olli; Shmulevich, Ilya; Dudley, Aimee M.
Aqua satellite orbiting the Earth
This animation shows the Aqua satellite orbiting the Earth on August 27, 2005 by revealing MODIS true-color imagery for that day. This animation is on a cartesian map projection, so the satellite w...
Informatics and Quantitative Analysis in Biological Imaging
NSDL National Science Digital Library
Biological imaging is now a quantitative technique for probing cellular structure and dynamics and is increasingly used for cell-based screens. However, the bioinformatics tools required for hypothesis-driven analysis of digital images are still immature. We are developing the Open Microscopy Environment (OME) as an informatics solution for the storage and analysis of optical microscope image data. OME aims to automate image analysis, modeling, and mining of large sets of images and specifies a flexible data model, a relational database, and an XML-encoded file standard that is usable by potentially any software tool. With this design, OME provides a first step toward biological image informatics.
Jason Swedlow (University of Dundee;); Ilya Goldberg (National Institutes of Health;Laboratory of Genetics, National Institute on Aging); Erik Brauner (Harvard Medical School;Institute of Chemistry and Cell Biology); Peter K. Sorger (Harvard Medical School/Massachusetts Institute of Technology;)
Using Qualitative Hazard Analysis to Guide Quantitative Safety Analysis
NASA Technical Reports Server (NTRS)
Quantitative methods can be beneficial in many types of safety investigations. However, there are many difficulties in using quantitative m ethods. Far example, there may be little relevant data available. This paper proposes a framework for using quantitative hazard analysis to prioritize hazard scenarios most suitable for quantitative mziysis. The framework first categorizes hazard scenarios by severity and likelihood. We then propose another metric "modeling difficulty" that desc ribes the complexity in modeling a given hazard scenario quantitatively. The combined metrics of severity, likelihood, and modeling difficu lty help to prioritize hazard scenarios for which quantitative analys is should be applied. We have applied this methodology to proposed concepts of operations for reduced wake separation for airplane operatio ns at closely spaced parallel runways.
Shortle, J. F.; Allocco, M.
Quantitative resilience analysis through control design.
Critical infrastructure resilience has become a national priority for the U. S. Department of Homeland Security. System resilience has been studied for several decades in many different disciplines, but no standards or unifying methods exist for critical infrastructure resilience analysis. Few quantitative resilience methods exist, and those existing approaches tend to be rather simplistic and, hence, not capable of sufficiently assessing all aspects of critical infrastructure resilience. This report documents the results of a late-start Laboratory Directed Research and Development (LDRD) project that investigated the development of quantitative resilience through application of control design methods. Specifically, we conducted a survey of infrastructure models to assess what types of control design might be applicable for critical infrastructure resilience assessment. As a result of this survey, we developed a decision process that directs the resilience analyst to the control method that is most likely applicable to the system under consideration. Furthermore, we developed optimal control strategies for two sets of representative infrastructure systems to demonstrate how control methods could be used to assess the resilience of the systems to catastrophic disruptions. We present recommendations for future work to continue the development of quantitative resilience analysis methods.
Sunderland, Daniel; Vugrin, Eric D.; Camphouse, Russell Chris (Sandia National Laboratories, Carlsbad, NM)
Towards quantitative connectivity analysis: reducing tractography biases.
Diffusion MRI tractography is often used to estimate structural connections between brain areas and there is a fast-growing interest in quantifying these connections based on their position, shape, size and length. However, a portion of the connections reconstructed with tractography is biased by their position, shape, size and length. Thus, connections reconstructed are not equally distributed in all white matter bundles. Quantitative measures of connectivity based on the streamline distribution in the brain such as streamline count (density), average length and spatial extent (volume) are biased by erroneous streamlines produced by tractography algorithms. In this paper, solutions are proposed to reduce biases in the streamline distribution. First, we propose to optimize tractography parameters in terms of connectivity. Then, we propose to relax the tractography stopping criterion with a novel probabilistic stopping criterion and a particle filtering method, both based on tissue partial volume estimation maps calculated from a T1-weighted image. We show that optimizing tractography parameters, stopping and seeding strategies can reduce the biases in position, shape, size and length of the streamline distribution. These tractography biases are quantitatively reported using in-vivo and synthetic data. This is a critical step towards producing tractography results for quantitative structural connectivity analysis. PMID:24816531
Girard, Gabriel; Whittingstall, Kevin; Deriche, Rachid; Descoteaux, Maxime
NASA Technical Reports Server (NTRS)
A little over ten years ago, in the early morning hours of May 4, 2002, crowds of spectators stood anxiously watching as the Delta II rocket carrying NASA's Aqua spacecraft lifted off from its launch pad at Vandenberg Air Force Base in California at 2:55 a.m. The rocket quickly went through a low-lying cloud cover, after which the main portion of the rocket fell to the waters below and the rockets second stage proceeded to carry Aqua south across the Pacific, onward over Antarctica, and north to Africa, where the spacecraft separated from the rocket 59.5 minutes after launch. Then, 12.5 minutes later, the solar array unfurled over Europe, and Aqua was on its way in the first of what by now have become over 50,000 successful orbits of the Earth.
Parkinson, Claire L.
Quantitative architectural analysis of bronchial intraepithelial neoplasia
NASA Astrophysics Data System (ADS)
Considerable variation exists among pathologist in the interpretation of intraepithelial neoplasia making it difficult to determine the natural history of these lesion and to establish management guidelines for chemoprevention. The aim of the study is to evaluate architectural features of pre-neoplastic progression in lung cancer, and to search for a correlation between architectural index and conventional pathology. Quantitative architectural analysis was performed on a series of normal lung biopsies and Carcinoma In Situ (CIS). Centers of gravity of the nuclei within a pre-defined region of interest were used as seeds to generate a Voronoi Diagram. About 30 features derived from the Voronoi diagram, its dual the Delaunay tessellation, and the Minimum Spanning Tree were extracted. A discriminant analysis was performed to separate between the two groups. The architectural Index was calculated for each of the bronchial biopsies that were interpreted as hyperplasia, metaplasia, mild, moderate or severe dysplasia by conventional histopathology criteria. As a group, lesions classified as CIS by conventional histopathology criteria could be distinguished from dysplasia using the architectural Index. Metaplasia was distinct from hyperplasia and hyperplasia from normal. There was overlap between severe and moderate dysplasia but mild dysplasia could be distinguished form moderate dysplasia. Bronchial intraepithelial neoplastic lesions can be degraded objectively by architectural features. Combination of architectural features and nuclear morphometric features may improve the quantitation of the changes occurring during the intra-epithelial neoplastic process.
Guillaud, Martial; MacAulay, Calum E.; Le Riche, Jean C.; Dawe, Chris; Korbelik, Jagoda; Lam, Stephen
Quantitative proteomic analysis of Myc oncoprotein function
This study applies a new quantitative proteomics technology to the analysis of the function of the Myc oncoprotein in mammalian cells. Employing isotope-coded affinity tag (ICATTM) reagent labeling and tandem mass spectrometry, the global pattern of protein expression in rat myc-null cells was compared with that of myc-plus cells (myc-null cells in which myc has been introduced) to generate a differential protein expression catalog. Expression differences among many functionally related proteins were identified, including reduction of proteases, induction of protein synthesis pathways and upregulation of anabolic enzymes in myc-plus cells, which are predicted to lead to increased cell mass (cell growth). In addition, reduction in the levels of adhesion molecules, actin network proteins and Rho pathway proteins were observed in myc-plus cells, leading to reduced focal adhesions and actin stress fibers as well as altered morphology. These effects are dependent on the highly conserved Myc Box�II region. Our results reveal a novel cytoskeletal function for Myc and indicate the feasibility of quantitative whole-proteome analysis in mammalian cells.
Shiio, Yuzuru; Donohoe, Sam; Yi, Eugene C.; Goodlett, David R.; Aebersold, Ruedi; Eisenman, Robert N.
[Quantitative analysis of smooth pursuit eye movement].
Abnormalities of smooth pursuit eye movement (SPEM) have been estimated, mainly using the wave form on an electro-oculogram, in a qualitative way. Many methods for quantitative analysis of SPEM have been designed, though most are still uncommon in present clinical use. Using a personal computer, we developed a method of automatic quantitative analysis of ocular tracking eye movement recorded by electro-oculography (EOG). The design concept of this method is based on the observation that eye movement during ocular tracking consists of two different kinds of eye movements, one is SPEM and the other is saccade. The combination of SPEM and saccade (composite eye movement: CEM) commonly appears during ocular tracking. These two kinds of eye movement are essentially different not only in behavior but also about involved neural pathway in the central nervous system. From this point of view, we believe that the two kinds of eye movements involved in ocular tracking should be evaluated separately. The analysis method is outlined as follows. A horizontal sinusoidally moving visual target was employed to elicit ocular tracking eye movements. The test frequencies were set at 0.1, 0.2, 0.4 and 0.8Hz, and the amplitude of target motion was 15 deg at each frequency. The 20 seconds of eye movement data measured by EOG were fed into the computer through a digital-analog converter for further analysis. Using our original saccade detection algorithm, based on the physiological behavior of saccades, the saccadic components were detected and removed from the eye movement wave. The remaining parts, fragments of SPEM, were connected by means of interpolating defective parts. The reconstructed wave was a slow cumulative eye position curve (SCEP). Sinusoidal target motion, CEM and SCEP were processed by the FFT (Fast Fourier Transformation) method. Bode plots were applied to summarize the gain and phase of responses to SCEP and the target motion wave. These processes enable us to estimate abnormalities of SPEM such as low gain, abnormal phase shift and large trends in tested duration. We conclude that the method described here is useful for quantitative estimation of SPEM in clinical neuro-otological examinations. PMID:7782976
Hashiba, M; Yasui, K; Watabe, H; Matsuoka, T; Baba, S
National Technical Information Service (NTIS)
A little over ten years ago, in the early morning hours of May 4, 2002, crowds of spectators stood anxiously watching as the Delta II rocket carrying NASA's Aqua spacecraft lifted off from its launch pad at Vandenberg Air Force Base in California at 2:55 ...
C. L. Parkinson
Error Propagation Analysis for Quantitative Intracellular Metabolomics
Model-based analyses have become an integral part of modern metabolic engineering and systems biology in order to gain knowledge about complex and not directly observable cellular processes. For quantitative analyses, not only experimental data, but also measurement errors, play a crucial role. The total measurement error of any analytical protocol is the result of an accumulation of single errors introduced by several processing steps. Here, we present a framework for the quantification of intracellular metabolites, including error propagation during metabolome sample processing. Focusing on one specific protocol, we comprehensively investigate all currently known and accessible factors that ultimately impact the accuracy of intracellular metabolite concentration data. All intermediate steps are modeled, and their uncertainty with respect to the final concentration data is rigorously quantified. Finally, on the basis of a comprehensive metabolome dataset of Corynebacterium glutamicum, an integrated error propagation analysis for all parts of the model is conducted, and the most critical steps for intracellular metabolite quantification are detected.
Tillack, Jana; Paczia, Nicole; Noh, Katharina; Wiechert, Wolfgang; Noack, Stephan
Materials characterization through quantitative digital image analysis
A digital image analysis system has been developed to allow advanced quantitative measurement of microstructural features. This capability is maintained as part of the microscopy facility at Sandia, Livermore. The system records images digitally, eliminating the use of film. Images obtained from other sources may also be imported into the system. Subsequent digital image processing enhances image appearance through the contrast and brightness adjustments. The system measures a variety of user-defined microstructural features--including area fraction, particle size and spatial distributions, grain sizes and orientations of elongated particles. These measurements are made in a semi-automatic mode through the use of macro programs and a computer controlled translation stage. A routine has been developed to create large montages of 50+ separate images. Individual image frames are matched to the nearest pixel to create seamless montages. Results from three different studies are presented to illustrate the capabilities of the system.
J. Philliber; B. Antoun; B. Somerday; N. Yang
Quantitative analysis of infrared contrast enhancement algorithms
NASA Astrophysics Data System (ADS)
Dynamic range reduction and contrast enhancement are two image-processing methods that are required when developing thermal camera systems. The two methods must be performed in such a way that the high dynamic range imagery output from current sensors are compressed in a pleasing way for display on lower dynamic range monitors. This research examines a quantitative analysis of infrared contrast enhancement algorithms found in literature and developed by the author. Four algorithms were studied, three of which were found in literature and one developed by the author: tail-less plateau equalization (TPE), adaptive plateau equalization (APE), the method according to Aare M�llo (MEAM), and infrared multi-scale retinex (IMSR). TPE and APE are histogram-based methods, requiring the calculation of the probability density of digital counts within an image. MEAM and IMSR are frequency-domain methods, methods that operate on input imagery that has been split into components containing differing spatial frequency content. After a rate of growth analysis and psychophysical trial were performed, MEAM was found to be the best algorithm.
Weith-Glushko, Seth; Salvaggio, Carl
NASA Technical Reports Server (NTRS)
This talk will focus on the afternoon constellation of EOS platforms and the scientific benefits that arise from this formation. The afternoon EOS constellation or the "A-train" will provide unprecedented information on clouds and aerosols. At 1:30 PM crossing time EOS-Aqua begins the train with the MODIS, CERES and AIRS instruments making aerosol, cloud, radiation budget , temperature and water vapor measurements. AMSR-E will also make total column water measurements. Following Aqua by one minute, Cloudsat will make active radar precipitation measurements as and PICASSOCENA will make lidar measurements of clouds and aerosols. Fourteen minutes later, EOS-Aura will pass through the same space making upper troposphere water vapor and ice profiles as well as some key trace gases associated with convective processes (MLS and HIRDLS). Additional measurements of aerosols will be made by Aura's OMI instrument.
Schoeberl, Mark; Einaudi, Franco (Technical Monitor)
Quantitative analysis of nanoparticle growth through plasmonics.
Plasmon excitation appears to be a powerful and flexible tool for probing in situ and in real time the growth of supported conducting metal nanoparticles. However, although models exist for analysing optical profiles, limitations arise in the realistic modelling of particle shape from the lack of knowledge of temperature effects and of broadening sources. This paper reports on the growth of silver on alumina at 190-675 K monitored by surface differential reflectivity spectroscopy in the UV-visible range. In the framework of plasmonic response analysis, particles are modelled by truncated spheres. Their polarizabilities are computed within the quasi-static approximation and used as an input to the interface susceptibilities model in order to determine the Fresnel reflection coefficient. The pivotal importance of the thermal variation of the metal dielectric constant is demonstrated. Finite-size effects are accounted for. As size distribution fluctuations contribute marginally to the lineshape compared to the aspect ratio (diameter/height) distribution, a convolution method for representing the experimental broadening is introduced. Effects of disorder on the lineshape are discussed. It is highlighted that beside the quality of the fit (not a proof by itself!), physical meaning of the parameters related to the sticking probability, growth and wetting is crucially required for validating models. The proposed modelling opens interesting perspectives for the quantitative study of growth via plasmonics, in particular in the case of noble metals. PMID:21975584
Lazzari, R�mi; Jupille, Jacques
Quantitative analysis of nanoparticle growth through plasmonics
NASA Astrophysics Data System (ADS)
Plasmon excitation appears to be a powerful and flexible tool for probing in situ and in real time the growth of supported conducting metal nanoparticles. However, although models exist for analysing optical profiles, limitations arise in the realistic modelling of particle shape from the lack of knowledge of temperature effects and of broadening sources. This paper reports on the growth of silver on alumina at 190-675 K monitored by surface differential reflectivity spectroscopy in the UV-visible range. In the framework of plasmonic response analysis, particles are modelled by truncated spheres. Their polarizabilities are computed within the quasi-static approximation and used as an input to the interface susceptibilities model in order to determine the Fresnel reflection coefficient. The pivotal importance of the thermal variation of the metal dielectric constant is demonstrated. Finite-size effects are accounted for. As size distribution fluctuations contribute marginally to the lineshape compared to the aspect ratio (diameter/height) distribution, a convolution method for representing the experimental broadening is introduced. Effects of disorder on the lineshape are discussed. It is highlighted that beside the quality of the fit (not a proof by itself!), physical meaning of the parameters related to the sticking probability, growth and wetting is crucially required for validating models. The proposed modelling opens interesting perspectives for the quantitative study of growth via plasmonics, in particular in the case of noble metals.
Lazzari, R�mi; Jupille, Jacques
Quantitative analysis of thallium-201 myocardial emission computed tomography
The clinical usefulness of quantitative analysis of exercise thallium-201 myocardial emission computed tomography (ECT) was evaluated in twenty coronary artery disease patients and 10 normal controls. Longaxial and shortaxial myocardial images of left ventricle were interpreted quantitatively using circumferential profile analysis and two types of abnormality were studied: (1) diminished initial distribution (stress defect) and (2) slow washout of thallium-201,
M. Okada; N. Kawai; S. Yamamoto; H. Matsushima; R. Kato; Y. Tanahashi; I. Sotobata; Y. Obata; S. Sakuma
Quantitative analysis of DNA-porphyrin interactions.
The binding of manganese(III)-tetra(4-N-methylpyridyl)porphyrin (MnTMpyP) with synthetic poly(dA-dT)2, poly(dI-dC)2, and poly(dG-dC)2 DNAs as well as calf thymus (CT) DNA has been quantitatively studied in detail using induced CD (circular dichroism) spectroscopy in the Soret absorption band. The CD spectra, which changed greatly depending on the porphyrin to DNA base-pair molar ratio (r), were normalized with respect to DNA concentration and deconvoluted. Three independent component binding modes (named mode 1, 2, and 3 in the order of increasing r values) were identified, which successfully simulated the observed CD spectra with negligibly small residuals for a wide range of r values. In the case of poly(dA-dT)2, poly (dI-dC)2, and CT DNA, all the three modes appeared, whereas in the case of poly(dG-dC)2 DNA, only modes 1 and 3 appeared in the r range studied. The r dependence of each binding mode, i.e., its relative affinity toward DNA, has been revealed by this analysis. Mode 1, which appeared as a single binding mode at very low r values (r < or = ca. 0.05), was inhibited by the addition of methyl green, a drug that preferentially binds to the major groove of poly (dA-dT)2 DNA. Berenil, a known minor groove binder to poly(dA-dT)2 or poly(dI-dC)2 DNA, inhibited modes 2 and 3. From these inhibition experiments as well as comparison of the component spectra for DNAs of different sequence, a binding site on DNA was proposed for each component binding mode. The number of DNA base pairs covered by a single molecule of porphyrin was estimated. PMID:16358258
Nitta, Y; Kuroda, R
Interspecific competition between Microcystis aeruginosa and Anabaena flos-aquae from Taihu Lake, China.
Microcystis and Anabaena are the main cyanobacteria that cause cyanobacterial blooms in Taihu Lake, China. The mechanism of population competition between M. aeruginosa and A. flos-aquae was studied by co-cultivation in the laboratory. The growth of M. aeruginosa was inhibited, while the growth of A. flos-aquae was promoted. The degree of inhibition or promotion was related to the ratio of the initial cell densities. Both cell-free filtrates of A. flos-aquae and co-culture inhibited M. aeruginosa growth, while both cell-free filtrates of M. aeruginosa and co-culture promoted A. flos-aquae growth. Analysis of the cell-free filtrate by gas chromatography-mass spectrometry indicated that M. aeruginosa and A. flos-aquae may secrete some extracellular allelochemicals that inhibit (promote) the growth of M. aeruginosa (A. flos-aquae) in co-culture. These compounds included sulfur compounds, naphthalene derivatives, cedrene derivatives, quinones, phenol derivatives, diphenyl derivatives, anthracene derivatives, and phthalate esters. This study can help to understand the characteristics of M. aeruginosa and A. flos-aquae and to provide new concepts for the control of cyanobacterial blooms in Taihu Lake. PMID:24772823
Zhang, Xue-Wei; Fu, Jie; Song, Shuang; Zhang, Ping; Yang, Xian-Hui; Zhang, Li-Rong; Luo, Yin; Liu, Chang-Hong; Zhu, Hai-Liang
Quantitative analysis of planetary reflectance spectra with principal components analysis
NASA Astrophysics Data System (ADS)
A technique is presented for quantitative analysis of planetary reflectance spectra as mixtures of particles on microscopic and macroscopic scales using principal components analysis. This technique allows for determination of the endmembers being mixed, their abundance, and the scale of mixing, as well as other physical parameters. Eighteen lunar telescopic reflectance spectra of the Copernicus crater region, from 600 nm to 1800 nm in wavelength, are modeled in terms of five likely endmembers: mare basalt, mature mare soil, anorthosite, mature highland soil, and clinopyroxene. These endmembers were chosen from a similar analysis of 92 lunar soil and rock samples. The models fit the data to within 2 percent rms. It is found that the goodness of fit is marginally better for intimate mixing over macroscopic mixing.
Johnson, P. E.; Smith, M. O.; Adams, J. B.
A Full Snow Season in Yellowstone: A Database of Restored Aqua Band 6
NASA Technical Reports Server (NTRS)
The algorithms for estimating snow extent for the Moderate Resolution Imaging Spectroradiometer (MODIS) optimally use the 1.6- m channel which is unavailable for MODIS on Aqua due to detector damage. As a test bed to demonstrate that Aqua band 6 can be restored, we chose the area surrounding Yellowstone and Grand Teton national parks. In such rugged and difficult-to-access terrain, satellite images are particularly important for providing an estimation of snow-cover extent. For the full 2010-2011 snow season covering the Yellowstone region, we have used quantitative image restoration to create a database of restored Aqua band 6. The database includes restored radiances, normalized vegetation index, normalized snow index, thermal data, and band-6-based snow-map products. The restored Aqua-band-6 data have also been regridded and combined with Terra data to produce a snow-cover map that utilizes both Terra and Aqua snow maps. Using this database, we show that the restored Aqua-band-6-based snow-cover extent has a comparable performance with respect to ground stations to the one based on Terra. The result of a restored band 6 from Aqua is that we have an additional band-6 image of the Yellowstone region each day. This image can be used to mitigate cloud occlusion, using the same algorithms used for band 6 on Terra. We show an application of this database of restored band-6 images to illustrate the value of creating a cloud gap filling using the National Aeronautics and Space Administration s operational cloud masks and data from both Aqua and Terra.
Gladkova, Irina; Grossberg, Michael; Bonev, George; Romanov, Peter; Riggs, George; Hall, Dorothy
Aqua's First 10 Years: An Overview
NASA Technical Reports Server (NTRS)
NASA's Aqua spacecraft was launched at 2:55 a.m. on May 4, 2002, from Vandenberg Air Force Base in California, into a near-polar, sun-synchronous orbit at an altitude of 705 km. Aqua carries six Earth-observing instruments to collect data on water in all its forms (liquid, vapor, and solid) and on a wide variety of additional Earth system variables (Parkinson 2003). The design lifetime for Aqua's prime mission was 6 years, and Aqua is now well into its extended mission, approaching 10 years of successful operations. The Aqua data have been used for hundreds of scientific studies and continue to be used for scientific discovery and numerous practical applications.
Parkinson, Claire L.
Database design and implementation for quantitative image analysis research
Quantitative image analysis (QIA) goes beyond sub- jective visual assessment to provide computer measurements of the image content, typically following image segmentation to iden- tify anatomical regions of interest (ROIs). Commercially available picture archiving and communication systems focus on storage of image data. They are not well suited to efficient storage and mining of new types of quantitative data. In
Matthew S. Brown; Sumit K. Shah; Richard C. Pais; Yeng-zhong Lee; Michael F. Mcnitt-gray; Jonathan G. Goldin; Alfonso F. Cardenas; Denise R. Aberle
Addressing an inadequacy in quantitative analysis: examining NMP technology selection
In its early years NASA's New Millennium Program (NMP) applied quantitative analysis methods in making complex decision in selecting technology for flight validation. In 1997, the quantitative approach showed serious signs of weakness in the selection of technologies for DS3. In response to this, the NMP began to explore new methods to select its technologies. To understand this inadequacy in
M. Bergmann; Martin G. Buehler
Quantitative analysis of diffusion tensor orientation: Theoretical framework
Diffusion-tensor MRI (DT-MRI) yields information about the magnitude, anisotropy, and orientation of water diffusion of brain tissues. Although white matter tractography and eigen- vector color maps provide visually appealing displays of white matter tract organization, they do not easily lend themselves to quantitative and statistical analysis. In this study, a set of visual and quantitative tools for the investigation of
Yu-Chien Wu; Moo K. Chung; Benham Badie; Andrew L. Alexander
[Application of SVR in quantitative analysis of wines].
Fourier transform infrared spectroscopy has been widely used in some related fields, thus induces the rapid development of quantitative analysis method based on Lambert-Beer's Law and chemometrics in recent years. The selection of appropriate pre-processing method and calibration model is extremely crucial to the quantitative analysis. The present paper selected 30 wine samples and used infrared spectroscopy combined with vector regression algorithm SVR quantitative analysis model with standard normal variate, baseline correction and outliers elimination to analyze four representative components of wine. Satisfactory results were gained while the relative errors were limited to less than 5%. This method can be applied to the wine representative quantitative analysis for the material content. PMID:24555371
Luo, Tao; Wei, Ji-Ping; Zhao, Yu-Ping; Zhang, Jun
The quantitative analysis approach for a heart sound information system
This paper presents quantitative heart sound analysis, based on which the Heart Sound Information System (HSIS) has been built. Heart sound analysis provides important information of cardiovascular diseases so it has been a basic requirement for every doctor and medical student. We use objective measurement and analysis in terms of physiology and pathology of heart sound and approaches of knowledge
Cao Zehan; Zhou Shiyong; Fu Li; Pei Yuli; Xiao Shouzhong
Quantitative Risk Analysis Approach on Construction Project Feasibility Research
The traditional methodology on risk analysis in construction project feasibility research has remained for a long time in the atmosphere of qualitative analysis. A thorough quantitative analysis approach in the same field has been carried out in this paper based on the properties and mechanisms of value mining. Taking advantages of value mining theory, the practical evaluation on potential revenue
Guan Jun; Wang Haiyan
Quantitative data analysis of ESAR data
NASA Astrophysics Data System (ADS)
A synthetic aperture radar (SAR) data processing uses the backscattered electromagnetic wave to map radar reflectivity of the ground surface. The polarization property in radar remote sensing was used successfully in many applications, especially in target decomposition. This paper presents a case study to the experiments which are performed on ESAR L-Band full polarized data sets from German Aerospace Center (DLR) to demonstrate the potential of coherent target decomposition and the possibility of using the weather radar measurement parameter, such as the differential reflectivity and the linear depolarization ratio to obtain the quantitative information of the ground surface. The raw data of ESAR has been processed by the SAR simulator developed using MATLAB program code with Range-Doppler algorithm.
Phruksahiran, N.; Chandra, M.
Towards a Quantitative OCT Image Analysis
Background Optical coherence tomography (OCT) is an invaluable diagnostic tool for the detection and follow-up of retinal pathology in patients and experimental disease models. However, as morphological structures and layering in health as well as their alterations in disease are complex, segmentation procedures have not yet reached a satisfactory level of performance. Therefore, raw images and qualitative data are commonly used in clinical and scientific reports. Here, we assess the value of OCT reflectivity profiles as a basis for a quantitative characterization of the retinal status in a cross-species comparative study. Methods Spectral-Domain Optical Coherence Tomography (OCT), confocal Scanning-La�ser Ophthalmoscopy (SLO), and Fluorescein Angiography (FA) were performed in mice (Mus musculus), gerbils (Gerbillus perpadillus), and cynomolgus monkeys (Macaca fascicularis) using the Heidelberg Engineering Spectralis system, and additional SLOs and FAs were obtained with the HRA I (same manufacturer). Reflectivity profiles were extracted from 8-bit greyscale OCT images using the ImageJ software package (http://rsb.info.nih.gov/ij/). Results Reflectivity profiles obtained from OCT scans of all three animal species correlated well with ex vivo histomorphometric data. Each of the retinal layers showed a typical pattern that varied in relative size and degree of reflectivity across species. In general, plexiform layers showed a higher level of reflectivity than nuclear layers. A comparison of reflectivity profiles from specialized retinal regions (e.g. visual streak in gerbils, fovea in non-human primates) with respective regions of human retina revealed multiple similarities. In a model of Retinitis Pigmentosa (RP), the value of reflectivity profiles for the follow-up of therapeutic interventions was demonstrated. Conclusions OCT reflectivity profiles provide a detailed, quantitative description of retinal layers and structures including specialized retinal regions. Our results highlight the potential of this approach in the long-term follow-up of therapeutic strategies.
Garcia Garrido, Marina; Beck, Susanne C.; Muhlfriedel, Regine; Julien, Sylvie; Schraermeyer, Ulrich; Seeliger, Mathias W.
Synergism of MODIS Aerosol Remote Sensing from Terra and Aqua
NASA Technical Reports Server (NTRS)
The MODerate-resolution Imaging Spectro-radiometer (MODIS) sensors, aboard the Earth Observing System (EOS) Terra and Aqua satellites, are showing excellent competence at measuring the global distribution and properties of aerosols. Terra and Aqua were launched on December 18, 1999 and May 4, 2002 respectively, with daytime equator crossing times of approximately 10:30 am and 1:30 pm respectively. Several aerosol parameters are retrieved at 10-km spatial resolution from MODIS daytime data over land and ocean surfaces. The parameters retrieved include: aerosol optical thickness (AOT) at 0.47, 0.55 and 0.66 micron wavelengths over land, and at 0.47, 0.55, 0.66, 0.87, 1.2, 1.6, and 2.1 microns over ocean; Angstrom exponent over land and ocean; and effective radii, and the proportion of AOT contributed by the small mode aerosols over ocean. Since the beginning of its operation, the quality of Terra-MODIS aerosol products (especially AOT) have been evaluated periodically by cross-correlation with equivalent data sets acquired by ground-based (and occasionally also airborne) sunphotometers, particularly those coordinated within the framework of the AErosol Robotic NETwork (AERONET). Terra-MODIS AOT data have been found to meet or exceed pre-launch accuracy expectations, and have been applied to various studies dealing with local, regional, and global aerosol monitoring. The results of these Terra-MODIS aerosol data validation efforts and studies have been reported in several scientific papers and conferences. Although Aqua-MODIS is still young, it is already yielding formidable aerosol data products, which are also subjected to careful periodic evaluation similar to that implemented for the Terra-MODIS products. This paper presents results of validation of Aqua-MODIS aerosol products with AERONET, as well as comparative evaluation against corresponding Terra-MODIS data. In addition, we show interesting independent and synergistic applications of MODIS aerosol data from both Terra and Aqua. In certain situations, this combined analysis of Terra- and Aqua-MODIS data offers an insight into the diurnal cycle of aerosol loading.
Ichoku, Charles; Kaufman, Yoram J.; Remer, Lorraine A.
Advances in Quantitative Trait Analysis in Yeast
Understanding the genetic mechanisms underlying complex traits is one of the next frontiers in biology. The budding yeast Saccharomyces cerevisiae has become an important model for elucidating the mechanisms that govern natural genetic and phenotypic variation. This success is partially due to its intrinsic biological features, such as the short sexual generation time, high meiotic recombination rate, and small genome size. Precise reverse genetics technologies allow the high throughput manipulation of genetic information with exquisite precision, offering the unique opportunity to experimentally measure the phenotypic effect of genetic variants. Population genomic and phenomic studies have revealed widespread variation between diverged populations, characteristic of man-made environments, as well as geographic clusters of wild strains along with naturally occurring recombinant strains (mosaics). Here, we review these recent studies and provide a perspective on how these previously unappreciated levels of variation can help to bridge our understanding of the genotype-phenotype gap, keeping budding yeast at the forefront of genetic studies. Not only are quantitative trait loci (QTL) being mapped with high resolution down to the nucleotide, for the first time QTLs of modest effect and complex interactions between these QTLs and between QTLs and the environment are being determined experimentally at unprecedented levels using next generation techniques of deep sequencing selected pools of individuals as well as multi-generational crosses.
Liti, Gianni; Louis, Edward J.
Using fire tests for quantitative risk analysis
Fires can be considered a causal chain-of-events in which the growth and spread of fire may cause damage and injury if it is rapid enough to overcome the barriers placed in its way. Fire tests for fire resistance of the barriers can be used in a quantitative risk assessment. The fire growth and spread is modelled in a State Transition Model (STM). The fire barriers are presented as part of the Fire Protection Model (FPM) which is based on a portion of the NFPA Decision Tree. An Emergency Equivalent Network is introduced to couple the Fire Growth Model (FGM) and the FPM so that the spread of fire beyond the room-of-origin can be computed. An example is presented in which a specific building floor plan is analyzed to obtain the shortest expected time for fire to spread between two points. To obtain the probability and time for each link in the network, data from the results of fire tests were used. These results were found to be lacking and new standards giving better data are advocated.
Ling, W.C.T.; Williamson, R.B.
Quantitative infrared analysis of hydrogen fluoride
This work was performed at the Portsmouth Gaseous Diffusion Plant where hydrogen fluoride is produced upon the hydrolysis of UF{sub 6}. This poses a problem for in this setting and a method for determining the mole percent concentration was desired. HF has been considered to be a non-ideal gas for many years. D. F. Smith utilized complex equations in his HF studies in the 1950s. We have evaluated HF behavior as a function of pressure from three different perspectives. (1) Absorbance at 3877 cm{sup -1} as a function of pressure for 100% HF. (2) Absorbance at 3877 cm{sup -1} as a function of increasing partial pressure HF. Total pressure = 300 mm HgA maintained with nitrogen. (3) Absorbance at 3877 cm{sup -1} for constant partial pressure HF. Total pressure is increased to greater than 800 mm HgA with nitrogen. These experiments have shown that at partial pressures up to 35mm HgA, HIF follows the ideal gas law. The absorbance at 3877 cm{sup -1} can be quantitatively analyzed via infrared methods.
Manuta, D.M.
Quantitative analysis of patient-specific dosimetric IMRT verification
Patient-specific dosimetric verification methods for IMRT treatments are variable, time-consuming and frequently qualitative, preventing evidence-based reduction in the amount of verification performed. This paper addresses some of these issues by applying a quantitative analysis parameter to the dosimetric verification procedure. Film measurements in different planes were acquired for a series of ten IMRT prostate patients, analysed using the quantitative parameter,
G J Budgell; B A Perrin; J H L Mott; J Fairfoul; R I Mackay
The quantitative failure of human reliability analysis
This philosophical treatise argues the merits of Human Reliability Analysis (HRA) in the context of the nuclear power industry. Actually, the author attacks historic and current HRA as having failed in informing policy makers who make decisions based on risk that humans contribute to systems performance. He argues for an HRA based on Bayesian (fact-based) inferential statistics, which advocates a systems analysis process that employs cogent heuristics when using opinion, and tempers itself with a rational debate over the weight given subjective and empirical probabilities.
Bennett, C.T.
Trend Analysis of global AOT based on various Polar Orbiting Satellite Observations: MODIS (Terra), MISR (Terra), SeaWiFS (OrbView-2), and MODIS (Aqua)
NASA Astrophysics Data System (ADS)
Many studies have investigated temporal trends of cloud-free AOTs derived from polar orbiting satellite observations since aerosol retrieval accuracy has been improved substantially. However, only few studies have discussed the fundamental limitation of incomplete sampling originated from frequent cloud disturbance and restricted temporal coverage. Furthermore, the AOT trends derived from various polar orbiting satellite observations are hardly comparable due to different sensor calibration, retrieval accuracy, and cloud screening. Therefore, the present paper integrates various analyses of AOT trends derived from multiple observations (i.e. MODIS-Terra (MOD) from 2000/03 to 2009/12, MISR-Terra (MIS) from 2000/03 to 2010/12, SeaWiFS-OrbView-2 (SEA) from 1998/01 to 2007/12, and MODIS-Aqua (MYD) from 2003/01 to 2008/12) using a weighted least squares regression in order to minimize the above mentioned issues. With high statistical confidence, the weighted trends of MOD AOT (550 nm), MIS AOT (558 nm), SEA AOT (510 nm), and MYD AOT (550 nm) over OECD Europe showed a significant decrease (-0.00274�0.00126, -0.00303�0.00169, -0.00077�0.00044, and -0.00530�0.00304 per year respectively) while increasing over East Asia (+0.00727�0.00385, +0.00673�0.00401, +0.00342�0.00171, and +0.01939�0.00986 per year respectively).
Yoon, J.; Vountas, M.; von Hoyningen-Huene, W.; Chang, D. Y.; Burrows, J. P.
Quantitative echotexture analysis of bovine ovarian follicles
Computer-assisted image analysis was used to evaluate ultrasound images of bovine ovarian follicles. The ovaries of 8 sexually mature heifers were examined daily by transrectal ultrasonography for 2 estrous cycles. Ultrasonographic examinations of the ovaries were then videotaped, and the dominant and subordinate follicles of successive waves were individually identified and monitored. Recorded images of the dominant anovulatory follicle of
J. W Tom; R. A Pierson; G. P Adams
Quantitive and Sociological Analysis of Blog Networks
NASA Astrophysics Data System (ADS)
This paper examines the emerging phenomenon of blogging, using three different Polish blogging services as the base of the research. Authors show that blog networks are sharing their characteristics with complex networks (gamma coefficients, small worlds, cliques, etc.). Elements of sociometric analysis were used to prove existence of some social structures in the blog networks.
Bachnik, W.; Szymczyk, S.; Leszczynski, S.; Podsiadlo, R.; Rymszewicz, E.; Kurylo, L.; Makowiec, D.; Bykowska, B.
Quantitative Analysis of Iterated Local Research.
National Technical Information Service (NTIS)
We present a probabilistic analysis of the average case-behavior of the 2-opt algorithm for the Traveling Salesman Problem. We derive an expression for the distribution of local minima of the 2-opt neighborhood. This distribution is numerically computed a...
T. W. M. Vossen M. G. A. Verhoeven H. M. M. ten Eikelder E. H. L. Aarts
A Comparative Assessment of Greek Universities' Efficiency Using Quantitative Analysis
ERIC Educational Resources Information Center
In part due to the increased demand for higher education, typical evaluation frameworks for universities often address the key issue of available resource utilisation. This study seeks to estimate the efficiency of 20 public universities in Greece through quantitative analysis (including performance indicators, data envelopment analysis (DEA) and�
Katharaki, Maria; Katharakis, George
Integrating qualitative and quantitative techniques in network analysis
Purpose � This article introduces a method for assessing network dynamics over time. It integrates a qualitative approach to data collection with a bifocal approach to data analysis, i.e. where data are interpreted with two lenses: qualitative and quantitative. Design\\/methodology\\/approach � The dynamics of an entrepreneurial firm's network are analyzed by combining: content and event analysis of case data and
Nicole E. Coviello
Quantitative landslide risk analysis Examples from B�ldudalur, NW-Iceland
Risk analysis, risk evaluation and risk management are integrated in the holistic concept of risk assessment. Internationally, various quantitative, semiquantitative and qualitative approaches exist to analyse the risk to life and\\/or the economic risk caused by landslides. In Iceland, a method to carry out snow avalanche risk analysis was developed in 1999, followed by rough guidelines on how to integrate
R. Bell; T. Glade
Quantitative Analysis of Chromatin Proteomes in Disease
In the nucleus reside the proteomes whose functions are most intimately linked with gene regulation. Adult mammalian cardiomyocyte nuclei are unique due to the high percentage of binucleated cells,1 the predominantly heterochromatic state of the DNA, and the non-dividing nature of the cardiomyocyte which renders adult nuclei in a permanent state of interphase.2 Transcriptional regulation during development and disease have been well studied in this organ,3-5 but what remains relatively unexplored is the role played by the nuclear proteins responsible for DNA packaging and expression, and how these proteins control changes in transcriptional programs that occur during disease.6 In the developed world, heart disease is the number one cause of mortality for both men and women.7 Insight on how nuclear proteins cooperate to regulate the progression of this disease is critical for advancing the current treatment options. Mass spectrometry is the ideal tool for addressing these questions as it allows for an unbiased annotation of the nuclear proteome and relative quantification for how the abundance of these proteins changes with disease. While there have been several proteomic studies for mammalian nuclear protein complexes,8-13 until recently14 there has been only one study examining the cardiac nuclear proteome, and it considered the entire nucleus, rather than exploring the proteome at the level of nuclear sub compartments.15 In large part, this shortage of work is due to the difficulty of isolating cardiac nuclei. Cardiac nuclei occur within a rigid and dense actin-myosin apparatus to which they are connected via multiple extensions from the endoplasmic reticulum, to the extent that myocyte contraction alters their overall shape.16 Additionally, cardiomyocytes are 40% mitochondria by volume17 which necessitates enrichment of the nucleus apart from the other organelles. Here we describe a protocol for cardiac nuclear enrichment and further fractionation into biologically-relevant compartments. Furthermore, we detail methods for label-free quantitative mass spectrometric dissection of these fractions-techniques amenable to in vivo experimentation in various animal models and organ systems where metabolic labeling is not feasible.
Monte, Emma; Chen, Haodong; Kolmakova, Maria; Parvatiyar, Michelle; Vondriska, Thomas M.; Franklin, Sarah
Quantitative analysis of heart rate variability
In the modern industrialized countries every year several hundred thousands of people diedue to the sudden cardiac death. The individual risk for this sudden cardiac death cannot bedefined precisely by common available, non-invasive diagnostic tools like Holter-monitoring,highly amplified ECG and traditional linear analysis of heart rate variability (HRV). Therefore,we apply some rather unconventional methods of nonlinear dynamics to analyse the
J. Kurths; A. Voss; P. Saparin; A. Witt; H. J. Kleiner; N. Wessel
Chromatic Image Analysis For Quantitative Thermal Mapping
NASA Technical Reports Server (NTRS)
Chromatic image analysis system (CIAS) developed for use in noncontact measurements of temperatures on aerothermodynamic models in hypersonic wind tunnels. Based on concept of temperature coupled to shift in color spectrum for optical measurement. Video camera images fluorescence emitted by phosphor-coated model at two wavelengths. Temperature map of model then computed from relative brightnesses in video images of model at those wavelengths. Eliminates need for intrusive, time-consuming, contact temperature measurements by gauges, making it possible to map temperatures on complex surfaces in timely manner and at reduced cost.
Buck, Gregory M.
Accurate quantitative measurements of asbestos in XRPD analysis.
X-ray Powder Diffraction (XRPD) quantitative analysis of fibrous substances like asbestos, is strongly influenced by systematic errors due to preferred orientation, as a consequence of their morphology. In the present work we have compared the accuracy of quantitative measurements performed by using the Internal Standard (IS) method and the Reference Intensity Ratio (RIR) method in the analysis of the same diffractographs. Both these analytical methods are based on the same principle but the data analysis procedures are different. We have particularly studied how, in the RIR case, the evaluation of several diffraction lines of both phases, standard and unknown, increases the accuracy of a quantitative determination, balancing the different effect due to systematic errors on the measurements of distinct peaks. PMID:11507831
Buccolieri, G; De Stefano, L
Quantitative transcriptome analysis using RNA-seq.
RNA-seq has emerged as the technology of choice to quantify gene expression. This technology is a convenient accurate tool to quantify diurnal changes in gene expression, gene discovery, differential use of promoters, and splice variants for all genes expressed in a single tissue. Thus, RNA-seq experiments provide sequence information and absolute expression values about transcripts in addition to relative quantification available with microarrays or qRT-PCR. The depth of information by sequencing requires careful assessment of RNA intactness and DNA contamination. Although the RNA-seq is comparatively recent, a standard analysis framework has emerged with the packages of Bowtie2, TopHat, and Cufflinks. With rising popularity of RNA-seq tools have become manageable for researchers without much bioinformatical knowledge or programming skills. Here, we present a workflow for a RNA-seq experiment from experimental planning to biological data extraction. PMID:24792045
K�lahoglu, Canan; Br�utigam, Andrea
Quantitative analysis of cardiac electrical restitution.
Electrical restitution (ER) of cardiac cells is an aggregate of events that rhythmically restore the initial conditions of electric signal (action potential) generation. Its analysis represents an important insight into cardiac arrhythmogenesis. The aim of this work is to theoretically substantiate and verify a novel approach allowing for the quantification of the individual ionic current components of ER. A method of analysis of the primary, initial conditions-setting restitution processes (apart from the secondary, test pulse-affected ones) is proposed. Both processes are described as sums of their measurable constituents. It is demonstrated that the optimum parameter of ER is the electric charge that is transferred through ionic channels and carriers during the test impulse. The theory was tested by using voltage-clamped canine ventricular preparations and by computer simulations. The experimental ER curve of canine ventricular muscle was constructed using action potential (AP) plateau voltage and half-repolarization time as parameters. At 30 degrees C and 0.5 Hz stimulation, the ER curve peaked, on average, after 400 ms with a 10% overshoot. Of this plateau elevation, 50% was due to 4-aminopyridine-sensitive transient outward current and 44% was due to verapamil-sensitive current. The delayed outward current antagonized the overshoot by about 6%. It was found that the initial conditions (i.e. the primary restitution processes) tend to strongly alter the plateau voltage of the premature AP. However, the final deviation is by about one order less. It is concluded that the voltage-dependent secondary processes counteract the effect of the primary processes, thereby suggesting strong negative feedback control of natural APs. PMID:11820394
Simurda, J; Simurdov�, M; P�sek, M; Braven�, P
Control of separation and quantitative analysis by GC-FTIR
NASA Astrophysics Data System (ADS)
Software for 3-D representations of the 'Absorbance-Wavenumber-Retention time' is used to control the quality of the GC separation. Spectral information given by the FTIR detection allows the user to be sure that a chromatographic peak is 'pure.' The analysis of peppermint essential oil is presented as an example. This assurance is absolutely required for quantitative applications. In these conditions, we have worked out a quantitative analysis of caffeine. Correlation coefficients between integrated absorbance measurements and concentration of caffeine are discussed at two steps of the data treatment.
Semmoud, A.; Huvenne, Jean P.; Legrand, P.
[Qualitative and quantitative gamma-hydroxybutyrate analysis].
Gamma-hydroxybutyrate (GHB) is a naturally occurring compound present in the brain and peripheral tissues of mammals. It is a minor metabolite and precursor of gamma-aminobutyric acid (GABA). Just as GABA, GHB is believed to play a role in neurotransmission. GHB was first synthesized in vitro in 1960, when it revealed depressive and hypnotic effects on the central nervous system. In 1960s it was used as an anaesthetic and later as an alternative to anabolic steroids, in order to enhance muscle growth. However, after it was shown that it caused strong physical dependence and severe side effects, GHB was banned. For the last fifteen years, GHB has been abused for its intoxicating effects such as euphoria, reduced inhibitions and sedation. Illicitly it is available as white powder or as clear liquid. Paradoxically GHB can easily be manufactured from its precursor gamma-butyrolactone (GBL), which has not yet been banned. Because of many car accidents and criminal acts in which it is involved, GHB has become an important object of forensic laboratory analysis. This paper describes gas and liquid chromatography, infrared spectroscopy, microscopy, colourimetry and nuclear magnetic resonance as methods for detection and quantification of GHB in urine and illicit products. PMID:17265679
Petek, Maja Jelena; Vrdoljak, Ana Luci?
Quantitative EEG in hospital encephalopathy: review and microstate analysis.
Hospital-acquired encephalopathy is a widely prevalent disorder. The quantitative changes in EEG associated with this condition have long been noted, including slowing of the background frequency and changes in the frequency band power. EEG has had limited clinical use, despite its ability to continuously track clinical severity. We review the development of the use of EEG and particularly quantitative EEG in the assessment of hospital-acquired encephalopathy. Recent advances in EEG technology have included network and microstate analyses, and continuous EEG monitoring, leading to renewed interest in the use of quantitative EEG. We describe the development of microstate analysis that has allowed novel quantitative analysis of the resting state background. We examined the microstates of 16 inpatients with encephalopathy and 20 control patients. The global variance explained by the four standard resting microstates was smaller in patients with encephalopathy. This suggests a decrease in microstate stability, indicating a breakdown in the resting state network dynamics. Modern analysis and acquisition techniques hold the promise of renewed interest in quantitative EEG techniques in the assessment of hospital-acquired encephalopathy. PMID:24084185
Sarkis, Rani A; Lee, Jong Woo
A quantitative analysis of the F18 flight control system
NASA Technical Reports Server (NTRS)
This paper presents an informal quantitative analysis of the F18 flight control system (FCS). The analysis technique combines a coverage model with a fault tree model. To demonstrate the method's extensive capabilities, we replace the fault tree with a digraph model of the F18 FCS, the only model available to us. The substitution shows that while digraphs have primarily been used for qualitative analysis, they can also be used for quantitative analysis. Based on our assumptions and the particular failure rates assigned to the F18 FCS components, we show that coverage does have a significant effect on the system's reliability and thus it is important to include coverage in the reliability analysis.
Doyle, Stacy A.; Dugan, Joanne B.; Patterson-Hine, Ann
Issues Related to Data Analysis and Quantitative Methods in PER
NSDL National Science Digital Library
This paper, presented at the 2002 Physics Education Research Conference, offers authors' discussion of some issues that always arise, implicitly or explicitly, when conducting quantitative research and carrying out data analysis in Physics Education Research. (Most are relevant for qualitative research as well.)
Meltzer, David (David Elliott)
Issues Related to Data Analysis and Quantitative Methods in PER
NSDL National Science Digital Library
This paper, presented at the 2002 Physics Education Research Conference, offers authors' discussion of some issues that always arise, implicitly or explicitly, when conducting quantitative research and carrying out data analysis in Physics Education Research. (Most are relevant for qualitative research as well.)
Meltzer, David E.
Analysis of quantitative trait loci that influence animal behavior
Behavioral differences between in- bred strains of mice and rats have a genetic basis that can now be dissected using quantitative trait locus (QTL) analysis. Over the last 10 years, a large number of genetic loci that influence behavior have been mapped. In this article I review what that information has revealed about the genetic architecture of behavior. I show
Jonathan Flint
Insight into quantitative environmental emission analysis of printed circuit board
This paper presents quantitative analysis of environmental emissions in different life cycle stages such as raw material preparation (RMP) and production processing (PP) of printed circuit board. A general emission model for printed circuit board (PCB) has been developed to analyze the emissions to air, fresh water, sea water and industrial soil. This work also demonstrates the quantities of renewable
Rajeev K. Kanth; Pasi Liljeberg; Hannu Tenhunen; Qiansu Wan; Lirong Zheng
Understanding customer needs through quantitative analysis of Kano's model
Purpose � The paper aims to help companies develop a better understanding of customer needs through quantitative analysis of Kano's model. Design\\/methodology\\/approach � A novel approach is developed to measure and quantify the relationships between customer satisfaction and the fulfillment of customer requirements (S-CR) as depicted in Kano's model. A case study concerning notebook computer design is conducted to illustrate
Ting Wang; Ping Ji
Quantitative analysis of trace OH in garnet and pyroxenes
To calibrate infrared (IR) spectroscopy for quantitative analysis of trace structural OH in specific minerals, we have determined concentrations of H in pure separates of mantle- derived pyrope garnet (56 :t 6 ppm H20 by weight), augite (268 :t 8, ppm H20), and enstatite (217 :t 11 ppm H20) by manometry after heating the samples and extracting H2 gas under
Quantitative transverse flow measurement using OCT speckle decorrelation analysis
We propose an inter-Ascan speckle decorrelation based method that can quantitatively assess blood flow normal to the direction of the OCT imaging beam. To validate this method, we performed a systematic study using both phantom and in vivo animal models. Results show that our speckle analysis method can accurately extract transverse flow speed with high spatial and temporal resolution.
Liu, Xuan; Huang, Yong; Ramella-Roman, Jessica C.; Mathews, Scott A.; Kang, Jin U.
Quantitative analysis using remote laser-induced breakdown spectroscopy (LIBS)
A measurement system for quantitative, remote materials analysis has been realised. It is based on the method of laser-induced breakdown spectroscopy (LIBS), utilising an optical fibre system, both to deliver the laser radiation to the sample specimen and to collect the light emission from the luminous plasma plume. Distances of up to 100 m between the remote location and the
C. M. Davies; H. H. Telle; D. J. Montgomery; R. E. Corbett
Using quantitative analysis to implement autonomic IT systems
The software underpinning today's IT systems needs to adapt dynamically and predictably to rapid changes in sys- tem workload, environment and objectives. We describe a software framework that achieves such adaptiveness for IT systems whose components can be modelled as Markov chains. The framework comprises (i) an autonomic archi- tecture that uses Markov-chain quantitative analysis to dy- namically adjust the
Radu Calinescu
INTRODUCTION: GETTING FROM TOXICOLOGY TO QUANTITATIVE ANALYSIS FOR CUMULATIVE RISK Hugh A. Barton1 and Carey N. Pope2 1US EPA, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Research Triangle Park, NC 2Department of...
Quantitative analysis of thallium-201 myocardial emission computed tomography
The clinical usefulness of quantitative analysis of exercise thallium-201 myocardial emission computed tomography (ECT) was evaluated in twenty coronary artery disease patients and 10 normal controls. Longaxial and shortaxial myocardial images of left ventricle were interpreted quantitatively using circumferential profile analysis and two types of abnormality were studied: (1) diminished initial distribution (stress defect) and (2) slow washout of thallium-201, evidenced by patients' initial thallium-201 uptake and 3-hour washout rate profiles falling below the normal limits, respectively. Two diagnostic criteria, stress defect criterion and combined one of stress defect and slow washout, were used to detect significant coronary artery lesions (greater than or equal to75% luminal narrowing). The ischemic volume was also evaluated with quantitative analysis of thallium-201 ECT. The diagnostic accuracy of stress defect criterion was 95% in left ascending, 90% in right coronary and 78% in left circumflex coronary artery lesions. The combined criterion of stress defect and low washout increased detection sensitivity with moderate loss of specificity for identification of individual coronary artery lesions. The ischemic myocardial volume evaluated with combined criterion was significantly larger in triple vessel than in single vessel disease (p<0.05). It was concluded that quantitative analysis of exercise thallium-201 myocardial ECT images was useful for evaluation of coronary artery lesions.
Okada, M.; Kawai, N.; Yamamoto, S.; Matsushima, H.; Kato, R.; Tanahashi, Y.; Sotobata, I.; Obata, Y.; Sakuma, S.
The Evolution of a Laboratory Syllabus for Quantitative Analysis
In this paper, we describe the evolution of a laboratory syllabus for a course in Quantitative Analysis. Over the past two decades, the syllabus has changed from one having individual students do mostly �wet� chemical analyses on commercial unknowns to one having groups of students do instrumental analyses on �real� samples. We describe, in some detail, the current laboratory syllabus,
Quantitating the subtleties of microglial morphology with fractal analysis
It is well established that microglial form and function are inextricably linked. In recent years, the traditional view that microglial form ranges between �ramified resting� and �activated amoeboid� has been emphasized through advancing imaging techniques that point to microglial form being highly dynamic even within the currently accepted morphological categories. Moreover, microglia adopt meaningful intermediate forms between categories, with considerable crossover in function and varying morphologies as they cycle, migrate, wave, phagocytose, and extend and retract fine and gross processes. From a quantitative perspective, it is problematic to measure such variability using traditional methods, but one way of quantitating such detail is through fractal analysis. The techniques of fractal analysis have been used for quantitating microglial morphology, to categorize gross differences but also to differentiate subtle differences (e.g., amongst ramified cells). Multifractal analysis in particular is one technique of fractal analysis that may be useful for identifying intermediate forms. Here we review current trends and methods of fractal analysis, focusing on box counting analysis, including lacunarity and multifractal analysis, as applied to microglial morphology.
Karperien, Audrey; Ahammer, Helmut; Jelinek, Herbert F.
Quantitative analysis of regional myocardial performance in coronary artery disease
NASA Technical Reports Server (NTRS)
Findings from a group of subjects with significant coronary artery stenosis are given. A group of controls determined by use of a quantitative method for the study of regional myocardial performance based on the frame-by-frame analysis of biplane left ventricular angiograms are presented. Particular emphasis was placed upon the analysis of wall motion in terms of normalized segment dimensions, timing and velocity of contraction. The results were compared with the method of subjective assessment used clinically.
Stewart, D. K.; Dodge, H. T.; Frimer, M.
Compound Quantitative Ultrasonic Tomography of Long Bones Using Wavelets Analysis
NASA Astrophysics Data System (ADS)
Compound Quantitative Ultrasonic Tomography (CQUT)is used to long bones imaging. We showed that an iterative tool might be used to provide, from reflection tomography, qualitative images of the shape of the object, and to provide, from transmission tomography, quantitative images of the velocity map. Both tomographies are based on ultrasonic propagation in bones, particularly perturbed by this high-contrasted heterogeneous medium. Reflected and transmitted signal are composed of several packages of waves. We propose a novel algorithm based on the wavelet analysis tool adapted to ultrasonic signals that allow the transmitted signals to be cleaned and filtered and the useful information to be separated from the unwanted noise
Lasaygues, P.
Markov chain Monte Carlo linkage analysis of complex quantitative phenotypes.
We report a Markov chain Monte Carlo analysis of the five simulated quantitative traits in Genetic Analysis Workshop 12 using the Loki software. Our objectives were to determine the efficacy of the Markov chain Monte Carlo method and to test a new scoring technique. Our initial blind analysis, on replicate 42 (the "best replicate") successfully detected four out of the five disease loci and found no false positives. A power analysis shows that the software could usually detect 4 of the 10 trait/gene combinations at an empirical point-wise p-value of 1.5 x 10(-4). PMID:11793758
Hinrichs, A; Reich, T
Quantitative risk analysis of oil storage facilities in seismic areas.
Quantitative risk analysis (QRA) of industrial facilities has to take into account multiple hazards threatening critical equipment. Nevertheless, engineering procedures able to evaluate quantitatively the effect of seismic action are not well established. Indeed, relevant industrial accidents may be triggered by loss of containment following ground shaking or other relevant natural hazards, either directly or through cascade effects ('domino effects'). The issue of integrating structural seismic risk into quantitative probabilistic seismic risk analysis (QpsRA) is addressed in this paper by a representative study case regarding an oil storage plant with a number of atmospheric steel tanks containing flammable substances. Empirical seismic fragility curves and probit functions, properly defined both for building-like and non building-like industrial components, have been crossed with outcomes of probabilistic seismic hazard analysis (PSHA) for a test site located in south Italy. Once the seismic failure probabilities have been quantified, consequence analysis has been performed for those events which may be triggered by the loss of containment following seismic action. Results are combined by means of a specific developed code in terms of local risk contour plots, i.e. the contour line for the probability of fatal injures at any point (x, y) in the analysed area. Finally, a comparison with QRA obtained by considering only process-related top events is reported for reference. PMID:15908107
Fabbrocino, Giovanni; Iervolino, Iunio; Orlando, Francesca; Salzano, Ernesto
Quantitative High-Resolution Genomic Analysis of Single Cancer Cells
During cancer progression, specific genomic aberrations arise that can determine the scope of the disease and can be used as predictive or prognostic markers. The detection of specific gene amplifications or deletions in single blood-borne or disseminated tumour cells that may give rise to the development of metastases is of great clinical interest but technically challenging. In this study, we present a method for quantitative high-resolution genomic analysis of single cells. Cells were isolated under permanent microscopic control followed by high-fidelity whole genome amplification and subsequent analyses by fine tiling array-CGH and qPCR. The assay was applied to single breast cancer cells to analyze the chromosomal region centred by the therapeutical relevant EGFR gene. This method allows precise quantitative analysis of copy number variations in single cell diagnostics.
Hannemann, Juliane; Meyer-Staeckling, Sonke; Kemming, Dirk; Alpers, Iris; Joosse, Simon A.; Pospisil, Heike; Kurtz, Stefan; Gorndt, Jennifer; Puschel, Klaus; Riethdorf, Sabine; Pantel, Klaus; Brandt, Burkhard
The finger-tapping test. A quantitative analysis.
A quantitative analysis of the so-called finger-tapping test was performed on 111 normal subjects. Quantitative analysis was also performed on 17 patients with cerebellar diseases, 14 with parkinsonism, and 14 with hemiparesis. All analyses were performed in a simple fashion using an 8-bit microcomputer fed through an electrocardiographic apparatus. The results in normal subjects were as follows: (1) tapping frequency lowered with advancing age; (2) men tapped faster than women; and (3) tapping with the dominant finger was faster than tapping with the nondominant finger in normal subjects. Tapping frequency can distinguish patients with motor dysfunctions of cerebellar, basal ganglia, and cerebral origins from normal subjects. Only the time-sequential histograms of tapping intervals could distinguish the motor dysfunctions studied. PMID:2346396
Shimoyama, I; Ninchoji, T; Uemura, K
Quantitative Analysis of Phospholipids Using Nanostructured Laser Desorption Ionization Targets
Since its introduction as an ionization technique in mass spectrometry, matrix-assisted laser desorption ionization (MALDI)\\u000a has been applied to a wide range of applications. Quantitative small molecule analysis by MALDI, however, is limited due to\\u000a the presence of intense signals from the matrix coupled with non-homogeneous surfaces. The surface used in nano-structured\\u000a laser desorption ionization (NALDI) eliminates the need for
Simona ColantonioJohn; John T. Simpson; Robert J. Fisher; Amichai Yavlovich; Julie M. Belanger; Anu Puri; Robert Blumenthal
Theoretical Sensitivity Analysis for Quantitative Operational Risk Management
We study the asymptotic behaviour of the difference between the Value at Risks VaR(L) and VaR(L+S) for heavy tailed random variables L and S as an application to the sensitivity analysis of quantitative operational risk management in the framework of an advanced measurement approach (AMA) of Basel II. Here the variable L describes the loss amount of the present risk
Takashi Kato
Quantitative analysis of lipids by thin-layer chromatography
A procedure is described for the quantitative analysis of neutral and phospholipids by thinlayer chromatography (TLC) employing\\u000a densitometry. The chromatophates are prepared with the usual solvent systems. The spots are charred under standard conditions\\u000a and analyzed with a Photovolt Corp. densitometer equipped with a special stage designed for holding 20�20 cm chromatoplates.\\u000a Each spot on the chromatoplate gives a peak
M. L. Blank; J. A. Schmit; O. S. Privett
Lipid analysis by quantitative thin-layer chromatography
Techniques for the quantitative analysis of lipids using thin-layer chromatography (TLC) are reviewed. The general procedures\\u000a are divided into two groups on the basis of whether or not the methods involve the recovery of substances from chromatoplates.\\u000a \\u000a Recovery methods are elaborated under detection of spots, recovery of substances and quantification. Methods are described\\u000a for the recovery of labile compounds from
O. S. Privett; M. L. Blank; D. W. Codding; E. C. Nickell
Quantitative analysis of SCIAMACHY carbon monoxide total column measurements
This paper presents a first quantitative and systematic analysis of one year of SCIAMACHY Carbon Monoxide (CO) total column retrievals from the IMLM algorithm (v6.3) using a chemistry-transport model simulation. The global distribution of modeled and measured CO show similar spatial patterns: a north-south gradient, low CO over mountains, and high CO over emission regions. CO column errors due to
A. T. J. de Laat; A. M. S. Gloudemans; H. Schrijver; J. F. Meirink; I. Aben; M. C. Krol
Quantitative analysis of food fatty acids by capillary gas chromatography
The superior efficiency of capillary columns is desirable for the gas chromatographic analysis of complex mixtures of fatty\\u000a acids, but there have been some reservations regarding quantitation and reproducibility. This paper discusses the use of wall-coated\\u000a glass capillary columns in a semiautomated system for the determination of food fatty acids. Glass columns coated with SP2340\\u000a were used for extended periods
H. T. Slover; E. Lanza
A quantitative analysis of coupled oscillations using mobile accelerometer sensors
NASA Astrophysics Data System (ADS)
In this paper, smartphone acceleration sensors were used to perform a quantitative analysis of mechanical coupled oscillations. Symmetric and asymmetric normal modes were studied separately in the first two experiments. In the third, a coupled oscillation was studied as a combination of the normal modes. Results indicate that acceleration sensors of smartphones, which are very familiar to students, represent valuable measurement instruments for introductory and first-year physics courses.
Castro-Palacio, Juan Carlos; Vel�zquez-Abad, Luisberis; Gim�nez, Fernando; Monsoriu, Juan A.
Qualitative and quantitative analysis of the adult Drosophila melanogaster proteome.
Drosophila melanogaster is one of the most widely used model organisms in life sciences. Mapping its proteome is of great significance for understanding the biological characteristics and tissue functions of this species. However, the comprehensive coverage of its proteome remains a challenge. Here, we describe a high-coverage analysis of whole fly through a 1D gel electrophoresis and LC-MS/MS approach. By combining the datasets of two types of SDS-PAGE and two kinds of tagmata, the high-coverage analysis resulted in the identification of 5262 genes, which correspond to 38.23% of the entire coding genes. Moreover, we found that the fly head and body have different molecular weight distributions of their proteomes when the proteins were resolved with SDS-PAGE and image analysis of the stained gel. This phenomenon was further confirmed by both label-free and isobaric tags for relative and absolute quantitation-based quantitative approaches. The consistent results of the two different quantitation methods also demonstrated the stability and accuracy of the LC-MS/MS platform. The MS proteomics data have been deposited to the ProteomeXchange with identifiers PXD000454 and PXD000455 (http://proteomecentral.proteomexchange.org/dataset/PXD000454; (http://proteomecentral.proteomexchange.org/dataset/PXD000455). PMID:24259522
Xing, Xiaohua; Zhang, Chengpu; Li, Ning; Zhai, Linhui; Zhu, Yunping; Yang, Xiaoming; Xu, Ping
Mini-Column Ion-Exchange Separation and Atomic Absorption Quantitation of Nickel, Cobalt, and Iron: An Undergraduate Quantitative Analysis Experiment.
ERIC Educational Resources Information Center
Presents an undergraduate quantitative analysis experiment, describing an atomic absorption quantitation scheme that is fast, sensitive and comparatively simple relative to other titration experiments. (CS)
Anderson, James L.; And Others
Aquaculture Network Information Center (AquaNIC)
NSDL National Science Digital Library
Links to national and international level electronic resources for aquaculture information including: scientific institutions, agencies, industries, news, newsletters, job listings, discussion groups, courses, species, publications, and commercial products. Goals include: providing self-paced aquaculture instruction to the aquaculture industry, and obtaining user input in directing AquaNIC services. A version in Spanish is being prepared.
Status of terra MODIS and aqua modis
Nearly identical copies of the Moderate Resolution Imaging Spectroradiometer (MODIS) have been operating onboard the Earth Observing System (EOS) Terra and Aqua satellites for 34 and 5 months respectively. Both are performing as designed. Sensitivities, with minor exceptions, are better than specified. Short- and long-term stability is very good. Trending of the Terra sensor has revealed degradation of the solar
W. L. Barnes; X. Xiong; V. V. Salomonson
Quantitative Analysis of Phospholipids Using Nanostructured Laser Desorption Ionization Targets�
Since its introduction as an ionization technique in mass spectrometry, matrix assisted laser desorption ionization (MALDI) has been applied to a wide range of applications. Quantitative small molecule analysis by MALDI, however, is limited due to the presence of intense signals from the matrix coupled with non-homogeneous surfaces. The surface used in nanostructured laser desorption ionization (NALDI) eliminates the need for a matrix and the resulting interferences, and allows for quantitative analysis of small molecules. This study was designed to analyze and quantitate phospholipid components of liposomes. Here we have developed an assay to quantitate the DPPC and DC8,9PC in liposomes by NALDI following various treatments. To test our method we chose to analyze a liposome system composed of DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) and DC8,9PC (1,2-bis (tricosa-10,12-diynoyl)-sn-glycero-3-phosphocholine), as DC8,9PC is known to undergo cross-linking upon treatment with UV (254 nm) and this reaction converts the monomer into a polymer. First, calibration curves for pure lipids (DPPC and DC8,9PC) were created using DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) as an internal standard. The calibration curve for both DPPC and DC8,9PC showed an R2 of 0.992, obtained using the intensity ratio of analyte and internal standard. Next, DPPC:DC8,9PC liposomes were treated with UV radiation (254 nm). Following this treatment, lipids were extracted from the liposomes and analyzed. The analysis of the lipids before and after UV exposure confirmed a decrease in the signal of DC8,9PC of about 90%. In contrast, there was no reduction in DPPC signal.
Colantonio, Simona; Simpson, John T.; Fisher, Robert J.; Yavlovich, Amichai; Belanger, Julie M.; Puri, Anu; Blumenthal, Robert
Quantitative analysis of phospholipids using nanostructured laser desorption ionization targets.
Since its introduction as an ionization technique in mass spectrometry, matrix-assisted laser desorption ionization (MALDI) has been applied to a wide range of applications. Quantitative small molecule analysis by MALDI, however, is limited due to the presence of intense signals from the matrix coupled with non-homogeneous surfaces. The surface used in nano-structured laser desorption ionization (NALDI) eliminates the need for a matrix and the resulting interferences, and allows for quantitative analysis of small molecules. This study was designed to analyze and quantitate phospholipid components of liposomes. Here we have developed an assay to quantitate the DPPC and DC(8,9)PC in liposomes by NALDI following various treatments. To test our method we chose to analyze a liposome system composed of DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) and DC(8,9)PC (1,2-bis(tricosa-10,12-diynoyl)-sn-glycero-3-phosphocholine), as DC(8,9)PC is known to undergo cross-linking upon treatment with UV (254 nm) and this reaction converts the monomer into a polymer. First, calibration curves for pure lipids (DPPC and DC(8,9)PC) were created using DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) as an internal standard. The calibration curve for both DPPC and DC(8,9)PC showed an R(2) of 0.992, obtained using the intensity ratio of analyte and internal standard. Next, DPPC:DC(8,9)PC liposomes were treated with UV radiation (254 nm). Following this treatment, lipids were extracted from the liposomes and analyzed. The analysis of the lipids before and after UV exposure confirmed a decrease in the signal of DC(8,9)PC of about 90%. In contrast, there was no reduction in DPPC signal. PMID:21327726
Colantonio, Simona; Simpson, John T; Fisher, Robert J; Yavlovich, Amichai; Belanger, Julie M; Puri, Anu; Blumenthal, Robert
A comparison of three quantitative motor unit analysis algorithms.
This study assessed the accuracy of three automatic motor unit analysis algorithms--multi-motor unit analysis, decomposition quantitative EMG, and EMGtools--on a set of real EMG signals whose true composition was determined by manual decomposition. All three algorithms correctly identified all the MUs in signals with up to 5 active MUs, and most of the MUs in signals with up to 10 active MUs. The algorithms accurately estimated MUAP amplitudes and firing rates, but they estimated duration less accurately because of baseline noise. These findings support the validity and utility of these algorithms. PMID:20715389
McGill, Kevin C
Universal quantitative NMR analysis of complex natural samples.
Nuclear Magnetic Resonance (NMR) is a universal and quantitative analytical technique. Being a unique structural tool, NMR also competes with metrological techniques for purity determination and reference material analysis. In pharmaceutical research, applications of quantitative NMR (qNMR) cover mostly the identification and quantification of drug and biological metabolites. Offering an unbiased view of the sample composition, and the possibility to simultaneously quantify multiple compounds, qNMR has become the method of choice for metabolomic studies and quality control of complex natural samples such as foods, plants or herbal remedies, and biofluids. In this regard, NMR-based metabolomic studies, dedicated to both the characterization of herbal remedies and clinical diagnosis, have increased considerably. PMID:24484881
Simmler, Charlotte; Napolitano, Jos� G; McAlpine, James B; Chen, Shao-Nong; Pauli, Guido F
Quantitative analysis of herpes simplex virus in cranial nerve ganglia.
A susceptible individual exposed to herpes simplex virus (HSV) will develop latent infection in multiple cranial nerve ganglia. There are a few quantitative studies of the viral load within the trigeminal ganglion, but none that investigate other cranial nerve ganglia. In this study, human trigeminal, geniculate, vestibular (Scarpa's) and cochlear (spiral) ganglia were obtained from willed body donors. Real time quantitative polymerase chain reaction (PCR) analysis of the HSV DNA polymerase gene was performed on ipsilateral ganglion sets from the same individual. Viral load, expressed as HSV genomes per 105 cells, was significantly greater in the vestibular ganglion (mean +/- SD, 176705 +/- 255916) than in the geniculate (9948 +/- 22066), cochlear (3527 +/- 9360), or trigeminal (2017 +/- 5578) ganglia. There was not a significant correlation among ganglia from the same individual. The results support the hypothesis that neuronal subpopulations have variable susceptibility to HSV infection. PMID:15371151
Vrabec, Jeffrey T; Alford, Raye L
Label-Free Technologies for Quantitative Multiparameter Biological Analysis
In the post-genomic era, information is king and information-rich technologies are critically important drivers in both fundamental biology and medicine. It is now known that single-parameter measurements provide only limited detail and that quantitation of multiple biomolecular signatures can more fully illuminate complex biological function. Label-free technologies have recently attracted significant interest for sensitive and quantitative multiparameter analysis of biological systems. There are several different classes of label-free sensors that are currently being developed both in academia and in industry. In this critical review, we highlight, compare, and contrast some of the more promising approaches. We will describe the fundamental principles of these different methodologies and discuss advantages and disadvantages that might potentially help one in selecting the appropriate technology for a given bioanalytical application.
Qavi, Abraham J.; Washburn, Adam L.; Byeon, Ji-Yeon; Bailey, Ryan C.
Chroma analysis for quantitative immunohistochemistry using active learning
NASA Astrophysics Data System (ADS)
Protein expression analysis has traditionally relied upon visual evaluation of immunohistochemical reaction by a pathologist, who analyzes the grade of staining intensity and estimates the percentage of cells stained in the area of interest. This method is effective in experienced hands but has potential limitations in its reproducibility due to subjectivity between and within operators. These limitations are particularly pronounced in gray areas where a distinction of weak from moderate protein expression can be clinically significant. Some research also suggests that sub localization of the protein expression into different components such as nuclei versus cytoplasm may be of great importance. This distinction can be particularly difficult to quantify using manual methods. In this paper, we formulate the problem of quantitative protein expression analysis as an active learning classification problem, where a very small set of pre-sampled user data is used for understanding expert evaluation. The expert coveted confidence is mapped to derive an uncertainty region to select the supplemental learning data. This is done by posing a structured query to the unknown data set. The newly identified samples are then augmented to the training set for incremental learning. The strength of our algorithm is measured in its ability to learn with minimum user interaction. Chroma analysis results of a Tissue Micro-array (TMA) images are presented to demonstrate the user interaction and learning ability. The chroma analysis results are then processed to obtain quantitative results.
Patel, Nilesh; Ma, Aiyesha; Shah, Rajal; Sethi, Ishwar
Quantitative Remote Laser-Induced Breakdown Spectroscopy by Multivariate Analysis
NASA Astrophysics Data System (ADS)
The ChemCam instrument selected for the Mars Science Laboratory (MSL) rover includes a remote Laser- Induced Breakdown Spectrometer (LIBS) that will quantitatively probe samples up to 9m from the rover mast. LIBS is fundamentally an elemental analysis technique. LIBS involves focusing a Nd:YAG laser operating at 1064 nm onto the surface of the sample. The laser ablates material from the surface, generating an expanding plasma containing electronically excited ions, atoms, and small molecules. As these electronically excited species relax back to the ground state, they emit light at wavelengths characteristic of the species present in the sample. Some of this emission is directed into one of three dispersive spectrometers. In this paper, we studied a suite of 18 igneous and highly-metamorphosed samples from a wide variety of parageneses for which chemical analyses by XRF were already available. Rocks were chosen to represent a range of chemical composition from basalt to rhyolite, thus providing significant variations in all of the major element contents (Si, Fe, Al, Ca, Na, K, O, Ti, Mg, and Mn). These samples were probed at a 9m standoff distance under experimental conditions that are similar to ChemCam. Extracting quantitative elemental concentrations from LIBS spectra is complicated by the chemical matrix effects. Conventional methods for obtaining quantitative chemical data from LIBS analyses are compared with new multivariate analysis (MVA) techniques that appear to compensate for these chemical matrix effects. The traditional analyses use specific elemental peak heights or areas, which compared with calibration curves for each element at one or more emission lines for a series of standard samples. Because of matrix effects, the calibration standards generally must have similar chemistries to the unknown samples, and thus this conventional approach imposes severe limitations on application of the technique to remote analyses. In this suite of samples, the use of traditional methods results in chemical analyses with significant uncertainties. Alternatively, greatly-improved quantitative elemental analysis was accomplished by using a Partial Least Squares (PLS) calibration model for all of the major elements of interest. Principal Components Analysis (PCA) and Soft Independent Modeling of Class Analogy (SIMCA) are then employed to predict the rock-type of the sample. These MVA techniques appear to compensate for these matrix effects because the analysis finds correlations between the spectra (independent variables), the individual elements of interest (dependent variables such as Si) as well as the other elements in the matrix.
Clegg, S. M.; Sklute, E. C.; Dyar, M. D.; Barefield, J. E.; Wiens, R. C.
Operational Experiences in Planning and Reconstructing Aqua Inclination Maneuvers
NASA Technical Reports Server (NTRS)
As the lead satellite in NASA's growing Earth Observing System (EOS) PM constellation, it is increasingly critical that Aqua maintain its various orbit requirements. The two of interest for this paper are maintaining an orbit inclination that provides for a consistent mean local time and a semi-major Axis (SMA) that allows for ground track repeatability. Maneuvers to adjust the orbit inclination involve several flight dynamics constraints and complexities which make planning such maneuvers challenging. In particular, coupling between the orbital and attitude degrees of freedom lead to changes in SMA when changes in inclination are effected. A long term mission mean local time trend analysis was performed in order to determine the size and placement of the required inclination maneuvers. Following this analysis, detailed modeling of each burn and its Various segments was performed to determine its effects on the immediate orbit state. Data gathered from an inclination slew test of the spacecraft and first inclination maneuver uncovered discrepancies in the modeling method that were investigated and resolved. The new modeling techniques were applied and validated during the second spacecraft inclination maneuver. These improvements should position Aqua to successfully complete a series of inclination maneuvers in the fall of 2004. The following paper presents the events and results related
Rand, David; Reilly, Jacqueline; Schiff, Conrad
Quantitative analysis of liver Golgi proteome in the cell cycle.
During mitosis, the Golgi membranes in mammalian cells undergo a continuous disassembly process and generate mitotic fragments that are distributed into the daughter cells and reassembled into new Golgi after mitosis. This disassembly and reassembly process is critical for Golgi biogenesis during cell division, but the underlying molecular mechanism is poorly understood. In this study, we have recapitulated this process using an in vitro assay and analyzed the proteins that are associated with interphase and mitotic Golgi membranes using quantitative proteomics that combines the isobaric tags for relative and absolute quantification approach with OFFGEL isoelectric focusing separation and LC-MALDI-MS/MS. A total of 1,193 Golgi-associated proteins were identified and quantified. These included broad functional categories: Golgi structural proteins, Golgi resident enzymes, SNAREs, Rab GTPases, and secretory and cytoskeletal proteins. More importantly, the combination of the quantitative proteomic approach with Western blot analysis allowed us to unveil 86 proteins with significant changes in abundance under the mitotic condition compared to the interphase condition. Altogether, this systematic quantitative proteomic study revealed candidate proteins of the molecular machinery that controls the Golgi disassembly and reassembly processes in the cell cycle. PMID:22903713
Chen, Xuequn; Andrews, Philip C; Wang, Yanzhuang
A quantitative analysis of IRAS maps of molecular clouds
NASA Technical Reports Server (NTRS)
We present an analysis of IRAS maps of five molecular clouds: Orion, Ophiuchus, Perseus, Taurus, and Lupus. For the classification and description of these astrophysical maps, we use a newly developed technique which considers all maps of a given type to be elements of a pseudometric space. For each physical characteristic of interest, this formal system assigns a distance function (a pseudometric) to the space of all maps: this procedure allows us to measure quantitatively the difference between any two maps and to order the space of all maps. We thus obtain a quantitative classification scheme for molecular clouds. In this present study we use the IRAS continuum maps at 100 and 60 micrometer(s) to produce column density (or optical depth) maps for the five molecular cloud regions given above. For this sample of clouds, we compute the 'output' functions which measure the distribution of density, the distribution of topological components, the self-gravity, and the filamentary nature of the clouds. The results of this work provide a quantitative description of the structure in these molecular cloud regions. We then order the clouds according to the overall environmental 'complexity' of these star-forming regions. Finally, we compare our results with the observed populations of young stellar objects in these clouds and discuss the possible environmental effects on the star-formation process. Our results are consistent with the recently stated conjecture that more massive stars tend to form in more 'complex' environments.
Wiseman, Jennifer J.; Adams, Fred C.
Variability in quantitative cardiac magnetic resonance perfusion analysis
By taking advantage of its high spatial resolution, noninvasive and nontoxic nature first-pass perfusion cardiovascular magnetic resonance (CMR) has rendered an indispensable tool for the noninvasive detection of reversible myocardial ischemia. A potential advantage of perfusion CMR is its ability to quantitatively assess perfusion reserve within a myocardial segment, as expressed semi- quantitatively by myocardial perfusion reserve index (MPRI) and fully- quantitatively by absolute myocardial blood flow (MBF). In contrast to the high accuracy and reliability of CMR in evaluating cardiac function and volumes, perfusion CMR is adversely affected by multiple potential reasons during data acquisition as well as post-processing. Various image acquisition techniques, various contrast agents and doses as well as variable blood flow at rest as well as variable reactions to stress all influence the acquired data. Mechanisms underlying the variability in perfusion CMR post processing, as well as their clinical significance, are yet to be fully elucidated. The development of a universal, reproducible, accurate and easily applicable tool in CMR perfusion analysis remains a challenge and will substantially enforce the role of perfusion CMR in improving clinical care.
Bratis, K.
Quantitative analysis of lipid deposits from Schnyder's corneal dystrophy
AIM�To report the quantitation of the lipid composition of a corneal button from a Japanese woman in her 60s with clinically and histopathologically proved Schnyder's corneal dystrophy.?METHODS�Total lipids extracted from the corneal button of the patient were analysed by the method of thin layer chromatography flame ionisation detection. Two different solvent systems were used for neutral lipid analysis and phospholipid analysis. Results were compared with three age matched corneal buttons obtained from cadaveric eyes.?RESULTS�The lipids that accumulated in the cornea in Schnyder's dystrophy consisted mainly of unesterified cholesterol and phospholipids. The analysis of phospholipids showed sphingomyelin to be the predominant phospholipid in the patient's cornea.?CONCLUSION�Findings suggest that this disorder involves a disturbance of the metabolism of cholesterol and/or sphingomyelin metabolism that is limited to the cornea.?? Keywords: Schnyder's dystrophy; lipids; unesterified cholesterol; sphingomyelin
Yamada, M.; Mochizuki, H.; Kamata, Y.; Nakamura, Y.; Mashima, Y.
Analysis of fungal gene expression by Real Time quantitative PCR.
The Real-Time quantitative PCR (qPCR) method has become central for the quantification of gene expression as well as other applications. The major advantages of qPCR are the utilization of small amount of template, high sensitivity and the ability to detect products during the reaction. After selecting qPCR among other options (northern blot, semi-quantitative PCR), one should consider several factors. The first and critical step in qPCR of fungi is the selection of an appropriate growth medium and RNA extraction method, which will avoid accumulation of inhibitors. In this chapter, we focus on detection of the accumulating product with the Syber Green dye, but other detection technologies, such as hybridization probes, might be considered as well. Accurate qPCR analysis with Syber Green depends mainly on optimal PCR reaction, and therefore it is important to design primers that will avoid formation of interfering structures. It is possible to use absolute quantification of the template in the sample, or to conduct a relative analysis, as described in this protocol. In the relative analysis method, expression of the gene of interest is compared with expression of a reference gene. According to our experience as well as according to the literature, it is recommended to use at least three reference genes in order to obtain reliable results. PMID:20238263
Ish-Shalom, Shahar; Lichter, Amnon
Quantitative proteomic analysis of drug-induced changes in mycobacteria.
A new approach for qualitative and quantitative proteomic analysis using capillary liquid chromatography and mass spectrometry to study the protein expression response in mycobacteria following isoniazid treatment is discussed. In keeping with known effects on the fatty acid synthase II pathway, proteins encoded by the kas operon (AcpM, KasA, KasB, Accd6) were significantly overexpressed, as were those involved in iron metabolism and cell division suggesting a complex interplay of metabolic events leading to cell death. PMID:16396495
Hughes, Minerva A; Silva, Jeffrey C; Geromanos, Scott J; Townsend, Craig A
Quantitative analysis of a noninvasive stereotactic image registration technique.
Our group has developed and tested a noninvasive image registration technique that does not require a special imaging study following the application of a head frame or radiological markers on the patient. This registration method involves performing automatic alignment between segmented scalp reconstructions from CT or MRI fitted with are surfaces traced with the Regulus Navigator. This paper will present a quantitative analysis of this technique compared to other stereotactic and image-guided registration techniques. This noninvasive surface alignment technique has been found to be a viable, quick and accurate method of performing image-guided registration. PMID:8938935
Kall, B A; Goerss, S J; Stiving, S O; Davis, D H; Kelly, P J
Quantitative analysis of neutral glycosphingolipids from human lymphocyte subpopulations.
The glycosphingolipids of normal human lymphocytes from individual donors were analysed by high-pressure liquid chromatography. In addition, purified T- and B-lymphocytes were examined separately. Lactosylceramide was shown to be the major neutral glycosphingolipid in human lymphocytes, and monohexosylceramide, trihexosylceramide, globoside and paragloboside were all detected in smaller amounts. Analysis of purified B- and T-cell fractions revealed that each of these populations contained a similar qualitative profile for neutral glycosphingolipids, but that quantitatively, B-cells contained several times more of each glycosphingolipid per cell than did T-cells.
Schwarting, G A
Quantitative analysis of neutral glycosphingolipids from human lymphocyte subpopulations.
The glycosphingolipids of normal human lymphocytes from individual donors were analysed by high-pressure liquid chromatography. In addition, purified T- and B-lymphocytes were examined separately. Lactosylceramide was shown to be the major neutral glycosphingolipid in human lymphocytes, and monohexosylceramide, trihexosylceramide, globoside and paragloboside were all detected in smaller amounts. Analysis of purified B- and T-cell fractions revealed that each of these populations contained a similar qualitative profile for neutral glycosphingolipids, but that quantitatively, B-cells contained several times more of each glycosphingolipid per cell than did T-cells. PMID:6971095
Schwarting, G A
Lipid biomarker analysis for the quantitative analysis of airborne microorganisms
There is an ever increasing concern regarding the presence of airborne microbial contaminants within indoor air environments. Exposure to such biocontaminants can give rise to large numbers of different health effects including infectious diseases, allergenic responses and respiratory problems, Biocontaminants typically round in indoor air environments include bacteria, fungi, algae, protozoa and dust mites. Mycotoxins, endotoxins, pollens and residues of organisms are also known to cause adverse health effects. A quantitative detection/identification technique independent of culturability that assays both culturable and non culturable biomass including endotoxin is critical in defining risks from indoor air biocontamination. Traditionally, methods employed for the monitoring of microorganism numbers in indoor air environments involve classical culture based techniques and/or direct microscopic counting. It has been repeatedly documented that viable microorganism counts only account for between 0.1-10% of the total community detectable by direct counting. The classic viable microbiologic approach doe`s not provide accurate estimates of microbial fragments or other indoor air components that can act as antigens and induce or potentiate allergic responses. Although bioaerosol samplers are designed to damage the microbes as little as possible, microbial stress has been shown to result from air sampling, aerosolization and microbial collection. Higher collection efficiency results in greater cell damage while less cell damage often results in lower collection efficiency. Filtration can collect particulates at almost 100% efficiency, but captured microorganisms may become dehydrated and damaged resulting in non-culturability, however, the lipid biomarker assays described herein do not rely on cell culture. Lipids are components that are universally distributed throughout cells providing a means to assess independent of culturability.
Macnaughton, S.J.; Jenkins, T.L.; Cormier, M.R. [Microbial Insights Inc., Rockford, TN (United States)] [and others
Enhanced efficiency of quantitative trait loci mapping analysis based on multivariate complexes of quantitative traits.
An approach to increase the efficiency of mapping quantitative trait loci (QTL) was proposed earlier by the authors on the basis of bivariate analysis of correlated traits. The power of QTL detection using the log-likelihood ratio (LOD scores) grows proportionally to the broad sense heritability. We found that this relationship holds also for correlated traits, so that an increased bivariate heritability implicates a higher LOD score, higher detection power, and better mapping resolution. However, the increased number of parameters to be estimated complicates the application of this approach when a large number of traits are considered simultaneously. Here we present a multivariate generalization of our previous two-trait QTL analysis. The proposed multivariate analogue of QTL contribution to the broad-sense heritability based on interval-specific calculation of eigenvalues and eigenvectors of the residual covariance matrix allows prediction of the expected QTL detection power and mapping resolution for any subset of the initial multivariate trait complex. Permutation technique allows chromosome-wise testing of significance for the whole trait complex and the significance of the contribution of individual traits owing to: (a) their correlation with other traits, (b) dependence on the chromosome in question, and (c) both a and b. An example of application of the proposed method on a real data set of 11 traits from an experiment performed on an F(2)/F(3) mapping population of tetraploid wheat (Triticum durum x T. dicoccoides) is provided.
Korol, A B; Ronin, Y I; Itskovich, A M; Peng, J; Nevo, E
Quantitative analysis of volume images: electron microscopic tomography of HIV
NASA Astrophysics Data System (ADS)
Three-dimensional objects should be represented by 3D images. So far, most of the evaluation of images of 3D objects have been done visually, either by looking at slices through the volumes or by looking at 3D graphic representations of the data. In many applications a more quantitative evaluation would be valuable. Our application is the analysis of volume images of the causative agent of the acquired immune deficiency syndrome (AIDS), namely human immunodeficiency virus (HIV), produced by electron microscopic tomography (EMT). A structural analysis of the virus is of importance. The representation of some of the interesting structural features will depend on the orientation and the position of the object relative to the digitization grid. We describe a method of defining orientation and position of objects based on the moment of inertia of the objects in the volume image. In addition to a direct quantification of the 3D object a quantitative description of the convex deficiency may provide valuable information about the geometrical properties. The convex deficiency is the volume object subtracted from its convex hull. We describe an algorithm for creating an enclosing polyhedron approximating the convex hull of an arbitrarily shaped object.
Nystroem, Ingela; Bengtsson, Ewert W.; Nordin, Bo G.; Borgefors, Gunilla
Multivariate calibration applied to the quantitative analysis of infrared spectra
Multivariate calibration methods are very useful for improving the precision, accuracy, and reliability of quantitative spectral analyses. Spectroscopists can more effectively use these sophisticated statistical tools if they have a qualitative understanding of the techniques involved. A qualitative picture of the factor analysis multivariate calibration methods of partial least squares (PLS) and principal component regression (PCR) is presented using infrared calibrations based upon spectra of phosphosilicate glass thin films on silicon wafers. Comparisons of the relative prediction abilities of four different multivariate calibration methods are given based on Monte Carlo simulations of spectral calibration and prediction data. The success of multivariate spectral calibrations is demonstrated for several quantitative infrared studies. The infrared absorption and emission spectra of thin-film dielectrics used in the manufacture of microelectronic devices demonstrate rapid, nondestructive at-line and in-situ analyses using PLS calibrations. Finally, the application of multivariate spectral calibrations to reagentless analysis of blood is presented. We have found that the determination of glucose in whole blood taken from diabetics can be precisely monitored from the PLS calibration of either mind- or near-infrared spectra of the blood. Progress toward the non-invasive determination of glucose levels in diabetics is an ultimate goal of this research. 13 refs., 4 figs.
Haaland, D.M.
[Quantitative analysis of butachlor, oxadiazon and simetryn by gas chromatography].
The quantitative analysis of the ingredients in 26% B-O-S (butachlor, oxadiazon and simetryn) emulsion by gas chromatographic method was carried out with a 5% SE-30 on Chromosorb AW DMCS, 2 m x 3 mm i.d., glass column at column temperature of 210 degrees C and detector temperature of 230 degrees C. The internal standard is di-n-butyl sebacate. The retentions of simetryn, internal standard, butachlor and oxadiazon were 6.5, 8.3, 9.9 and 11.9 min respectively. This method has a recovery of 98.62%-100.77% and the coefficients of variation of this analysis of butachlor, oxadiazon and simetryn were 0.46%, 0.32% and 0.57% respectively. All coefficients of linear correlation were higher than 0.999. PMID:12549176
Liu, F; Mu, W; Wang, J
Quantitative Analysis of Genetic and Neuronal Multi-Perturbation Experiments
Perturbation studies, in which functional performance is measured after deletion, mutation, or lesion of elements of a biological system, have been traditionally employed in many fields in biology. The vast majority of these studies have been qualitative and have employed single perturbations, often resulting in little phenotypic effect. Recently, newly emerging experimental techniques have allowed researchers to carry out concomitant multi-perturbations and to uncover the causal functional contributions of system elements. This study presents a rigorous and quantitative multi-perturbation analysis of gene knockout and neuronal ablation experiments. In both cases, a quantification of the elements' contributions, and new insights and predictions, are provided. Multi-perturbation analysis has a potentially wide range of applications and is gradually becoming an essential tool in biology.
Meilijson, Isaac; Kupiec, Martin; Ruppin, Eytan
Fusing Quantitative Requirements Analysis with Model-based Systems Engineering
NASA Technical Reports Server (NTRS)
A vision is presented for fusing quantitative requirements analysis with model-based systems engineering. This vision draws upon and combines emergent themes in the engineering milieu. "Requirements engineering" provides means to explicitly represent requirements (both functional and non-functional) as constraints and preferences on acceptable solutions, and emphasizes early-lifecycle review, analysis and verification of design and development plans. "Design by shopping" emphasizes revealing the space of options available from which to choose (without presuming that all selection criteria have previously been elicited), and provides means to make understandable the range of choices and their ramifications. "Model-based engineering" emphasizes the goal of utilizing a formal representation of all aspects of system design, from development through operations, and provides powerful tool suites that support the practical application of these principles. A first step prototype towards this vision is described, embodying the key capabilities. Illustrations, implications, further challenges and opportunities are outlined.
Cornford, Steven L.; Feather, Martin S.; Heron, Vance A.; Jenkins, J. Steven
AMSR-E/Aqua Gridded Brightness Temperatures
NASA Astrophysics Data System (ADS)
Passive microwave brightness temperature data are a major component in many geophysical models and algorithms. For many researchers, a major difficulty in using these data is transforming the satellite swath data into a model-friendly, gridded format. Two new data sets and improvements to a toolkit at the National Snow and Ice Data Center (NSIDC) will help scientists incorporate these data into their research. We have produced "AMSR-E/Aqua Daily EASE-Grid Brightness Temperatures" from the Advanced Microwave Scanning Radiometer - Earth Observing System (AMSR-E) instrument aboard NASA's Earth Observing System (EOS) Aqua satellite. This data set will complement and extend NSIDC's existing EASE-grid brightness temperature data sets, with new data beginning June 2002 and continuing throughout the life-cycle of the instrument. Additionally, in order to respond to user demand for quarter-degree data, we are distributing "AMSR-E/Aqua Daily Global Quarter-Degree Gridded Brightness Temperatures" also spanning the AMSR-E time period. Researchers whose needs are not met by the above data sets can create customized grids with our AMSR-E Swath to Grid Toolkit. Recent improvements to the toolkit allow subsetted swath data as input, greatly reducing the initial data volume required to produce customized grids.
Savoie, M.; Brodzik, M. J.; Knowles, K.
Quantitative image analysis in sonograms of the thyroid gland
NASA Astrophysics Data System (ADS)
High-resolution, real-time ultrasound is a routine examination for assessing the disorders of the thyroid gland. However, the current diagnosis practice is based mainly on qualitative evaluation of the resulting sonograms, therefore depending on the physician's experience. Computerized texture analysis is widely employed in sonographic images of various organs (liver, breast), and it has been proven to increase the sensitivity of diagnosis by providing a better tissue characterization. The present study attempts to characterize thyroid tissue by automatic texture analysis. The texture features that are calculated are based on co-occurrence matrices as they have been proposed by Haralick. The sample consists of 40 patients. For each patient two sonographic images (one for each lobe) are recorded in DICOM format. The lobe is manually delineated in each sonogram, and the co-occurrence matrices for 52 separation vectors are calculated. The texture features extracted from each one of these matrices are: contrast, correlation, energy and homogeneity. Primary component analysis is used to select the optimal set of features. The statistical analysis resulted in the extraction of 21 optimal descriptors. The optimal descriptors are all co-occurrence parameters as the first-order statistics did not prove to be representative of the images characteristics. The bigger number of components depends mainly on correlation for very close or very far distances. The results indicate that quantitative analysis of thyroid sonograms can provide an objective characterization of thyroid tissue.
Catherine, Skouroliakou; Maria, Lyra; Aristides, Antoniou; Lambros, Vlahos
Epistasis analysis for quantitative traits by functional regression model.
The critical barrier in interaction analysis for rare variants is that most traditional statistical methods for testing interactions were originally designed for testing the interaction between common variants and are difficult to apply to rare variants because of their prohibitive computational time and poor ability. The great challenges for successful detection of interactions with next-generation sequencing (NGS) data are (1) lack of methods for interaction analysis with rare variants, (2) severe multiple testing, and (3) time-consuming computations. To meet these challenges, we shift the paradigm of interaction analysis between two loci to interaction analysis between two sets of loci or genomic regions and collectively test interactions between all possible pairs of SNPs within two genomic regions. In other words, we take a genome region as a basic unit of interaction analysis and use high-dimensional data reduction and functional data analysis techniques to develop a novel functional regression model to collectively test interactions between all possible pairs of single nucleotide polymorphisms (SNPs) within two genome regions. By intensive simulations, we demonstrate that the functional regression models for interaction analysis of the quantitative trait have the correct type 1 error rates and a much better ability to detect interactions than the current pairwise interaction analysis. The proposed method was applied to exome sequence data from the NHLBI's Exome Sequencing Project (ESP) and CHARGE-S study. We discovered 27 pairs of genes showing significant interactions after applying the Bonferroni correction (P-values < 4.58 � 10(-10)) in the ESP, and 11 were replicated in the CHARGE-S study. PMID:24803592
Zhang, Futao; Boerwinkle, Eric; Xiong, Momiao
Quantitative infrared analysis of borophosphosilicate films using multivariate statistical methods
Infrared (IR) spectroscopy can serve as a rapid method for the quantitative analysis of borophosphosilicate glass (BPSG) films on Si wafers for the microelectronics industry. The advantages of using statistically designed calibration sets are emphasized. Classical least-squares (CLS), partial least-squares (PLS), and principal component regression (PCR) methods are all found to provide improved precision over traditional peak-height measurements. The quantitative results from spectral measurements taken in transmission mode at both 0/sup 0/ and 60/sup 0/ incident angles were also compared. PLS and PCR methods yielded results that were comparable within the sampling error, and each exhibited a better analysis precision than that obtained from the CLS analysis. Both PLS and PCR methods yielded the best results when applied to the original 60/sup 0/ incident angle data, which was not corrected for film thickness. PLS and PCR analyses each gave a standard error of prediction (SEP) for boron of approx. = 0.1 wt% and approx. = 0.2 wt % for phosphorus for a set of 44 calibration samples which spanned a range of concentrations from 1 to 5 wt % B and 2 to 6 wt % P. The PLS and PCR methods applied to the IR spectra were also capable of monitoring film thickness with a SEP of 14 nm for films that varied in thickness from 430 to 1000 nm. The importance of using these full-spectrum multivariate methods for outlier sample detection is presented, and the ability to extract qualitative spectral information from the CLS and PLS calibrations is demonstrated.
Haaland, D.M.
Fractal Spectrum Technique for Quantitative Analysis of Volcanic Particle Shapes
NASA Astrophysics Data System (ADS)
The shapes of volcanic particles reflect numerous eruptive parameters (e.g. magma viscosity, volatile content, degree of interaction with water) and are useful for understanding fragmentation and transport processes associated with volcanic eruptions. However, quantitative analysis of volcanic particle shapes has proven difficult due to their morphological complexity and variability. Shape analysis based on fractal geometry has been successfully applied to a wide variety of particles and appears to be well suited for describing complex features. The technique developed and applied to volcanic particles in this study uses fractal data produced by dilation of the 2-D particle boundary to produce a full spectrum of fractal dimensions over a range of scales for each particle. Multiple fractal dimensions, which can be described as a fractal spectrum curve, are calculated by taking the first derivative of data points on a standard Richardson plot. Quantitative comparisons are carried out using multivariate statistical techniques such as cluster and principal components analysis. Compared with previous fractal methods that express shape in terms of only one or two fractal dimensions, use of multiple fractal dimensions results in more effective discrimination between samples. In addition, the technique eliminates the subjectivity associated with selecting linear segments on Richardson plots for fractal dimension calculation, and allows direct comparison of particles as long as instantaneous dimensions used as input to multivariate analyses are selected at the same scales for each particle. Applications to samples from well documented eruptions (e.g. Mt. St. Helens, Tambora, Surtsey) indicate that the fractal spectrum technique provides a useful means of characterizing volcanic particles and can be helpful for identifying the products of specific fragmentation processes (volatile exsolution, phreatomagmatic, quench granulation) and modes of volcanic deposition (tephra fall, pyroclastic flow, blast/surge).
Maria, A. H.; Carey, S. N.
Quantitative modeling and data analysis of SELEX experiments
NASA Astrophysics Data System (ADS)
SELEX (Systematic Evolution of Ligands by Exponential Enrichment) is an experimental procedure that allows extracting, from an initially random pool of DNA, those oligomers with high affinity for a given DNA-binding protein. We address what is a suitable experimental and computational procedure to infer parameters of transcription factor-DNA interaction from SELEX experiments. To answer this, we use a biophysical model of transcription factor-DNA interactions to quantitatively model SELEX. We show that a standard procedure is unsuitable for obtaining accurate interaction parameters. However, we theoretically show that a modified experiment in which chemical potential is fixed through different rounds of the experiment allows robust generation of an appropriate data set. Based on our quantitative model, we propose a novel bioinformatic method of data analysis for such modified experiment and apply it to extract the interaction parameters for a mammalian transcription factor CTF/NFI. From a practical point of view, our method results in a significantly improved false positive/false negative trade-off, as compared to both the standard information theory based method and a widely used empirically formulated procedure. This work will appear in Physical Biology. This work was supported by NIH grant GM67794. Final parts of this work were supported by NSF under Agreement No. 0112050 and NSF grant MCB-0418891.
Djordjevic, Marko; Sengupta, Anirvan M.
Quantitative modeling and data analysis of SELEX experiments
NASA Astrophysics Data System (ADS)
SELEX (systematic evolution of ligands by exponential enrichment) is an experimental procedure that allows the extraction, from an initially random pool of DNA, of those oligomers with high affinity for a given DNA-binding protein. We address what is a suitable experimental and computational procedure to infer parameters of transcription factor-DNA interaction from SELEX experiments. To answer this, we use a biophysical model of transcription factor-DNA interactions to quantitatively model SELEX. We show that a standard procedure is unsuitable for obtaining accurate interaction parameters. However, we theoretically show that a modified experiment in which chemical potential is fixed through different rounds of the experiment allows robust generation of an appropriate dataset. Based on our quantitative model, we propose a novel bioinformatic method of data analysis for such a modified experiment and apply it to extract the interaction parameters for a mammalian transcription factor CTF/NFI. From a practical point of view, our method results in a significantly improved false positive/false negative trade-off, as compared to both the standard information theory based method and a widely used empirically formulated procedure.
Djordjevic, Marko; Sengupta, Anirvan M.
Quantitative analysis of gene function in the Drosophila embryo.
The specific functions of gene products frequently depend on the developmental context in which they are expressed. Thus, studies on gene function will benefit from systems that allow for manipulation of gene expression within model systems where the developmental context is well defined. Here we describe a system that allows for genetically controlled overexpression of any gene of interest under normal physiological conditions in the early Drosophila embryo. This regulated expression is achieved through the use of Drosophila lines that express a maternal mRNA for the yeast transcription factor GAL4. Embryos derived from females that express GAL4 maternally activate GAL4-dependent UAS transgenes at uniform levels throughout the embryo during the blastoderm stage of embryogenesis. The expression levels can be quantitatively manipulated through the use of lines that have different levels of maternal GAL4 activity. Specific phenotypes are produced by expression of a number of different developmental regulators with this system, including genes that normally do not function during Drosophila embryogenesis. Analysis of the response to overexpression of runt provides evidence that this pair-rule segmentation gene has a direct role in repressing transcription of the segment-polarity gene engrailed. The maternal GAL4 system will have applications both for the measurement of gene activity in reverse genetic experiments as well as for the identification of genetic factors that have quantitative effects on gene function in vivo.
Tracey, W D; Ning, X; Klingler, M; Kramer, S G; Gergen, J P
Quantitative analysis of incipient mineral loss in hard tissues
NASA Astrophysics Data System (ADS)
A coupled diffuse-photon-density-wave and thermal-wave theoretical model was developed to describe the biothermophotonic phenomena in multi-layered hard tissue structures. Photothermal Radiometry was applied as a safe, non-destructive, and highly sensitive tool for the detection of early tooth enamel demineralization to test the theory. Extracted human tooth was treated sequentially with an artificial demineralization gel to simulate controlled mineral loss in the enamel. The experimental setup included a semiconductor laser (659 nm, 120 mW) as the source of the photothermal signal. Modulated laser light generated infrared blackbody radiation from teeth upon absorption and nonradiative energy conversion. The infrared flux emitted by the treated region of the tooth surface and sub-surface was monitored with an infrared detector, both before and after treatment. Frequency scans with a laser beam size of 3 mm were performed in order to guarantee one-dimensionality of the photothermal field. TMR images showed clear differences between sound and demineralized enamel, however this technique is destructive. Dental radiographs did not indicate any changes. The photothermal signal showed clear change even after 1 min of gel treatment. As a result of the fittings, thermal and optical properties of sound and demineralized enamel were obtained, which allowed for quantitative differentiation of healthy and non-healthy regions. In conclusion, the developed model was shown to be a promising tool for non-invasive quantitative analysis of early demineralization of hard tissues.
Matvienko, Anna; Mandelis, Andreas; Hellen, Adam; Jeon, Raymond; Abrams, Stephen; Amaechi, Bennett
Quantitative colorimetric-imaging analysis of nickel in iron meteorites.
A quantitative analytical imaging approach for determining the nickel content of metallic meteorites is proposed. The approach uses a digital image of a series of standard solutions of the nickel-dimethylglyoxime coloured chelate and a meteorite sample solution subjected to the same treatment as the nickel standards for quantitation. The image is processed with suitable software to assign a colour-dependent numerical value (analytical signal) to each standard. Such a value is directly proportional to the analyte concentration, which facilitates construction of a calibration graph where the value for the unknown sample can be interpolated to calculate the nickel content of the meteorite. The results thus obtained were validated by comparison with the official, ISO-endorsed spectrophotometric method for nickel. The proposed method is fairly simple and inexpensive; in fact, it uses a commercially available digital camera as measuring instrument and the images it provides are processed with highly user-friendly public domain software (specifically, ImageJ, developed by the National Institutes of Health and freely available for download on the Internet). In a scenario dominated by increasingly sophisticated and expensive equipment, the proposed method provides a cost-effective alternative based on simple, robust hardware that is affordable and can be readily accessed worldwide. This can be especially advantageous for countries were available resources for analytical equipment investments are scant. The proposed method is essentially an adaptation of classical chemical analysis to current, straightforward, robust, cost-effective instrumentation. PMID:21238754
Zamora, L Lahuerta; L�pez, P Alem�n; Fos, G M Ant�n; Algarra, R Mart�n; Romero, A M Mellado; Calatayud, J Mart�nez
Application of Synchrotron-XRF to Quantitative Elemental Aerosol Analysis
NASA Astrophysics Data System (ADS)
Recent advances in synchrotron x-ray fluorescence (s-XRF) analysis of atmospheric particulate matter have improved elemental sensitivity, quantification and time-resolution. Analysis of both filter and impactor based aerosol samples have yielded quantitative data for elements Na-U, if present, in ambient aerosols. The increased sensitivity allows higher time resolution through either smaller spatial analysis of time-resolved impactor samples or shorter sample time-integration using filter-based samplers. Of particular interest is the application of s-XRF to aerodynamically sized rotating substrate impactor samples. These samplers, 8- and 3-stage DRUM's, have the ability to aerodynamically size-classify particles in either 8 or 3 categories, respectively. In addition, the rotating substrate allows time-resolved analysis of samples with little or no loss in elemental sensitivity. The s-XRF analyses are performed on Beamline 10.3.1 at the Advanced Light Source-Lawrence Berkeley Laboratory (ALS-LBL). Beamline 10.3.1, originally designed for materials analysis, has been supplemented with aerosol analysis capability from several substrate options. Typical analysis involves Teflon filters or Mylar impaction substrates. The newly formed Participating Research Team (PRT) for beamline 10.3.1 encompasses both global climate and material science research. The s-XRF capabilities of beamline 10.3.1 are now available for PRT researchers and independent investigators through a proposal process to the ALS. The technology, application to aerosol research and monitoring, and availability of the facility to the aerosol research community will be presented.
Cliff, S. S.; Perry, K. D.; Jimenez-Cruz, M. P.; Cahill, T. A.
Multipoint quantitative-trait linkage analysis in general pedigrees.
Multipoint linkage analysis of quantitative-trait loci (QTLs) has previously been restricted to sibships and small pedigrees. In this article, we show how variance-component linkage methods can be used in pedigrees of arbitrary size and complexity, and we develop a general framework for multipoint identity-by-descent (IBD) probability calculations. We extend the sib-pair multipoint mapping approach of Fulker et al. to general relative pairs. This multipoint IBD method uses the proportion of alleles shared identical by descent at genotyped loci to estimate IBD sharing at arbitrary points along a chromosome for each relative pair. We have derived correlations in IBD sharing as a function of chromosomal distance for relative pairs in general pedigrees and provide a simple framework whereby these correlations can be easily obtained for any relative pair related by a single line of descent or by multiple independent lines of descent. Once calculated, the multipoint relative-pair IBDs can be utilized in variance-component linkage analysis, which considers the likelihood of the entire pedigree jointly. Examples are given that use simulated data, demonstrating both the accuracy of QTL localization and the increase in power provided by multipoint analysis with 5-, 10-, and 20-cM marker maps. The general pedigree variance component and IBD estimation methods have been implemented in the SOLAR (Sequential Oligogenic Linkage Analysis Routines) computer package.
Almasy, L; Blangero, J
Quantitative analysis of the reconstruction performance of interpolants
NASA Technical Reports Server (NTRS)
The analysis presented provides a quantitative measure of the reconstruction or interpolation performance of linear, shift-invariant interpolants. The performance criterion is the mean square error of the difference between the sampled and reconstructed functions. The analysis is applicable to reconstruction algorithms used in image processing and to many types of splines used in numerical analysis and computer graphics. When formulated in the frequency domain, the mean square error clearly separates the contribution of the interpolation method from the contribution of the sampled data. The equations provide a rational basis for selecting an optimal interpolant; that is, one which minimizes the mean square error. The analysis has been applied to a selection of frequently used data splines and reconstruction algorithms: parametric cubic and quintic Hermite splines, exponential and nu splines (including the special case of the cubic spline), parametric cubic convolution, Keys' fourth-order cubic, and a cubic with a discontinuous first derivative. The emphasis in this paper is on the image-dependent case in which no a priori knowledge of the frequency spectrum of the sampled function is assumed.
Lansing, Donald L.; Park, Stephen K.
Analysis of three-dimensional images in quantitative microscopy
NASA Astrophysics Data System (ADS)
In bright field microscopy, quantitative analysis of acquired images is customarily performed using the `best' image. Since an image with sufficient detail and clarity is required for consistent classification and discrimination of objects in the image, the image with higher magnification is commonly chosen for the analysis, which generally corresponds to lower focal depths. The objectively determined `best' focus level, although optimal for the extraction of some features from the chosen objects, may not correspond to the best focal level for the extraction of some other features. To obtain tighter distribution of all features, we have been searching for a method which employs analysis of images acquired at different focal planes. In this work, we analyzed images of stained cervical cells using three different approaches. In the first approach, different features were extracted from images taken at different focal planes. In the second approach, we used simultaneously all the in-focus and out-of-focus information from the images to reconstruct the focussed images at various focal planes. In the third approach, the in-focus three-dimensional scene was compressed to two dimensions to simulate an image taken from a system with a very large depth of focus. The latter method reduced the data storage size and simplified subsequent scene analysis. The advantages and disadvantages of the above approaches are discussed.
Poon, Steven S. S.; Ward, Rabab K.; Palcic, Branko
Quantitative analysis of dinuclear manganese(II) EPR spectra
NASA Astrophysics Data System (ADS)
A quantitative method for the analysis of EPR spectra from dinuclear Mn(II) complexes is presented. The complex [(Me 3TACN) 2Mn(II) 2(?-OAc) 3]BPh 4 ( 1) (Me 3TACN= N, N', N''-trimethyl-1,4,7-triazacyclononane; OAc=acetate 1-; BPh 4=tetraphenylborate 1-) was studied with EPR spectroscopy at X- and Q-band frequencies, for both perpendicular and parallel polarizations of the microwave field, and with variable temperature (2-50 K). Complex 1 is an antiferromagnetically coupled dimer which shows signals from all excited spin manifolds, S=1 to 5. The spectra were simulated with diagonalization of the full spin Hamiltonian which includes the Zeeman and zero-field splittings of the individual manganese sites within the dimer, the exchange and dipolar coupling between the two manganese sites of the dimer, and the nuclear hyperfine coupling for each manganese ion. All possible transitions for all spin manifolds were simulated, with the intensities determined from the calculated probability of each transition. In addition, the non-uniform broadening of all resonances was quantitatively predicted using a lineshape model based on D- and r-strain. As the temperature is increased from 2 K, an 11-line hyperfine pattern characteristic of dinuclear Mn(II) is first observed from the S=3 manifold. D- and r-strain are the dominate broadening effects that determine where the hyperfine pattern will be resolved. A single unique parameter set was found to simulate all spectra arising for all temperatures, microwave frequencies, and microwave modes. The simulations are quantitative, allowing for the first time the determination of species concentrations directly from EPR spectra. Thus, this work describes the first method for the quantitative characterization of EPR spectra of dinuclear manganese centers in model complexes and proteins. The exchange coupling parameter J for complex 1 was determined ( J=-1.5�0.3 cm-1; H ex=-2J S1� S2) and found to be in agreement with a previous determination from magnetization. The phenomenon of exchange striction was found to be insignificant for 1.
Golombek, Adina P.; Hendrich, Michael P.
Quantitative comparison of analysis methods for spectroscopic optical coherence tomography
Spectroscopic optical coherence tomography (sOCT) enables the mapping of chromophore concentrations and image contrast enhancement in tissue. Acquisition of depth resolved spectra by sOCT requires analysis methods with optimal spectral/spatial resolution and spectral recovery. In this article, we quantitatively compare the available methods, i.e. the short time Fourier transform (STFT), wavelet transforms, the Wigner-Ville distribution and the dual window method through simulations in tissue-like media. We conclude that all methods suffer from the trade-off in spectral/spatial resolution, and that the STFT is the optimal method for the specific application of the localized quantification of hemoglobin concentration and oxygen saturation.
Bosschaart, Nienke; van Leeuwen, Ton G.; Aalders, Maurice C. G.; Faber, Dirk J.
Quantitative multielement analysis using high energy particle bombardment
NASA Technical Reports Server (NTRS)
Charged particles ranging in energy from 0.8 to 4.0 MeV are used to induce resonant nuclear reactions, Coulomb excitation (gamma-rays), and X-ray emission in both thick and thin targets. Quantitative analysis is possible for elements from Li to Pb in complex environmental samples, although the matrix can severely reduce the sensitivity. It is necessary to use a comparator technique for the gamma-rays while for X-rays an internal standard can be used. A USGS standard rock is analyzed for a total of 28 elements. Water samples can be analyzed either by nebulizing the sample doped with Cs or Y a thin Formvar film or by extracting the sample onto ion exchange resin which is pressed into a pellet.
Clark, P. J.; Neal, G. F.; Allen, R. O.
Quantitative multielement analysis using high energy particle bombardment
NASA Technical Reports Server (NTRS)
Charged particles ranging in energy from 0.8 to 4.0 MeV are used to induce resonant nuclear reactions, Coulomb excitation (gamma X-rays), and X-ray emission in both thick and thin targets. Quantitative analysis is possible for elements from Li to Pb in complex environmental samples, although the matrix can severely reduce the sensitivity. It is necessary to use a comparator technique for the gamma-rays, while for X-rays an internal standard can be used. A USGS standard rock is analyzed for a total of 28 elements. Water samples can be analyzed either by nebulizing the sample doped with Cs or Y onto a thin formvar film or by extracting the sample (with or without an internal standard) onto ion exchange resin which is pressed into a pellet.
Clark, P. J.; Neal, G. F.; Allen, R. O.
Quantitative image analysis of WE43-T6 cracking behavior
NASA Astrophysics Data System (ADS)
Environment-assisted cracking of WE43 cast magnesium (4.2 wt.% Yt, 2.3 wt.% Nd, 0.7% Zr, 0.8% HRE) in the T6 peak-aged condition was induced in ambient air in notched specimens. The mechanism of fracture was studied using electron backscatter diffraction, serial sectioning and in situ observations of crack propagation. The intermetallic (rare earthed-enriched divorced intermetallic retained at grain boundaries and predominantly at triple points) material was found to play a significant role in initiating cracks which leads to failure of this material. Quantitative measurements were required for this project. The populations of the intermetallic and clusters of intermetallic particles were analyzed using image analysis of metallographic images. This is part of the work to generate a theoretical model of the effect of notch geometry on the static fatigue strength of this material.
Ahmad, A.; Yahya, Z.
Quantitative analysis of gallstones using laser-induced breakdown spectroscopy
The utility of laser-induced breakdown spectroscopy (LIBS) for categorizing different types of gallbladder stone has been demonstrated by analyzing their major and minor constituents. LIBS spectra of three types of gallstone have been recorded in the 200-900 nm spectral region. Calcium is found to be the major element in all types of gallbladder stone. The spectrophotometric method has been used to classify the stones. A calibration-free LIBS method has been used for the quantitative analysis of metal elements, and the results have been compared with those obtained from inductively coupled plasma atomic emission spectroscopy (ICP-AES) measurements. The single-shot LIBS spectra from different points on the cross section (in steps of 0.5 mm from one end to the other) of gallstones have also been recorded to study the variation of constituents from the center to the surface. The presence of different metal elements and their possible role in gallstone formation is discussed.
Singh, Vivek K.; Singh, Vinita; Rai, Awadhesh K.; Thakur, Surya N.; Rai, Pradeep K.; Singh, Jagdish P
Quantitative analysis of creatinine in urine by metalized nanostructured parylene
NASA Astrophysics Data System (ADS)
A highly accurate, real-time multisensor agent monitor for biomarker detection is required for early detection of kidney diseases. Urine creatinine level can provide useful information on the status of the kidney. We prepare nanostructured surface-enhanced Raman spectroscopy (SERS) substrates without template or lithography, which provides controllable, well-organized nanostructures on the surface, for the quantitative analysis of creatinine concentration in urine. We present our work on sensitivity of the SERS substrate to urine samples collected from diabetic patients and healthy persons. We report the preparation of a new type of SERS substrate, which provides fast (<10 s), highly sensitive (creatinine concentration <0.5 ?g/mL) and reproducible (<5% variation) detection of urine. Our method to analyze the creatinine level in urine is in good agreement with the enzymatic method.
Wang, Hui; Malvadkar, Niranjan; Koytek, S.; Bylander, J.; Reeves, W. Brian; Demirel, Melik C.
A quantitative histological analysis of the dilated ureter of childhood.
A quantitative histological study of the dilated ureter of childhood was performed on 26 ureters. The specimens were from 15 male and 11 female patients 10 days to 12 years old (mean age 2.0 years). A color image analysis system was used to examine and compare collagen and smooth muscle components of the muscularis layers to normal control ureters of similar age. In comparing primary obstructed (12) to primary refluxing (14) megaureters and control ureters (6), there was a statistically different collagen-to-smooth muscle ratio (p < 0.001) between the primary obstructed and primary refluxing megaureter groups. For patients with primary refluxing megaureter there was a 2-fold increase in the tissue matrix ratio of collagen-to-smooth muscle when compared to patients with primary obstructed megaureter. In the primary obstructed megaureters the amount of collagen and smooth muscle was not statistically different from controls (p > 0.01). The increased tissue matrix ratio of 2.0 +/- 0.35 (collagen-to-smooth muscle) in the refluxing megaureter group compared to 0.78 +/- 0.22 in the obstructed megaureter group and 0.52 +/- 0.12 in controls was found to be due not only to a marked increase in collagen but also a significant decrease in the smooth muscle component of the tissue. Primary obstructed and normal control ureters had similar quantitative amounts of smooth muscle with 60 +/- 5% and 61 +/- 6%, respectively, while refluxing megaureters had only 40 +/- 5% smooth muscle. The percentage collagen was 36 +/- 5 in the obstructed megaureter group and 30 +/- 5 in controls, with refluxing megaureters having 58 +/- 5% collagen on analysis. Our findings emphasize the significant differences in the structural components (collagen and smooth muscle) of the dilated ureter of childhood, and provide us with further insight into the pathological nature of these dilated ureters and their surgical repair. PMID:1433552
Lee, B R; Partin, A W; Epstein, J I; Quinlan, D M; Gosling, J A; Gearhart, J P
QTL analysis for some quantitative traits in bread wheat*
Quantitative trait loci (QTL) analysis was conducted in bread wheat for 14 important traits utilizing data from four different mapping populations involving different approaches of QTL analysis. Analysis for grain protein content (GPC) suggested that the major part of genetic variation for this trait is due to environmental interactions. In contrast, pre-harvest sprouting tolerance (PHST) was controlled mainly by main effect QTL (M-QTL) with very little genetic variation due to environmental interactions; a major QTL for PHST was detected on chromosome arm 3AL. For grain weight, one QTL each was detected on chromosome arms 1AS, 2BS and 7AS. QTL for 4 growth related traits taken together detected by different methods ranged from 37 to 40; nine QTL that were detected by single-locus as well as two-locus analyses were all M-QTL. Similarly, single-locus and two-locus QTL analyses for seven yield and yield contributing traits in two populations respectively allowed detection of 25 and 50 QTL by composite interval mapping (CIM), 16 and 25 QTL by multiple-trait composite interval mapping (MCIM) and 38 and 37 QTL by two-locus analyses. These studies should prove useful in QTL cloning and wheat improvement through marker aided selection.
Pushpendra, Kumar Gupta; Harindra, Singh Balyan; Pawan, Laxminarayan Kulwal; Neeraj, Kumar; Ajay, Kumar; Reyazul, Rouf Mir; Amita, Mohan; Jitendra, Kumar
Quantitative Medical Image Analysis for Clinical Development of Therapeutics
NASA Astrophysics Data System (ADS)
There has been significant progress in development of therapeutics for prevention and management of several disease areas in recent years, leading to increased average life expectancy, as well as of quality of life, globally. However, due to complexity of addressing a number of medical needs and financial burden of development of new class of therapeutics, there is a need for better tools for decision making and validation of efficacy and safety of new compounds. Numerous biological markers (biomarkers) have been proposed either as adjunct to current clinical endpoints or as surrogates. Imaging biomarkers are among rapidly increasing biomarkers, being examined to expedite effective and rational drug development. Clinical imaging often involves a complex set of multi-modality data sets that require rapid and objective analysis, independent of reviewer's bias and training. In this chapter, an overview of imaging biomarkers for drug development is offered, along with challenges that necessitate quantitative and objective image analysis. Examples of automated and semi-automated analysis approaches are provided, along with technical review of such methods. These examples include the use of 3D MRI for osteoarthritis, ultrasound vascular imaging, and dynamic contrast enhanced MRI for oncology. Additionally, a brief overview of regulatory requirements is discussed. In conclusion, this chapter highlights key challenges and future directions in this area.
Analoui, Mostafa
Quantitative analysis of triple-mutant genetic interactions.
The quantitative analysis of genetic interactions between pairs of gene mutations has proven to be effective for characterizing cellular functions, but it can miss important interactions for functionally redundant genes. To address this limitation, we have developed an approach termed triple-mutant analysis (TMA). The procedure relies on a query strain that contains two deletions in a pair of redundant or otherwise related genes, which is crossed against a panel of candidate deletion strains to isolate triple mutants and measure their growth. A central feature of TMA is to interrogate mutants that are synthetically sick when two other genes are deleted but interact minimally with either single deletion. This approach has been valuable for discovering genes that restore critical functions when the principal actors are deleted. TMA has also uncovered double-mutant combinations that produce severe defects because a third protein becomes deregulated and acts in a deleterious fashion, and it has revealed functional differences between proteins presumed to act together. The protocol is optimized for Singer ROTOR pinning robots, takes 3 weeks to complete and measures interactions for up to 30 double mutants against a library of 1,536 single mutants. PMID:25010907
Braberg, Hannes; Alexander, Richard; Shales, Michael; Xu, Jiewei; Franks-Skiba, Kathleen E; Wu, Qiuqin; Haber, James E; Krogan, Nevan J
Detection, Quantitation, and Phylogenetic Analysis of Noroviruses in Japanese Oysters
Noroviruses (NVs) cause many cases of oyster- or clam-associated gastroenteritis in various countries. We collected 191 samples from Japanese oysters intended for raw consumption that had been harvested from the sea in two different areas between December 2001 and February 2002. To detect, quantitate, and phylogenetically analyze the NV genome in purified concentrates from the stomachs and digestive diverticula of these oysters, we amplified the NV capsid gene by reverse transcription-PCR. Phylogenetic analysis was performed by using the neighbor-joining method. We detected the NV genome in 17 of 191 oysters (9%). Phylogenetic analysis indicated genogroup I (Norwalk virus type) in 3 of the 17 oysters and genogroup II (Snow Mountain virus type) in the other 14. Both genogroups showed wide genetic diversity. To quantify the NV capsid gene in these oysters, we performed real-time PCR using genogroup-specific probes. More than 102 copies of the NV genome were detected in 11 of 17 oysters. The results suggested that about 10% of Japanese oysters intended for raw consumption harbored NVs, and more than 50% of those oysters in which NVs were detected had a large amount.
Nishida, Tomoko; Kimura, Hirokazu; Saitoh, Mika; Shinohara, Michiyo; Kato, Masahiko; Fukuda, Shinji; Munemura, Tetsuya; Mikami, Toshiyuki; Kawamoto, Ayumi; Akiyama, Miho; Kato, Yumiko; Nishi, Kanako; Kozawa, Kunihisa; Nishio, Osamu
Quantitative analysis of fluorescence lifetime imaging made easy
Fluorescence lifetime imaging is a valuable and versatile tool for the investigation of the molecular environment of fluorophores in living cells. It is ideally suited�and is therefore increasingly used�for the quantification of the occurrence of F�rster Resonance Energy Transfer, a powerful microscopy method for the detection of subnanometer conformational changes, protein-protein interactions, and protein biochemical status. However, careful quantitative analysis is required for the correct and meaningful interpretation of fluorescence lifetime data. This can be a daunting task to the nonexpert user, and is the source for many avoidable errors and unsound interpretations. Digman and colleagues (Digman et al., 2007, Biophys. J. 94, L14�6) present an analysis technique that avoids data fitting in favor of a simple graphical polar data representation. In this �phasor� space, the physics of lifetime imaging becomes more intuitive and accessible also to the inexperienced user. The cumulated information from image pixels, even over different cells, describes patterns and trajectories that can be visually interpreted in physically meaningful ways. Its usefulness is demonstrated in the study of the dimerization of the uPAR receptor (Caiolfa et al., 2007, J. Cell Biol. 179, 1067�1082).
Wouters, Fred S.; Esposito, Alessandro
A PCR primer bank for quantitative gene expression analysis
Although gene expression profiling by microarray analysis is a useful tool for assessing global levels of transcriptional activity, variability associated with the data sets usually requires that observed differences be validated by some other method, such as real-time quantitative polymerase chain reaction (real-time PCR). However, non-specific amplification of non-target genes is frequently observed in the latter, confounding the analysis in ?40% of real-time PCR attempts when primer-specific labels are not used. Here we present an experimentally validated algorithm for the identification of transcript-specific PCR primers on a genomic scale that can be applied to real-time PCR with sequence-independent detection methods. An online database, PrimerBank, has been created for researchers to retrieve primer information for their genes of interest. PrimerBank currently contains 147 404 primers encompassing most known human and mouse genes. The primer design algorithm has been tested by conventional and real-time PCR for a subset of 112 primer pairs with a success rate of 98.2%.
Wang, Xiaowei; Seed, Brian
Quantitative RNA-seq analysis of the Campylobacter jejuni transcriptome
Campylobacter jejuni is the most common bacterial cause of foodborne disease in the developed world. Its general physiology and biochemistry, as well as the mechanisms enabling it to colonize and cause disease in various hosts, are not well understood, and new approaches are required to understand its basic biology. High-throughput sequencing technologies provide unprecedented opportunities for functional genomic research. Recent studies have shown that direct Illumina sequencing of cDNA (RNA-seq) is a useful technique for the quantitative and qualitative examination of transcriptomes. In this study we report RNA-seq analyses of the transcriptomes of C. jejuni (NCTC11168) and its rpoN mutant. This has allowed the identification of hitherto unknown transcriptional units, and further defines the regulon that is dependent on rpoN for expression. The analysis of the NCTC11168 transcriptome was supplemented by additional proteomic analysis using liquid chromatography-MS. The transcriptomic and proteomic datasets represent an important resource for the Campylobacter research community.
Chaudhuri, Roy R.; Yu, Lu; Kanji, Alpa; Perkins, Timothy T.; Gardner, Paul P.; Choudhary, Jyoti; Maskell, Duncan J.
Quantitative EEG analysis in post-traumatic anosmia.
Many objective and quantitative methods have been developed to create a procedure or a device to prove, describe and quantify olfactory deficit and anosmia, especially after a head trauma. Electrophysiological testing throughout olfactoelectroencephalography (olfactoEEG) is based on brain activity desynchronisation, and on the subsequent disappearance of alpha activity on the posterior regions after an olfactory stimulus. Yet traditional evaluation of EEG can be difficult, because of little or hardly detectable alpha activity on the posterior regions ('alpha rare'). The aim of this study was to evaluate the Olfactory Stop Reaction (OSR) by means of frequency band power calculation and subsequent topographical mapping in patients with post-traumatic anosmia, who presented 'alpha rare' EEG. Twenty-five consecutive patients, affected by anosmia caused by head trauma, were submitted to an EEG recording with olfactory stimulation. After signal processing and analysis, an Olfactory Stop Reaction was detected in 17 out of 25 patients; moreover, in these patients we detected a significant decrease in alpha band power in the occipital regions and an increase in theta band power on midline frontal and central regions after olfactory stimulation. In the remaining eight patients, no significant variation in band power was observed. In conclusion, an objective evaluation of the olfactory function with this method of automatic EEG signal analysis allows the limits given by psychophysical methods and traditional EEG to be overcome and attempts to fulfil the requirements for standardization of olfactory function evalution. PMID:17113930
Bonanni, E; Borghetti, D; Fabbrini, M; Maestri, M; Cignoni, F; Sartucci, F; Murri, L
Understanding Maneuver Uncertainties during Inclination Maneuvers of the Aqua Spacecraft
NASA Technical Reports Server (NTRS)
During the Fall 2006 inclination campaign for the Aqua spacecraft it was discovered that there was significant uncertainty in the prediction of the semimajor axis change during a maneuver. The low atmospheric drag environment at the time of the maneuvers amplified the effects of this uncertainty leading to a potential violation of the spacecraft ground-track requirements. In order to understand the uncertainty, a Monte Carlo simulation was developed to characterize the expected semi-major axis change uncertainty given the observed behavior of the spacecraft propulsion and attitude control systems during a maneuver. This expected uncertainty was then used to develop new analysis tools to ensure that future inclination maneuver plans will .meet ground-track control requirements in the presence of the error.
McKinley, David P.
AQUA AMSR-E Sea Surface Temperature
NASA Astrophysics Data System (ADS)
NASA's AQUA satellite carries the JAXA's Advanced Microwave Scanning Radiometer - Earth Observing System (AMSR-E). The AQUA satellite was launched in May 2002 into a polar, sun-synchronous orbit at an altitude of 705 km, with a LECT of 1:30 AM/PM. AMSR-E has 12 channels corresponding to 6 frequencies; all except 23.8 GHz measure both vertical and horizontal polarizations. Geophysical retrievals of SST, wind speed, water vapor, cloud liquid water, and rain rates are calculated using a multi-stage linear regression algorithm derived through comprehensive radiative transfer model simulations. SST retrievals are prevented by rain, sun glint, near land emissions, and radio frequency interference due to geostationary satellite broadcasts. Since only a small number of retrievals are unsuccessful, almost complete global coverage is available daily. At high latitudes, where cloud cover regularly prevents infrared observations of SSTs, the microwave observations of SST provide a significant improvement to measurement capabilities. Validation of the datasets through comparison to the global drifting buoy networks yields mean biases of -0.02 K and standard deviations of 0.50 K. AMSR-E SSTs have been widely used for numerical weather prediction, ocean modeling, fisheries, and oceanographic research.
Gentemann, C. L.
Ecotoxicological impact of sunlight assisted photoreduction of hexavalent chromium present in wastewater with zinc oxide nanoparticles on common Anabaena flos-aquae.
Hexavalent chromium is more toxic and carcinogenic compared to its trivalent counterpart. Hexavalent chromium can be photocatalytically reduced to trivalent one using zinc oxide semiconductor and solar or UV radiation as light source. But an important ecological aspect is whether the net toxicity decreases after the photocatalytic process. In the present work, we have selected Anabaena flos-aquae as the model organism and examined whether the net toxicity to which it has been exposed in water decreases after photocatalytic reduction of hexavalent chromium using ZnO semiconductor as photocatalyst. We have studied the cumulative toxicities of both chromium (before and after treatment) and ZnO (both nano and micro) separately and as a suspension of ZnO in chromium. Quantitative cell surface roughness analysis was conducted using AFM to confirm the changes in cell surface properties. PMID:23025895
Nandi, Isita; Mitra, Pallavi; Banerjee, Prantik; Chakrabarti, Anirban; Ghosh, Mahua; Chakrabarti, Sampa
Teaching Quantitative Literacy through a Regression Analysis of Exam Performance
ERIC Educational Resources Information Center
Quantitative literacy is increasingly essential for both informed citizenship and a variety of careers. Though regression is one of the most common methods in quantitative sociology, it is rarely taught until late in students' college careers. In this article, the author describes a classroom-based activity introducing students to regression�
Lindner, Andrew M.
Comparison of multivariate calibration methods for quantitative spectral analysis
The quantitative prediction abilities of four multivariate calibration methods for spectral analyses are compared by using extensive Monte Carlo simulations. The calibration methods compared include inverse least-squares (ILS), classical least-squares (CLS), partial least-squares (PLS), and principal component regression (PCR) methods. ILS is a frequency-limited method while the latter three are capable of full-spectrum calibration. The simulations were performed assuming Beer's law holds and that spectral measurement errors and concentration errors associated with the reference method are normally distributed. Eight different factors that could affect the relative performance of the calibration methods were varied in a two-level, eight-factor experimental design in order to evaluate their effect on the prediction abilities of the four methods. It is found that each of the three full-spectrum methods has its range of superior performance. The frequency-limited ILS method was never the best method, although in the presence of relatively large concentration errors it sometimes yields comparable analysis precision to the full-spectrum methods for the major spectral component. The importance of each factor in the absolute and relative performances of the four methods is compared.
Thomas, E.V.; Haaland, D.M. (Sandia National Laboratories, Albuquerque, NM (USA))
Genomewide Analysis of Epistatic Effects for Quantitative Traits in Barley
The doubled-haploid (DH) barley population (Harrington � TR306) developed by the North American Barley Genome Mapping Project (NABGMP) for QTL mapping consisted of 145 lines and 127 markers covering a total genome length of 1270 cM. These DH lines were evaluated in ?25 environments for seven quantitative traits: heading, height, kernel weight, lodging, maturity, test weight, and yield. We applied an empirical Bayes method that simultaneously estimates 127 main effects for all markers and 127(127?1)/2=8001 interaction effects for all marker pairs in a single model. We found that the largest main-effect QTL (single marker) and the largest epistatic effect (single pair of markers) explained ?18 and 2.6% of the phenotypic variance, respectively. On average, the sum of all significant main effects and the sum of all significant epistatic effects contributed 35 and 6% of the total phenotypic variance, respectively. Epistasis seems to be negligible for all the seven traits. We also found that whether two loci interact does not depend on whether or not the loci have individual main effects. This invalidates the common practice of epistatic analysis in which epistatic effects are estimated only for pairs of loci of which both have main effects.
Xu, Shizhong; Jia, Zhenyu
Quantitative analysis of biomedical samples using synchrotron radiation microbeams
NASA Astrophysics Data System (ADS)
X-ray fluorescence (XRF) using a synchrotron radiation (SR) microbeam was applied to investigate distributions and concentrations of elements in single neurons of patients with neurodegenerative diseases. In this paper we introduce a computer code that has been developed to quantify the trace elements and matrix elements at the single cell level. This computer code has been used in studies of several important neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD) and parkinsonism-dementia complex (PDC), as well as in basic biological experiments to determine the elemental changes in cells due to incorporation of foreign metal elements. The substantial nigra (SN) tissue obtained from the autopsy specimens of patients with Guamanian parkinsonism-dementia complex (PDC) and control cases were examined. Quantitative XRF analysis showed that neuromelanin granules of Parkinsonian SN contained higher levels of Fe than those of the control. The concentrations were in the ranges of 2300-3100 ppm and 2000-2400 ppm respectively. On the contrary, Zn and Ni in neuromelanin granules of SN tissue from the PDC case were lower than those of the control. Especially Zn was less than 40 ppm in SN tissue from the PDC case while it was 560-810 ppm in the control. These changes are considered to be closely related to the neuro-degeneration and cell death. .
Ektessabi, Ali; Shikine, Shunsuke; Yoshida, Sohei
Regulators of yeast endocytosis identified by systematic quantitative analysis
Endocytosis of receptors at the plasma membrane is controlled by a complex mechanism that includes clathrin, adaptors, and actin regulators. Many of these proteins are conserved in yeast yet lack observable mutant phenotypes, which suggests that yeast endocytosis may be subject to different regulatory mechanisms. Here, we have systematically defined genes required for internalization using a quantitative genome-wide screen that monitors localization of the yeast vesicle-associated membrane protein (VAMP)/synaptobrevin homologue Snc1. Genetic interaction mapping was used to place these genes into functional modules containing known and novel endocytic regulators, and cargo selectivity was evaluated by an array-based comparative analysis. We demonstrate that clathrin and the yeast AP180 clathrin adaptor proteins have a cargo-specific role in Snc1 internalization. We additionally identify low dye binding 17 (LDB17) as a novel conserved component of the endocytic machinery. Ldb17 is recruited to cortical actin patches before actin polymerization and regulates normal coat dynamics and actin assembly. Our findings highlight the conserved machinery and reveal novel mechanisms that underlie endocytic internalization.
Burston, Helen E.; Maldonado-Baez, Lymarie; Davey, Michael; Montpetit, Benjamen; Schluter, Cayetana; Wendland, Beverly
Quantitative analysis of chromosome motion in Drosophila melanogaster
NASA Astrophysics Data System (ADS)
We present an algorithm for estimating nonrigid motion of chromosomes in 4D microscopic images. Chromosomes are represented by a graph and motion estimation is formulated as a graph matching problem. All chromosomes within the graph are located, and then simulated annealing is used to find the mapping of chromosomes at time t onto chromosomes at time t+1 that minimizes the integrated displacement along each chromosome. Results with actual 4D images indicate that this model-based approach is sufficiently robust to correctly track the motion of chromosomes under conditions of limited spatial and temporal resolution. Using the motion estimate, previously developed methods for the quantitative analysis of 3D structure are extended to four dimensions, allowing chromosome mobility, flexibility, and interactions to be measured. Application of these algorithms to 4D images of Drosophila metaphase chromosomes in vivo allows visualization of clearly defined domains of high chromosomal flexibility, as well as other regions of distinctly lower chromosomal mobility which may coincide with centrometers.
Marshall, Wallace F.; Agard, David A.; Sedat, John W.
Neutrophil extracellular traps in bronchial aspirates: a quantitative analysis.
Neutrophil extracellular traps (NETs) are structures composed of DNA and granular proteins, which rapidly trap and kill pathogens. The formation of NETs has been detected during infection in animal experiments, but their role in humans is unclear. The purposes of this study were to quantitatively evaluate the production of NETs during acute respiratory infection and to study the relationship between the NET length and various inflammatory mediators. We examined bronchial aspirates collected from nine intubated patients in an intensive care unit. Samples were collected at the onset of acute respiratory infection (day 0) and on days 1, 3-5, and 6-8. The NET length was visualised by immunohistochemistry and quantified using computer tracing software. The NET length was measured and compared at each time point. The length differed significantly between time points (p<0.001). NETs were significantly longer on day 1 than on day 0 (p<0.001). Neutrophils released NETs abundantly in response to respiratory infection and regression analysis showed that NET length correlated with six clinical parameters (white blood cells, platelets, lactate, CXC ligand-2, interleukin-8, and procalcitonin) as the explanatory variables. NETs in bronchial aspirates may reflect disease progression of respiratory infections. Quantification of NETs in bronchial aspirates may provide a new indicator of inflammation. PMID:24603817
Hamaguchi, Shigeto; Hirose, Tomoya; Matsumoto, Naoya; Akeda, Yukihiro; Irisawa, Taro; Seki, Masafumi; Hosotsubo, Hideo; Yamamoto, Kouji; Tasaki, Osamu; Oishi, Kazunori; Shimazu, Takeshi; Tomono, Kazunori
SILAC-based quantitative proteomic analysis of gastric cancer secretome
Purpose Gastric cancer is a commonly occurring cancer in Asia and one of the leading causes of cancer deaths. However, there is no reliable blood-based screening test for this cancer. Identifying proteins secreted from tumor cells could lead to the discovery of clinically useful biomarkers for early detection of gastric cancer. Experimental design A SILAC-based quantitative proteomic approach was employed to identify secreted proteins that were differentially expressed between neoplastic and non-neoplastic gastric epithelial cells. Proteins from the secretome were subjected to SDS-PAGE and SCX-based fractionation, followed by mass spectrometric analysis on an LTQ-Orbitrap Velos mass spectrometer. Immunohistochemical labeling was employed to validate a subset of candidates using tissue microarrays. Results We identified 2,205 proteins in the gastric cancer secretome of which 263 proteins were overexpressed >4-fold in gastric cancer-derived cell lines as compared to non-neoplastic gastric epithelial cells. Three candidate proteins, proprotein convertase subtilisin/kexin type 9 (PCSK9), lectin mannose binding 2 (LMAN2) and PDGFA associated protein 1 (PDAP1), were validated by immunohistochemical labeling. Conclusions and clinical relevance We report here the largest cancer secretome described to date. The novel biomarkers identified in the current study are excellent candidates for further testing as early detection biomarkers for gastric adenocarcinoma.
Marimuthu, Arivusudar; Subbannayya, Yashwanth; Sahasrabuddhe, Nandini A.; Balakrishnan, Lavanya; Syed, Nazia; Sekhar, Nirujogi Raja; Katte, Teesta V.; Pinto, Sneha M.; Srikanth, Srinivas M.; Kumar, Praveen; Pawar, Harsh; Kashyap, Manoj K.; Maharudraiah, Jagadeesha; Ashktorab, Hassan; Smoot, Duane T; Ramaswamy, Girija; Kumar, Rekha V.; Cheng, Yulan; Meltzer, Stephen J; Roa, Juan Carlos; Chaerkady, Raghothama; Prasad, T.S. Keshava; Harsha, H. C.; Chatterjee, Aditi; Pandey, Akhilesh
Quantitative analysis of regulatory flexibility under changing environmental conditions
The circadian clock controls 24-h rhythms in many biological processes, allowing appropriate timing of biological rhythms relative to dawn and dusk. Known clock circuits include multiple, interlocked feedback loops. Theory suggested that multiple loops contribute the flexibility for molecular rhythms to track multiple phases of the external cycle. Clear dawn- and dusk-tracking rhythms illustrate the flexibility of timing in Ipomoea nil. Molecular clock components in Arabidopsis thaliana showed complex, photoperiod-dependent regulation, which was analysed by comparison with three contrasting models. A simple, quantitative measure, Dusk Sensitivity, was introduced to compare the behaviour of clock models with varying loop complexity. Evening-expressed clock genes showed photoperiod-dependent dusk sensitivity, as predicted by the three-loop model, whereas the one- and two-loop models tracked dawn and dusk, respectively. Output genes for starch degradation achieved dusk-tracking expression through light regulation, rather than a dusk-tracking rhythm. Model analysis predicted which biochemical processes could be manipulated to extend dusk tracking. Our results reveal how an operating principle of biological regulators applies specifically to the plant circadian clock.
Edwards, Kieron D; Akman, Ozgur E; Knox, Kirsten; Lumsden, Peter J; Thomson, Adrian W; Brown, Paul E; Pokhilko, Alexandra; Kozma-Bognar, Laszlo; Nagy, Ferenc; Rand, David A; Millar, Andrew J
Quantitative analysis of plasma interleiukin-6 by immunoassay on microchip
NASA Astrophysics Data System (ADS)
Sandwich enzyme-linked immunoassay (ELISA) is one of the most frequently employed assays for clinical diagnosis, since this enables the investigator to identify specific protein biomarkers. However, the conventional assay using a 96-well microtitration plate is time- and sample-consuming, and therefore is not suitable for rapid diagnosis. To overcome these drawbacks, we performed a sandwich ELISA on a microchip. We employed the piezoelectric inkjet printing for deposition and fixation of 1st antibody on the microchannnel surface (300 ?m width and 100 ?m depth). Model analyte was interleukin-6 (IL-6) which was one of the inflammatory cytokine. After blocking the microchannel, antigen, biotin-labeled 2nd antibody, and avidin-labeled peroxidase were infused into the microchannel and incubated for 20 min, 10 min, and 5 min, respectively. This assay could detect 2 pg/ml and quantitatively measure the range of 0-32 pg/ml. Liner regression analysis of plasma IL-6 concentration obtained by microchip and conventional methods exhibited a significant relationship (R2 = 0.9964). This assay reduced the time for the antigen-antibody reaction to 1/6, and the consumption of samples and reagents to 1/50 compared with the conventional method. This assay enables us to determine plasma IL-6 with accuracy, high sensitivity, time saving ability, and low consumption of sample and reagents, and thus will be applicable to clinic diagnosis.
Abe, K.; Hashimoto, Y.; Yatsushiro, S.; Yamamura, S.; Tanaka, M.; Ooie, T.; Baba, Y.; Kataoka, M.
Databases and their analysis for applications in quantitative risk analysis of NPP
There are several equipment failure databases originating in the nuclear power plant that are successfully used in quantitative risk analysis applications Le, probabilistic safety assessment (PSA). Regulatory bodies (like AERB, India) now accept the importance and use of databases for safety and reliability studies in the nuclear industry as industry practice. Databases containing human error data originated from studies carried
U. Rastogi; V. K. Jain; G. Srinivas; R. Guptan
A DArT platform for quantitative bulked segregant analysis
Background Bulked segregant analysis (BSA) identifies molecular markers associated with a phenotype by screening two DNA pools of phenotypically distinct plants for markers with skewed allele frequencies. In contrast to gel-based markers, hybridization-based markers such as SFP, DArT or SNP generate quantitative allele-frequency estimates. Only DArT, however, combines this advantage with low development and assay costs and the ability to be deployed for any plant species irrespective of its ploidy level. Here we investigate the suitability of DArT for BSA applications using a barley array as an example. Results In a first test experiment, we compared two bulks of 40 Steptoe/Morex DH plants with contrasting pubescent leaves (mPub) alleles on chromosome 3H. At optimized levels of experimental replication and marker-selection threshold, the BSA scan identified 433 polymorphic markers. The relative hybridization contrast between bulks accurately reflected the between-bulk difference in the frequency of the mPub allele (r = 0.96). The 'platform noise' of DArT assays, estimated by comparing two identical aliquots of a DNA mixture, was significantly lower than the 'pooling noise' reflecting the binomial sampling variance of the bulking process. The allele-frequency difference on chromosome 3H increased in the vicinity of mPub and peaked at the marker with the smallest distance from mPub (4.6 cM). In a validation experiment with only 20 plants per bulk we identified an aluminum (Al) tolerance locus in a Dayton/Zhepi2 DH population on chromosome 4H with < 0.8 cM precision, the same Al-tolerance locus that had been mapped before in other barley populations. Conclusion DArT-BSA identifies genetic loci that influence phenotypic characters in barley with at least 5 cM accuracy and should prove useful as a generic tool for high-throughput, quantitative BSA in plants irrespective of their ploidy level.
Wenzl, Peter; Raman, Harsh; Wang, Junping; Zhou, Meixue; Huttner, Eric; Kilian, Andrzej
Bivariate association analysis for quantitative traits using generalized estimation equation.
Quantitative traits often underlie risk for complex diseases. Many studies collect multiple correlated quantitative phenotypes and perform univariate analyses on each of them respectively. However, this strategy may not be powerful and has limitations to detect pleiotropic genes that may underlie correlated quantitative traits. In addition, testing multiple traits individually will exacerbate perplexing problem of multiple testing. In this study, generalized estimating equation 2 (GEE2) is applied to association mapping of two correlated quantitative traits. We suppose that a quantitative trait locus is located in a chromosome region that exerts pleiotropic effects on multiple quantitative traits. In that region, multiple SNPs are genotyped. Genotypes of these SNPs and the two quantitative traits affected by a causal SNP were simulated under various parameter values: residual correlation coefficient between two traits, causal SNP heritability, minor allele frequency of the causal SNP, extent of linkage disequilibrium with the causal SNP, and the test sample size. By power analytical analyses, it is showed that the bivariate method is generally more powerful than the univariate method. This method is robust and yields false-positive rates close to the pre-set nominal significance level. Our real data analyses attested to the usefulness of the method. PMID:20129400
Yang, Fang; Tang, Zihui; Deng, Hongwen
Is the new AquaTrainer� snorkel valid for VO2 assessment in swimming?
The Cosmed AquaTrainer� snorkel, in connection with the K4b2 analyzer, is the most recent instrument used for real time gas analysis during swimming. This study aimed to test if a new AquaTrainer� snorkel with 2 (SV2) or 4 (SV4) valves is comparable to a standard face mask (Mask) being valid for real time gas analysis under controlled laboratory and swimming pool conditions. 9 swimmers performed 2 swimming and 3 cycling tests at 3 different workloads on separate days. Tests were performed in random order, at constant exercise load with direct turbine temperature measurements, breathing with Mask, SV4 and SV2 while cycling, and with SV2 and SV4 while swimming. A high agreement was obtained using Passing - Bablok regression analysis in oxygen consumption, carbon dioxide production, tidal volumes, pulmonary ventilation, expiratory fraction of oxygen and carbon dioxide, and heart rate comparing different conditions in swimming and cycling. Proportional and fixed differences were always rejected (95% CI always contained the value 1 for the slope and the 0 for the intercept). In conclusion, the new SV2 AquaTrainer� snorkel, can be considered a valid device for gas analysis, being comparable to the Mask and the SV4 in cycling, and to the SV4 in swimming. PMID:23041962
Baldari, C; Fernandes, R J; Meucci, M; Ribeiro, J; Vilas-Boas, J P; Guidetti, L
Quantitative Analysis of p-Phthalic Acid by Infrared Spectrum.
National Technical Information Service (NTIS)
A quantitative method is described for determining p-phthalic acid in synthetic resins, synthetic fibers, and plastifiers by infrared absorption spectrum. The apparatus used was a infrared spectrometer. Infrared absorption spectra of p- and o-phthalic aci...
Ch'en Chang-ch'iang Chang Yu-ch'ien
Quantitative Analysis and Characterization of DNA Immobilized on Gold.
National Technical Information Service (NTIS)
We describe the complementary use of X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared (FTIR) spectroscopy to quantitatively characterize the immobilization of thiolated (dT)25 single- stranded DNA (ssDNA) on gold. When electron attenu...
D. Y. Petrovykh H. Kimura-Suda L. J. Whitman M. J. Tarlov
Comparison of audio and video data sources for quantitative analysis of echocardiographic Doppler velocity profiles
Computer based, off-line quantitative Doppler velocity profile image analysis can utilize either the audio or video formats of the echocardiography machine. The audio and video data are each corrupted, in some way, relative to the Doppler information from which they originate. To compare the suitability of each source for quantitative model-based image processing analysis, audio and video transmitral Doppler data
Andrew F. Hall; S. J. Kovacs
Quantitative Analysis of Urban Expansion in Central China
NASA Astrophysics Data System (ADS)
Quantifying urban expansion forms is important to understanding regional urbanization processes and urban planning. For this purpose, conventional landscape indices are commonly used for quantitative analysis of urban landscape patterns. However, these landscape indices only reflect information for one particular temporal phase of landscape patterns. This paper studies and quantifies the dynamic changes of urban landscape from 1993 to 2006 in Changsha-Zhuzhou-Xiangtan metropolitan areas in Hunan province of China using landscape expansion index (LEI), which contains information of the formation processes of landscape patterns. The results indicate that there are three types of urban expansions: infilling, edge-expansion and outlying in the study area. The change of proportion of the three urban expansion types reveals that urban expansion patterns have changed from a messy, dispersed early development phase to more compact and reasonable layout from 1993 to 2006. Moreover, the urban expansion modes varied in different periods. From 1993 to 1996, the edge-expansion and outlying were the main types of urban expansion forms, indicating an early stage of rapid urban developments. Comparing with the edge-expansion, the outlying expansion increased rapidly in this period, which indicates urban development is messy and dispersion. Overall, the edge-expansion was the major type of urban expansion form during the study period with outlying as the second and rapidly-increasing major form of expansion prior to 1998, which indicates urbanization is in the early stage of rapid urban developments, and infilling as the second and rapidly-increasing major form of expansion after 1998.
Zeng, Y.; Xu, Y.; Li, S.; He, L.; Yu, F.; Zhen, Z.; Cai, C.
Quantitative analysis of analgoantipyretics in dosage form using planar chromatography.
In the therapy of pain of weaker genesis, frequently used drugs usually represent a mix of analgoantipyretics of different chemical structures, mostly derivatives of salicylic acid, pyrazolone and p-aminophenol as well as derivatives of propionic and acetylsalicylic acid. For the determination of these drugs, different chromatographic methods have been applied, mostly HPLC, due to the the lower polarity (pyrazolones derivatives) and thermolability, as well as nonvolatility of compounds investigated. TLC method, considering advantages which include simplicity, reasonable sensitivity, rapidity, excellent resolving power and low cost has been successfully explored for the determination of analgoantipyretic compounds. The aim of this work was to develop a simple and rapid HPTLC method for the determination of acetylsalicylic acid, paracetamol, caffeine and phenobarbitone in dosage form. The determination of analgoantipyretics were performed on pre-coated HPTLC silica gel plates (10 x 20 cm(2)) by development in the mobile phase dichlormethane-ethyl acetate-cyclohexane-isopropanol-0.1 M HCL-formic acid (9:8:3:1.5:0.2:0.2 v/v/v/v/v/v). Migration distances (68.6+0.2 mm, 54.1+0.1 mm, 36.4+0.14 mm and 85.9+0.11 mm for acetylsalicylic acid, paracetamol, caffeine and phenobarbitone, respectively) with low RSD values (0.13--0.39%) showed a satisfactory reproductivity of the chromatographic system. TLC scanner was used for direct evaluation of the chromatograms in the reflectance/absorbance mode. Established calibration curves (r>0.999), precision (0.3--1.02%) and detection limits, as well as recovery values (96.51--98.1%) were validated and found to be satisfactory. The method was found to be reproducible and convenient for the quantitative analysis of compounds investigated in their dosage forms. PMID:11248516
Franeta, J T; Agbaba, D D; Eric, S M; Pavkov, S P; Vladimirov, S D; Aleksic, M B
Hydrocarbons on Phoebe, Iapetus, and Hyperion: Quantitative Analysis
NASA Technical Reports Server (NTRS)
We present a quantitative analysis of the hydrocarbon spectral bands measured on three of Saturn's satellites, Phoebe, Iaperus, and Hyperion. These bands, measured with the Cassini Visible-Infrared Mapping Spectrometer on close fly-by's of these satellites, are the C-H stretching modes of aromatic hydrocarbons at approximately 3.28 micrometers (approximately 3050 per centimeter), and the are four blended bands of aliphatic -CH2- and -CH3 in the range approximately 3.36-3.52 micrometers (approximately 2980- 2840 per centimeter) bably indicating the presence of polycyclic aromatic hydrocarbons (PAH), is unusually strong in comparison to the aliphatic bands, resulting in a unique signarure among Solar System bodies measured so far, and as such offers a means of comparison among the three satellites. The ratio of the C-H bands in aromatic molecules to those in aliphatic molecules in the surface materials of Phoebe, NAro:NAliph approximately 24; for Hyperion the value is approximately 12, while laperus shows an intermediate value. In view of the trend of the evolution (dehydrogenation by heat and radiation) of aliphatic complexes toward more compact molecules and eventually to aromatics, the relative abundances of aliphatic -CH2- and -CH3- is an indication of the lengths of the molecular chain structures, hence the degree of modification of the original material. We derive CH2:CH3 approximately 2.2 in the spectrum of low-albedo material on laperus; this value is the same within measurement errors to the ratio in the diffuse interstellar medium. The similarity in the spectral signatures of the three satellites, plus the apparent weak trend of aromatic/aliphatic abundance from Phoebe to Hyperion, is consistent with, and effectively confirms that the source of the hydrocarbon-bearing material is Phoebe, and that the appearance of that material on the other two satellites arises from the deposition of the inward-spiraling dust that populates the Phoebe ring.
Cruikshank, Dale P.; MoreauDalleOre, Cristina; Pendleton, Yvonne J.; Clark, Roger Nelson
Quantitative analysis of the immune cells in the anal mucosa.
The prevalence of anoperineal diseases, i.e. sexual transmitted infections, is increasing particularly in AIDS, a fact which is likely due to the alteration of mucosal immunity. However, no data were available on normal anal status. In order to study anal immunity in man, we characterized lymphocytes subtypes and Langerhans' cells (LC) using quantitative morphometric analysis and immunohistochemistry. Anal normal mucosal samples obtained from surgical specimens of 45 patients (30 suffering from hemorrhoids and 15 from fissurations) were analyzed. Immunohistochemistry was performed on frozen sections with antibodies recognizing CD1a (LC), CD3 (T lymphocytes), CD4 (T4), CD8 (T8) and CD22 (B-lymphocytes). Immunostained cells were counted per square millimeter of mucosal epithelium. The surface of CD1a cells was measured using a computerized software program and a percentage of CD1a immunostained area was calculated in comparison to the whole mucosal surface. LC and T-Lymphocytes were found in the squamous epithelium in all analyzed samples. The mean values of LC number were 84.13 +/- 9.6 and 64.77 +/- 9.8 in hemorroid- and fissure-patients, respectively. The mean values of LC area (% of CD1a stained area over total mucosal surface) were 3.89 +/- 0.44 and 4.84 +/- 0.64, respectively. In the two groups, the number of intraepithelial CD8 lymphocytes was higher than that of CD4 lymphocytes. These data suggest for the first time that anal mucosa could be considered as a part of MALT system. PMID:8822106
Gervaz, E; Dauge-Geffroy, M D; Sobhani, I; Vissuzaine, C; Mignon, M; Benhamou, G; Potet, F
Quantitative Analysis of the Effective Functional Structure in Yeast Glycolysis
The understanding of the effective functionality that governs the enzymatic self-organized processes in cellular conditions is a crucial topic in the post-genomic era. In recent studies, Transfer Entropy has been proposed as a rigorous, robust and self-consistent method for the causal quantification of the functional information flow among nonlinear processes. Here, in order to quantify the functional connectivity for the glycolytic enzymes in dissipative conditions we have analyzed different catalytic patterns using the technique of Transfer Entropy. The data were obtained by means of a yeast glycolytic model formed by three delay differential equations where the enzymatic rate equations of the irreversible stages have been explicitly considered. These enzymatic activity functions were previously modeled and tested experimentally by other different groups. The results show the emergence of a new kind of dynamical functional structure, characterized by changing connectivity flows and a metabolic invariant that constrains the activity of the irreversible enzymes. In addition to the classical topological structure characterized by the specific location of enzymes, substrates, products and feedback-regulatory metabolites, an effective functional structure emerges in the modeled glycolytic system, which is dynamical and characterized by notable variations of the functional interactions. The dynamical structure also exhibits a metabolic invariant which constrains the functional attributes of the enzymes. Finally, in accordance with the classical biochemical studies, our numerical analysis reveals in a quantitative manner that the enzyme phosphofructokinase is the key-core of the metabolic system, behaving for all conditions as the main source of the effective causal flows in yeast glycolysis.
De la Fuente, Ildefonso M.; Cortes, Jesus M.
Quantitative Analysis by Isotopic Dilution Using Mass Spectroscopy: The Determination of Caffeine by GC-MS.
ERIC Educational Resources Information Center
Describes a laboratory technique for quantitative analysis of caffeine by an isotopic dilution method for coupled gas chromatography-mass spectroscopy. Discusses caffeine analysis and experimental methodology. Lists sample caffeine concentrations found in common products. (MVL)
Hill, Devon W.; And Others
Quantitative proton nuclear magnetic resonance for the structural and quantitative analysis of atropine sulfate.
This study assessed a general method of quantitative nuclear magnetic resonance (qNMR) for the calibration of atropine sulfate (Active Pharmaceutical Ingredient, API) as reference standard. The spectra were acquired in D2O using maleic acid as the internal standard. Conformational behaviors of tropane ring were observed and studied by means of NMR and ROESY experiments at different temperature, which showed that the azine methyl group was at equilibrium for axial and equatorial conformations at room temperature. Signal delay and monitor signals of qNMR experimentation were optimized for quantification. The study reported here validated the method's linearity, range, limit of quantification, stability and precision. The results were consistent with the results obtained from mass balance approach. PMID:24280740
Shen, Shi; Yao, Jing; Shi, Yaqin
A new quantitative method for gunshot residue analysis by ion beam analysis.
Imaging and analyzing gunshot residue (GSR) particles using the scanning electron microscope equipped with an energy dispersive X-ray spectrometer (SEM-EDS) is a standard technique that can provide important forensic evidence, but the discrimination power of this technique is limited due to low sensitivity to trace elements and difficulties in obtaining quantitative results from small particles. A new, faster method using a scanning proton microbeam and Particle Induced X-ray Emission (?-PIXE), together with Elastic Backscattering Spectrometry (EBS) is presented for the non-destructive, quantitative analysis of the elemental composition of single GSR particles. In this study, the GSR particles were all Pb, Ba, Sb. The precision of the method is assessed. The grouping behaviour of different makes of ammunition is determined using multivariate analysis. The protocol correctly groups the cartridges studied here, with a confidence >99%, irrespective of the firearm or population of particles selected. PMID:23775063
Christopher, Matthew E; Warmenhoeven, John-William; Romolo, Francesco S; Donghi, Matteo; Webb, Roger P; Jeynes, Christopher; Ward, Neil I; Kirkby, Karen J; Bailey, Melanie J
Quantitative analysis of localized surface plasmons based on molecular probing.
We report on the quantitative characterization of the plasmonic optical near-field of a single silver nanoparticle. Our approach relies on nanoscale molecular molding of the confined electromagnetic field by photoactivated molecules. We were able to directly image the dipolar profile of the near-field distribution with a resolution better than 10 nm and to quantify the near-field depth and its enhancement factor. A single nanoparticle spectral signature was also assessed. This quantitative characterization constitutes a prerequisite for developing nanophotonic applications. PMID:20687536
Deeb, Claire; Bachelot, Renaud; Plain, J�r�me; Baudrion, Anne-Laure; Jradi, Safi; Bouhelier, Alexandre; Soppera, Olivier; Jain, Prashant K; Huang, Libai; Ecoffet, Carole; Balan, Lavinia; Royer, Pascal
Quantitative analysis of autophagy using advanced 3D fluorescence microscopy.
Prostate cancer is the leading form of malignancies among men in the U.S. While surgery carries a significant risk of impotence and incontinence, traditional chemotherapeutic approaches have been largely unsuccessful. Hormone therapy is effective at early stage, but often fails with the eventual development of hormone-refractory tumors. We have been interested in developing therapeutics targeting specific metabolic deficiency of tumor cells. We recently showed that prostate tumor cells specifically lack an enzyme (argininosuccinate synthase, or ASS) involved in the synthesis of the amino acid arginine(1). This condition causes the tumor cells to become dependent on exogenous arginine, and they undergo metabolic stress when free arginine is depleted by arginine deiminase (ADI)(1,10). Indeed, we have shown that human prostate cancer cells CWR22Rv1 are effectively killed by ADI with caspase-independent apoptosis and aggressive autophagy (or macroautophagy)(1,2,3). Autophagy is an evolutionarily-conserved process that allows cells to metabolize unwanted proteins by lysosomal breakdown during nutritional starvation(4,5). Although the essential components of this pathway are well-characterized(6,7,8,9), many aspects of the molecular mechanism are still unclear - in particular, what is the role of autophagy in the death-response of prostate cancer cells after ADI treatment? In order to address this question, we required an experimental method to measure the level and extent of autophagic response in cells - and since there are no known molecular markers that can accurately track this process, we chose to develop an imaging-based approach, using quantitative 3D fluorescence microscopy(11,12). Using CWR22Rv1 cells specifically-labeled with fluorescent probes for autophagosomes and lysosomes, we show that 3D image stacks acquired with either widefield deconvolution microscopy (and later, with super-resolution, structured-illumination microscopy) can clearly capture the early stages of autophagy induction. With commercially available digital image analysis applications, we can readily obtain statistical information about autophagosome and lysosome number, size, distribution, and degree of colocalization from any imaged cell. This information allows us to precisely track the progress of autophagy in living cells and enables our continued investigation into the role of autophagy in cancer chemotherapy. PMID:23665532
Changou, Chun A; Wolfson, Deanna L; Ahluwalia, Balpreet Singh; Bold, Richard J; Kung, Hsing-Jien; Chuang, Frank Y S
Calibration Adjustments to the MODIS Aqua Ocean Color Bands
NASA Technical Reports Server (NTRS)
After the end of the SeaWiFS mission in 2010 and the MERIS mission in 2012, the ocean color products of the MODIS on Aqua are the only remaining source to continue the ocean color climate data record until the VIIRS ocean color products become operational (expected for summer 2013). The MODIS on Aqua is well beyond its expected lifetime, and the calibration accuracy of the short wavelengths (412nm and 443nm) has deteriorated in recent years_ Initially, SeaWiFS data were used to improve the MODIS Aqua calibration, but this solution was not applicable after the end of the SeaWiFS mission_ In 2012, a new calibration methodology was applied by the MODIS calibration and support team using desert sites to improve the degradation trending_ This presentation presents further improvements to this new approach. The 2012 reprocessing of the MODIS Aqua ocean color products is based on the new methodology.
Meister, Gerhard
Quantitative Analysis of Human Milk Oligosaccharides by Capillary Electrophoresis
Human milk oligosaccharides may have important biological activities. 1 We developed a sensitive, convenient, quantitative method for the routine study of sialylated (acidic, negatively charged) oligosaccharides in large numbers of milk samples. Capillary electrophoresis (CE) with detection at 205 nm was sensitive to the femtomole level and could resolve and quantify nine acidic oligosaccharides in milk, ranging from tri- to
David S. Newburg; Zuojun Shen; Christopher D. Warren
Today I will talk about the use of quantitative or Real time PCR for the standardized identification and quantification of molds. There are probably at least 100,000 species of molds or fungi. But there are actually about 100 typically found indoors. Some pose a threat to human...
Detection, Quantitation, and Phylogenetic Analysis of Noroviruses in Japanese Oysters
Noroviruses (NVs) cause many cases of oyster- or clam-associated gastroenteritis in various countries. We collected 191 samples from Japanese oysters intended for raw consumption that had been harvested from the sea in two different areas between December 2001 and February 2002. To detect, quantitate, and phylogeneti- cally analyze the NV genome in purified concentrates from the stomachs and digestive diverticula
Tomoko Nishida; Hirokazu Kimura; Mika Saitoh; Michiyo Shinohara; Masahiko Kato; Shinji Fukuda; Tetsuya Munemura; Toshiyuki Mikami; Ayumi Kawamoto; Miho Akiyama; Yumiko Kato; Kanako Nishi; Kunihisa Kozawa; Osamu Nishio
Quantitative XRD analysis of zirconia-toughened alumina ceramics
An equation is proposed to give, from XRD data, the tetragonal to monoclinic phase ratio of zirconia in a toughened alumina ceramic material. Using several X-ray wavelengths, with different depths of penetration, quantitative analyses of the tetragonal to monoclinic phase ratio of zirconia as a function of depth were performed, on an as-sintered sample as well as on treated specimens.
R. Fillit; R. P. Homerin; R. J. Schafer; R. H. Bruyas; R. F. Thevenot
Quantitative Mineralogical Analysis by X-ray diffraction.
National Technical Information Service (NTIS)
Work was done in two phases on different combinations of soil-like crystalline materials that were mixed in the laboratory to develop a simple, rapid, and inexpensive method of doing quantitative mineralogical analyses, largely by X-ray diffraction (XRD)....
A. D. Buck
Quantitative structure-activity relationship analysis of phenolic antioxidants
In this report, the quantitative structure-activity relationship (QSAR) analyses of substituted phenols, vitamin E derivatives and flavonoids are presented. Two models have been derived using calculated parameters such as the heat of formation (Hf), the energy of the lowest unoccupied molecular orbital of radicals (Elumo-r), the energy of the highest occupied molecular orbital of the parent compounds (Ehomo) and the
Eric J. Lien; Shijun Ren; Huynh-Hoa Bui; Rubin Wang
Depression in Parkinson's disease: a quantitative and qualitative analysis
Depression is a common feature of Parkinson's disease, a fact of both clinical and theoretical significance. Assessment of depression in Parkinson's disease is complicated by overlapping symptomatology in the two conditions, making global assessments based on observer or self-ratings of doubtful validity. The present study aimed to provide both a quantitative and qualitative description of the nature of the depressive
A M Gotham; R G Brown; C D Marsden
Ground application of AquaReslin and AquaKontrol against Anopheles quadrimaculatus, Aedes aegypti, and Aedes albopictus.
Two permethrin formulations, AquaReslin and AquaKontrol, were applied by ultra-low volume truck-mounted sprayers on test plots under appropriate meteorological condition at Jacksonville, FL. The method of application was followed from the product label. The application rate for each formulation was 0.79 g permethrin per acre. AquaReslin and AquaKontrol demonstrated similar results against Anopheles quadrimaculatus; the former was superior to the latter used against Aedes aegypti, and Ae. albopictus. Teflon-coated standard glass slides were used to collect the aerosol components. Volume median-diameter droplets per square centimeter varied with pesticides and distance from spray source, and the mortality of the 3 species at 18 h ranged from 61.3% to 91.7%. PMID:22017102
Brown, James R; Xue, Rui-De
Quantitative X-Ray Diffraction Analysis of Crocidolite and Amosite in Bulk or Settled Dust Samples
A quantitative procedure for determining crocidolite and amosite in bulk or settled dust samples is described. Crocidolite and amosite are two of the three major types of asbestos fibers used in the United States asbestos industry. Each has a crystalline structure which provides a distinct x-ray diffraction pattern of sufficient intensity to be used in quantitative analysis. Quartz is used
John V. Crable; Marta J. Knott
An Inexpensive Electrodeposition Device and Its Use in a Quantitative Analysis Laboratory Exercise
ERIC Educational Resources Information Center
An experimental procedure, using an apparatus that is easy to construct, was developed to incorporate a quantitative electrogravimetric determination of the solution nickel content into an undergraduate or advanced high school quantitative analysis laboratory. This procedure produces results comparable to the procedure used for the gravimetric�
Parker, Richard H.
Optimal sibship selection for genotyping in quantitative trait locus linkage analysis
In this paper we present a novel method for selecting optimally informative sibships of any size for quantitative trait locus (QTL) linkage analysis. The method allocates a quantitative index of potential informativeness to each sibship on the basis of observed trait scores and an assumed true QTL model. Any sample of phenotypically screened sibships can therefore be easily rank-ordered for
S. Purcell; S. S. Cherny; J. K. Hewitt; P. C. Sham
Optimal Sibship Selection for Genotyping in Quantitative Trait Locus Linkage Analysis
In this paper we present a novel method for selecting optimally informative sibships of any size for quantitative trait locus (QTL) linkage analysis. The method allocates a quantitative index of potential informativeness to each sibship on the basis of observed trait scores and an assumed true QTL model. Any sample of phenotypically screened sibships can therefore be easily rank-ordered for
S. Purcell; S.S. Cherny; J. K. Hewitt; P. C. Sham
An integrated quantitative risk analysis method for natural gas pipeline network
Natural gas industry is developing rapidly, and its accidents are threatening the urban safety. Risk management through quantitative assessment has become an important way to improve the safety performance of the natural gas supply system. In this paper, an integrated quantitative risk analysis method for natural gas pipeline network is proposed. This method is composed of the probability assessment of
Z. Y. Han; W. G. Weng
Quantitative Analysis of Endodontic Treatment for Periapical Lesions in Intraoral Radiographs
Intraoral radiographs have been taken to diagnose periapical lesions. Subsequent endodontic treatment needs to be evaluated quantitatively, that is often difficul t due to various imaging factors as well as subjective visua l interpretation. Therefore, we sought to establish an image analysis based quantitative model to evaluate endod ontic treatments (40 effective and 43 noneffective cases) . To normalize an
Taeju Lee; Hyekyung Jeong; Desok Kim; Byung-do Lee
Quantitative and qualitative HPLC analysis of thermogenic weight loss products.
An HPLC qualitative and quantitative method of seven analytes (caffeine, ephedrine, forskolin, icariin, pseudoephedrine, synephrine, and yohimbine) in thermogenic weight loss preparations available on the market is described in this paper. After 45 min the seven analytes were separated and detected in the acetonitrile: water (80:20) extract. The method uses a Waters XTerra RP18 (5 microm particle size) column as the stationary phase, a gradient mobile phase of water (5.0 mM SDS) and acetonitrile, and a UV detection of 210 nm. The correlation coefficients for the calibration curves and the recovery rates ranged from 0.994 to 0.999 and from 97.45% to 101.05%, respectively. The qualitative and quantitative results are discussed. PMID:15587578
Schaneberg, B T; Khan, I A
Pooled analysis of data from multiple quantitative trait locus mapping populations
Quantitative trait locus (QTL) analysis on pooled data from multiple populations (pooled analysis) provides a means for evaluating, as a whole, evidence for existence of a QTL from different studies and examining differences in gene effect of a QTL among different populations. Objectives of this study were to: (1) develop a method for pooled analysis and (2) conduct pooled analysis
B. Guo; D. A. Sleper; J. Sun; H. T. Nguyen; P. R. Arelli; J. G. Shannon
Quantitative NMR spectroscopy--applications in drug analysis.
NMR spectroscopy being a primary ratio method of measurement is highly suitable to evaluate the quality of drugs. NMR spectroscopy can be used for the identification of a drug substance, the identification and quantification of impurities arising from the synthesis pathway and degradation, or residual solvents as well as the determination of the content in the assay. This review gives an overview of the application of quantitative NMR spectroscopy in International Pharmacopoeias and for licensing purposes. PMID:15893899
Holzgrabe, U; Deubner, R; Schollmayer, C; Waibel, B
Quantitative analysis of the electroencephalogram during cranial electrotherapy stimulation
Objective: Normal individuals were used to quantitate electroencephalographic (EEG) changes during concurrent administration of 0.5 and 100 Hz cranial electrotherapy stimulation (CES).Methods: Twelve normal, right-handed males were used in a randomized, double-blind crossover design study. A 3 amplifier system incorporating noise-cancellation was used to collect one channel of EEG (O1-Cz configuration) for 30 min. Either 0.5, 100 Hz, or sham
M. j. Schroeder; R. e. Barr
Genome-Wide Analysis of Expression Quantitative Trait Loci in Breast Cancer - Nicholas Knoblauch, TCGA Scientitifc Symposium 2012
Home News and Events Multimedia Library Videos Genome-Wide Analysis of Expression Quantitative Trait Loci in Breast Cancer - Nicholas Knoblauch Genome-Wide Analysis of Expression Quantitative Trait Loci in Breast Cancer - Nicholas Knoblauch, TCGA
How closely correlated are molecular and quantitative measures of genetic variation? A meta-analysis.
The ability of populations to undergo adaptive evolution depends on the presence of quantitative genetic variation for ecologically important traits. Although molecular measures are widely used as surrogates for quantitative genetic variation, there is controversy about the strength of the relationship between the two. To resolve this issue, we carried out a meta-analysis based on 71 datasets. The mean correlation between molecular and quantitative measures of genetic variation was weak (r = 0.217). Furthermore, there was no significant relationship between the two measures for life-history traits (r = -0.11) or for the quantitative measure generally considered as the best indicator of adaptive potential, heritability (r = -0.08). Consequently, molecular measures of genetic diversity have only a very limited ability to predict quantitative genetic variability. When information about a population's short-term evolutionary potential or estimates of local adaptation and population divergence are required, quantitative genetic variation should be measured directly. PMID:11475045
Reed, D H; Frankham, R
Software for quantitative analysis of radiotherapy: overview, requirement analysis and design solutions.
Radiotherapy is a fast-developing discipline which plays a major role in cancer care. Quantitative analysis of radiotherapy data can improve the success of the treatment and support the prediction of outcome. In this paper, we first identify functional, conceptional and general requirements on a software system for quantitative analysis of radiotherapy. Further we present an overview of existing radiotherapy analysis software tools and check them against the stated requirements. As none of them could meet all of the demands presented herein, we analyzed possible conceptional problems and present software design solutions and recommendations to meet the stated requirements (e.g. algorithmic decoupling via dose iterator pattern; analysis database design). As a proof of concept we developed a software library "RTToolbox" following the presented design principles. The RTToolbox is available as open source library and has already been tested in a larger-scale software system for different use cases. These examples demonstrate the benefit of the presented design principles. PMID:23523366
Zhang, Lanlan; Hub, Martina; Mang, Sarah; Thieke, Christian; Nix, Oliver; Karger, Christian P; Floca, Ralf O
Quantitative Gas Analysis of Sulfur Dioxide in Nitrogen by Fourier Transform Infrared Spectrophotometer.
National Technical Information Service (NTIS)
A method for quantitative gas analysis of sulfur dioxide contained in nitrogen using the Fourier transform infrared spectrophotometer has been established. On account of the strong adsorption properties of sulfur dioxide, the measuring method adopted is o...
Y. Koga M. Sugie S. Kondo S. Saeki
ANSI/ASHRAE/INESNA Standard 90.1-2007 Final Determination Quantitative Analysis.
National Technical Information Service (NTIS)
The United States (U.S.) Department of Energy (DOE) conducted a final quantitative analysis to assess whether buildings constructed according to the requirements of the American National Standards Institute (ANSI)/American Society of Heating, Refrigeratin...
B. Liu D. Winiarski E. Richman M. Halverson
Quantitative Analysis of a Hybrid Electric HMMWV for Fuel Economy Improvement.
National Technical Information Service (NTIS)
This paper presents a quantitative analysis and comparison of fuel economy and performance of a series hybrid electric HMMWV (High Mobility Multi- purpose Wheeled Vehicle) military vehicle with a conventional HMMWV of equivalent size. Hybrid vehicle power...
A. Masrur A. Nedungadi R. Smith
Porous polymer packings have been used successfully in many applications of direct aqueous injection gas chromatography. The authors have expanded the use of aqueous injection to the quantitative analysis of 68 alcohols, acetates, ketones, ethers, sulfides, aldehydes, diols, dion...
Rapid Quantitative Analysis of Proteins or Protein Function in Complex Mixtures.
National Technical Information Service (NTIS)
Analytical reagents and mass spectrometry-based methods using these reagents for the rapid, and quantitative analysis of proteins or protein function in mixtures of proteins. The methods employ affinity labeled protein reactive reagents having three porti...
R. H. Aebersold M. H. Gelb S. P. Gygi C. R. Scott F. Turecek S. A. Gerber B. Rist
Status of Terra and Aqua MODIS Instruments
NASA Technical Reports Server (NTRS)
Currently, two nearly identical MODIS instruments are operating in space: one on the Terra spacecraft launched in December 1999 and another on the Aqua spacecraft launched in May 2002. MODIS has 36 spectral bands with wavelengths covering from visible (VIS) to long-wave infrared (LWIR). Since launch, MODIS observations and data products have contributed significantly to studies of changes in the Earth system of land, oceans, and atmosphere. To maintain its on-orbit calibration and data product quality, MODIS was built with a comprehensive set of on-board calibrators, consisting of a solar diffuser (SD) and a solar diffuser stability monitor (SDSM) for the reflective solar bands (RSB) and an on-board blackbody (BB) for the thermal emissive bands (TEB). Both instruments have demonstrated good performance. The primary Level 1 B (LIB) data products are top of the atmosphere (TOA) reflectance for RSB and radiance for TEB This paper provides an overview of MODIS calibration methodologies, activities, lifetime on-orbit performance and challenging issues for each MODIS, the impact on LIB product quality, and lessons learned for future sensors such as the NPOESS VIIRS.
Xiong, Xiaoxiong; Wenny, Brian N.; Kuyper, James; Salomonson, Vicent; Barmes. William
Quantitative analysis and measurements of near-field interactions in terahertz microscopes.
We demonstrated quantitative analysis and measurements of near-fields interactions in a terahertz pulse near-field microscope. We developed a self-consistent line dipole image method for the quantitative analysis of the near-field interaction in THz scattering-type scanning optical microscopes. The measurements of approach curves and relative contrasts on gold and silicon substrates were in excellent agreement with calculations. PMID:21716385
Moon, Kiwon; Jung, Euna; Lim, Meehyun; Do, Youngwoong; Han, Haewook
Evaluation of quantitative parametric analysis for characterization of breast lesions in contrast-enhanced MR mammography
Our aim was to evaluate quantitative parametric analysis for characterization of breast lesions in contrast-enhanced magnetic resonance (MR) mammography. In 62 patients, contrast-enhanced MR mammography revealed 75 suspicious lesions, of which 18 were benign and 57 were malignant. The quantitative parametric analysis delineates signal intensity changes of contrast-enhanced lesions on a pixel-by-pixel basis. The initial rate of enhancement is coded
E. A. M. Hauth; H. Jaeger; S. Maderwald; C. Stockamp; A. M�hler; R. Kimmig; M. Forsting
Optimal climate policy is a utopia: from quantitative to qualitative cost-benefit analysis
The dominance of quantitative cost-benefit analysis (CBA) and optimality concepts in the economic analysis of climate policy is criticised. Among others, it is argued to be based in a misplaced interpretation of policy for a complex climate�economy system as being analogous to individual inter-temporal welfare optimisation. The transfer of quantitative CBA and optimality concepts reflects an overly ambitious approach that
Plural Analysis: Developing Multiple Approaches to Quantitative Research. Phase 1.
National Technical Information Service (NTIS)
The project proposes a methodology of plural analysis, with a decision-science focus, which is to be grounded in sound science and be practically useful. The methodology comprises guidelines and computer aids for conducting plural analysis and methods for...
R. V. Brown D. V. Lindley J. W. Ulvila D. V. Winterfeldt
Quantitative phenotypic analysis of multistress response in Zygosaccharomyces rouxii complex.
Zygosaccharomyces rouxii complex comprises three yeasts clusters sourced from sugar- and salt-rich environments: haploid Zygosaccharomyces rouxii, diploid Zygosaccharomyces sapae and allodiploid/aneuploid strains of uncertain taxonomic affiliations. These yeasts have been characterized with respect to gene copy number variation, karyotype variability and change in ploidy, but functional diversity in stress responses has not been explored yet. Here, we quantitatively analysed the stress response variation in seven strains of the Z.�rouxii complex by modelling growth variables via model and model-free fitting methods. Based on the spline fit as most reliable modelling method, we resolved different interstrain responses to 15 environmental perturbations. Compared with Z.�rouxii CBS 732(T) and Z.�sapae strains ABT301(T) and ABT601, allodiploid strain ATCC 42981 and aneuploid strains CBS 4837 and CBS 4838 displayed higher multistress resistance and better performance in glycerol respiration even in the presence of copper. ?-based logarithmic phenotypic index highlighted that ABT601 is a slow-growing strain insensitive to stress, whereas ABT301(T) grows fast on rich medium and is sensitive to suboptimal conditions. Overall, the differences in stress response could imply different adaptation mechanisms to sugar- and salt-rich niches. The obtained phenotypic profiling contributes to provide quantitative insights for elucidating the adaptive mechanisms to stress in halo- and osmo-tolerant Zygosaccharomyces yeasts. PMID:24533625
Solieri, Lisa; Dakal, Tikam C; Bicciato, Silvio
Quantitative Analysis of Transferred Nuclear Overhauser Effects in Complex Spin Systems by Full Relaxation Matrix Analysis
NASA Astrophysics Data System (ADS)
A computer program was developed for studying transferred nuclear Overhauser effects in complex spin systems. It permits quantitative analysis of nuclear Overhauser effects observed in biologically important systems, such as ligands interacting with transmembrane receptors in the presence of lipid bilayers. The full generalized relaxation matrix approach takes into account the local mobility, spin equivalence, finite exchange rates, and spectral overlap. The program can be used either to simulate theoretical nuclear Overhauser effect buildup curves or to fit a relaxation matrix of a given model to experimental data. Selected examples illustrate the program's performance.
Czaplicki, J.; Milon, A.
A novel image-analysis toolbox enabling quantitative analysis of root system architecture.
We present in this paper a novel, semiautomated image-analysis software to streamline the quantitative analysis of root growth and architecture of complex root systems. The software combines a vectorial representation of root objects with a powerful tracing algorithm that accommodates a wide range of image sources and quality. The root system is treated as a collection of roots (possibly connected) that are individually represented as parsimonious sets of connected segments. Pixel coordinates and gray level are therefore turned into intuitive biological attributes such as segment diameter and orientation as well as distance to any other segment or topological position. As a consequence, user interaction and data analysis directly operate on biological entities (roots) and are not hampered by the spatially discrete, pixel-based nature of the original image. The software supports a sampling-based analysis of root system images, in which detailed information is collected on a limited number of roots selected by the user according to specific research requirements. The use of the software is illustrated with a time-lapse analysis of cluster root formation in lupin (Lupinus albus) and an architectural analysis of the maize (Zea mays) root system. The software, SmartRoot, is an operating system-independent freeware based on ImageJ and relies on cross-platform standards for communication with data-analysis software. PMID:21771915
Lobet, Guillaume; Pag�s, Lo�c; Draye, Xavier
Quantitative analysis of Op18 phosphorylation in childhood acute leukemia.
Oncoprotein 18 (Op18) is a major cystolic phosphoprotein constituent of leukemia cells. There is cumulative evidence that suggests a role for Op18 in integrating signals from diverse pathways involved in cell growth. Op18 phosphorylation is induced with proliferation in a variety of cell types, and is essential for cell cycle progression. In this study we analyzed the level of unphosphorylated Op18 and of its major phosphorylated forms, Op18a and Op18b, in a series of 177 childhood acute leukemias by means of quantitative two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). Op18 phosphorylation was significantly correlated with the white blood count at the time of diganosis, and with a high percentage of cells in the S phase. Our findings suggest that strategies to inhibit Op18 expression or phosphorylation may be effective in inhibiting leukemia cell proliferation. PMID:9324290
Melhem, R; Hailat, N; Kuick, R; Hanash, S M
Quantitative Analysis of Matrine in Liquid Crystalline Nanoparticles by HPLC
A reversed-phase high-performance liquid chromatographic method has been developed to quantitatively determine matrine in liquid crystal nanoparticles. The chromatographic method is carried out using an isocratic system. The mobile phase was composed of methanol-PBS(pH6.8)-triethylamine (50?:?50?:?0.1%) with a flow rate of 1?mL/min with SPD-20A UV/vis detector and the detection wavelength was at 220?nm. The linearity of matrine is in the range of 1.6 to 200.0??g/mL. The regression equation is y = 10706x ? 2959 (R2 = 1.0). The average recovery is 101.7%; RSD = 2.22%??(n = 9). This method provides a simple and accurate strategy to determine matrine in liquid crystalline nanoparticle.
Peng, Xinsheng; Hu, Min; Ling, Yahao; Tian, Yuan; Zhou, Yanxing; Zhou, Yanfang
Cross-bridge model of muscle contraction. Quantitative analysis.
We recently presented, in a qualitative manner, a cross-bridge model of muscle contraction which was based on a biochemical kinetic cycle for the actomyosin ATPase activity. This cross-bridge model consisted of two cross-bridge states detached from actin and two cross-bridge states attached to actin. In the present paper, we attempt to fit this model quantitatively to both biochemical and physiological data. We find that the resulting complete cross-bridge model is able to account reasonably well for both the isometric transient data observed when a muscle is subjected to a sudden change in length and for the relationship between the velocity of muscle contraction in vivo and the actomyosin ATPase activity in vitro. This model also illustrates the interrelationship between biochemical and physiological data necessary for the development of a complete cross-bridge model of muscle contraction.
Eisenberg, E; Hill, T L; Chen, Y
Quantitative analysis of matrine in liquid crystalline nanoparticles by HPLC.
A reversed-phase high-performance liquid chromatographic method has been developed to quantitatively determine matrine in liquid crystal nanoparticles. The chromatographic method is carried out using an isocratic system. The mobile phase was composed of methanol-PBS(pH6.8)-triethylamine (50?:?50?:?0.1%) with a flow rate of 1?mL/min with SPD-20A UV/vis detector and the detection wavelength was at 220?nm. The linearity of matrine is in the range of 1.6 to 200.0? ? g/mL. The regression equation is y = 10706x - 2959 (R (2) = 1.0). The average recovery is 101.7%; RSD = 2.22%??(n = 9). This method provides a simple and accurate strategy to determine matrine in liquid crystalline nanoparticle. PMID:24834359
Peng, Xinsheng; Li, Baohong; Hu, Min; Ling, Yahao; Tian, Yuan; Zhou, Yanxing; Zhou, Yanfang
On the quantitative analysis of liquid flow in physiological tubes
NASA Astrophysics Data System (ADS)
We review three benchmark quantitative models for flow generation by physiological tube pumps. In each case significant differences between model predictions and tube behavior was emphasized. In order to close these gaps both modeler and Physiologist (often the same investigator) need to find paths which can grow to bridges. The modeler must develop more exact solutions to provide Physiologists with plug-in equations which will accept measurements. The Physiologist must make the kind of measurements which can be reasonably tested by a meaningful model. The measurements which have been features in this review are pressure, viscosity and geometry--or where geometry varies with time, kinematic data. A number of diagnostic marker formulas have been presented as stepping stones to modeling. These include R sub e, Beta, slenderness etc. which translates physiological data into indicators for modeling directions.
Winet, H.
AQUA� as predictor of allergy in elite marathon runners
Background The prevalence of allergy in athletes is increasing, and its risk varies across sports. The risk is dependent mainly on the ventilation rate and environmental factors; however, the prevalence of allergy in elite runners remains unknown. Therefore, the aim of this study was to screen allergy symptoms in elite marathon runners by using a validated questionnaire for screening allergy in athletes. Methods Two hundred and one elite marathoners, who participated in the most competitive Brazilian marathons and half-marathons during 2011, were invited to complete a validated self-report Allergy Questionnaire for Athletes (AQUA�), with additional questions pertaining to training history, such as running experience, running distance per week and their best race time in marathon or half-marathon events. Results Sixty percent of the assessed athletes reported allergy symptoms as defined by a positive AQUA outcome (score [greater than or equal to] 5). No significant differences (p?>?0.05) between groups (AQUA?+?and AQUA-) were observed for gender, age, running experience, weekly training volume and best performance time in the half-marathon and marathon. The most frequently reported symptoms were related to the respiratory tract and physical effort. Conclusions This study demonstrates that AQUA� can be used to predict allergy in elite marathon runners. In addition, these athletes have a higher prevalence of allergy symptoms to elite athletes from other sports.
Response Neighborhoods in Online Learning Networks: A Quantitative Analysis
ERIC Educational Resources Information Center
Theoretical foundation of Response mechanisms in networks of online learners are revealed by Statistical Analysis of p* Markov Models for the Networks. Our comparative analysis of two networks shows that the minimal-effort hunt-for-social-capital mechanism controls a major behavior of both networks: negative tendency to respond. Differences in�
Aviv, Reuven; Erlich, Zippy; Ravid, Gilad
Compensation for Time-Dependent Star Tracker Thermal Deformation on the Aqua Spacecraft
NASA Technical Reports Server (NTRS)
Analysis of attitude sensor data from the Aqua mission showed small but systematic differences between batch least-squares and extended Kalman filter attitudes. These differences were also found to be correlated with star tracker residuals, gyro bias estimates, and star tracker baseplate temperatures. This paper describes the analysis that shows that these correlations are all consistent with a single cause: time-dependent thermal deformation of star tracker alignments. These varying alignments can be separated into relative and common components. The relative misalignments can be determined and compensated for. The common misalignments can only be determined in special cases.
Hashmall, Joseph A.; Natanson, Gregory; Glickman, Jonathan; Sedlak, Joseph
[Research progress of quantitative analysis for respiratory sinus arrhythmia].
Respiratory sinus arrhythmia (RSA) is known as fluctuations of heart rate associated with breathing. It has been increasingly used as a noninvasive index of cardiac vagal tone in psychophysiological research recently. Its analysis is often influenced or distorted by respiratory parameters, posture and action, etc. This paper reviews five methods of quantification, including the root mean square of successive differences (RMSSD), peak valley RSA (pvRSA), cosinor fitting, spectral analysis, and joint timing-frequency analysis (JTFA). Paced breathing, analysis of covariance, residua method and msRSA per liter tidal volume are adjustment strategies of measurement and analysis of RSA in this article as well. At last, some prospects of solutions of the problems of RSA research are given. PMID:22295719
Sun, Congcong; Zhang, Zhengbo; Wang, Buqing; Liu, Hongyun; Ang, Qing; Wang, Weidong
Quantitative assessment of human motion using video motion analysis
NASA Technical Reports Server (NTRS)
In the study of the dynamics and kinematics of the human body, a wide variety of technologies was developed. Photogrammetric techniques are well documented and are known to provide reliable positional data from recorded images. Often these techniques are used in conjunction with cinematography and videography for analysis of planar motion, and to a lesser degree three-dimensional motion. Cinematography has been the most widely used medium for movement analysis. Excessive operating costs and the lag time required for film development coupled with recent advances in video technology have allowed video based motion analysis systems to emerge as a cost effective method of collecting and analyzing human movement. The Anthropometric and Biomechanics Lab at Johnson Space Center utilizes the video based Ariel Performance Analysis System to develop data on shirt-sleeved and space-suited human performance in order to plan efficient on orbit intravehicular and extravehicular activities. The system is described.
Probe, John D.
Quantitative proteomic analysis of amphotericin B resistance in Leishmania infantum.
Amphotericin B (AmB) in its liposomal form is now considered as either first- or second-line treatment against Leishmania infections in different part of the world. Few cases of AmB resistance have been reported and resistance mechanisms toward AmB are still poorly understood. This paper reports a large-scale comparative proteomic study in the context of AmB resistance. Quantitative proteomics using stable isotope labeling of amino acids in cell culture (SILAC) was used to better characterize cytoplasmic and membrane-enriched (ME) proteomes of the in vitro generated Leishmania infantum AmB resistant mutant AmB1000.1. In total, 97 individual proteins were found as differentially expressed between the mutant and its parental sensitive strain (WT). More than half of these proteins were either metabolic enzymes or involved in transcription or translation processes. Key energetic pathways such as glycolysis and TCA cycle were up-regulated in the mutant. Interestingly, many proteins involved in reactive oxygen species (ROS) scavenging and heat-shock proteins were also up-regulated in the resistant mutant. This work provides a basis for further investigations to understand the roles of proteins differentially expressed in relation with AmB resistance. PMID:25057462
Brotherton, Marie-Christine; Bourassa, Sylvie; L�gar�, Danielle; Poirier, Guy G; Droit, Arnaud; Ouellette, Marc
Temporal kinetics and quantitative analysis of Cryptococcus neoformans nonlytic exocytosis.
Cryptococcus neoformans is a facultative intracellular pathogen and the causative agent of cryptococcosis, a disease that is often fatal to those with compromised immune systems. C. neoformans has the capacity to escape phagocytic cells through a process known as nonlytic exocytosis whereby the cryptococcal cell is released from the macrophage into the extracellular environment, leaving both the host and pathogen alive. Little is known about the mechanism behind nonlytic exocytosis, but there is evidence that both the fungal and host cells contribute to the process. In this study, we used time-lapse movies of C. neoformans-infected macrophages to delineate the kinetics and quantitative aspects of nonlytic exocytosis. We analyzed approximately 800 macrophages containing intracellular C. neoformans and identified 163 nonlytic exocytosis events that were further characterized into three subcategories: type I (complete emptying of macrophage), type II (partial emptying of macrophage), and type III (cell-to-cell transfer). The majority of type I and II events occurred after several hours of intracellular residence, whereas type III events occurred significantly (P < 0.001) earlier in the course of macrophage infection. Our results show that nonlytic exocytosis is a morphologically and temporally diverse process that occurs relatively rapidly in the course of macrophage infection. PMID:24595144
Stukes, Sabriya A; Cohen, Hillel W; Casadevall, Arturo
Quantitative Analysis of Chromosome Condensation in Fission Yeast
Chromosomes undergo extensive conformational rearrangements in preparation for their segregation during cell divisions. Insights into the molecular mechanisms behind this still poorly understood condensation process require the development of new approaches to quantitatively assess chromosome formation in vivo. In this study, we present a live-cell microscopy-based chromosome condensation assay in the fission yeast Schizosaccharomyces pombe. By automatically tracking the three-dimensional distance changes between fluorescently marked chromosome loci at high temporal and spatial resolution, we analyze chromosome condensation during mitosis and meiosis and deduct defined parameters to describe condensation dynamics. We demonstrate that this method can determine the contributions of condensin, topoisomerase II, and Aurora kinase to mitotic chromosome condensation. We furthermore show that the assay can identify proteins required for mitotic chromosome formation de novo by isolating mutants in condensin, DNA polymerase ?, and F-box DNA helicase I that are specifically defective in pro-/metaphase condensation. Thus, the chromosome condensation assay provides a direct and sensitive system for the discovery and characterization of components of the chromosome condensation machinery in a genetically tractable eukaryote.
Petrova, Boryana; Dehler, Sascha; Kruitwagen, Tom; Heriche, Jean-Karim; Miura, Kota
Quantitative analysis of pheromone-binding protein specificity.
Many pheromones have very low water solubility, posing experimental difficulties for quantitative binding measurements. A new method is presented for determining thermodynamically valid dissociation constants for ligands binding to pheromone-binding proteins, using ?-cyclodextrin as a solubilizer and transfer agent. The method is applied to LUSH, a Drosophila odorant-binding protein that binds the pheromone 11-cis vaccenyl acetate (cVA). Refolding of LUSH expressed in Escherichia?coli was assessed by measuring N-phenyl-1-naphthylamine (NPN) binding and F�rster resonance energy transfer between LUSH tryptophan 123 (W123) and NPN. Binding of cVA was measured from quenching of W123 fluorescence as a function of cVA concentration. The equilibrium constant for transfer of cVA between ?-cyclodextrin and LUSH was determined from a linked equilibria model. This constant, multiplied by the ?-cyclodextrin-cVA dissociation constant, gives the LUSH-cVA dissociation constant: ?100 nM. It was also found that other ligands quench W123 fluorescence. The LUSH-ligand dissociation constants were determined to be ?200?nM for the silk moth pheromone bombykol and ?90?nM for methyl oleate. The results indicate that the ligand-binding cavity of LUSH can accommodate a variety ligands with strong binding interactions. Implications of this for the Laughlin, Ha, Jones and Smith model of pheromone reception are discussed. PMID:23121132
Katti, S; Lokhande, N; Gonz�lez, D; Cassill, A; Renthal, R
Physicochemical basis of the universal genetic codes--quantitative analysis.
Quantitative mathematic models have been developed to correlate the fragment hydrophobicity contribution constants (faa) of 20 amino acids with the physicochemical properties (mu, Hb, and square root of MW) of the four bases (U, A, C, G) of the codons, or those of the anticodons. Using the general equation faa = a mu 1 + b mu 2 + c mu 3 + d square root of MW1 + e square root of MW2 + f square root of MW3 + g Hb1 + h Hb2 + i Hb3 + j, where 1, 2, 3 refer to the first, the second and the third base respectively, correlation coefficient of about 0.82 can be obtained for all 20 amino acids coded by 61 different triplet codes. These correlations are statistically highly significant, even though they do not take into account the involvement of various factors and peptidyl transferases. Furthermore, the reasons for the three stop codons are revealed. The graphic presentation of the codons and the amino acids coded separates the acidic and the basic, the aromatic and the heterocyclic amino acids into different quadrants of an octagon. This is in agreement with the ancient Chinese Ying-Yang theory embedded in the classical I-Ching. PMID:9204681
Lien, E J; Das, A; Nandy, P; Ren, S
Quantitative analysis of molecular absorption into PDMS microfluidic channels.
Microfluidic devices fabricated using poly(dimethylsiloxane) (PDMS) polymer are routinely used for in vitro cell culture for a wide range of cellular assays. These assays typically involve the incubation of cultured cells with a drug molecule or a fluorescent marker while monitoring a cellular response. The accuracy of these assays depends on achieving a consistent and reproducible concentration of solute molecules in solution. However, hydrophobic therapeutic and fluorescent molecules tend to diffuse into the PDMS walls of the microfluidic devices, which reduce their concentration in solution and consequently affect the accuracy and reliability of these assays. In this paper, we quantitatively investigate the relationship between the partition coefficient (log P) of a series of markers routinely used in in vitro cellular assays including [3H]-dexamethasone, [3H]-diazepam, [14C]-mannitol, [3H]-phenytoin, and rhodamine 6G and their absorption into PDMS microfluidic channels. Our results show that the absorption of a given solute into PDMS depends on the hydrophilic/hydrophobic balance defined by its log P value. Specifically, results demonstrate that molecules with log P less than 2.47 exhibit minimal absorption (<10%) into PDMS channels whereas molecules with log P larger than 2.62 exhibit extensive absorption (>90%) into PDMS channels. Further investigations showed that TiO(2) and glass coatings of PDMS channels reduced the absorption of hydrophobic molecules (log P > 2.62) by 2- and 4.5-folds, respectively. PMID:22484830
Wang, Jack D; Douville, Nicholas J; Takayama, Shuichi; ElSayed, Mohamed
Quantitative proteomic analysis of amphotericin B resistance in Leishmania infantum
Amphotericin B (AmB) in its liposomal form is now considered as either first- or second-line treatment against Leishmania infections in different part of the world. Few cases of AmB resistance have been reported and resistance mechanisms toward AmB are still poorly understood. This paper reports a large-scale comparative proteomic study in the context of AmB resistance. Quantitative proteomics using stable isotope labeling of amino acids in cell culture (SILAC) was used to better characterize cytoplasmic and membrane-enriched (ME) proteomes of the in vitro generated Leishmania infantum AmB resistant mutant AmB1000.1. In total, 97 individual proteins were found as differentially expressed between the mutant and its parental sensitive strain (WT). More than half of these proteins were either metabolic enzymes or involved in transcription or translation processes. Key energetic pathways such as glycolysis and TCA cycle were up-regulated in the mutant. Interestingly, many proteins involved in reactive oxygen species (ROS) scavenging and heat-shock proteins were also up-regulated in the resistant mutant. This work provides a basis for further investigations to understand the roles of proteins differentially expressed in relation with AmB resistance.
Brotherton, Marie-Christine; Bourassa, Sylvie; Legare, Danielle; Poirier, Guy G.; Droit, Arnaud; Ouellette, Marc
Quantitative analysis of in-air output ratio
Output factor (Scp) is one of the important factors required to calculate monitor unit (MU), and is divided into two components: phantom scatter factor (Sp) and in-air output ratio (Sc). Generally, Sc for arbitrary fields are calculated using several methods based on Sc determined by the absorbed dose measurement for several square fields. However, there are calculation errors when the treatment field has a large aspect ratio and the opening of upper and lower collimator are exchanged. To determine Sc accurately, scattered photons from the treatment head and backscattered particles into the monitor chamber must be analyzed individually. In this report, a simulation model that agreed well with measured Sc was constructed and dose variation by scattered photons from the treatment head and by backscattered particles into the monitor chamber was analyzed quantitatively. The results showed that the contribution of scattered photons from the primary collimator was larger than that of the flattening filter, and backscattered particles were affected by not only the upper jaw but also the lower jaw. In future work, a new Sc determination algorism based on the result of this report will be proposed.
Miyashita, Hisayuki; Hatanaka, Shogo; Fujita, Yukio; Hashimoto, Shimpei; Myojyoyama, Atsushi; Saitoh, Hidetoshi
Quantitative analysis of virus and plasmid trafficking in cells
NASA Astrophysics Data System (ADS)
Intracellular transport of DNA carriers is a fundamental step of gene delivery. By combining both theoretical and numerical approaches we study here single and several viruses and DNA particles trafficking in the cell cytoplasm to a small nuclear pore. We present a physical model to account for certain aspects of cellular organization, starting with the observation that a viral trajectory consists of epochs of pure diffusion and epochs of active transport along microtubules. We define a general degradation rate to describe the limitations of the delivery of plasmid or viral particles to a nuclear pore imposed by various types of direct and indirect hydrolysis activity inside the cytoplasm. By replacing the switching dynamics by a single steady state stochastic description, we obtain estimates for the probability and the mean time for the first one of many particles to go from the cell membrane to a small nuclear pore. Computational simulations confirm that our model can be used to analyze and interpret viral trajectories and estimate quantitatively the success of nuclear delivery.
Lagache, Thibault; Dauty, Emmanuel; Holcman, David
Quantitative analysis of TALE-DNA interactions suggests polarity effects.
Transcription activator-like effectors (TALEs) have revolutionized the field of genome engineering. We present here a systematic assessment of TALE DNA recognition, using quantitative electrophoretic mobility shift assays and reporter gene activation assays. Within TALE proteins, tandem 34-amino acid repeats recognize one base pair each and direct sequence-specific DNA binding through repeat variable di-residues (RVDs). We found that RVD choice can affect affinity by four orders of magnitude, with the relative RVD contribution in the order NG > HD ? NN > NI > NK. The NN repeat preferred the base G over A, whereas the NK repeat bound G with 10(3)-fold lower affinity. We compared AvrBs3, a naturally occurring TALE that recognizes its target using some atypical RVD-base combinations, with a designed TALE that precisely matches 'standard' RVDs with the target bases. This comparison revealed unexpected differences in sensitivity to substitutions of the invariant 5'-T. Another surprising observation was that base mismatches at the 5' end of the target site had more disruptive effects on affinity than those at the 3' end, particularly in designed TALEs. These results provide evidence that TALE-DNA recognition exhibits a hitherto un-described polarity effect, in which the N-terminal repeats contribute more to affinity than C-terminal ones. PMID:23408851
Meckler, Joshua F; Bhakta, Mital S; Kim, Moon-Soo; Ovadia, Robert; Habrian, Chris H; Zykovich, Artem; Yu, Abigail; Lockwood, Sarah H; Morbitzer, Robert; Els�esser, Janett; Lahaye, Thomas; Segal, David J; Baldwin, Enoch P
Quantitative analysis of the tremor wavefield at Etna Volcano, Italy
The properties of volcanic tremor wavefield at Mt. Etna Volcano, Italy, are investigated using data from two dense, small-aperture arrays of short-period seismometers deployed on the North and South flank of the volcano. Spectral analysis shows that most of the seismic energy is associated to several, narrow spectral peaks spanning the 1�5 Hz frequency band. Analysis of simultaneous recordings evidences
Gilberto Saccorotti; Luciano Zuccarellosupbsu; Edoardo Del Pezzo; Jesus Ibanez; Stefano Gresta
[Quantitative spectrum analysis of characteristic gases of spontaneous combustion coal].
Aimed at the characteristics of spontaneous combustion gas such as a variety of gases, lou limit of detection, and critical requirement of safety, Fourier transform infrared (FTIR) spectral analysis is presented to analyze characteristic gases of spontaneous combustion In this paper, analysis method is introduced at first by combing characteristics of absorption spectra of analyte and analysis requirement. Parameter setting method, sample preparation, feature variable abstract and analysis model building are taken into consideration. The methods of sample preparation, feature abstraction and analysis model are introduced in detail. And then, eleven kinds of gases were tested with Tensor 27 spectrometer. CH4, C2H6, C3H8, iC4H10, nC4H10, C2 H4, C3 H6, C3 H2, SF6, CO and CO2 were included. The optical path length was 10 cm while the spectra resolution was set as 1 cm(-1). The testing results show that the detection limit of all analytes is less than 2 x 10(-6). All the detection limits fit the measurement requirement of spontaneous combustion gas, which means that FTIR may be an ideal instrument and the analysis method used in this paper is competent for spontaneous combustion gas measurement on line. PMID:22097853
Liang, Yun-Tao; Tang, Xiao-Jun; Luo, Hai-Zhu; Sun, Yong
Advancing genetic theory and application by metabolic quantitative trait loci analysis.
This review describes recent advances in the analysis of metabolism using quantitative genetics. It focuses on how recent metabolic quantitative trait loci (QTL) studies enhance our understanding of the genetic architecture underlying naturally variable phenotypes and the impact of this fundamental research on agriculture, specifically crop breeding. In particular, the role of whole-genome duplications in generating quantitative genetic variation within a species is highlighted and the potential uses of this phenomenon presented. Additionally, the review describes how new observations from metabolic QTL mapping analyses are helping to shape and expand the concepts of genetic epistasis. PMID:19525414
Kliebenstein, Danielj
AquaSMART: Water & Boating Safety, Grades K-2. Teacher's Guide.
ERIC Educational Resources Information Center
This teacher's guide accompanies a program designed to teach water and boating safety to students in grades K-2. The written curriculum accompanies a video, AquaSMART K-2. The theme of the curriculum is AquaSMART. To become AquaSMART, students must learn 10 basic lessons for water and boating safety. The teacher's guide begins with an overview of�
Texas State Dept. of Parks and Wildlife, Austin.
AquaSMART: Water & Boating Safety, Grades 3-5. Teacher's Guide.
ERIC Educational Resources Information Center
This teacher's guide accompanies a program designed to teach water and boating safety to students in grades 3-5. The written curriculum accompanies a video, AquaSMART 3-5. The theme of the curriculum is AquaSMART. To become AquaSMART, students must learn 10 basic lessons for water and boating safety. The written curriculum begins with an overview�
Texas State Dept. of Parks and Wildlife, Austin.
Software applications toward quantitative metabolic flux analysis and modeling.
Metabolites and their pathways are central for adaptation and survival. Metabolic modeling elucidates in silico all the possible flux pathways (flux balance analysis, FBA) and predicts the actual fluxes under a given situation, further refinement of these models is possible by including experimental isotopologue data. In this review, we initially introduce the key theoretical concepts and different analysis steps in the modeling process before comparing flux calculation and metabolite analysis programs such as C13, BioOpt, COBRA toolbox, Metatool, efmtool, FiatFlux, ReMatch, VANTED, iMAT and YANA. Their respective strengths and limitations are discussed and compared to alternative software. While data analysis of metabolites, calculation of metabolic fluxes, pathways and their condition-specific changes are all possible, we highlight the considerations that need to be taken into account before deciding on a specific software. Current challenges in the field include the computation of large-scale networks (in elementary mode analysis), regulatory interactions and detailed kinetics, and these are discussed in the light of powerful new approaches. PMID:23142828
Dandekar, Thomas; Fieselmann, Astrid; Majeed, Saman; Ahmed, Zeeshan
Quantitative assessment of human motion using video motion analysis
NASA Technical Reports Server (NTRS)
In the study of the dynamics and kinematics of the human body a wide variety of technologies has been developed. Photogrammetric techniques are well documented and are known to provide reliable positional data from recorded images. Often these techniques are used in conjunction with cinematography and videography for analysis of planar motion, and to a lesser degree three-dimensional motion. Cinematography has been the most widely used medium for movement analysis. Excessive operating costs and the lag time required for film development, coupled with recent advances in video technology, have allowed video based motion analysis systems to emerge as a cost effective method of collecting and analyzing human movement. The Anthropometric and Biomechanics Lab at Johnson Space Center utilizes the video based Ariel Performance Analysis System (APAS) to develop data on shirtsleeved and space-suited human performance in order to plan efficient on-orbit intravehicular and extravehicular activities. APAS is a fully integrated system of hardware and software for biomechanics and the analysis of human performance and generalized motion measurement. Major components of the complete system include the video system, the AT compatible computer, and the proprietary software.
Probe, John D.
iTRAQ-based quantitative proteomic analysis of Thermobifida fusca reveals metabolic pathways of cellulose utilization
Thermobifida fusca is an aerobic, thermophilic, cellulose degrading bacterium identified in heated organic materials. This study applied iTRAQ quantitative proteomic analysis to the cellular and membrane proteomes of T. fusca grown in presence and absence of cellulose to elucidate the cellular processes induced by cellulose nutrient. Using an iTRAQ-based quantitative proteomic approach, 783 cytosolic and 181 membrane proteins expressed during
Sunil S. Adav; Chee Sheng Ng; Siu Kwan Sze
Dynamic and still microcirculatory image analysis for quantitative microcirculation research
NASA Astrophysics Data System (ADS)
Based on analyses of various types of digital microcirculatory image (DMCI), we summed up the image features of DMCI, the digitizing demands for digital microcirculatory imaging, and the basic characteristics of the DMCI processing. A dynamic and still imaging separation processing (DSISP) mode was designed for developing a DMCI workstation and the DMCI processing. Original images in this study were clinical microcirculatory images from human finger nail-bed and conjunctiva microvasculature, and intravital microvascular network images from animal tissue or organs. A series of dynamic and still microcirculatory image analysis functions were developed in this study. The experimental results indicate most of the established analog video image analysis methods for microcirculatory measurement could be realized in a more flexible way based on the DMCI. More information can be rapidly extracted from the quality improved DMCI by employing intelligence digital image analysis methods. The DSISP mode is very suitable for building a DMCI workstation.
Ying, Xiaoyou; Xiu, Rui-juan
Quantitative analysis of single aerosol particles with confocal micro-X-ray fluorescence spectrometer
NASA Astrophysics Data System (ADS)
A laboratory confocal micro-X-ray fluorescence (XRF) spectrometer based on polycapillary X-ray optics (PXRO) was proposed to carry out the quantitative XRF analysis of single aerosol particles with smaller sizes than that of focal spot of the PXRO. The PXRO in the detection channel can both increase the collecting angle of the detector and lower the minimum detection limits of the XRF spectrometer. In order to reduce the effects of the PXRO on the analysis results, the sensitivities were corrected using a Gaussian function for the quantitative XRF analysis of single aerosol particles.
Sun, Tianxi; Liu, Zhiguo; Li, Yude; Lin, Xiaoyan; Wang, Guangfu; Zhu, Guanghua; Xu, Qing; Luo, Ping; Pan, Qiuli; Liu, Hui; Ding, Xunliang
Quantitative proteomics analysis of adsorbed plasma proteins classifies nanoparticles with different surface properties and size
In biofluids (e.g., blood plasma) nanoparticles are readily embedded in layers of proteins that can affect their biological activity and biocompatibility. Herein, we report a study on the interactions between human plasma proteins and nanoparticles with a controlled systematic variation of properties using stable isotope labeling and liquid chromatography-mass spectrometry (LC-MS) based quantitative proteomics. Novel protocol has been developed to simplify the isolation of nanoparticle bound proteins and improve the reproducibility. Plasma proteins associated with polystyrene nanoparticles with three different surface chemistries and two sizes as well as for four different exposure times (for a total of 24 different samples) were identified and quantified by LC-MS analysis. Quantitative comparison of relative protein abundances were achieved by spiking an 18 O-labeled 'universal reference' into each individually processed unlabeled sample as an internal standard, enabling simultaneous application of both label-free and isotopic labeling quantitation across the sample set. Clustering analysis of the quantitative proteomics data resulted in distinctive pattern that classifies the nanoparticles based on their surface properties and size. In addition, data on the temporal study indicated that the stable protein 'corona' that was isolated for the quantitative analysis appeared to be formed in less than 5 minutes. The comprehensive results obtained herein using quantitative proteomics have potential implications towards predicting nanoparticle biocompatibility.
Zhang, Haizhen; Burnum, Kristin E.; Luna, Maria L.; Petritis, Brianne O.; Kim, Jong Seo; Qian, Weijun; Moore, Ronald J.; Heredia-Langner, Alejandro; Webb-Robertson, Bobbie-Jo M.; Thrall, Brian D.; Camp, David G.; Smith, Richard D.; Pounds, Joel G.; Liu, Tao
The Quantitative Analysis of an Analgesic Tablet: An NMR Experiment for the Instrumental Analysis Course
NASA Astrophysics Data System (ADS)
A quantitative analysis experiment is outlined that uses 13C NMR. Initial work utilizes a known compound (acenapthene) to assess the type of NMR experiment necessary to achieve a proportional response from all of the carbons in the compound. Both gated decoupling and inverse gated decoupling routines with a variety of delay times are inspected, in addition to investigation of paramagnetic additives in conjunction with inverse gated decoupling. Once the experiments with the known compound have illuminated the merits of the differing strategies for obtaining a proportional carbon response, a quantitative assessment of an unknown analgesic tablet is undertaken. The amounts of the two major components of the tablet, acetaminophen and aspirin, are determined following addition of an internal standard to the mixture. The carbon resonances emanating from each compound can be identified using spectra of the pure analgesic components and internal standard. Knowing the concentration of the internal standard and assuming a proportional response to all carbons in the sample allows calculation of the amount of both analytes in the analgesic tablets. Data from an initial laboratory trial is presented that illustrates the accuracy of the procedure.
Schmedake, Thomas A.; Welch, Lawrence E.
Reflectance spectroscopy: quantitative analysis techniques for remote sensing applications.
Several methods for the analysis of remotely sensed reflectance data are compared, including empirical methods and scattering theories, both of which are important for solving remote sensing problems. The concept of the photon mean path length and the implications for use in modeling reflectance spectra are presented.-from Authors
Clark, R. N.; Roush, T. L.
Procedures for Quantitative Analysis of Change Facilitator Interventions.
ERIC Educational Resources Information Center
The procedures and coding schema that have been developed by the Research on the Improvement Process (RIP) Program for analyzing the frequency of interventions and for examining their internal characteristics are described. In two in-depth ethnographic studies of implementation efforts, interventions were the focus of data collection and analysis.�
Hord, Shirley M.; Hall, Gene E.
Reflectance Spectroscopy: Quantitative Analysis Techniques for Remote Sensing Applications
Several methods for the analysis of remotely sensed reflectance data are compared, including empirical methods and scattering theories, both of which are important for solving remote sensing problems. The concept of the photon mean optical path length and the implications for use in modeling reflectance spectra are presented. It is shown that the mean optical path length in a particulate
Roger N. Clark; Ted L. Roush
The PMPA Standards Committee is developing a new test method for determining the porosity of powder metallurgy products by image analysis techniques. This technique would be used to evaluate the local density variation in complex P\\/M parts. An inter-laboratory study was conducted to estimate the uncertainty of this new measurement technique. The results found the accuracy of the test method
Howard I. Sanderow; Tom Murphy
Analytical Modeling and Quantitative Analysis of Scratch Drive Actuator
A new analytical model of Scratch Drive Actuator (SDA) is proposed, which considers its deforming states and geometry characteristics. This model contains three kinds of conditions: low driving voltage, critical driving voltage and high driving voltage. The storing strain energy in the SDA is studied under different conditions because the working performance of the SDA mainly depends on it. Analysis
Jean W. Zu; Qiuzhen Qu; Gong Cheng
Quantitative analysis of cell migration using optical flow.
Neural crest cells exhibit dramatic migration behaviors as they populate their distant targets. Using a line of zebrafish expressing green fluorescent protein (sox10:EGFP) in neural crest cells we developed an assay to analyze and quantify cell migration as a population, and use it here to characterize in detail the subtle defects in cell migration caused by ethanol exposure during early development. The challenge was to quantify changes in the in vivo migration of all Sox10:EGFP expressing cells in the visual field of time-lapse movies. To perform this analysis we used an Optical Flow algorithm for motion detection and combined the analysis with a fit to an affine transformation. Through this analysis we detected and quantified significant differences in the cell migrations of Sox10:EGFP positive cranial neural crest populations in ethanol treated versus untreated embryos. Specifically, treatment affected migration by increasing the left-right asymmetry of the migrating cells and by altering the direction of cell movements. Thus, by applying this novel computational analysis, we were able to quantify the movements of populations of cells, allowing us to detect subtle changes in cell behaviors. Because cranial neural crest cells contribute to the formation of the frontal mass these subtle differences may underlie commonly observed facial asymmetries in normal human populations. PMID:23936049
Boric, Katica; Orio, Patricio; Vi�ville, Thierry; Whitlock, Kathleen
Quantitative analysis of sequence alignment applications on multiprocessor architectures
The exponential growth of databases that contains biological information (such as protein and DNA data) demands great efforts to improve the performance of computational platforms. In this work we investigate how bioinformatics applications benefit from parallel architectures that combine different alternatives to exploit coarse- and fine-grain parallelism. As a case of analysis we study the performance behavior of the Ssearch
Friman S�nchez; Alex Ram�rez; Mateo Valero
Regression Commonality Analysis: A Technique for Quantitative Theory Building
ERIC Educational Resources Information Center
When it comes to multiple linear regression analysis (MLR), it is common for social and behavioral science researchers to rely predominately on beta weights when evaluating how predictors contribute to a regression model. Presenting an underutilized statistical technique, this article describes how organizational researchers can use commonality�
Nimon, Kim; Reio, Thomas G., Jr.
Development of Quantitative Risk Analysis tool for the fire safety in railway tunnel
In the context of strengthening fire safety level in the transport tunnel, much effort has been made to develop techniques to quantify the fire risk in the transport tunnel system. In this paper, the development of quantitative risk analysis tool for the fire safety in railway tunnel will be described. Inside the analysis tool, a number of scenarios are constructed
Sungwook Yoon; Hang Choi
Integrating Data Analysis (IDA): Working with Sociology Departments to Address the Quantitative Literacy Gap
ERIC Educational Resources Information Center
The NSF-funded Integrating Data Analysis (IDA) Project undertaken by the American Sociological Association (ASA) and the Social Science Data Analysis Network sought to close the quantitative literacy gap for sociology majors. Working with twelve departments, the project built on lessons learned from ASA's Minority Opportunities through School�
Howery, Carla B.; Rodriguez, Havidan
Quantitative risk analysis of aflatoxin toxicity for the consumers of �kenkey� � a fermented maize product
The introduction of quantitative risk analysis into food safety assurance systems has been suggested. This paper presents an attempt to quantify the risk posed to consumers of �kenkey�, a traditional fermented staple food of Ghana. The risk analysis is conducted exclusively for adverse health effects caused by aflatoxins, contaminants frequently found in the raw materials used for kenkey production. It
L. Nickelsen; M. Jakobsen
A Quantitative Analysis of the Extrinsic and Intrinsic Turnover Factors of Relational Database Support Professionals
ERIC Educational Resources Information Center
This quantitative analysis explored the intrinsic and extrinsic turnover factors of relational database support specialists. Two hundred and nine relational database support specialists were surveyed for this research. The research was conducted based on Hackman and Oldham's (1980) Job Diagnostic Survey. Regression analysis and a univariate ANOVA�
Takusi, Gabriel Samuto
Digitally Enhanced Thin-Layer Chromatography: An Inexpensive, New Technique for Qualitative and Quantitative Analysis
ERIC Educational Resources Information Center
A study conducted shows that if digital photography is combined with regular thin-layer chromatography (TLC), it could perform highly improved qualitative analysis as well as make accurate quantitative analysis possible for a much lower cost than commercial equipment. The findings suggest that digitally enhanced TLC (DE-TLC) is low-cost and easy�
Hess, Amber Victoria Irish
Quantitative analysis of ATM safety issues using retrospective accident data: The dynamic risk modelling project
The �dynamic risk modelling project� was a research activity aimed at developing a simulation approach able to provide a quantitative analysis of some critical activities of air traffic control (ATC) operators considering the organizational context in which they take place, the main cognitive processes underneath, and the possibility to inform the analysis using retrospective accident data.The pilot study presented in
Maria Chiara Leva; Massimiliano De Ambroggi; Daniela Grippa; Randall De Garis; Paolo Trucco; Oliver Str�ter
Quantitative Fourier Transform Infrared Analysis of Gas Phase Cigarette Smoke and Other Gas Mixtures
A new method for the analysis of selected components in complex gas mixtures has been developed utilizing a relatively inexpensive Fourier transform infrared spectrometer and a continuous flow gas cell. the method was used to monitor nitric oxide and nitrogen dioxide concentrations in cigarette smoke with time.Using multivariate least-square regression analysis, it is possible to simultaneously quantitate both NO and
Rafael Cueto; Daniel R. Church; William A. Piyor
Quantitative image analysis of bubble cavities in iron ore green pellets
Scanning electron microscopy and image analysis was used for quantitative analysis of bubble cavities in iron ore green pellets. Two types of pellets prepared with and without addition of flotation reagent prior to balling were studied. The bubble cavity porosity amounted to 2.8% in the pellets prepared without addition of flotation reagent prior to balling. When flotation reagent was added
I. U. Bhuiyan; J. Mouzon; S. P. E. Forsmo; J. Hedlund
A simple approach to quantitative analysis using three-dimensional spectra based on selected Zernike moments.
A very simple approach to quantitative analysis is proposed based on the technology of digital image processing using three-dimensional (3D) spectra obtained by high-performance liquid chromatography coupled with a diode array detector (HPLC-DAD). As the region-based shape features of a grayscale image, Zernike moments with inherently invariance property were employed to establish the linear quantitative models. This approach was applied to the quantitative analysis of three compounds in mixed samples using 3D HPLC-DAD spectra, and three linear models were obtained, respectively. The correlation coefficients (R(2)) for training and test sets were more than 0.999, and the statistical parameters and strict validation supported the reliability of established models. The analytical results suggest that the Zernike moment selected by stepwise regression can be used in the quantitative analysis of target compounds. Our study provides a new idea for quantitative analysis using 3D spectra, which can be extended to the analysis of other 3D spectra obtained by different methods or instruments. PMID:23183354
Zhai, Hong Lin; Zhai, Yue Yuan; Li, Pei Zhen; Tian, Yue Li
Mass spectrometry for real-time quantitative breath analysis.
Breath analysis research is being successfully pursued using a variety of analytical methods, prominent amongst which are gas chromatography with mass spectrometry, GC-MS, ion mobility spectrometry, IMS, and the fast flow and flow-drift tube techniques called selected ion flow tube mass spectrometry, SIFT-MS, and proton transfer reaction mass spectrometry, PTR-MS. In this paper the case is made for real-time breath analysis by obviating sample collection into bags or onto traps that can suffer from partial degradation of breath metabolites or the introduction of impurities. Real-time analysis of a broad range of volatile chemical compounds can be best achieved using SIFT-MS and PTR-MS, which are sufficiently sensitive and rapid to allow the simultaneous analyses of several trace gas metabolites in single breath exhalations. The basic principles and the ion chemistry that underpin these two analytical techniques are briefly described and the differences between them, including their respective strengths and weaknesses, are revealed, especially with reference to the analysis of the complex matrix that is exhaled breath. A recent innovation is described that combines time-of-flight mass spectrometry with the proton transfer flow-drift tube reactor, PTR-TOFMS, which provides greater resolution in the analytical mass spectrometer and allows separation of protonated isobaric molecules. Examples are presented of some recent data that well illustrate the quality and real-time feature of SIFT-MS and PTR-MS for the analysis of exhaled breath for physiological/biochemical/pharmacokinetics studies and for the identification and quantification of biomarkers relating to specific disease states. PMID:24682047
Smith, David; Span?l, Patrik; Herbig, Jens; Beauchamp, Jonathan
A quantitative analysis of fish consumption and stroke risk.
Although a rich source of n-3 polyunsaturated fatty acids (PUFAs) that may confer multiple health benefits, some fish contain methyl mercury (MeHg), which may harm the developing fetus. U.S. government recommendations for women of childbearing age are to modify consumption of high-MeHg fish to reduce MeHg exposure, while recommendations encourage fish consumption among the general population because of the nutritional benefits. The Harvard Center for Risk Analysis convened an expert panel (see acknowledgements) to quantify the net impact of resulting hypothetical changes in fish consumption across the population. This paper estimates the impact of fish consumption on stroke risk. Other papers quantify coronary heart disease mortality risk and the impacts of both prenatal MeHg exposure and maternal intake of n-3 PUFAs on cognitive development. This analysis identified articles in a recent qualitative literature review that are appropriate for the development of a dose-response relationship between fish consumption and stroke risk. Studies had to satisfy quality criteria, quantify fish intake, and report the precision of the relative risk estimates. The analysis combined the relative risk results, weighting each proportionately to its precision. Six studies were identified as appropriate for inclusion in this analysis, including five prospective cohort studies and one case-control study (total of 24 exposure groups). Our analysis indicates that any fish consumption confers substantial relative risk reduction compared to no fish consumption (12% for the linear model), with the possibility that additional consumption confers incremental benefits (central estimate of 2.0% per serving per week). PMID:16242601
Bouzan, Colleen; Cohen, Joshua T; Connor, William E; Kris-Etherton, Penny M; Gray, George M; K�nig, Ariane; Lawrence, Robert S; Savitz, David A; Teutsch, Steven M
Concentration analysis: A quantitative assessment of student states
NSDL National Science Digital Library
Multiple-choice tests such as the Force Concept Inventory (FCI) provide useful instruments to probe the distribution of student difficulties on a large scale. However, traditional analysis often relies solely on scores (number of students giving the correct answer). This ignores what can be significant and important information: The distribution of wrong answers given by the class. In this paper we introduce a new method, concentration analysis, to measure how students' responses on multiple-choice questions are distributed. This information can be used to study if the students have common incorrect models or if the question is effective in detecting student models. When combined with information obtained from qualitative research, the method allows us to identify cleanly what FCI results are telling us about student knowledge.
Bao, Lei; Redish, Edward F.
Quantitative full time course analysis of nonlinear enzyme cycling kinetics
Enzyme inhibition due to the reversible binding of reaction products is common and underlies the origins of negative feedback inhibition in many metabolic and signaling pathways. Product inhibition generates non-linearity in steady-state time courses of enzyme activity, which limits the utility of well-established enzymology approaches developed under the assumption of irreversible product release. For more than a century, numerous attempts to find a mathematical solution for analysis of kinetic time courses with product inhibition have been put forth. However, no practical general method capable of extracting common enzymatic parameters from such non-linear time courses has been successfully developed. Here we present a simple and practical method of analysis capable of efficiently extracting steady-state enzyme kinetic parameters and product binding constants from non-linear kinetic time courses with product inhibition and/or substrate depletion. The method is general and applicable to all enzyme systems, independent of reaction schemes and pathways.
Cao, Wenxiang; De La Cruz, Enrique M.
Quantitative analysis of structural neuroimaging of mesial temporal lobe epilepsy
Mesial temporal lobe epilepsy (MTLE) is the most common of the surgically remediable drug-resistant epilepsies. MRI is the primary diagnostic tool to detect anatomical abnormalities and, when combined with EEG, can more accurately identify an epileptogenic lesion, which is often hippocampal sclerosis in cases of MTLE. As structural imaging technology has advanced the surgical treatment of MTLE and other lesional epilepsies, so too have the analysis techniques that are used to measure different structural attributes of the brain. These techniques, which are reviewed here and have been used chiefly in basic research of epilepsy and in studies of MTLE, have identified different types and the extent of anatomical abnormalities that can extend beyond the affected hippocampus. These results suggest that structural imaging and sophisticated imaging analysis could provide important information to identify networks capable of generating spontaneous seizures and ultimately help guide surgical therapy that improves postsurgical seizure-freedom outcomes.
Memarian, Negar; Thompson, Paul M; Engel, Jerome; Staba, Richard J
Functionally oriented and clinically feasible quantitative gait analysis method
A protocol for clinical gait analysis is described, and data from 30 normal adult female subjects are presented. Extensive\\u000a application to pathologic subjects has proven to be feasible and sufficiently accurate. The method is based on a particular\\u000a location and attachment of retro-reflective markers on the body and on a particular arrangement of four TV cameras. A motion\\u000a analyser measures
C. Frigo; M. Rabuffetti; D. C. Kerrigan; L. C. Deming; A. Pedotti
Quantitative Analysis of Corn Zeins by Capillary Electrophoresis
Cereal Chem. 74(6):766-770 Kjeldahl analysis is commonly used to measure zein proteins in corn maize (N ? 5.7) with no attempt to eliminate contribution from other nitrogen sources. In this study, dry milled corn was extracted with 70% ethanol or 0.1N NaOH and the zein content of the extract measured using capillary electrophoresis in the presence of sodium dodecyl sulfate.
Nicholas Parris; Leland Dickey; James Craig
Quantitative analysis of calcium spikes in noisy fluorescent background.
Intracellular calcium signals are studied by laser-scanning confocal fluorescence microscopy. The required spatio-temporal resolution makes description of calcium signals difficult because of the low signal-to-noise ratio. We designed a new procedure of calcium spike analysis based on their fitting with a model. The accuracy and precision of calcium spike description were tested on synthetic datasets generated either with randomly varied spike parameters and Gaussian noise of constant amplitude, or with constant spike parameters and Gaussian noise of various amplitudes. Statistical analysis was used to evaluate the performance of spike fitting algorithms. The procedure was optimized for reliable estimation of calcium spike parameters and for dismissal of false events. A new algorithm was introduced that corrects the acquisition time of pixels in line-scan images that is in error due to sequential acquisition of individual pixels along the space coordinate. New software was developed in Matlab and provided for general use. It allows interactive dissection of temporal profiles of calcium spikes from x-t images, their fitting with predefined function(s) and acceptance of results on statistical grounds, thus allowing efficient analysis and reliable description of calcium signaling in cardiac myocytes down to the in situ function of ryanodine receptors. PMID:23741324
Janicek, Radoslav; Hotka, Matej; Zahradn�kov�, Alexandra; Zahradn�kov�, Alexandra; Zahradn�k, Ivan
Quantitative Analysis of Calcium Spikes in Noisy Fluorescent Background
Intracellular calcium signals are studied by laser-scanning confocal fluorescence microscopy. The required spatio-temporal resolution makes description of calcium signals difficult because of the low signal-to-noise ratio. We designed a new procedure of calcium spike analysis based on their fitting with a model. The accuracy and precision of calcium spike description were tested on synthetic datasets generated either with randomly varied spike parameters and Gaussian noise of constant amplitude, or with constant spike parameters and Gaussian noise of various amplitudes. Statistical analysis was used to evaluate the performance of spike fitting algorithms. The procedure was optimized for reliable estimation of calcium spike parameters and for dismissal of false events. A new algorithm was introduced that corrects the acquisition time of pixels in line-scan images that is in error due to sequential acquisition of individual pixels along the space coordinate. New software was developed in Matlab and provided for general use. It allows interactive dissection of temporal profiles of calcium spikes from x-t images, their fitting with predefined function(s) and acceptance of results on statistical grounds, thus allowing efficient analysis and reliable description of calcium signaling in cardiac myocytes down to the in situ function of ryanodine receptors.
Janicek, Radoslav; Hotka, Matej; Zahradnikova, Alexandra; Zahradnikova, Alexandra; Zahradnik, Ivan
Photobacterium aquae sp. nov., isolated from a recirculating mariculture system.
A Gram-staining-negative, heterotrophic, facultatively anaerobic bacterium, designated AE6(T), was isolated from a grouper (Epinephelus malabaricas) culture tank in a recirculating mariculture system located in Tianjin, China. Strain AE6(T) was able to grow at 15-40 �C (optimum, 30-35 �C), at pH 5.5-10.0 (optimum, pH 7.0-7.5) and in the presence of 0.5-7% (w/v) NaCl (optimum, 2-3%). It contained Q-8 as the predominant respiratory quinone, phosphatidylethanolamine (PE) and phosphatidylglycerol (PG) as the major polar lipids and C(16 : 1)?7c/C(16 : 1)?6c (40.4%), C(18 : 1)?7c (15.5%) and C(16 : 0) (13.5%) as the predominant cellular fatty acids. The genomic DNA G+C content was 47.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain AE6(T) belonged to the genus Photobacterium (94.2-96.8% of 16S rRNA gene sequence similarity) and formed a distinct phylogenetic lineage within the genus and exhibited the highest sequence similarity to Photobacterium aphoticum CECT 7614(T) (96.8%). Multilocus sequence analysis (MLSA) using four loci (gyrB, rpoA, pyrH and recA) also revealed that strain AE6(T) was phylogenetically related to the genus Photobacterium. Based on the phylogenetic, chemotaxonomic and phenotypic evidence, strain AE6(T) is considered to represent a novel species of the genus Photobacterium, for which the name Photobacterium aquae sp. nov. is proposed. The type strain is AE6(T) (?=?CGMCC 1.12159(T)?=?JCM 18480(T)). PMID:24096359
Liu, Ying; Liu, Liang-Zi; Song, Lei; Zhou, Yu-Guang; Qi, Fang-Jun; Liu, Zhi-Pei
Label-Free Quantitative Proteomics and N-terminal Analysis of Human Metastatic Lung Cancer Cells
Proteomic analysis is helpful in identifying cancer-associated proteins that are differentially expressed and fragmented that can be annotated as dysregulated networks and pathways during metastasis. To examine meta-static process in lung cancer, we performed a proteomics study by label-free quantitative analysis and N-terminal analysis in 2 human non-small-cell lung cancer cell lines with disparate metastatic potentials�NCI-H1703 (primary cell, stage I) and NCI-H1755 (metastatic cell, stage IV). We identified 2130 proteins, 1355 of which were common to both cell lines. In the label-free quantitative analysis, we used the NSAF normalization method, resulting in 242 differential expressed proteins. For the N-terminal proteome analysis, 325 N-terminal peptides, including 45 novel fragments, were identified in the 2 cell lines. Based on two proteomic analysis, 11 quantitatively expressed proteins and 8 N-terminal peptides were enriched for the focal adhesion pathway. Most proteins from the quantitative analysis were upregulated in metastatic cancer cells, whereas novel fragment of CRKL was detected only in primary cancer cells. This study increases our understanding of the NSCLC metastasis proteome.
Min, Hophil; Han, Dohyun; Kim, Yikwon; Cho, Jee Yeon; Jin, Jonghwa; Kim, Youngsoo
Quantitative Colocalization Analysis of Multicolor Confocal Immunofluorescence Microscopy Images: Pushing Pixels to Explore Biological Phenomena
Quantitative colocalization analysis is an advanced digital imaging tool to examine antigens of interest in immunofluorescence images obtained using confocal microscopes. It employs specialized algorithms to estimate the degree of overlap of fluorescence signals and thus enables acquiring important new information not otherwise obtainable using qualitative approaches alone. As raw confocal images have high levels of background, they should be prepared to become suitable for reliable calculation of colocalization coefficients by correcting it. We provide concise theoretical basis of quantitative colocalization analysis, discuss its limitations, and describe proper use of the technique. The use of quantitative colocalization analysis is demonstrated by studying bile salt export pump and multidrug resistance associated protein 2 in the liver and major basic protein and platelet activating factor receptor antigens in conjunctiva. The review is focused on the applicability and correct interpretation of the results of colocalization coefficients calculations.
Zinchuk, Vadim; Zinchuk, Olga; Okada, Teruhiko
Enabling Quantitative Analysis in Ambient Ionization Mass Spectrometry: Internal Standard Coated Capillary Samplers
We describe a sampling method using glass capillaries for quantitative analysis of trace analytes in small volumes of complex mixtures (~1 ?L) using ambient ionization mass spectrometry. The internal surface of a sampling glass capillary was coated with internal standard then used to draw liquid sample and so transfer both the analyte and internal standard in a single fixed volume onto a substrate for analysis. The internal standard was automatically mixed into the sample during this process and the volumes of the internal standard solution and sample are both fixed by the capillary volume. Precision in quantitation is insensitive to variations in length of the capillary, making the preparation of the sampling capillary simple and providing a robust sampling protocol. Significant improvements in quantitation accuracy were obtained for analysis of 1 ?L samples using various ambient ionization methods.
Liu, Jiangjiang; Cooks, R. Graham; Ouyang, Zheng
Quantitation of satellite cell proliferation in vivo using image analysis.
A nonisotopic, double fluorescence technique was developed to study myogenic satellite cell proliferation in posthatch turkey skeletal muscle. Labeled satellite cell nuclei were identified on enzymatically isolated myofiber segments using a mouse monoclonal antibody (anti-BrdU) followed by fluorescein-5-isothiocyanate (FITC) conjugated goat anti-mouse IgG secondary antibody. Myofiber nuclei (myonuclei+satellite cell nuclei) were counterstained with propidium iodide (PI). The myofiber segment length, myofiber segment diameter, and the number of PI and FITC labeled nuclei contained in each segment was determined using a Nikon fluorescence microscope, a SIT video camera and Image-1 software. Data collected by three different operators of the image analysis system revealed 5.0 +/- 1.4 satellite cell nuclei per 1000 myofiber nuclei and 5284 +/- 462 microns3 of cytoplasm surrounding each myofiber nucleus in the pectoralis thoracicus of 9-week-old tom turkeys. BrdU immunohistochemistry coupled with the new approach of PI staining of whole myofiber mounts is an effective combination to allow the use of an efficient semi-automated image analysis protocol. PMID:7819418
Mozdziak, P E; Fassel, T; Gregory, R; Schultz, E; Greaser, M L; Cassens, R G
Combining ability analysis of some quantitative characters in hexaploid Triticale.
Seven parental lines of hexaploid Triticale were selected to study the nature of inheritance of various agronomic characters. Combining ability analysis was carried out for eleven characters following Method 4, Model I of diallel cross analysis given by Griffing (1956).Both the general and specific combining ability variances were highly significant or significant for all the characters studied. However, the former were greater than the latter for each of the characters, except for spike length and number of days to maturity, indicating the predominance of additive gene action in the material studied.The corresponding general combining ability effects for grain yield and one or two of its components suggest the importance of the component method of selection in Triticale breeding. The important yield contributing characters were found to be productive tillers per plant, 1000 kernel weight, kernels per spike and kernels per spikelet.The possibility of capitalising both the additive and non-additive portions of genetic variability by practising selections successively on the basis of general and specific combining abilities is discussed. PMID:24414759
Reddy, L V
Quantitative phosphoproteomic analysis of prion-infected neuronal cells
Prion diseases or transmissible spongiform encephalopathies (TSEs) are fatal diseases associated with the conversion of the cellular prion protein (PrPC) to the abnormal prion protein (PrPSc). Since the molecular mechanisms in pathogenesis are widely unclear, we analyzed the global phospho-proteome and detected a differential pattern of tyrosine- and threonine phosphorylated proteins in PrPSc-replicating and pentosan polysulfate (PPS)-rescued N2a cells in two-dimensional gel electrophoresis. To quantify phosphorylated proteins, we performed a SILAC (stable isotope labeling by amino acids in cell culture) analysis and identified 105 proteins, which showed a regulated phosphorylation upon PrPSc infection. Among those proteins, we validated the dephosphorylation of stathmin and Cdc2 and the induced phosphorylation of cofilin in PrPSc-infected N2a cells in Western blot analyses. Our analysis showed for the first time a differentially regulated phospho-proteome in PrPSc infection, which could contribute to the establishment of novel protein markers and to the development of novel therapeutic intervention strategies in targeting prion-associated disease.
Quantitative proteomic analysis of cold-responsive proteins in rice.
Rice is susceptible to cold stress and with a future of climatic instability we will be unable to produce enough rice to satisfy increasing demand. A thorough understanding of the molecular responses to thermal stress is imperative for engineering cultivars, which have greater resistance to low temperature stress. In this study we investigated the proteomic response of rice seedlings to 48, 72 and 96?h of cold stress at 12-14�C. The use of both label-free and iTRAQ approaches in the analysis of global protein expression enabled us to assess the complementarity of the two techniques for use in plant proteomics. The approaches yielded a similar biological response to cold stress despite a disparity in proteins identified. The label-free approach identified 236 cold-responsive proteins compared to 85 in iTRAQ results, with only 24 proteins in common. Functional analysis revealed differential expression of proteins involved in transport, photosynthesis, generation of precursor metabolites and energy; and, more specifically, histones and vitamin B biosynthetic proteins were observed to be affected by cold stress. PMID:21433000
Neilson, Karlie A; Mariani, Michael; Haynes, Paul A
Quantitative assessment of human body shape using Fourier analysis
NASA Astrophysics Data System (ADS)
Fall protection harnesses are commonly used to reduce the number and severity of injuries. Increasing the efficiency of harness design requires the size and shape variation of the user population to be assessed as detailed and as accurately as possible. In light of the unsatisfactory performance of traditional anthropometry with respect to such assessments, we propose the use of 3D laser surface scans of whole bodies and the statistical analysis of elliptic Fourier coefficients. Ninety-eight male and female adults were scanned. Key features of each torso were extracted as a 3D curve along front, back and the thighs. A 3D extension of Elliptic Fourier analysis4 was used to quantify their shape through multivariate statistics. Shape change as a function of size (allometry) was predicted by regressing the coefficients onto stature, weight and hip circumference. Upper and lower limits of torso shape variation were determined and can be used to redefine the design of the harness that will fit most individual body shapes. Observed allometric changes are used for adjustments to the harness shape in each size. Finally, the estimated outline data were used as templates for a free-form deformation of the complete torso surface using NURBS models (non-uniform rational B-splines).
Friess, Martin; Rohlf, F. J.; Hsiao, Hongwei
A quantitative analysis of passive electrolocation behavior in electric fish.
Weakly electric fish of the families Gymnotidae and Hypopomidae (Gymnotiformes) are able to locate the electric discharges from conspecifics or from dipole electrodes, and they demonstrate this by making rapid, well-directed approaches toward these electrical sources. A video tracking system was used to follow the movements of electric fish in a large tank and an analytic method was used for computing the direction and magnitude of the electric field anywhere within the cylindrical test tank. Using a static analysis method, we describe the posture of test fish relative to the electric fields during their approaches to stationary or moving electrical stimuli. Using a dynamic analysis, we examine the movements of the fish including the sign and magnitude of velocity and bending in response to electric fields. Electric fish seek to maintain a zero error angle between their body orientation and the local electric field. They do so by bending their body in the direction of the local electric field. The response has a delay of approximately 0.5 s. Swimming in reverse inverts the direction of the bend. These fish also use 'V-turns' to redirect their swim directions when encountering rapidly-changing electric fields. PMID:9217992
Hopkins, C D; Shieh, K T; McBride, D W; Winslow, M
Quantitative Analysis of Spectral Impacts on Silicon Photodiode Radiometers: Preprint
Inexpensive broadband pyranometers with silicon photodiode detectors have a non-uniform spectral response over the spectral range of 300-1100 nm. The response region includes only about 70% to 75% of the total energy in the terrestrial solar spectral distribution from 300 nm to 4000 nm. The solar spectrum constantly changes with solar position and atmospheric conditions. Relative spectral distributions of diffuse hemispherical irradiance sky radiation and total global hemispherical irradiance are drastically different. This analysis convolves a typical photodiode response with SMARTS 2.9.5 spectral model spectra for different sites and atmospheric conditions. Differences in solar component spectra lead to differences on the order of 2% in global hemispherical and 5% or more in diffuse hemispherical irradiances from silicon radiometers. The result is that errors of more than 7% can occur in the computation of direct normal irradiance from global hemispherical irradiance and diffuse hemispherical irradiance using these radiometers.
Myers, D. R.
Quantitative radiographic analysis of fiber reinforced polymer composites.
X-ray radiographic examination of the bone fracture healing process is a widely used method in the treatment and management of patients. Medical devices made of metallic alloys reportedly produce considerable artifacts that make the interpretation of radiographs difficult. Fiber reinforced polymer composite materials have been proposed to replace metallic alloys in certain medical devices because of their radiolucency, light weight, and tailorable mechanical properties. The primary objective of this paper is to provide a comparable radiographic analysis of different fiber reinforced polymer composites that are considered suitable for biomedical applications. Composite materials investigated consist of glass, aramid (Kevlar-29), and carbon reinforcement fibers, and epoxy and polyether-ether-ketone (PEEK) matrices. The total mass attenuation coefficient of each material was measured using clinical X-rays (50 kev). The carbon fiber reinforced composites were found to be more radiolucent than the glass and kevlar fiber reinforced composites. PMID:11261603
Baidya, K P; Ramakrishna, S; Rahman, M; Ritchie, A
Assessment of graphene quality by quantitative optical contrast analysis
NASA Astrophysics Data System (ADS)
We show that contrast analysis carried out by standard optical microscopy can be employed as a simple and quick technique to monitor the cleanness of graphene during the process steps required for device fabrication. Graphene flakes deposited by adhesive tape exfoliation can display a strong contrast increase upon processing, due to the organic contamination arising from the diffusion of glue residues over the samples. On the other hand, graphene deposited by an adhesive-free method, such as electrostatic deposition, does not show any contrast variation, suggesting a low degree of contamination. Therefore, the fabrication process of graphene-based devices may be monitored and optimized on the basis of an easy optical inspection.
Bruna, Matteo; Borini, Stefano
Microscopy environment for quantitative spatial and temporal analysis of multicellular interactions
Quantitative analysis of spatial and temporal concurrent responses of multiple markers in 3-dimensional cell cultures is hampered by the routine mode of sequential image acquisition, measurement and analysis of specific targets. A system was developed for detailed analysis of multi-dimensional, time-sequence responses and in order to relate features in novel and meaningful ways that will further our understanding of basic
Damir Sudar; Bahram Parvin; Daniel E. Callahan; Richard I. Schwarz; David W. Knowles; Carlos Ortiz de Solorzano; Mary H. Barcellos-Hoff
Development of a method for automated quantitative analysis of ores using LIBS
This paper reports the development of a method for real-time automated quantitative analysis of mineral ores using a commercial laser-induced breakdown spectroscopy instrument, TRACER� 2100, fitted with a recently developed computer controlled auto-sampler. The auto-sampler permits the execution of methods for performing calibrations and analysis of multiple elements on multiple samples. Furthermore, the analysis is averaged over multiple locations on
S. Rosenwasser; G Asimellis; B Bromley; R Hazlett; J Martin; T Pearce; A Zigler
Synthesis, structure, and application of self-assembled copper(II) aqua complex by H-bonding for acceleration of the nitroaldol reaction on water.
Simple addition: Copper(II) aqua complex 1 can be prepared in a one-pot synthesis and is self-assembled by H-bond interactions. Complex 1 is shown to accelerate the nitroaldol reaction on water, which is a heterogeneous process, requiring no additive or base, and 1 can be recycled without loss of activity. Copper(II) aqua complex 1 has been prepared in a one-pot synthesis. The single crystal X-ray analysis showed that the complex is self-assembled through aqua ligands by H-bond interactions and the copper(II) atoms are pentacoordinated with square pyramidal geometry. Complex 1 has been studied for the acceleration of the nitroalodol reaction on water. It is a clean technological process and the catalyst can be recycled without loss of activity. PMID:19003846
Jammi, Suribabu; Ali, Md Ashif; Sakthivel, Sekarpandi; Rout, Laxmidhar; Punniyamurthy, Tharmalingam
Qualitative and quantitative analysis of synapses in Hirschsprung's disease.
In Hirschsprung's disease (HD), certain intestinal nervous plexuses are absent. Sprouting nerve endings contain different amounts of synaptophysin (SY), a protein and main constituent of acetylcholinesterase (AChE) storage compartments. Due to the lack of specific markers for synapses, a qualitative analysis of nerve endings of intestinal segments affected by HD has not yet been undertaken. For this study, resected colorectal specimens from patients with HD (n = 8, mean age 2.1 years) were investigated in parallel for AChE, SY, and content of small synaptic vesicles by biochemical, immunohistochemical, and electronmicroscopic means. In the microdissected muscular layer, reduced SY (1.4 microgram/mg total protein, normal 24 +/- 0.3) was observed. Immunohistochemistry showed in affected tissues reduced numbers of SY-positive nerve fibers and nerve endings, which in turn were thickened and distorted, in both the muscle proper and the muscularis mucosae. Combining both morphologic and biochemical findings, in HD the number of cholinergic vesicles in the remaining nerve endings seems to be increased as measured by SY, a marker molecule specific for synaptic vesicles. Our data also suggest that nerve endings in HD may contain high concentrations of cholinergic vesicles, paralleling the known high amounts of acetylcholine and AChE found in intestinal segments of patients with HD. PMID:9716672
Wiedenmann, B; Riedel, C; John, M; Ahnert-Hilger, G; Stoltenburg, G; Waldschmidt, J; von Deimling, K; Riecken, E O; Schier, F
Quantitative Analysis of the Microstructure of Auxetic Foams
The auxetic foams first produced by Lakes have been modelled in a variety of ways, each model trying to reproduce some observed feature of the microscale of the foams. Such features include bent or broken ribs or inverted angles between ribs. These models can reproduce the Poisson's ratio or Poisson's function of auxetic foam if the model parameters are carefully chosen. However these model parameters may not actually reflect the internal structure of the foams. A big problem is that measurement of parameters such as lengths and angles is not straightforward within a 3-d sample. In this work a sample of auxetic foam has been imaged by 3-d X-ray computed tomography. The resulting image is translated to a form that emphasises the geometrical structure of connected ribs. This connected rib data are suitably analysed to describe both the microstructural construction of auxetic foams and the statistical spread of structure, that is, the heterogeneity of an auxetic foam. From the analysis of the microstructure, observations are made about the requirements for microstructural models and comparisons made to previous existing models. From the statistical data, measures of heterogeneity are made that will help with future modelling that includes the heterogeneous aspect of auxetic foams.
Gaspar, N.; Smith, C.W.; Miller, E.A.; Seidler, G.T.; Evans, K.E. (Exeter); (UWASH)
Quantitative analysis of DNA methylation in chronic lymphocytic leukemia patients.
Changes in the genomic DNA methylation level have been found to be closely associated with tumorigenesis. In order to analyze the relation of aberrant DNA methylation to clinical and biological risk factors, we have determined the cytosine methylation level of 81 patients diagnosed with chronic lymphocytic leukemia (CLL). The analysis was based on DNA hydrolysis followed by derivatization of the 2'-desoxyribonucleoside-3'-monophosphates with BODIPY FL EDA. Derivatives were separated by micellar electrokinetic chromatography, and laser-induced fluorescence was used for detection. We analyzed potential correlations between DNA methylation levels and numerous patient parameters, including clinical observations and biological data. As a result, we observed a significant correlation with the immunoglobulin variable heavy chain gene (VH) mutation status. This factor has been repeatedly proposed as a reliable prognostic marker for CLL, which suggests that the methylation level might be a valuable factor in determining the prognostic outcome of CLL. We are now in the process of refining our method to broaden its application potential. In this context, we show here that the oxidation of the fluorescence marker in the samples and the evaporation of methanol in the electrolytes can be prevented by a film of paraffin oil. In summary, our results thus establish capillary electrophoresis as a valuable tool for analyzing the DNA methylation status of clinical samples. PMID:15188237
Lyko, Frank; Stach, Dirk; Brenner, Axel; Stilgenbauer, Stephan; D�hner, Hartmut; Wirtz, Michaela; Wiessler, Manfred; Schmitz, Oliver J
Leukoaraiosis is associated with arterial wall thickness: a quantitative analysis.
Leukoaraiosis refers to an age-related, abnormal appearance of the brain white matter on neuroimaging. The association between leukoaraiosis and cerebrovascular disease suggests that ischemia may be an important contributing factor; however, the pathogenesis of the condition remains controversial. We hypothesized that physical abnormalities of blood vessels might be culpable and compared the external and internal measurements of blood vessel walls between brains that demonstrated leukoaraiosis on imaging and normal control brains. Fourteen brains of individuals who had been diagnosed as having severe leukoaraiosis and five non-leukoaraiosis control brains were studied. Arterial cross-sections were evaluated by length measurements with an image analysis device. Arterial wall thickness and the ratio of the outer and inner diameters of the vessel were measured. We measured a total of 108 vessels in the leukoaraiosis group and 95 vessels in the control group. The vessel walls of the leukoaraiosis patients were an average of 5.5?�m thicker than the walls of control vessels of the same inside diameter (P?=?0.0000, 95% CI 3.01-8.08) and an average of 2.3?�m thicker than walls of control vessels of the same outside diameter (P?=?0.016, 95% CI 0.48-4.17). Our data provide evidence that leukoaraiosis is associated with vessel wall thickening in an additive fashion and indicate that structural vascular abnormalities are associated with leukoaraiosis. PMID:22017293
Auriel, Eitan; Csiba, Laszlo; Berenyi, Ervin; Varkonyi, Ildiko; Mehes, Gabor; Kardos, Laszlo; Karni, Arnon; Bornstein, Natan M
Quantitative Analysis with Heavy Ion E-TOF ERD
Heavy ion TOF ERD combined with energy detection (E-TOF-ERD) is a powerful analytical technique taking advantage of the following facts: the scattering cross section is usually very high ({approximately}10{sup {minus}21} cm{sup 2}/sr) compared to regular He RBS ({approximately}10{sup {minus}25} cm{sup 2}/sr), contrary to what happens with the energy resolution in ordinary surface solid barrier detectors, time resolution is almost independent of the atomic mass of the detected element, and the detection in coincidence of time and energy signals allows for the mass separation of overlapping signals with the same energy (or time of flight). Measurements on several oxides have been performed with the E-TOF-ERD set up at Sandia National Laboratories using an incident beam of 10-15 MeV Au. The information on the composition of the sample is obtained from the time domain spectrum, which is converted to energy domain, and then, using existing software codes, the analysis is performed. During the quantification of the results, they have found problems related to the interaction of the beam with the sample and to the tabulated values of the stopping powers for heavy ions.
Banks, J.C.; Doyle, B.L.; Font, A. Climent
Quantitative Analysis of Single Nucleotide Polymorphisms within Copy Number Variation
Background Single nucleotide polymorphisms (SNPs) have been used extensively in genetics and epidemiology studies. Traditionally, SNPs that did not pass the Hardy-Weinberg equilibrium (HWE) test were excluded from these analyses. Many investigators have addressed possible causes for departure from HWE, including genotyping errors, population admixture and segmental duplication. Recent large-scale surveys have revealed abundant structural variations in the human genome, including copy number variations (CNVs). This suggests that a significant number of SNPs must be within these regions, which may cause deviation from HWE. Results We performed a Bayesian analysis on the potential effect of copy number variation, segmental duplication and genotyping errors on the behavior of SNPs. Our results suggest that copy number variation is a major factor of HWE violation for SNPs with a small minor allele frequency, when the sample size is large and the genotyping error rate is 0?1%. Conclusions Our study provides the posterior probability that a SNP falls in a CNV or a segmental duplication, given the observed allele frequency of the SNP, sample size and the significance level of HWE testing.
Lee, Soohyun; Kasif, Simon; Weng, Zhiping; Cantor, Charles R.
Machine learning methods for quantitative analysis of Raman spectroscopy data
NASA Astrophysics Data System (ADS)
The automated identification and quantification of illicit materials using Raman spectroscopy is of significant importance for law enforcement agencies. This paper explores the use of Machine Learning (ML) methods in comparison with standard statistical regression techniques for developing automated identification methods. In this work, the ML task is broken into two sub-tasks, data reduction and prediction. In well-conditioned data, the number of samples should be much larger than the number of attributes per sample, to limit the degrees of freedom in predictive models. In this spectroscopy data, the opposite is normally true. Predictive models based on such data have a high number of degrees of freedom, which increases the risk of models over-fitting to the sample data and having poor predictive power. In the work described here, an approach to data reduction based on Genetic Algorithms is described. For the prediction sub-task, the objective is to estimate the concentration of a component in a mixture, based on its Raman spectrum and the known concentrations of previously seen mixtures. Here, Neural Networks and k-Nearest Neighbours are used for prediction. Preliminary results are presented for the problem of estimating the concentration of cocaine in solid mixtures, and compared with previously published results in which statistical analysis of the same dataset was performed. Finally, this paper demonstrates how more accurate results may be achieved by using an ensemble of prediction techniques.
Madden, Michael G.; Ryder, Alan G.
Direct Quantitative Analysis of Arsenic in Coal Fly Ash
A rapid, simple method based on graphite furnace atomic absorption spectrometry is described for the direct determination of arsenic in coal fly ash. Solid samples were directly introduced into the atomizer without preliminary treatment. The direct analysis method was not always free of spectral matrix interference, but the stabilization of arsenic by adding palladium nitrate (chemical modifier) and the optimization of the parameters in the furnace program (temperature, rate of temperature increase, hold time, and argon gas flow) gave good results for the total arsenic determination. The optimal furnace program was determined by analyzing different concentrations of a reference material (NIST1633b), which showed the best linearity for calibration. The optimized parameters for the furnace programs for the ashing and atomization steps were as follows: temperatures of 500�1200 and 2150�C, heating rates of 100 and 500�C?s?1, hold times of 90 and 7?s, and medium then maximum and medium argon gas flows, respectively. The calibration plots were linear with a correlation coefficient of 0.9699. This method was validated using arsenic-containing raw coal samples in accordance with the requirements of the mass balance calculation; the distribution rate of As in the fly ashes ranged from 101 to 119%.
Hartuti, Sri; Kambara, Shinji; Takeyama, Akihiro; Kumabe, Kazuhiro; Moritomi, Hiroshi
Quantitative analysis of American woodcock nest and brood habitat
Sixteen nest and 19 brood sites of American woodcock (Philohela minoI) were examined in northern lower Michigan between 15 April and 15 June 1974 to determine habitat structure associated with these sites. Woodcock hens utilized young, second-growth forest stands which were similar in species composition for both nesting and brood rearing. A multi-varIate discriminant function analysis revealed a significant (P< 0.05) difference, however, in habitat structure. Nest habitat was characterized by lower tree density (2176 trees/ha) and basal area (8.6 m2/ha), by being close to forest openings (7 m) and by being situated on dry, relatively well drained sites. In contrast, woodcock broods were located in sites that had nearly twice the tree density (3934 trees/hal and basal area (16.5 m2/ha), was located over twice as far from forest openings (18 m) and generally occurred on damp sites, near (8 m) standing water. Importance of the habitat features to the species and possible management implications are discussed.
Bourgeois, A.
Quantitative analysis of scale sensitivity in geographic cellular automata
NASA Astrophysics Data System (ADS)
Geographical Cellular Automata (GCA) approach is based on complexity theory and is widely used in geospatial modeling. A reason for the increasing attention given to GCA models is that they can easily be integrated with rasterbased GIS environment. However, the behavior of the GCA models is affected by uncertainties arising from the interaction between model elements, structures, and the quality of data sources used as model input. The objective of this study is to examine the impacts of model elements on the generated outputs of a GIS-based GCA land-use growth model using sensitivity analysis (SA) approach. The proposed SA method consists of KAPPA index with different spatial metrics. A stochastic GCA model was built to model land use change in the changsha region (Hunan,China). The transition rules were empirically derived from four Landsat-TM (30m resolution) images taken in 1996,1999, 2002 and 2005 that have been resampled to four resolutions (30, 60, 90, 120m). Five different neighbourhood configurations were considered (Moore, Von Neumann, and circular approximations of 2, 3 and 4 cell radii). Simulations were performed for each of the twenty spatial scale scenarios. Results show that spatial scale has a considerable impact on simulation dynamics in terms of both land use area and spatial structure. The spatial scale domains present in the results reveal the nonlinear relationships that link the spatial scale components to the simulation results.
Zhang, Honghui; Zeng, Yongnian; Yin, Changlin; Jin, Xiaobin; Chen, Guanghui; You, Shenjin; Zou, Bin
Quantitative analysis of bloggers' collective behavior powered by emotions
NASA Astrophysics Data System (ADS)
Large-scale data resulting from users' online interactions provide the ultimate source of information to study emergent social phenomena on the Web. From individual actions of users to observable collective behaviors, different mechanisms involving emotions expressed in the posted text play a role. Here we combine approaches of statistical physics with machine-learning methods of text analysis to study the emergence of emotional behavior among Web users. Mapping the high-resolution data from digg.com onto bipartite networks of users and their comments onto posted stories, we identify user communities centered around certain popular posts and determine emotional contents of the related comments by the emotion classifier developed for this type of text. Applied over different time periods, this framework reveals strong correlations between the excess of negative emotions and the evolution of communities. We observe avalanches of emotional comments exhibiting significant self-organized critical behavior and temporal correlations. To explore the robustness of these critical states, we design a network-automaton model on realistic network connections and several control parameters, which can be inferred from the dataset. Dissemination of emotions by a small fraction of very active users appears to critically tune the collective states.
Mitrovi?, Marija; Paltoglou, Georgios; Tadi?, Bosiljka
Quantitative analysis of urinary stone composition with micro-Raman spectroscopy
NASA Astrophysics Data System (ADS)
Urolithiasis is a common, disturbing disease with high recurrent rate (60% in five years). Accurate identification of urinary stone composition is important for treatment and prevention purpose. Our previous studies have demonstrated that micro-Raman spectroscopy (MRS)-based approach successfully detects the composition of tiny stone powders after minimal invasive urological surgery. But quantitative analysis of urinary stones was not established yet. In this study, human urinary stone mixed with two compositions of COM, HAP, COD, and uric acid, were analyzed quantitatively by using a 632.98 nm Raman spectrometric system. This quantitative analysis was based on the construction of calibration curves of known mixtures of synthetically prepared pure COM, HAP, COD and uric acid. First, the various concentration (mole fraction) ratio of binary mixtures including COM and HAP, COM and COD, or COM and uric acid, were produced. Second, the intensities of the characteristic bands at 1462cm -1(IRCOM), 1477cm-1(IRCOD), 961cm-1(IRHAP) and 1402cm-1(IRuric acid), for COD, COM, HAP and uric acid were used respectively for intensity calculation. Various binary mixtures of known concentration ratio were recorded as the basis for the quantitative analysis. The ratios of the relative intensities of the Raman bands corresponding to binary mixtures of known composition on the inverse of the COM concentration yielded a linear dependence. Third, urinary stone fragments collected from patients after management were analyzed with the use of the calibration curve and the quantitative analysis of unknown samples was made by the interpolation analysis. We successfully developed a MRS-based quantitative analytical method for measuring two composition.
Huang, Yi-Yu; Chiu, Yi-Chun; Chiang, Huihua Kenny; Chou, Y. H. Jet; Lu, Shing-Hwa; Chiu, Allen W.
Quantitative Surface Analysis of NBS Standard Materials and Mt. St. Helens Ash by Electron Spectroscopy for Chemical Analysis
Results are presented which develop a quantitative method of surface analysis by ESCA for complex heterogeneous systems. Calibration and application of the method to determination of surface weight percentages are discussed. Mt. St. Helens Ash is used to authenticate the method; results agree with bulk analysis to �20%. Results from NBS standard materials are used to establish detection limits of
Joseph A. Gardella Jr; David M. Hercules
Quantitative analysis of contrast-enhanced ultrasonography: differentiating focal nodular hyperplasia from hepatocellular carcinoma
Objective: To explore the potential of quantitative analysis of contrast-enhanced ultrasonography (CEUS) in differentiating focal nodular hyperplasia (FNH) from hepatocellular carcinoma (HCC). Methods: 34 cases of FNH and 66 cases of HCC (all lesions <5?cm) were studied using CEUS to evaluate enhancement patterns and using analytic software Sonoliver� (Image-Arena� v.4.0, TomTec Imaging Systems, Munich, Germany) to obtain quantitative features of CEUS in the region of interest. The quantitative features of maximum of intensity (IMAX), rise slope (RS), rise time (RT) and time to peak (TTP) were compared between the two groups and applied to further characterise both FNH and HCC with hypoenhancing patterns in the late phase on CEUS. Results: The sensitivity and specificity of CEUS for diagnosis of FNH were 67.6% and 93.9%, respectively. For quantitative analysis, IMAX and RS in FNHs were significantly higher than those in HCCs (p<0.05), while RT and TTP in FNHs were significantly shorter (p<0.05). Both the 11 FNHs and 62 HCCs with hypo-enhancing patterns in the late phase were further characterised with their quantitative features, and the sensitivity and specificity of IMAX for diagnosis of FNH were 90.9% and 43.5%, RS 81.8% and 80.6%, RT 90.9% and 71.0%, and TTP 90.9% and 71.0%, respectively. Conclusion: The quantitative features of CEUS in FNH and HCC were significantly different, and they could further differentiate FNH from HCC following conventional CEUS. Advances in knowledge: Our findings suggest that quantitative analysis of CEUS can improve the accuracy of differentiating FNH from HCC.
Pei, X-Q; Liu, L-Z; Xiong, Y-H; Zou, R-H; Chen, M-S; Cai, M-Y
Quantitative Analysis of Water Confined in Ion-Exchanged Zeolites
NASA Astrophysics Data System (ADS)
Zeolites, which host large quantities of water, are among the most important rock-forming and environmental minerals in the surface and near-surface regions of the Earth. The physical properties and geochemical behavior of water confined in zeolites differs substantially from that of bulk liquid water, and the energectics of confined water exerts a profound influence on the stability and behavior of zeolites in natural and engineered systems. Because the cations and water molecules are both located in the zeolitic channels, changes in cation content can influence the amount and site occupancies of water molecules in zeolites. In order to find out the relationship between the behavior of confined water and cation composition in zeolites, thermogravimetric and calorimetric experiments were conducted on the mordenite (one of the most common zeolites) samples of mixing Na+ and K+. These mordenite solid solutions were generated by binary ion exchange between pure synthetic Na-mordenite (CBV 10A, obtained from Zeolyst International) and chloride solutions containing Na+ and K+ of different equivalent concentration ratios. The results from dehydration and hydration of the mordenite solid solutions show that when the mole fraction of K+ in mordenite increases, the maximum water content of mordenite decreases and the enthalpy of hydration becomes less exothermic. More importantly, both maximum water content and enthalpy of hydration of mordenite are demonstrated to change linearly with mole fraction of K+. Two energetically distinct sets of water molecules have been observed in mordenite: W1 (relatively less energetic) and W2 (relatively high energetic). Thermodynamic analysis on the hydration of W1 and W2 reveals that these two sets of water molecules behave differently when cation composition of mordenite changes. The water content of W2 is independent of cation composition, whereas W1 loses water with when mole fraction of K+ increases; the enthalpy of hydration of W1 appears to be constant, but that of W2 becomes less exothermic with increasing mole fraction of K+.
Wang, J.; Neuhoff, P. S.
Quantitative flux analysis reveals folate-dependent NADPH production.
ATP is the dominant energy source in animals for mechanical and electrical work (for example, muscle contraction or neuronal firing). For chemical work, there is an equally important role for NADPH, which powers redox defence and reductive biosynthesis. The most direct route to produce NADPH from glucose is the oxidative pentose phosphate pathway, with malic enzyme sometimes also important. Although the relative contribution of glycolysis and oxidative phosphorylation to ATP production has been extensively analysed, similar analysis of NADPH metabolism has been lacking. Here we demonstrate the ability to directly track, by liquid chromatography-mass spectrometry, the passage of deuterium from labelled substrates into NADPH, and combine this approach with carbon labelling and mathematical modelling to measure NADPH fluxes. In proliferating cells, the largest contributor to cytosolic NADPH is the oxidative pentose phosphate pathway. Surprisingly, a nearly comparable contribution comes from serine-driven one-carbon metabolism, in which oxidation of methylene tetrahydrofolate to 10-formyl-tetrahydrofolate is coupled to reduction of NADP(+) to NADPH. Moreover, tracing of mitochondrial one-carbon metabolism revealed complete oxidation of 10-formyl-tetrahydrofolate to make NADPH. As folate metabolism has not previously been considered an NADPH producer, confirmation of its functional significance was undertaken through knockdown of methylenetetrahydrofolate dehydrogenase (MTHFD) genes. Depletion of either the cytosolic or mitochondrial MTHFD isozyme resulted in decreased cellular NADPH/NADP(+) and reduced/oxidized glutathione ratios (GSH/GSSG) and increased cell sensitivity to oxidative stress. Thus, although the importance of folate metabolism for proliferating cells has been long recognized and attributed to its function of producing one-carbon units for nucleic acid synthesis, another crucial function of this pathway is generating reducing power. PMID:24805240
Fan, Jing; Ye, Jiangbin; Kamphorst, Jurre J; Shlomi, Tomer; Thompson, Craig B; Rabinowitz, Joshua D
Quantitative underwater 3D motion analysis using submerged video cameras: accuracy analysis and trajectory reconstruction.
In this study we aim at investigating the applicability of underwater 3D motion capture based on submerged video cameras in terms of 3D accuracy analysis and trajectory reconstruction. Static points with classical direct linear transform (DLT) solution, a moving wand with bundle adjustment and a moving 2D plate with Zhang's method were considered for camera calibration. As an example of the final application, we reconstructed the hand motion trajectories in different swimming styles and qualitatively compared this with Maglischo's model. Four highly trained male swimmers performed butterfly, breaststroke and freestyle tasks. The middle fingertip trajectories of both hands in the underwater phase were considered. The accuracy (mean absolute error) of the two calibration approaches (wand: 0.96 mm - 2D plate: 0.73 mm) was comparable to out of water results and highly superior to the classical DLT results (9.74 mm). Among all the swimmers, the hands' trajectories of the expert swimmer in the style were almost symmetric and in good agreement with Maglischo's model. The kinematic results highlight symmetry or asymmetry between the two hand sides, intra- and inter-subject variability in terms of the motion patterns and agreement or disagreement with the model. The two outcomes, calibration results and trajectory reconstruction, both move towards the quantitative 3D underwater motion analysis. PMID:22435960
Silvatti, Amanda P; Cerveri, Pietro; Telles, Thiago; Dias, F�bio A S; Baroni, Guido; Barros, Ricardo M L
Optimization of Quantitative MGMT Promoter Methylation Analysis Using Pyrosequencing and Combined Bisulfite Restriction Analysis
Resistance to chemotherapy is a major complication during treatment of cancer patients. Hypermethylation of the MGMT gene alters DNA repair and is associated with longer survival of glioblastoma patients treated with alkylating agents. Therefore, MGMT promoter methylation plays an important role as a predictive biomarker for chemotherapy resistance. To adopt this established correlation into a molecular diagnosis procedure, we compared and optimized three experimental techniques [combined bisulfite restriction analysis, a primer extension- and denaturing high-performance liquid chromatography-based method named SIRPH (SNuPE ion pair-reverse phase high-performance liquid chromatography), and pyrosequencing] with regard to their accuracy of detecting MGMT promoter methylation. Initially, bisulfite sequencing was used to obtain a comprehensive methylation profile of the MGMT promoter region in 22 glioblastoma samples and in three normal brain controls. Next, we statistically identified CpG sites that best discriminate between methylated and unmethylated MGMT promoters. These results were then used to design optimal combined bisulfite restriction analysis, SIRPH, and pyrosequencing assays for accurate and cost-efficient assessment of MGMT promoter methylation. We compared all three techniques with regard to their reliability and reproducibility on well-characterized tumor samples. The optimized pyrosequencing assay performed best and provides a sensitive, robust, and easy-to-use method for quantitative assessment of MGMT methylation, for both snap-frozen and paraffin-embedded specimens.
Mikeska, Thomas; Bock, Christoph; El-Maarri, Osman; Hubner, Anika; Ehrentraut, Denise; Schramm, Johannes; Felsberg, Jorg; Kahl, Philip; Buttner, Reinhard; Pietsch, Torsten; Waha, Andreas
Quantitative energy-filtered image analysis in cytochemistry. II. Morphometric analysis of element-distribution images.
A combination of energy-filtered electron microscopy (EFEM) and an image-analysis system (IBAS/2000) is used for a morphometric analysis of chemical reaction products in cells. Electron energy-loss spectroscopic element-distribution images are acquired from cytochemical reaction products in a variety of cellular objects: (1) colloidal thorium particles in extra-cellular coat material, (2) iron-containing ferritin particles in liver parenchymal cells, (3) barium-containing reaction products in endoplasmic reticulum stacks, (4) elements present in lysosomal cerium- and barium-containing precipitates connected with acid phosphatase (AcPase) or aryl sulphatase (AS) enzyme activity. Areas or area fractions are determined from such element-distribution images by application of an objective image segmentation method. By superposition of two or more element-distribution images, mutual element relations are qualitatively established in lysosomal cerium- and barium-containing precipitates connected with acid phosphatase (AcPase) or aryl sulphatase (AS) enzyme activity. By comparing electron spectroscopic images (ESI) with element-distribution images, the mutual contrast per element relations are quantitatively investigated. The obtained gain in resolution in such electron energy-loss spectroscopic element-distribution images will be explained and discussed. PMID:2336735
Sorber, C W; Van Dort, J B; Ringeling, P C; Cleton-Soeteman, M I; De Bruijn, W C
Quantitative analysis of single aerosol particles using polycapillary X-ray optics
NASA Astrophysics Data System (ADS)
A laboratory micro X-ray fluorescence spectrometer based on polycapillary X-ray optics (PXRO) was used to carry out the quantitative X-ray fluorescence analysis of single aerosol particles with smaller size than that of focal spot of PXRO. The minimum detection limits measured with the thin-film reference standards were in the range from 13.3 to 0.7 ng cm - 2 when the operating current and voltage were 70 mA and 35 kV, respectively. In order to reduce the effects of the inhomogeneous distributions of the X-ray intensity in the focal spot of the PXRO on the analysis results, the sensitivities were corrected by using a Gaussian function for the quantitative analysis of single aerosol particles. The accuracy of the analysis of single standard solution drops was on average 25% depending on the element and concentration. The precision of the analysis was better than 5%.
Sun, Tianxi; Liu, Zhiguo; Li, Yude; Wang, Guangfu; Zhu, Guanghua; Ding, Xunliang; Xu, Qing; Liu, Hui; Luo, Ping; Pan, Qiuli; Lin, Xiaoyan; Teng, Yuepeng
Analysis of 129I in Groundwater Samples: Direct and Quantitative Results below the Drinking Water Standard
Due to its long half-life (15.7 million years) and relatively unencumbered migration in subsurface environments, 129I has been recognized as a contaminant of concern at numerous federal, private, and international facilities. In order to understand the long-term risk associated with 129I at these locations, quantitative analysis of groundwater samples must be performed. However, the ability to quantitatively assess the 129I content in groundwater samples requires specialized extraction and sophisticated analytical techniques, which are complicated and not always available to the general scientific community. This paper highlights an analytical method capable of directly quantifying 129I in groundwater samples at concentrations below the MCL without the need for sample pre-concentration. Samples were analyzed on a Perkin Elmer ELAN DRC II ICP-MS after minimal dilution using O2 as the reaction gas. Analysis of continuing calibration verification standards indicated that the DRC mode could be used for quantitative analysis of 129I in samples below the drinking water standard (0.0057 ng/ml or 1 pCi/L). The low analytical detection limit of 129I analysis in the DRC mode coupled with minimal sample dilution (1.02x) resulted in a final sample limit of quantification of 0.0051 ng/ml. Subsequent analysis of three groundwater samples containing 129I resulted in fully quantitative results in the DRC mode, and spike recovery analyses performed on all three samples confirmed that the groundwater matrix did not adversely impact the analysis of 129I in the DRC mode. This analytical approach has been proven to be a cost-effective, high-throughput technique for the direct, quantitative analysis of 129I in groundwater samples at concentrations below the current MCL.
Brown, Christopher F.; Geiszler, Keith N.; Lindberg, Michael J.
Possibility of quantitative estimation of blood cell forms by the spatial-frequency spectrum analysis
NASA Astrophysics Data System (ADS)
At present in hematology there are no quantitative estimates of such important for the cell classification parameters: cell form and nuclear form. Due to the absence of the correlation between morphological parameters and parameters measured by hemoanalyzers, both flow cytometers and computer recognition systems, do not provide the completeness of the clinical blood analysis. Analysis of the spatial-frequency spectra of blood samples (smears and liquid probes) permit the estimate the forms quantitatively. On the results of theoretical and experimental researches carried out an algorithm of the form quantitative estimation by means of SFS parameters has been created. The criteria of the quality of these estimates have been proposed. A test bench based on the coherent optical and digital processors. The received results could be applied for the automated classification of ether normal or pathological blood cells in the standard blood smears.
Spiridonov, Igor N.; Safonova, Larisa P.; Samorodov, Andrey V.
CERES Edition2 Cloud Property Retrievals Using TRMM VIRS and Terra and Aqua MODIS Data�Part II: Examples of Average Results and Comparisons With Other Data
Cloud properties were retrieved by applying the Clouds and Earth's Radiant Energy System (CERES) project Edition-2 algorithms to 3.5 years of Tropical Rainfall Measuring Mission Visible and Infrared Scanner data and 5.5 and 8 years of MODerate Resolution Imaging Spectroradiometer (MODIS) data from Aqua and Terra, respectively. The cloud products are consistent quantitatively from all three imagers; the greatest dis-
Patrick Minnis; Szedung Sun-Mack; Yan Chen; Mandana M. Khaiyer; Yuhong Yi; J. Kirk Ayers; Ricky R. Brown; Xiquan Dong; Sharon C. Gibson; Patrick W. Heck; Bing Lin; Michele L. Nordeen; Louis Nguyen; Rabindra Palikonda; William L. Smith; Douglas A. Spangenberg; Qing Z. Trepte; Baike Xi
Direct evidence for the role of light-mediated gas vesicle collapse in the buoyancy regulation of Anabaena flos-aquae (cyanobacteria)
Quantitative measurements were made of the changes in gas vacuole volume and the major components of cell mass (protein and carbohydrate) on cultures of Anabaenaflos-aquae which lost buoyancy as they were shifted from low to high light intensity. Assuming densities of 1,300 kg. rn-' for protein and 1,600 for carbohydrate, we calculated the change in ballast brought about by changes
Aqua-planet simulations of the formation of the South Atlantic convergence zone
NASA Technical Reports Server (NTRS)
The impact of Amazon Basin convection and cold fronts on the formation and maintenance of the South Atlantic convergence zone (SACZ) is studied using aqua-planet simulations with a general circulation model. In the model, a circular patch of warm sea-surface temperature (SST) is used to mimic the effect of the Amazon Basin on South American monsoon convection. The aqua-planet simulations were designed to study the effect of the strength and latitude of Amazon Basin convection on the formation of the SACZ. The simulations indicate that the strength of the SACZ increases as the Amazon convection intensifies and is moved away from the equator. Of the two controls studied here, the latitude of the Amazon convection exerts the strongest effect on the strength of the SACZ. An analysis of the synoptic-scale variability in the simulations shows the importance of frontal systems in the formation of the aqua-planet SACZ. Composite time series of frontal systems that occurred in the simulations show that a robust SACZ occurs when fronts penetrate into the subtropics and become stationary there as they cross eastward of the longitude of the Amazon Basin. Moisture convergence associated with these frontal systems produces rainfall not along the model SACZ region and along a large portion of the northern model Amazon Basin. Simulations in which the warm SST patch was too weak or too close to the equator did not produce frontal systems that extended into the tropics and became stationary, and did not form a SACZ. In the model, the SACZ forms as Amazon Basin convection strengthens and migrates far enough southward to allow frontal systems to penetrate into the tropics and stall over South America. This result is in agreement with observations that the SACZ tends to form after the onset of the monsoon season in the Amazon Basin.
Nieto Ferreira, Rosana; Chao, Winston C.
Quantitative analysis of melt elongational behavior of LLDPE\\/LDPE blends
Shear and elongational data of blends of linear (LLDPE) and branched (LDPE) polyethylene are reported. Blends show thermo-rheological complex behavior. Also, in unidirectional shear or elongational flow, the linear-viscoelastic deformation regime of the blends is significantly reduced, and the terminal relaxation times of the blends are shifted in the direction of the LDPE homopolymer. Quantitative analysis of elongational viscosity data
Manfred H. Wagner; Saeid Kheirandish; Masayuki Yamaguchi
Development of motion analysis system for quantitative evaluation of teamwork in soccer games
We present a motion analysis system of soccer games. The purpose of this system is to evaluate the teamwork quantitatively based on the movement of all the players in a game. Space management and cooperative movement by the players are two major factors for teamwork evaluation. To quantify them from motion images, we propose two new features; �minimum moving time
Tsuyoshi Taki; Jun-ichi Hasegawa; Teruo Fukumura
Bayesian model selection for genome-wide epistatic quantitative trait loci analysis
The problem of identifying complex epistatic quantitative trait loci (QTL) across the entire genome continues to be a formidable challenge for geneticists. The complexity of genome-wide epistatic analysis results mainly from the number of QTL being unknown and the number of possible epistatic effects being huge. In this article, we use a composite model space approach to develop a Bayesian
Nengjun Yi; Brian S. Yandell; David B. Allison; Eugene J. Eisen; Daniel Pomp
Gas chromatograph-mass spectrometer (GC/MS) system for quantitative analysis of reactive chemical compounds
Described is a new gas chromatograph-mass spectrometer (GC/MS) system and method for quantitative analysis of reactive chemical compounds. All components of such a GC/MS system external to the oven of the gas chromatograph are programmably temperature controlled to operate at a volatilization temperature specific to the compound(s) sought to be separated and measured.
Grindstaff, Quirinus G. (Oak Ridge, TN)
Multi-observation PET image analysis for patient follow-up quantitation and therapy assessment
In positron emission tomography (PET) imaging, an early therapeutic response is usually characterized by variations of semi-quantitative parameters restricted to maximum SUV measured in PET scans during the treatment. Such measurements do not reflect overall tumor volume and radiotracer uptake variations. The proposed approach is based on multi-observation image analysis for merging several PET acquisitions to assess tumor metabolic volume
S. David; D. Visvikis; C. Roux; M. Hatt
Multidimensional Analysis System for Quantitative Chemistry Problems: Symbol, Macro, Micro, and Process Aspects.
ERIC Educational Resources Information Center
Explores teaching methods to improve students' understanding of quantitative chemistry and their ability to solve related problems using the Multidimensional Analysis System (MAS). Investigates the relationships between MAS-classified chemistry problems and student achievement in solving these problems. Shows that improvement in student�
Dori, Yehudit J.; Hameiri, Mira
Clinical applications of a quantitative analysis of regional lift ventricular wall motion
NASA Technical Reports Server (NTRS)
Observations were summarized which may have clinical application. These were obtained from a quantitative analysis of wall motion that was used to detect both hypokinesis and tardokinesis in left ventricular cineangiograms. The method was based on statistical comparisons with normal values for regional wall motion derived from the cineangiograms of patients who were found not to have heart disease.
Leighton, R. F.; Rich, J. M.; Pollack, M. E.; Altieri, P. I.
Quantitative analysis of genetically modified organisms (GMO) in processed food by PCR-based methods
Two different PCR-based approaches for the quantitative analysis of genetically modified organism (GMO) � components in foods are presented using Soybean derived samples as an example. The first method � a double competitive PCR � is well suited to determine threshold levels of GMO content in food. The other � PCR on-line measurement � is suited to determine ratios of
A. Wurz; A. Bluth; P. Zeltz; C. Pfeifer; R. Willmund
Most conflicts between countries, originate from issues regarding the quantity and quality of shared water resources. During the last decades, many tools and models for river basin management have been developed according to the international and European law, conventions and other agreements. The proposed methodology is a quantitative outlook of the popular SWOT analysis. The technique suggested in this article
Christina Mitsiani
Collaborative study of quantitative coal mineral analysis using computer-controlled scanning electron microscopy
Six laboratories collaborated in an international study of the computer-controlled scanning electron microscopy (CCSEM) method of quantitative coal mineral analysis. A total of five analyses were performed by most of the laboratories on three bituminous coal samples: Pittsburgh No. 8, Illinois No. 6 and Prince. Repeatability relative standard deviation (RSDr) was <20% for the four minerals analysed: calcite, kaolinite, pyrite
Kevin Galbreath; Christopher Zygarlicke; Gary Casuccio; Tracy Moore; Paul Gottlieb; Nicki Agron-Olshina; Gerald Huffman; Anup Shah; Nancy Yang; John Vleeskens; Gerrit Hamburg
Quantitative Policy Analysis of Sanitary, Phytosanitary and Technical Barriers to Trade
This paper surveys and analyses existing methodologies to model and quantify non-tariff trade barriers (NTBs) in the agricultural and food sectors. The analysis centers on sanitary, phytosanitary, and technical regulations that can have an impact on trade. The paper stresses methods that provide some quantitative estimates of the impact of such barriers on market equilibrium, trade flows, economic efficiency, and
John C. Beghin; Jean-Christophe Bureau
The vacuum bag (VB) dust was analyzed by mold specific quantitative PCR. These results were compared to the analysis survey calculated for each of the homes. The mean and standard deviation (SD) of the ERMI values in the homes of the NC asthmatic children was 16.4 (6.77), compa...
Quantitative analysis of plasma neutral glycosphingolipids by high performance liquid chromatography of their perbenzoyl derivatives
A quantitative high performance liquid chro- matography method for the analysis of neutral glycosyl- ceramides as their perbenzoyl derivatives has been devised. Samples containing more than 2.5 nmol each of mono-, di-, tri-, and tetraglycosylceramide are benzoylated with 10% benzoyl chloride in pyridine at 37�C for 16 hr. The products are separated from excess reagents by solvent distribution and injected
M. David Ullman; Robert H. McCluer
Quantitative Neutronographic Analysis of Fibre Texture of Zirconium by the Time-of-Flight Method.
National Technical Information Service (NTIS)
Quantitative neutronographic analysis of fibre texture of zirconium has been done by the time-of-flight method. On the IBR-30 pulsed reactor 16 diffraction spectra are measured on each of three deformation states of the sample. Pole figures have been dete...
M. Betzl K. Walther W. Matz K. Feldmann
Multiple regression analysis of sib-pair data on reading to detect quantitative trait loci
A simple extension of the DeFries and Fulker multiple regression model for twin analysis is applied to the problem of detecting linkage in a quantitative trait. The method, employing sib pairs, is based on that of Haseman and Elston. Reading data from 19 extended pedigrees were analyzed employing RLFPs as markers on chromosome 15 and using the widely available statistical
D. W. Fulker; L. R. Cardon; J. C. Defries; W. J. Kimberling; B. F. Pennington; S. D. Smith
Quantitative Analysis of Thymidine Phosphorylase and Dihydropyrimidine Dehydrogenase in Renal Cell Carcinoma
Objective: The purpose of the present study was to clarify the clinicopathological significance of both thymidine phosphorylase (TP) and dihydropyrimidine dehydrogenase (DPD) in renal cell carcinoma (RCC) based on a quantitative analysis of RCC patients. Methods: Levels of TP and DPD in RCC and\\/or uninvolved renal tissues from 65 RCC patients were measured by enzyme-linked immunosorbent assay. Results: The TP
Tatsuo Morita; Atsushi Matsuzaki; Akihiko Tokue
Quantitative analysis of multi-periodic supply chain contracts with options via stochastic programming
We propose a stochastic programming approach for quantitative analysis of supply contracts, involving flexibility, between a buyer and a supplier, in a supply chain framework. Specifically, we consider the case of multi-periodic contracts in the face of correlated demands. To design such contracts, one has to estimate the savings or costs induced for both parties, as well as the optimal
Christian VAN DELFT; Jean-Philippe VIAL
A Colorimetric Analysis Experiment Not Requiring a Spectrophotometer: Quantitative Determination of Albumin in Powdered Egg White
ERIC Educational Resources Information Center
A general science experiment for high school chemistry students might serve as an excellent review of the concepts of solution preparation, solubility, pH, and qualitative and quantitative analysis of a common food product. The students could learn to use safe laboratory techniques, collect and analyze data using proper scientific methodology and�
Charlton, Amanda K.; Sevcik, Richard S.; Tucker, Dorie A.; Schultz, Linda D.
Quantitative analysis of in situ wafer bowing measurements for III-nitride growth on sapphire
Wafer bowing measurements have been recently developed into an efficient tool for MOVPE and MBE process optimization. In combination with temperature and reflectance measurements they are applied for direct but mostly qualitative evaluation of III-nitride epitaxial growth processes. In this work, applying a quantitative analysis of wafer bowing throughout the full epitaxial process, we are able to trace the lattice
F. Brunner; A. Knauer; T. Schenk; M. Weyers; J.-T. Zettler
Quantitative Analysis of Lipid Droplet Fusion: Inefficient Steady State Fusion but Rapid Stimulation by Chemical Fusogens
Lipid droplets (LDs) are dynamic cytoplasmic organelles containing neutral lipids and bounded by a phospholipid monolayer. Previous studies have suggested that LDs can undergo constitutive homotypic fusion, a process linked to the inhibitory effects of fatty acids on glucose transporter trafficking. Using strict quantitative criteria for LD fusion together with refined light microscopic methods and real-time analysis, we now show
Samantha Murphy; Sally Martin; Robert G. Parton; Jean Gruenberg
Quantitative measurement of stability in human gait through computer simulation and Floquet analysis
The purpose of this investigation was to develop and test quantitative measures to assess the dynamic stability of human locomotion in normal and pathologic gait. Through computer simulation the stability of joint trajectories were specified under a variety of conditions. The resulting joint trajectory time series data were used to calculate the overall stability of the walking using Floquet analysis.
A. Scheiner; D. C. Ferencz; Howard J. Chizeck
Quantitative X-Ray Diffraction Analysis of Oxides Formed on Superalloys.
National Technical Information Service (NTIS)
Methods were developed for quantitative analysis by X-ray diffraction of the oxides Al2O3, NiO, Cr2O3, CoO, and CoCr2O4 within a standard deviation of about 10 percent of the weight fraction reported or within 1 percent absolute. These error limits assume...
R. G. Garlick
Quantitative fluid inclusion gas analysis of airburst, nuclear, impact and fulgurite glasses
We present quantitative fluid inclusion gas analysis on a suite of violently-formed glasses. We used the incremental crush mass spectrometry method (Norman & Blamey, 2001) to analyze eight pieces of Libyan Desert Glass (LDG). As potential analogues we also analyzed trinitite, three impact crater glasses, and three fulgurites. The 'clear' LDG has the lowest CO content and O\\/Ar ratios are
John Parnell; Horton E. Newsom; Nigel J. F. Blamey; Mark Bruce Elrick Boslough
A Computer Program for Calculation of Calibration Curves for Quantitative X-Ray Diffraction Analysis.
ERIC Educational Resources Information Center
Describes a FORTRAN IV program written to supplement a laboratory exercise dealing with quantitative x-ray diffraction analysis of mixtures of polycrystalline phases in an introductory course in x-ray diffraction. Gives an example of the use of the program and compares calculated and observed calibration data. (Author/GS)
Blanchard, Frank N.
Quantitative and Qualitative Analysis of Nutrition and Food Safety Information in School Science Textbooks of India
ERIC Educational Resources Information Center
Objective: To assess quantity and quality of nutrition and food safety information in science textbooks prescribed by the Central Board of Secondary Education (CBSE), India for grades I through X. Design: Content analysis. Methods: A coding scheme was developed for quantitative and qualitative analyses. Two investigators independently coded the�
Subba Rao, G. M.; Vijayapushapm, T.; Venkaiah, K.; Pavarala, V.
Quantitative and visual analysis of the impact of music on perceived emotion of film
This paper presents quantitative and visual methods for the analysis of the effect of music on emotion perceived in film. We discover strong, visible, and quantifiable trends in the effect of music on perceived emotion of film. We perform studies using both selected classical and composed music segments annotated with diverse emotions, paired with ambiguous film clips. We collect and
Rob Parke; Elaine Chew; Chris Kyriakakis
Analytical strategies based on multiple headspace extraction for the quantitative analysis of aroma components in mushrooms.
Headspace (HS) and headspace solid phase microextraction (HS-SPME) analysis by gas chromatography-mass spectrometry (GC/MS) have been found to be suitable methods for the analysis of volatile organic compounds. The objectives of this paper are to study the possibilities of multiple headspace extraction (MHE) for the quantitative determination of volatile compounds in mushroom samples and to compare the results obtained using three different sample treatment techniques. For this purpose, HS with two different injection techniques (pressure-loop system and gas-tight syringe autosampling system) and HS-SPME have been studied. Three processes were optimized for the analysis of 20 volatile compounds by experimental design technique based on Central Composite Design (CCD) and Full Factorial Design depending on the used methodology. Once the designs were finished, a trade off among optimum conditions for each compound analyzed was reached. At optimum conditions, appropriate extraction time and sample amount for the three techniques used were established. Finally, the methods were validated in terms of linearity, detection and quantitation limits and repeatability. The most suitable method was then applied to the quantitative analysis of seven mushroom samples. A detailed comparison of the analytical performance characteristics of HS and HS-SPME as sample treatment techniques for final GC/MS determination is given. In addition, MHE has been proved to be an adequate technique to avoid matrix effects in complex samples quantitation. Its applicability to the determination of volatile mushroom components, along with its limitations, is discussed in this work. PMID:24725884
San Rom�n, I; Alonso, M L; Bartolom�, L; Alonso, R M; Fa�an�s, R
Quantitative Thermal Analysis of Poly(butylene Terephthalate) by Temperature-Modulated Differential Scanning Calorimetry
Quantitative thermal analysis is performed on poly(butylene terephthalate), PBT, between 5 and 600 K based on the measured heat capacity by adiabatic calorimertry, standard differential scanning calorimetry (DSC) and temperature-modulated differential scanning calorimetry (TMDSC). Based on the new data, the low temperature heat capacity is linked to the vibrational spectrum, using the ATHAS method to calculate the solid heat capacity
M. Pyda; E. Nowak-Pyda; B. Wunderlich
Identification of Candidate Periodontal Pathogens and Beneficial Species by Quantitative 16S Clonal Analysis
Most studies of the bacterial etiology of periodontitis have used either culture-based or targeted DNA approaches, and so it is likely that pathogens remain undiscovered. The purpose of this study was to use culture-independent, quantitative analysis of biofilms associated with chronic periodontitis and periodontal health to identify pathogens and beneficial species. Samples from subjects with periodontitis and controls were analyzed
Purnima S. Kumar; Ann L. Griffen; Melvin L. Moeschberger; Eugene J. Leys
The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks
Motivation: Analysis of cellular signaling interactions is expected to pose an enormous informatics challenge, per- haps even larger than analyzing the genome. The complex networks arising from signaling processes are traditionally represented as block diagrams. A key step in the evolu- tion toward a more quantitative understanding of signal- ing is to explicitly specify the kinetics of all chemical reac-
Sudhir Sivakumaran; Sridhar Hariharaputran; Jyoti Mishra; Upinder S. Bhalla
Quantitative Analysis of Organic Compounds: A Simple and Rapid Method for Use in Schools
ERIC Educational Resources Information Center
Describes the procedure for making a quantitative analysis of organic compounds suitable for secondary school chemistry classes. Using the Schoniger procedure, the organic compound, such as PVC, is decomposed in a conical flask with oxygen. The products are absorbed in a suitable liquid and analyzed by titration. (JR)
Schmidt, Hans-Jurgen
A Quantitative Categorical Analysis of Metadata Elements in Image-Applicable Metadata Schemas.
ERIC Educational Resources Information Center
Reports on a quantitative categorical analysis of metadata elements in the Dublin Core, VRA (Visual Resource Association) Core, REACH (Record Export for Art and Cultural Heritage), and EAD (Encoded Archival Description) metadata schemas, all of which can be used for organizing and describing images. Introduces a new schema comparison methodology�
Greenberg, Jane
Quantitative Intersectionality: A Critical Race Analysis of the Chicana/o Educational Pipeline
ERIC Educational Resources Information Center
Utilizing the critical race framework of intersectionality, this research reexamines the Chicana/o educational pipeline through a quantitative intersectional analysis. This approach disaggregates data along the intersection of race, class, gender, and citizenship status to provide a detailed portrait of the educational trajectory of Mexican-origin�
Covarrubias, Alejandro
A Quantitative Analysis of Cognitive Strategy Usage in the Marking of Two GCSE Examinations
ERIC Educational Resources Information Center
Diverse strategies for marking GCSE examinations have been identified, ranging from simple automatic judgements to complex cognitive operations requiring considerable expertise. However, little is known about patterns of strategy usage or how such information could be utilised by examiners. We conducted a quantitative analysis of previous verbal�
Suto, W. M. Irenka; Greatorex, Jackie
Forty Years of the "Journal of Librarianship and Information Science": A Quantitative Analysis, Part I
ERIC Educational Resources Information Center
This paper reports on the first part of a two-part quantitative analysis of volume 1-40 (1969-2008) of the "Journal of Librarianship and Information Science" (formerly the "Journal of Librarianship"). It provides an overview of the current state of LIS research journal publishing in the UK; a review of the publication and printing history of�
Furner, Jonathan
Quantitative analysis of bristle number in Drosophila mutants identifies genes involved in neural development
NASA Technical Reports Server (NTRS)
BACKGROUND: The identification of the function of all genes that contribute to specific biological processes and complex traits is one of the major challenges in the postgenomic era. One approach is to employ forward genetic screens in genetically tractable model organisms. In Drosophila melanogaster, P element-mediated insertional mutagenesis is a versatile tool for the dissection of molecular pathways, and there is an ongoing effort to tag every gene with a P element insertion. However, the vast majority of P element insertion lines are viable and fertile as homozygotes and do not exhibit obvious phenotypic defects, perhaps because of the tendency for P elements to insert 5' of transcription units. Quantitative genetic analysis of subtle effects of P element mutations that have been induced in an isogenic background may be a highly efficient method for functional genome annotation. RESULTS: Here, we have tested the efficacy of this strategy by assessing the extent to which screening for quantitative effects of P elements on sensory bristle number can identify genes affecting neural development. We find that such quantitative screens uncover an unusually large number of genes that are known to function in neural development, as well as genes with yet uncharacterized effects on neural development, and novel loci. CONCLUSIONS: Our findings establish the use of quantitative trait analysis for functional genome annotation through forward genetics. Similar analyses of quantitative effects of P element insertions will facilitate our understanding of the genes affecting many other complex traits in Drosophila.
Norga, Koenraad K.; Gurganus, Marjorie C.; Dilda, Christy L.; Yamamoto, Akihiko; Lyman, Richard F.; Patel, Prajal H.; Rubin, Gerald M.; Hoskins, Roger A.; Mackay, Trudy F.; Bellen, Hugo J.
Synthesis of quantitative and qualitative evidence for accident analysis in risk-based highway planning.
Accident analysis involves the use of both quantitative and qualitative data in decision-making. The aim of this paper is to demonstrate the synthesis of relevant quantitative and qualitative evidence for accident analysis and for planning a large and diverse portfolio of highway investment projects. The proposed analysis and visualization techniques along with traditional mathematical modeling serve as an aid to planners, engineers, and the public in comparing the benefits of current and proposed improvement projects. The analysis uses data on crash rates, average daily traffic, cost estimates from highway agency databases, and project portfolios for regions and localities. It also utilizes up to two motivations out of seven that are outlined in the Transportation Equity Act for the 21st Century (TEA-21). Three case studies demonstrate the risk-based approach to accident analysis for short- and long-range transportation plans. The approach is adaptable to other topics in accident analysis and prevention that involve the use of quantitative and qualitative evidence, risk analysis, and multi-criteria decision-making for project portfolio selection. PMID:16730627
Lambert, James H; Peterson, Kenneth D; Joshi, Nilesh N
Biomonitoring and risk assessment on earth and during exploratory missions using AquaHab �
NASA Astrophysics Data System (ADS)
Bioregenerative closed ecological life support systems (CELSS) will be necessary in the exploration context revitalizing atmosphere, waste water and producing food for the human CELSS mates. During these long-term space travels and stays far away from Earth in an hostile environment as well as far for example from any hospital and surgery potential, it will be necessary to know much more about chemical and drug contamination in the special sense and by human's themselves in detail. Additionally, there is a strong need on Earth for more relevant standardized test systems including aquatic ones for the prospective risk assessment of chemicals and drugs in general on a laboratory scale. Current standardized test systems are mono species tests, and thus do not represent system aspects and have reduced environmental relevance. The experience gained during the last years in our research group lead to the development of a self-sustaining closed aquatic habitat/facility, called AquaHab � which can serve regarding space exploration and Earth application. The AquaHab � module can be the home of several fish species, snails, plants, amphipods and bacteria. The possibility to use different effect endpoints with certain beneficial characteristics is the basis for the application of AquaHab � in different fields. Influence of drugs and chemicals can be tested on several trophic levels and ecosystem levels; guaranteeing a high relevance for aquatic systems in the real environment. Analyses of effect parameters of different complexity (e.g. general biological and water chemical parameters, activity of biotransforming enzymes) result in broad spectra of sensitivity. Combined with residual analyses (including all metabolites), this leads to an extended prospective risk assessment of a chemical on Earth and in a closed Life Support System. The possibility to measure also sensitive "online" parameters (e.g. behavior, respiration/photosynthetic activity) enables a quick and sensitive effect analysis of water contaminants in respective environments. AquaHab � is currently under development to an early warning biomonitoring system using genetically modified fish and green algae. The implementation of biosensors/biochip in addition is also discussed.
Slenzka, K.; D�nne, M.; Jastorff, B.
Quantitative analysis and chromatographic fingerprinting for the quality evaluation of Scutellaria baicalensis Georgi using capillary electrophoresis
Quantitative analysis and chromatographic fingerprinting for the quality evaluation of a Chinese herb Scutellaria baicalensis Georgi using capillary electrophoresis (CE) technique was developed. The separation was performed with a 50.0cm (42.0cm to the detector window)�75?m i.d. fused-silica capillary, and the CE fingerprint condition was optimized using the combination of central composite design and multivariate analysis. The optimized buffer system containing
Ke Yu; Yifei Gong; Zhongying Lin; Yiyu Cheng
The Replacement of Cytogenetic Analysis by Direct Chorionic Villi Sampling Preparation with Quantitative Fluorescence PCR
Aim: The aim of this study is to assess the replacement of chromosomal analysis of chorionic villi (CV) direct preparation samples (DIR) by quantitative fluorescence PCR (QF-PCR) and to determine its advantages in routine prenatal diagnosis. Methods: From a total of 4,020 CV samples, rapid results were obtained either by conventional cytogenetic analysis of DIR in 2,770 samples, or by
S. Christopoulou; G. Christopoulou; A. Hatzaki; A. Hatzipouliou; J. Donoghue; M. Karkaletsi; P. Kaminopetros; S. Sifakis; V. Velissariou
X-ray quantitative analysis of coal by the Reference Intensity Method. Final report
Twenty-four coal samples representing the four major rank types were analyzed by the x-ray RIM methodology which includes mass absorption analysis by x-ray transmission and quantitative x-ray powder diffraction. Twenty-three separate mineral species were observed in the samples, many of which could be quantified in the whole coal analysis. Several mineral species at levels of 5 wt % or less
B. L. Davis; L. R. Johnson; T. Mebrahtu
Multilayers quantitative X-ray fluorescence analysis applied to easel paintings
X-ray fluorescence spectrometry (XRF) allows a rapid and simple determination of the elemental composition of a material.\\u000a As a non-destructive tool, it has been extensively used for analysis in art and archaeology since the early 1970s. Whereas\\u000a it is commonly used for qualitative analysis, recent efforts have been made to develop quantitative treatment even with portable\\u000a systems. However, the interpretation
Laurence de Viguerie; V. Armando Sole; Philippe Walter
Quantitative analysis of hydroperoxyl radical using flow injection analysis with chemiluminescence detection.
The hydroperoxyl radical (HO2) is one of the most abundant free radicals in the atmosphere, where it participates in a series of photochemical reactions that determine the fate of natural and anthropogenic emissions. In addition, HO2 is found in droplets and surface water as a result of photochemical formation and gas-phase scavenging. We describe a quantitative method for determining trace concentrations of HO2 radicals that exploits the chemiluminescence produced upon reaction with a synthetic analogue of luciferin from the crustacean Cypridina. The technique is linear at least up to 1 microM HO2(aq) and has a minimum detection limit of 0.1 nM. A unique feature of this analysis is a calibration method using stable aqueous HO2 standards produced in submicromolar concentrations using 60Co gamma-radiolysis. The advantage of this method in comparison to others in consideration of field deployment is its simplicity, low cost, and minimal size and power requirements. One intended application of this technique is the measurement of atmospheric HO2 radicals following collection into aqueous solution. PMID:14632084
Zheng, Jun; Springston, Stephen R; Weinstein-Lloyd, Judith
Analysis of focal adhesion turnover: A quantitative live-cell imaging example.
Recent advances in optical and fluorescent protein technology have rapidly raised expectations in cell biology, allowing quantitative insights into dynamic intracellular processes like never before. However, quantitative live-cell imaging comes with many challenges including how best to translate dynamic microscopy data into numerical outputs that can be used to make meaningful comparisons rather than relying on representative data sets. Here, we use analysis of focal adhesion turnover dynamics as a straightforward specific example on how to image, measure, and analyze intracellular protein dynamics, but we believe this outlines a thought process and can provide guidance on how to understand dynamic microcopy data of other intracellular structures. PMID:24974036
Stehbens, Samantha J; Wittmann, Torsten
Functionalized Magnetic Nanoparticles for the Detection and Quantitative Analysis of Cell Surface Antigen
Cell surface antigens as biomarkers offer tremendous potential for early diagnosis, prognosis, and therapeutic response in a variety of diseases such as cancers. In this research, a simple, rapid, accurate, inexpensive, and easily available in vitro assay based on magnetic nanoparticles and magnetic cell separation principle was applied to identify and quantitatively analyze the cell surface antigen expression in the case of prostate cancer cells. Comparing the capability of the assay with flow cytometry as a gold standard method showed similar results. The results showed that the antigen-specific magnetic cell separation with antibody-coated magnetic nanoparticles has high potential for quantitative cell surface antigen detection and analysis.
Shahbazi-Gahrouei, Daryoush; Abdolahi, Mohammad; Zarkesh-Esfahani, Sayyed Hamid; Laurent, Sophie; Sermeus, Corine; Gruettner, Cordula
Quantitative analysis of the mixtures of illicit drugs using terahertz time-domain spectroscopy
NASA Astrophysics Data System (ADS)
A method was proposed to quantitatively inspect the mixtures of illicit drugs with terahertz time-domain spectroscopy technique. The mass percentages of all components in a mixture can be obtained by linear regression analysis, on the assumption that all components in the mixture and their absorption features be known. For illicit drugs were scarce and expensive, firstly we used common chemicals, Benzophenone, Anthraquinone, Pyridoxine hydrochloride and L-Ascorbic acid in the experiment. Then illicit drugs and a common adulterant, methamphetamine and flour, were selected for our experiment. Experimental results were in significant agreement with actual content, which suggested that it could be an effective method for quantitative identification of illicit drugs.
Jiang, Dejun; Zhao, Shusen; Shen, Jingling
Functionalized magnetic nanoparticles for the detection and quantitative analysis of cell surface antigen.
Cell surface antigens as biomarkers offer tremendous potential for early diagnosis, prognosis, and therapeutic response in a variety of diseases such as cancers. In this research, a simple, rapid, accurate, inexpensive, and easily available in vitro assay based on magnetic nanoparticles and magnetic cell separation principle was applied to identify and quantitatively analyze the cell surface antigen expression in the case of prostate cancer cells. Comparing the capability of the assay with flow cytometry as a gold standard method showed similar results. The results showed that the antigen-specific magnetic cell separation with antibody-coated magnetic nanoparticles has high potential for quantitative cell surface antigen detection and analysis. PMID:23484112
Shahbazi-Gahrouei, Daryoush; Abdolahi, Mohammad; Zarkesh-Esfahani, Sayyed Hamid; Laurent, Sophie; Sermeus, Corine; Gruettner, Cordula
Quantitative analysis of the effectiveness of pediatric therapy. Emphasis on the neurodevelopmental treatment approach.
We investigated the effectiveness of neurodevelopmental treatment when used both in isolation and in combination with other developmental therapies. The data were analyzed using recently developed methods of quantitatively synthesizing research results in which the literature review process is regarded as a unique type of research. Our analysis revealed that the subjects who received NDT performed slightly better than the control-comparison subjects who did not receive the intervention. The study outcomes are discussed in relation to several design variables and study characteristics associated with subject performance. The advantages and limitations of quantitative reviewing are identified briefly, and the potential use of the procedures in clinical research is emphasized. PMID:2941772
Ottenbacher, K J; Biocca, Z; DeCremer, G; Gevelinger, M; Jedlovec, K B; Johnson, M B
A combined qualitative and quantitative procedure for the chemical analysis of urinary calculi
A better understanding of the physico-chemical principles underlying the formation of calculus has led to a need for more precise information on the chemical composition of stones. A combined qualitative and quantitative procedure for the chemical analysis of urinary calculi which is suitable for routine use is presented. The procedure involves five simple qualitative tests followed by the quantitative determination of calcium, magnesium, inorganic phosphate, and oxalate. These data are used to calculate the composition of the stone in terms of calcium oxalate, apatite, and magnesium ammonium phosphate. Analytical results and derived values for five representative types of calculi are presented.
Hodgkinson, A.
[Quantitative analysis of Mn, Cr in steel based on laser-induced breakdown spectroscopy].
Quantitative analysis of trace elements such as manganese and chromium in steel was performed employing laser-induced breakdown spectroscopy (LIBS) technique in the present paper. The experimental measurements indicate that the optimal delay, focal plane and detecting position from the sample surface are 2 micros, -3.5 mm and 1.5 mm,respectively. Mn I: 403.07 nm and Cr I : 427.48 nm were selected as the analytical lines and their contents in the target steel sample were analyzed with traditional quantitative analysis and internal standard methods. Comparison of the results with two kinds of quantitatively analytical methods show that the coefficients of determination gained by internal standard method are 0.998 and 0.979 which are much better than the results obtained by traditional quantitative analysis method. According to the established calibration curve by internal standard method the detection limits of manganese and chromium calculated are 0.005% and 0.040 6%, respectively. PMID:22097868
Wang, Qi; Chen, Xing-Long; Yu, Rong-Hua; Xu, Ming-Ming; Yang, Yang; Wu, Bian; Ni, Zhi-Bo; Dong, Feng-Zhong
Quantitative image analysis for the characterization of microbial aggregates in biological wastewater treatment: a review.
Quantitative image analysis techniques have gained an undeniable role in several fields of research during the last decade. In the field of biological wastewater treatment (WWT) processes, several computer applications have been developed for monitoring microbial entities, either as individual cells or in different types of aggregates. New descriptors have been defined that are more reliable, objective, and useful than the subjective and time-consuming parameters classically used to monitor biological WWT processes. Examples of this application include the objective prediction of filamentous bulking, known to be one of the most problematic phenomena occurring in activated sludge technology. It also demonstrated its usefulness in classifying protozoa and metazoa populations. In high-rate anaerobic processes, based on granular sludge, aggregation times and fragmentation phenomena could be detected during critical events, e.g., toxic and organic overloads. Currently, the major efforts and needs are in the development of quantitative image analysis techniques focusing on its application coupled with stained samples, either by classical or fluorescent-based techniques. The use of quantitative morphological parameters in process control and online applications is also being investigated. This work reviews the major advances of quantitative image analysis applied to biological WWT processes. PMID:23716077
Costa, J C; Mesquita, D P; Amaral, A L; Alves, M M; Ferreira, E C
A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis.
New methods for performing quantitative proteome analyses based on differential labeling protocols or label-free techniques are reported in the literature on an almost monthly basis. In parallel, a correspondingly vast number of software tools for the analysis of quantitative proteomics data has also been described in the literature and produced by private companies. In this article we focus on the review of some of the most popular techniques in the field and present a critical appraisal of several software packages available to process and analyze the data produced. We also describe the importance of community standards to support the wide range of software, which may assist researchers in the analysis of data using different platforms and protocols. It is intended that this review will serve bench scientists both as a useful reference and a guide to the selection and use of different pipelines to perform quantitative proteomics data analysis. We have produced a web-based tool ( http://www.proteosuite.org/?q=other_resources ) to help researchers find appropriate software for their local instrumentation, available file formats, and quantitative methodology. PMID:22804616
Gonzalez-Galarza, Faviel F; Lawless, Craig; Hubbard, Simon J; Fan, Jun; Bessant, Conrad; Hermjakob, Henning; Jones, Andrew R
[Quantitative analysis model of multi-component complex oil spill source based on near infrared spectroscopy].
Near infrared spectroscopy technology was used for quantitative analysis of the simulation of complex oil spill source. Three light petroleum products, i. e. gasoline, diesel fuel and kerosene oil, were selected and configured as simulated mixture of oil spill samples in accordance with different concentrations proportion, and their near infrared spectroscopy in the range of 8 000 -12 000 cm(-1) was collected by Fourier transform near infrared spectrometer. After processing the NIR spectra with different pretreatment methods, partial least squares method was used to establish quantitative analysis model for the mixture of oil spill samples. For gasoline, diesel fuel and kerosene oil, the second derivative method is the optimal pretreatment method, and for these three oil components in the ranges of 8 501.3-7 999.8 and 6 102.1-4 597.8 cm(-1); 6 549.5-4 597.8; 7 999.8-7 498.4 and 102.1-4 597.8 cm(-1), the correlation coefficients R2 of the prediction model are 0.998 2, 0.990 2 and 0.993 6 respectively, while the forecast RMSEP indicators are 0.474 7, 0.936 1 and 1.013 1 respectively; The experimental results show that using near infrared spectroscopy can quantitatively determine the content of each component in the simulated mixed oil spill samples, thus this method can provide effective means for the quantitative detection and analysis of complex marine oil spill source. PMID:23427535
Tan, Ai-Ling; Bi, Wei-Hong
Joint Multipoint Linkage Analysis of Multivariate Qualitative and Quantitative Traits. I. Likelihood Formulation and Simulation Results
Summary We describe a variance-components method for multipoint linkage analysis that allows joint consideration of a discrete trait and a correlated continuous biological marker (e.g., a disease precursor or associated risk factor) in pedigrees of arbitrary size and complexity. The continuous trait is assumed to be multivariate normally distributed within pedigrees, and the discrete trait is modeled by a threshold process acting on an underlying multivariate normal liability distribution. The liability is allowed to be correlated with the quantitative trait, and the liability and quantitative phenotype may each include covariate effects. Bivariate discrete-continuous observations will be common, but the method easily accommodates qualitative and quantitative phenotypes that are themselves multivariate. Formal likelihood-based tests are described for coincident linkage (i.e., linkage of the traits to distinct quantitative-trait loci [QTLs] that happen to be linked) and pleiotropy (i.e., the same QTL influences both discrete-trait status and the correlated continuous phenotype). The properties of the method are demonstrated by use of simulated data from Genetic Analysis Workshop 10. In a companion paper, the method is applied to data from the Collaborative Study on the Genetics of Alcoholism, in a bivariate linkage analysis of alcoholism diagnoses and P300 amplitude of event-related brain potentials.
Williams, Jeff T.; Van Eerdewegh, Paul; Almasy, Laura; Blangero, John
Quantitative assessment of in-solution digestion efficiency identifies optimal protocols for unbiased protein analysis.
The majority of mass spectrometry-based protein quantification studies uses peptide-centric analytical methods and thus strongly relies on efficient and unbiased protein digestion protocols for sample preparation. We present a novel objective approach to assess protein digestion efficiency using a combination of qualitative and quantitative liquid chromatography-tandem MS methods and statistical data analysis. In contrast to previous studies we employed both standard qualitative as well as data-independent quantitative workflows to systematically assess trypsin digestion efficiency and bias using mitochondrial protein fractions. We evaluated nine trypsin-based digestion protocols, based on standard in-solution or on spin filter-aided digestion, including new optimized protocols. We investigated various reagents for protein solubilization and denaturation (dodecyl sulfate, deoxycholate, urea), several trypsin digestion conditions (buffer, RapiGest, deoxycholate, urea), and two methods for removal of detergents before analysis of peptides (acid precipitation or phase separation with ethyl acetate). Our data-independent quantitative liquid chromatography-tandem MS workflow quantified over 3700 distinct peptides with 96% completeness between all protocols and replicates, with an average 40% protein sequence coverage and an average of 11 peptides identified per protein. Systematic quantitative and statistical analysis of physicochemical parameters demonstrated that deoxycholate-assisted in-solution digestion combined with phase transfer allows for efficient, unbiased generation and recovery of peptides from all protein classes, including membrane proteins. This deoxycholate-assisted protocol was also optimal for spin filter-aided digestions as compared with existing methods. PMID:23792921
Le�n, Ileana R; Schw�mmle, Veit; Jensen, Ole N; Sprenger, Richard R
Stable isotope labeling of mammals (SILAM) for in vivo quantitative proteomic analysis.
Metabolic labeling of rodent proteins with �?N, a heavy stable isotope of nitrogen, provides an efficient way for relative quantitation of differentially expressed proteins. Here we describe a protocol for metabolic labeling of rats with an �?N-enriched spirulina diet. As a case study, we also demonstrate the application of �?N-enriched tissue as a common internal standard in quantitative analysis of differentially expressed proteins in neurodevelopment in rats at two different time points, postnatal day 1 and 45. We briefly discuss the bioinformatics tools, ProLucid and Census, which can easily be used in a sequential manner to identify and quantitate relative protein levels on a proteomic scale. PMID:23523555
Rauniyar, Navin; McClatchy, Daniel B; Yates, John R
iTRAQ-based quantitative analysis of protein mixtures with large fold change and dynamic range.
Quantitation of changes in protein abundance is key to understanding the alterations that biological systems undergo and to discovering novel biomarkers. Currently, HPLC-MS/MS can be used to quantify changes in protein expression levels [Ong, S. E. and Mann, M., Nat. Chem. Biol. 2005, 1, 252-262]. Nevertheless, quantitative analysis of protein mixtures by HPLC-MS/MS is still hampered by the wide range of protein expression levels, the high dynamic range of protein concentrations and the lack of reliable quantitation algorithms [D'Ascenzo, M., et al. Brief. Funct. Genomic. Proteomic. 2008, 7, 127-135; Lin, W. T., et al., J. Proteome Res. 2006, 5, 2328-2338; Matthiesen, R., et al. J. Proteome Res. 2005, 4, 2338-2347; Yu, C. Y., et al. Nucleic Acids Res. 2007, 35, W707-W712]. In this context, we describe two different samples (4-protmix and 8-protmix) suitable for relative protein quantitation using iTRAQ. Using the 4-protmix, relative protein changes of up to 24-fold were measured. The 8-protmix allowed the quantitation of the relative protein changes in a mixture of proteins within the range of two orders of magnitude in concentration and ten-fold differences in relative abundance. We propose that the two samples are suited to test the iTRAQ quantitative proteomic workflow. We analyzed the iTRAQ samples with a LTQ Orbitrap using "higher energy collision-induced dissociation" fragmentation [Olsen, J. V., et al., Nat. Methods 2007, 4, 709-712] and quantified with Proteome Discoverer v.1.1 (Thermo Fisher Scientific). We believe that the presented protein mixtures will be useful to assess the performance of the iTRAQ-based quantitation proteomic strategy in any laboratory. PMID:20029838
Casado-Vela, Juan; Mart�nez-Esteso, Mar�a Jos�; Rodriguez, Eva; Borr�s, Eva; Elortza, Felix; Bru-Mart�nez, Roque
The Trouble With Tailings: How Alteration Mineralogy can Hinder Quantitative Phase Analysis of Mineral Waste
NASA Astrophysics Data System (ADS)
Quantitative phase analysis, using the Rietveld method and X-ray powder-diffraction data, has become a standard technique for analysis of mineral waste from mining operations. This method relies upon the availability of well defined crystal structures for all detectable mineral phases in a sample. An even more basic assumption, central to quantitative mineralogy, is that all significant mineral phases can be detected from X-ray diffraction data. This is not always the case, because X-ray amorphous and nanocrystalline mineral phases can develop within geological samples as a result of chemical weathering. The extent of mineral-water interaction to which mine tailings are exposed, during processing and storage, makes these materials particularly susceptible to weathering and alteration. We have used the Rietveld method and X-ray powder-diffraction data to quantify the uptake of atmospheric CO2 into secondary carbonate minerals at two operating mines: the Diavik Diamond Mine, Northwest Territories, Canada, and the Mount Keith Nickel Mine, Western Australia, Australia. At Diavik, nominally anhydrous minerals in kimberlitic mine tailings have been found to contain X-ray amorphous material and hydroxyl groups detectable by Raman spectroscopy. A series of weighed mixtures, prepared to simulate kimberlite mine tailings, has been used to assess the effects of X-ray amorphous material on quantitative phase analysis of Diavik tailings. At Mount Keith, hydrated sulphate minerals and halide minerals develop efflorescent crusts at the surface of the tailings storage facility. Hydrated sulphate minerals in these mine tailings commonly decompose to amorphous substances rather than dehydrating to produce minerals detectable from X-ray powder-diffraction patterns. Nanocrystalline and X-ray amorphous material in mine tailings can affect the accuracy of quantitative determinations of CO2 trapping and abundances of sulphur-bearing minerals associated with redox reactions. Here we assess the impact of amorphous material on quantitative X-ray diffraction results with particular reference to CO2 sequestration and suggest strategies for detection and analysis.
Wilson, S. A.; Mills, S. J.; Dipple, G. M.; Raudsepp, M.
Accuracy improvement of quantitative analysis in laser-induced breakdown spectroscopy using modified wavelet transform.
A modified algorithm of background removal based on wavelet transform was developed for spectrum correction in laser-induced breakdown spectroscopy (LIBS). The optimal type of wavelet function, decomposition level and scaling factor ? were determined by the root-mean-square error of calibration (RMSEC) of the univariate regression model of the analysis element, which is considered as the optimization criteria. After background removal by this modified algorithm with RMSEC, the root-mean-square error of cross-validation (RMSECV) and the average relative error (ARE) criteria, the accuracy of quantitative analysis on chromium (Cr), vanadium (V), cuprum (Cu), and manganese (Mn) in the low alloy steel was all improved significantly. The results demonstrated that the algorithm developed is an effective pretreatment method in LIBS to significantly improve the accuracy in the quantitative analysis. PMID:24921726
Zou, X H; Guo, L B; Shen, M; Li, X Y; Hao, Z Q; Zeng, Q D; Lu, Y F; Wang, Z M; Zeng, X Y
Quantitative determination of sibutramine in adulterated herbal slimming formulations by TLC-image analysis method.
A simple thin layer chromatographic (TLC)-image analysis method was developed for rapid determination and quantitation of sibutramine hydrochloride (SH) adulterated in herbal slimming products. Chromatographic separation of SH was achieved on a silica gel 60 F(254) TLC plate, using toluene-n-hexane-diethylamine (9:1:0.3, v/v/v) as the mobile phase and Dragendorff reagent as spot detection. Image analysis of the scanned TLC plate was performed to quantify the amount of SH. The polynomial regression data for the calibration plots showed good linear relationship in the concentration range of 1-6 ?g/spot. The limits of detection and quantitation were 190 and 634 ng/spot, respectively. The method gave satisfactory specificity, precision, accuracy, robustness and was applied for determination of SH in herbal formulations. The contents of SH in adulterated samples determined by the TLC-image analysis and TLC-densitometry were also compared. PMID:22227151
Phattanawasin, Panadda; Sotanaphun, Uthai; Sukwattanasinit, Tasamaporn; Akkarawaranthorn, Jariya; Kitchaiya, Sarunyaporn
Quantitative trait locus analysis of susceptibility to diet-induced atherosclerosis in recombinant inbred mice
Quantitative trait locus (QTL) analysis is a statistical method that can be applied to identify loci making a significant impact on a phenotype. For the phenotype of susceptibility to diet-induced atherosclerosis in the mouse, we have studied four quantitative traits: area of aortic fatty streaks and serum concentrations of high-density lipoprotein-bound cholesterol (HDL-cholesterol), apolipoprotein A-I, and apolipoprotein A-II (apo A-II). QTL analysis revealed a significant locus on chromosome 1 distal impacting serum apo A-II concentration on a high-fat diet and serum HDL-cholesterol concentration on a chow diet. This locus is presumably Apoa-2, the structural gene for apo A-II. QTL analysis of aortic fatty streaks failed to reveal a significant locus. 19 refs., 3 tabs.
Hyman, R.W. [Stanford Univ. School of Medicine, CA (United States); Frank, S.; Warden, C.H. [Univ. of California, Los Angeles, CA (United States)] [and others
Chemometrics applied to quantitative analysis of ternary mixtures by terahertz spectroscopy.
Chemometrics was applied to qualitative and quantitative analyses of terahertz spectra obtained in transmission mode. A series of mixtures of three pure analytes, namely, citric acid, d-(-)fructose, and ?-lactose monohydrate under various concentrations, was prepared as pressed pellets with polyethylene as binder. Then, terahertz absorbance spectra were recorded by terahertz time domain spectroscopy and analyzed. First, principal component analysis allowed one to correctly locate the samples into a ternary diagram. Second, quantitative analysis was achieved by partial least-squares (PLS) regression and artificial neural networks (ANN). The concentrations were predicted with values of relative mean square error lower than 0.9% for the three constituents. As a conclusion, chemometrics was demonstrated to be very efficient for the analysis of the ternary mixtures prepared for this study. PMID:24738647
El Haddad, Josette; de Miollis, Frederick; Bou Sleiman, Joyce; Canioni, Lionel; Mounaix, Patrick; Bousquet, Bruno
Quantitative analysis of orofacial development and median clefts in Xenopus laevis.
Xenopus has become a useful tool to study the molecular mechanisms underlying orofacial development. However, few quantitative analyses exist to describe the anatomy of this region. In this study we combine traditional facial measurements with geometric morphometrics to describe anatomical changes in the orofacial region during normal and abnormal development. Facial measurements and principal component (PC) analysis indicate that during early tadpole development the face expands primarily in the midface region accounting for the development of the upper jaw and primary palate. The mouth opening correspondingly becomes flatter and wider as it incorporates the jaw elements. A canonical variate analysis of orofacial and mouth opening shape emphasized that changes in the orofacial shape occur gradually. Orofacial anatomy was quantified after altered levels of retinoic acid using all-trans retinoic acid or an inhibitor of retinoic acid receptors or by injecting antisense oligos targeting RALDH2. Such perturbations resulted in major decreases in the width of the midface and the mouth opening illustrated in facial measurements and a PC analysis. The mouth opening shape also had a gap in the primary palate resulting in a median cleft in the mouth opening that was only illustrated quantitatively in the morphometric analysis. Finally, canonical and discriminant function analysis statistically distinguished the orofacial and mouth opening shape changes among the different modes used to alter retinoic acid signaling levels. By combining quantitative analyses with molecular studies of orofacial development we will be better equipped to understand the complex morphogenetic processes involved in palate development and clefting. PMID:24443252
Kennedy, Allyson E; Dickinson, Amanda J
Summary of Terra and Aqua MODIS Long-Term Performance
NASA Technical Reports Server (NTRS)
Since launch in December 1999, the MODIS ProtoFlight Model (PFM) onboard the Terra spacecraft has successfully operated for more than 11 years. Its Flight Model (FM) onboard the Aqua spacecraft, launched in May 2002, has also successfully operated for over 9 years. MODIS observations are made in 36 spectral bands at three nadir spatial resolutions and are calibrated and characterized regularly by a set of on-board calibrators (OBC). Nearly 40 science products, supporting a variety of land, ocean, and atmospheric applications, are continuously derived from the calibrated reflectances and radiances of each MODIS instrument and widely distributed to the world-wide user community. Following an overview of MODIS instrument operation and calibration activities, this paper provides a summary of both Terra and Aqua MODIS long-term performance. Special considerations that are critical to maintaining MODIS data quality and beneficial for future missions are also discussed.
Xiong, Xiaoxiong (Jack); Wenny, Brian N.; Angal, Amit; Barnes, William; Salomonson, Vincent
Example MODIS Global Cloud Optical and Microphysical Properties: Comparisons between Terra and Aqua
NASA Technical Reports Server (NTRS)
MODIS observations from the NASA EOS Terra spacecraft (launched in December 1999, 1030 local time equatorial crossing) have provided a unique data set of Earth observations. With the launch of the NASA Aqua spacecraft in May 2002 (1330 local time), two MODIS daytime (sunlit) and nighttime observations are now available in a 24 hour period, allowing for some measure of diurnal variability. We report on an initial analysis of several operational global (Level-3) cloud products from the two platforms. The MODIS atmosphere Level-3 products, which include clear-sky and aerosol products in addition to cloud products, are available as three separate files providing daily, eight-day, and monthly aggregations; each temporal aggregation is spatially aggregated to a 1 degree grid. The files contain approximately 600 statisitical datasets (from simple means and standard deviations to 1 - and 2-dimensional histograms). Operational cloud products include detection (cloud fraction), cloud-top properties, and daytimeonly cloud optical thickness and particle effective radius for both water and ice clouds. We will compare example global Terra and Aqua cloud fraction, optical thickness, and effective radius aggregations.
Hubanks, P. A.; Platnick, S.; King, M. D.; Ackerman, S. A.; Frey, R. A.
Simulations of tropical sub-seasonal variability in the idealized aqua-planet AGCMs
NASA Astrophysics Data System (ADS)
The characteristics of the simulated tropical sub-seasonal variability (15-90days) in four atmospheric general circulation models (AGCMs) were compared in a simplified aqua-planet framework. The investigated models are the NASA/NSIPP, GFDL/AM2, SNU/SNUGCM and NASA/GEOS5 AGCMs. The experiment uses the same configuration as the Aqua-Planet Experiment (APE) proposed by Neale and Hoskins (2001), but with a simple mixed layer ocean of finite heat capacity at the lower boundary, which enables air-sea interaction processes. Although, as in the observation, the dominant tropical rainfall variability simulated by all the models consists of low-frequency eastward propagation signals, their amplitudes and speeds are quite different among the models. Two AGCMs (NSIPP and SNU) are characterized by small amplitude of sub-seasonal variances with fast propagation of convectively coupled equatorial waves, whereas the other two AGCMs (AM2 and GEOS5) are characterized by large amplitude of variances and much slower propagation of equatorial waves. Subsequent analysis and sensitivity experiments suggested that these differences are largely explained by the "Tokioka" modification in their Relaxed Arakawa-Schubert (RAS) convection scheme used in the latter models, which tends to suppress the parameterized convection and enhances the rainfall variability from grid- scale condensation process. The vertical distribution of diabatic heating, clouds, and surface fluxes are further analyzed to examine the structure of propagating waves and the role of air-sea interaction and of cloud- radiation feedback.
Lee, M.; Kim, D.; Suarez, M. J.; Kang, I.; Held, I. M.
Inter-Comparison of Terra and Aqua MODIS
NASA Technical Reports Server (NTRS)
Nearly identical copies of the Moderate Resolution Imaging Spectroradiometer (MODIS) have been operating on-board the NASA's Earth Observing System (EOS) Terra and Aqua satellites since their launches in December 1999 and May 2002, respectively. Each MODIS has 20 reflective solar bands (RSB) with center wavelengths ranging from 0.41 to 2.1 micrometers and 16 thermal emissive bands (TEB) from 3.7 to 14.4 micrometers. The absolute radiometric accuracy requirements (1 sigma) at the typical spectral radiance levels are plus or minus 2% for the RSB for the RSB reflectance factors and plus or minus 5% for the RSB radiance products. With few exceptions, the TEB requirements are plus or minus 1%. The sensor's on-orbit radiometric calibration is performed by the on-board calibrators, including a solar diffuser (SD) and a solar diffuser stability monitor (SDSM) system for the RSB and a V-groove flat panel blackbody (BB) for the TEB. In addition, the Moon has been extensively used by both Terra and Aqua MODIS to support their on-orbit calibration and characterization. This paper presents MODIS lunar calibration methodology and inter-comparison of Terra and Aqua MODIS in the VIS/NIR spectral regions. Current results from lunar observations show that the calibration difference between the two sensors is less than plus or minus 1%. Also discussed in this paper are the approaches and results of inter-comparison of Terra and Aqua MODIS in the TEB using closely matched thermal infrared (TIR) channels on the Advanced Very High Resolution Radiometer (AVHRR) at 11 and 12 micrometers.
Xiong, X.; Salomonson, V. V.; Sun, J.; Wu, A.; Barnes, W.; Guenther, B.
The First Day In The Life of Aqua-MODIS
NSDL National Science Digital Library
In its first day of operations, June 24, 2002, Aqua-MODIS observed significant Earth events occurring all over the globe. As Super Typhoon Chataan was rapidly approaching Japan, there was severe flooding in southeast Texas and a vast, thick pall of smoke from Canadian wildfires blanketed almost the entire U.S. East Coast. MODIS collected and beamed to Earth these images in very near real-time.
Rhodes, Greg; Herring, David
Quantitative approaches to utilizing mutational analysis and disulfide crosslinking for modeling a transmembrane domain.
The transmembrane domain of chemoreceptor Trg from Escherichia coli contains four transmembrane segments in its native homodimer, two from each subunit. We had previously used mutational analysis and sulfhydryl cross-linking between introduced cysteines to obtain data relevant to the three-dimensional organization of this domain. In the current study we used Fourier analysis to assess these data quantitatively for periodicity along the sequences of the segments. The analyses provided a strong indication of alpha-helical periodicity in the first transmembrane segment and a substantial indication of that periodicity for the second segment. On this basis, we considered both segments as idealized alpha-helices and proceeded to model the transmembrane domain as a unit of four helices. For this modeling, we calculated helical crosslinking moments, parameters analogous to helical hydrophobic moments, as a quantitative way of condensing and utilizing a large body of crosslinking data. Crosslinking moments were used to define the relative separation and orientation of helical pairs, thus creating a quantitatively derived model for the transmembrane domain of Trg. Utilization of Fourier transforms to provide a quantitative indication of periodicity in data from analyses of transmembrane segments, in combination with helical crosslinking moments to position helical pairs should be useful in modeling other transmembrane domains.
Lee, G. F.; Hazelbauer, G. L.
Multidimensional analysis system for quantitative chemistry problems: Symbol, macro, micro, and process aspects
NASA Astrophysics Data System (ADS)
There is a consensus regarding the fact that students encounter difficulties in understanding scientific concepts, such as the particulate nature of matter, the mole, and the interpretation of chemical symbols. Researchers and practitioners have been looking for teaching methods to improve students' understanding of quantitative chemistry and their ability to solve related problems. This study describes the Multidimensional Analysis System (MAS), an approach to constructing, classifying, and analyzing quantitative chemistry problems. MAS enables classification based on complexity and transformation levels of a quantitative problem. We define three transformation levels: symbol macro, symbol micro, and symbol process. Applying this framework to teaching and research, we investigated the relationships between MAS-classified chemistry problems and student achievement in solving these problems. The research population, 241 high school chemistry students, studied problem solving according to MAS for 9 weeks; the control group studied the same topic for the same duration in the traditional way. Student achievement was sorted by mathematics level and gender. We found that the success rate of the entire student population in solving these problems decreased as the problem difficulty increased. Experimental group students scored significantly higher than their control group peers. The improvement in student achievement was significantly dependent on the pretest score and the mathematics level, and independent of gender. Students who studied mathematics in the basic level benefited significantly more from MAS-based teaching than their peers, whose mathematics level was advanced. Based on the research findings, we recommend applying the multidimensional analysis approach while teaching quantitative problems in chemistry.
Dori, Yehudit J.; Hameiri, Mira
Quantitative proteomics analysis of adsorbed plasma proteins classifies nanoparticles with different surface properties and size
Nanoparticle biological activity, biocompatibility and fate can be directly affected by layers of readily adsorbed host proteins in biofluids. Here, we report a study on the interactions between human blood plasma proteins and nanoparticles with a controlled systematic variation of properties using 18O-labeling and LC-MS-based quantitative proteomics. We developed a novel protocol to both simplify isolation of nanoparticle bound proteins and improve reproducibility. LC-MS analysis identified and quantified 88 human plasma proteins associated with polystyrene nanoparticles consisting of three different surface chemistries and two sizes, as well as, for four different exposure times (for a total of 24 different samples). Quantitative comparison of relative protein abundances was achieved by spiking an 18O-labeled �universal� reference into each individually processed unlabeled sample as an internal standard, enabling simultaneous application of both label-free and isotopic labeling quantification across the entire sample set. Clustering analysis of the quantitative proteomics data resulted in distinctive patterns that classified the nanoparticles based on their surface properties and size. In addition, temporal data indicated that the formation of the stable protein corona was at equilibrium within 5 min. The comprehensive quantitative proteomics results obtained in this study provide rich data for computational modeling and have potential implications towards predicting nanoparticle biocompatibility.
Zhang, Haizhen; Burnum, Kristin E.; Luna, Maria L.; Petritis, Brianne O.; Kim, Jong-Seo; Qian, Wei-Jun; Moore, Ronald J.; Heredia-Langner, Alejandro; Webb-Robertson, Bobbie-Jo M.; Thrall, Brian D.; Camp, David G.; Smith, Richard D.; Pounds, Joel G.; Liu, Tao
Quantitative proteomics analysis of adsorbed plasma proteins classifies nanoparticles with different surface properties and size.
Nanoparticle biological activity, biocompatibility and fate can be directly affected by layers of readily adsorbed host proteins in biofluids. Here, we report a study on the interactions between human blood plasma proteins and nanoparticles with a controlled systematic variation of properties using (18)O-labeling and LC-MS-based quantitative proteomics. We developed a novel protocol to both simplify isolation of nanoparticle bound proteins and improve reproducibility. LC-MS analysis identified and quantified 88 human plasma proteins associated with polystyrene nanoparticles consisting of three different surface chemistries and two sizes, as well as, for four different exposure times (for a total of 24 different samples). Quantitative comparison of relative protein abundances was achieved by spiking an (18)O-labeled "universal" reference into each individually processed unlabeled sample as an internal standard, enabling simultaneous application of both label-free and isotopic labeling quantification across the entire sample set. Clustering analysis of the quantitative proteomics data resulted in distinctive patterns that classified the nanoparticles based on their surface properties and size. In addition, temporal data indicated that the formation of the stable protein corona was at equilibrium within 5 min. The comprehensive quantitative proteomics results obtained in this study provide rich data for computational modeling and have potential implications towards predicting nanoparticle biocompatibility. PMID:21956884
Zhang, Haizhen; Burnum, Kristin E; Luna, Maria L; Petritis, Brianne O; Kim, Jong-Seo; Qian, Wei-Jun; Moore, Ronald J; Heredia-Langner, Alejandro; Webb-Robertson, Bobbie-Jo M; Thrall, Brian D; Camp, David G; Smith, Richard D; Pounds, Joel G; Liu, Tao
Quantitative analysis of biological tissues using Fourier transform-second-harmonic generation imaging
NASA Astrophysics Data System (ADS)
We demonstrate the use of Fourier transform-second-harmonic generation (FT-SHG) imaging of collagen fibers as a means of performing quantitative analysis of obtained images of selected spatial regions in porcine trachea, ear, and cornea. Two quantitative markers, preferred orientation and maximum spatial frequency are proposed for differentiating structural information between various spatial regions of interest in the specimens. The ear shows consistent maximum spatial frequency and orientation as also observed in its real-space image. However, there are observable changes in the orientation and minimum feature size of fibers in the trachea indicating a more random organization. Finally, the analysis is applied to a 3D image stack of the cornea. It is shown that the standard deviation of the orientation is sensitive to the randomness in fiber orientation. Regions with variations in the maximum spatial frequency, but with relatively constant orientation, suggest that maximum spatial frequency is useful as an independent quantitative marker. We emphasize that FT-SHG is a simple, yet powerful, tool for extracting information from images that is not obvious in real space. This technique can be used as a quantitative biomarker to assess the structure of collagen fibers that may change due to damage from disease or physical injury.
Ambekar Ramachandra Rao, Raghu; Mehta, Monal R.; Toussaint, Kimani C., Jr.
Quantitative Surface Atomic Structure Analysis by Low-Energy Ion Scattering Spectroscopy (ISS)
NASA Astrophysics Data System (ADS)
Surface atomic structure analysis by low-energy ion scattering spectroscopy (ISS) is reviewed, with particular emphasis on quantitative surface atomic structure analysis by ISS. The important differences between ISS and Rutherford backscattering spectroscopy (RBS), some basic characteristics of ISS, a special type of ISS called impact-collision ion scattering spectroscopy (ICISS), and the general features of the shadow cone in the energy range of ISS are discussed as a basis for the description of particular examples of ISS studies which follow. The examples are mainly concerned with the analysis of the atomic arrangement, defect structure, thermal vibration, and electron spatial distribution of the (001) and (111) surfaces of TiC.
Aono, Masakazu; Souda, Ryutaro
Status of Aqua MODIS spatial characterization and performance
NASA Astrophysics Data System (ADS)
NASA's EOS Aqua spacecraft was launched on May 04, 2002. The Moderate Resolution Imaging Spectroradiometer (MODIS) is one of the six Earth-observing sensors aboard the EOS Aqua spacecraft. MODIS is the highest spatial resolution instrument on the Aqua platform with data products generated in 250m, 500m, and 1000m resolutions (nadir). It has 36 spectral bands, a total of 490 detectors, located on four focal plane assemblies (FPAs) with two of them controlled during operation at 83K by a passive radiative cooler. In addition to radiometric calibration and spectral characterization, MODIS spatial performance was extensively characterized pre-launch, including measurements of band-to-band registration (BBR), FPA to FPA registration (FFR), line spread function (LSF), modulation transfer function (MTF), and instantaneous field-of-view (IFOV). The sensor's spatial characterization is monitored by an on-board calibrator, the spectro-radiometric calibration assembly (SRCA). In this paper, we will briefly describe MODIS SRCA spatial characterization methodologies and operational activities. We will focus on the sensor's spatial performance using four years of on-orbit observations and, consequently, evaluate the SRCA's performance. On-orbit results of key spatial characterization parameters (BBR, FFR, and MTF) will be examined and compared to pre-launch measurements and design requirements.
Xiong, Xiaoxiong; Che, Nianzeng; Barnes, William; Xie, Yong; Wang, Lingli; Qu, John
Status of Terra and Aqua MODIS Instrument Operation and Calibration
NASA Astrophysics Data System (ADS)
Terra and Aqua MODIS have successfully operated for more than 13 and 11 years since their respective launches in 1999 and 2002. Nearly 40 data products, developed for studies of the earth's land, ocean, and atmosphere, have been routinely generated from calibrated and geo-located MODIS observations and widely distributed to the science and user community. MODIS on-orbit calibration is performed by a set of on-board calibrators, which include a solar diffuser for the reflective solar bands calibration and a blackbody for the thermal emissive bands calibration. MODIS on-board calibrators are regularly operated to monitor on-orbit changes in sensor responses and key performance parameters, such as radiometric calibration coefficients. Since launch, extensive instrument calibration and characterization activities have been scheduled and executed by the MODIS Characterization Support Team (MCST). This presentation provides an overview of both Terra and Aqua MODIS instrument status, their on-orbit operation and calibration activities, and overall long-term performance. It reports calibration improvements (algorithms and look-up tables) made in the latest MODIS data collection (C6). Lessons learned from both Terra and Aqua MODIS and their applications to the S-NPP VIIRS on-orbit calibration are also discussed.
Xiong, X.; Wenny, B. N.; Sun, J.; Angal, A.; Salomonson, V. V.
Models and methods for quantitative analysis of surface-enhanced Raman spectra.
The quantitative analysis of surface-enhanced Raman spectra using scattering nanoparticles has shown the potential and promising applications in in vivo molecular imaging. The diverse approaches have been used for quantitative analysis of Raman pectra information, which can be categorized as direct classical least squares models, full spectrum multivariate calibration models, selected multivariate calibration models, and latent variable regression (LVR) models. However, the working principle of these methods in the Raman spectra application remains poorly understood and a clear picture of the overall performance of each model is missing. Based on the characteristics of the Raman spectra, in this paper, we first provide the theoretical foundation of the aforementioned commonly used models and show why the LVR models are more suitable for quantitative analysis of the Raman spectra. Then, we demonstrate the fundamental connections and differences between different LVR methods, such as principal component regression, reduced-rank regression, partial least square regression (PLSR), canonical correlation regression, and robust canonical analysis, by comparing their objective functions and constraints.We further prove that PLSR is literally a blend of multivariate calibration and feature extraction model that relates concentrations of nanotags to spectrum intensity. These features (a.k.a. latent variables) satisfy two purposes: the best representation of the predictor matrix and correlation with the response matrix. These illustrations give a new understanding of the traditional PLSR and explain why PLSR exceeds other methods in quantitative analysis of the Raman spectra problem. In the end, all the methods are tested on the Raman spectra datasets with different evaluation criteria to evaluate their performance. PMID:24058035
Li, Shuo; Nyagilo, James O; Dave, Digant P; Gao, Jean
Quantitative proteomic analysis of post-translational modifications of human histones.
Histone proteins are subject to a range of post-transcriptional modifications in living cells. The combinatorial nature of these modifications constitutes the "histone code" that dictates chromatin structure and function during development, growth, differentiation, and homeostasis of cells. Deciphering of the histone code is hampered by the lack of analytical methods for monitoring the combinatorial complexity of reversible multisite modifications of histones, including acetylation and methylation. To address this problem, we used LC-MSMS technology and Virtual Expert Mass Spectrometrist software for qualitative and quantitative proteomic analysis of histones extracted from human small cell lung cancer cells. A total of 32 acetylations, methylations, and ubiquitinations were located in the human histones H2A, H2B, H3, and H4, including seven novel modifications. An LC-MSMS-based method was applied in a quantitative proteomic study of the dose-response effect of the histone deacetylase inhibitor (HDACi) PXD101 on histone acetylation in human cell cultures. Triplicate LC-MSMS runs at six different HDACi concentrations demonstrated that PXD101 affects acetylation of histones H2A, H2B, H3, and H4 in a site-specific and dose-dependent manner. This unbiased analysis revealed that a relative increase in acetylated peptide from the histone variants H2A, H2B, and H4 was accompanied by a relative decrease of dimethylated Lys(57) from histone H2B. The dose-response results obtained by quantitative proteomics of histones from HDACi-treated cells were consistent with Western blot analysis of histone acetylation, cytotoxicity, and dose-dependent expression profiles of p21 and cyclin A2. This demonstrates that mass spectrometry-based quantitative proteomic analysis of post-translational modifications is a viable approach for functional analysis of candidate drugs, such as HDAC inhibitors. PMID:16627869
Beck, Hans Christian; Nielsen, Eva C; Matthiesen, Rune; Jensen, Lars H; Sehested, Maxwell; Finn, Paul; Grauslund, Morten; Hansen, Anne Maria; Jensen, Ole N�rregaard
Direct quantitative analysis of nicotine alkaloids from biofluid samples using paper spray mass spectrometry.
The determination of tobacco derived nicotine alkaloids in biofluid samples is of great importance to testing for tobacco use, tobacco cessation treatment, and studies on exposure to secondhand smoke. Paper spray mass spectrometry (MS) has been adapted for direct, quantitative analysis of tobacco alkaloids from biofluid samples, such as blood, urine, and saliva in liquid and dried form. Limits of quantitation as low as several nanograms per milliliter were obtained for nicotine, cotinine, trans-3'-hydroxycotinine, and anabasine. Direct analysis of fresh blood samples has also been achieved with improved sensitivity using print paper substrates of high density. Quantitation of the cotinine in the blood of a rat was performed with both direct analysis using paper spray and a traditional analysis protocol using liquid chromatography MS. Comparable results were obtained and the precision of the two methods was similar. The paper spray MS method is rapid and shows potential for significantly improved analytical efficiency in clinical laboratories as well as for point-of-care tobacco use assessment. PMID:24195719
Wang, He; Ren, Yue; McLuckey, Morgan N; Manicke, Nicholas E; Park, Jonghyuck; Zheng, Lingxing; Shi, Riyi; Cooks, R Graham; Ouyang, Zheng
Optimisation of Lime-Soda process parameters for reduction of hardness in aqua-hatchery practices using Taguchi methods.
This paper presents the optimisation of Lime-Soda process parameters for the reduction of hardness in aqua-hatchery practices in the context of M. rosenbergii. The fresh water in the development of fisheries needs to be of suitable quality. Lack of desirable quality in available fresh water is generally the confronting restraint. On the Indian subcontinent, groundwater is the only source of raw water, having varying degree of hardness and thus is unsuitable for the fresh water prawn hatchery practices (M. rosenbergii). In order to make use of hard water in the context of aqua-hatchery, Lime-Soda process has been recommended. The efficacy of the various process parameters like lime, soda ash and detention time, on the reduction of hardness needs to be examined. This paper proposes to determine the parameter settings for the CIFE well water, which is pretty hard by using Taguchi experimental design method. Orthogonal Arrays of Taguchi, Signal-to-Noise Ratio, the analysis of variance (ANOVA) have been applied to determine their dosage and analysed for their effect on hardness reduction. The tests carried out with optimal levels of Lime-Soda process parameters confirmed the efficacy of the Taguchi optimisation method. Emphasis has been placed on optimisation of chemical doses required to reduce the total hardness using Taguchi method and ANOVA, to suit the available raw water quality for aqua-hatchery practices, especially for fresh water prawn M. rosenbergii. PMID:24749379
Yavalkar, S P; Bhole, A G; Babu, P V Vijay; Prakash, Chandra
Surgical Results of Patients with Peritoneal Carcinomatosis Treated with Cytoreductive Surgery Using a New Technique Named Aqua Dissection
During 2004 to 2011, 81, 420, and 166 patients with colorectal cancer (CRC), epithelial appendiceal neoplasm (APN), and gastric cancer (GC) with PC were treated with cytoreductive surgery (CRS) plus perioperative chemotherapy. CRS was performed by peritonectomy techniques using an aqua dissection. Results. Complete cytoreduction was done in 62/81 (76.5%), 228/420 (54.3%), and 101/166 (60.8%) of patients with CRC, APN, and GC. The main reasons of incomplete resections were involvement of all peritoneal regions and diffuse involvement of small bowel. The incidence (64%, 302/470) of CC-0 resection after introduction of an aqua dissection was significantly higher than before (42%, 82/197). A total of 41 (6.1%) patients died postoperatively. Major complication (grade 3-4 complications) occurred in 126 patients (18.9%). A reoperation was necessary in 36 patients (5.4%). By the multivariate analysis, PCI scores capable of serving as thresholds for favorable versus poor prognosis in each group and CC scores demonstrated as the independent prognostic factors. Conclusions. Peritonectomy using an aqua dissection improves the incidence of complete cytoreduction, and improves the survival of patients with PC. Patients with PCI larger than the threshold values should be treated with chemotherapy to improve the incidences of complete cytoreduction.
Yonemura, Y.; Elnemr, A.; Endou, Y.; Ishibashi, H.; Mizumoto, A.; Miura, M.; Li, Yan
Quantitative trait analysis in sequencing studies under trait-dependent sampling
It is not economically feasible to sequence all study subjects in a large cohort. A cost-effective strategy is to sequence only the subjects with the extreme values of a quantitative trait. In the National Heart, Lung, and Blood Institute Exome Sequencing Project, subjects with the highest or lowest values of body mass index, LDL, or blood pressure were selected for whole-exome sequencing. Failure to account for such trait-dependent sampling can cause severe inflation of type I error and substantial loss of power in quantitative trait analysis, especially when combining results from multiple studies with different selection criteria. We present valid and efficient statistical methods for association analysis of sequencing data under trait-dependent sampling. We pay special attention to gene-based analysis of rare variants. Our methods can be used to perform quantitative trait analysis not only for the trait that is used to select subjects for sequencing but for any other traits that are measured. For a particular trait of interest, our approach properly combines the association results from all studies with measurements of that trait. This meta-analysis is substantially more powerful than the analysis of any single study. By contrast, meta-analysis of standard linear regression results (ignoring trait-dependent sampling) can be less powerful than the analysis of a single study. The advantages of the proposed methods are demonstrated through simulation studies and the National Heart, Lung, and Blood Institute Exome Sequencing Project data. The methods are applicable to other types of genetic association studies and nongenetic studies.
Lin, Dan-Yu; Zeng, Donglin; Tang, Zheng-Zheng
Genetic basis for systems of skeletal quantitative traits: principal component analysis of the canid skeleton.
Evolution of mammalian skeletal structure can be rapid and the changes profound, as illustrated by the morphological diversity of the domestic dog. Here we use principal component analysis of skeletal variation in a population of Portuguese Water Dogs to reveal systems of traits defining skeletal structures. This analysis classifies phenotypic variation into independent components that can be used to dissect genetic networks regulating complex biological systems. We show that unlinked quantitative trait loci associated with these principal components individually promote both correlations within structures (e.g., within the skull or among the limb bones) and inverse correlations between structures (e.g., skull vs. limb bones). These quantitative trait loci are consistent with regulatory genes that inhibit growth of some bones while enhancing growth of others. These systems of traits could explain the skeletal differences between divergent breeds such as Greyhounds and Pit Bulls, and even some of the skeletal transformations that characterize the evolution of hominids. PMID:12114542
Chase, Kevin; Carrier, David R; Adler, Frederick R; Jarvik, Tyler; Ostrander, Elaine A; Lorentzen, Travis D; Lark, Karl G
New approach for quantitative analysis of myocardial perfusion with magnetic resonance first-pass bolus imaging
NASA Astrophysics Data System (ADS)
Myocardial perfusion reserve can be noninvasively assessed with cardiovascular magnetic resonance. With magnetic resonance (MR) multislice dynamic imaging techniques it is possible to acquire the complete heart during the first pass of a contrast agent bolus. For diagnostic reasons an important question is to obtain quantitative parameters of the perfusion of the myocardium. We developed a model for the analysis of the contrast agent bolus pass in the myocardium and established a process for the complete task, which will support a routine clinical use delivering these quantitative parameters in a reproducible way. To evaluate the analysis in a collective of patients with single vessel disease and without significant coronary artery disease the signal intensity curves of the first pass of a gadolinium-DTPA bolus injected via a central vein were estimated before and after dipyridamole infusion.
Oswald, Helmut; Schnackenburg, Bernd; Bornstedt, Axel; Gross, Michael; Al-Saadi, Nidal; Nagel, Eicke; Fleck, Eckart
Quantitative Analysis for Monitoring Formulation of Lubricating Oil Using Terahertz Time-Domain Transmission Spectroscopy
NASA Astrophysics Data System (ADS)
The quantitative analysis of zinc isopropyl-isooctyl-dithiophosphate (T204) mixed with lube base oil from Korea with viscosity index 70 (T204-Korea70) is presented by using terahertz time-domain spectroscopy (THz-TDS). Compared with the middle-infrared spectra of zinc n-butyl-isooctyl-dithiophosphate (T202) and T204, THz spectra of T202 and T204 show the weak broad absorption bands. Then, the absorption coefficients of the T204-Korea70 system follow Beer's law at the concentration from 0.124 to 4.024%. The experimental absorption spectra of T204-Korea70 agree with the calculated ones based on the standard absorption coefficients of T204 and Korea70. The quantitative analysis enables a strategy to monitor the formulation of lubricating oil in real time.
Tian, Lu; Zhao, Kun; Zhou, Qing-Li; Shi, Yu-Lei; Zhang, Cun-Lin
Measurement of DNA copy number at microsatellite loci using quantitative PCR analysis.
This report describes the development and validation of quantitative microsatellite analysis (QuMA) for rapid measurement of relative DNA sequence copy number. In QuMA, the copy number of a test locus relative to a pooled reference is assessed using quantitative, real-time PCR amplification of loci carrying simple sequence repeats. Use of simple sequence repeats is advantageous because of the large numbers that are mapped precisely. In addition, all markers are informative because QuMA does not require that they be polymorphic. The utility of QuMA is demonstrated in assessment of the extent of deletions of chromosome 2 in leukemias arising in radiation-sensitive inbred SJL mice and in analysis of the association of increased copy number of the putative oncogene ZNF217 with reduced survival duration in ovarian cancer patients. PMID:11034080
Ginzinger, D G; Godfrey, T E; Nigro, J; Moore, D H; Suzuki, S; Pallavicini, M G; Gray, J W; Jensen, R H
Quantitative analysis on the urban flood mitigation effect by the extensive green roof system.
Extensive green-roof systems are expected to have a synergetic effect in mitigating urban runoff, decreasing temperature and supplying water to a building. Mitigation of runoff through rainwater retention requires the effective design of a green-roof catchment. This study identified how to improve building runoff mitigation through quantitative analysis of an extensive green-roof system. Quantitative analysis of green-roof runoff characteristics indicated that the extensive green roof has a high water-retaining capacity response to rainfall of less than 20 mm/h. As the rainfall intensity increased, the water-retaining capacity decreased. The catchment efficiency of an extensive green roof ranged from 0.44 to 0.52, indicating reduced runoff comparing with efficiency of 0.9 for a concrete roof. Therefore, extensive green roofs are an effective storm water best-management practice and the proposed parameters can be applied to an algorithm for rainwater-harvesting tank design. PMID:23892044
Lee, J Y; Moon, H J; Kim, T I; Kim, H W; Han, M Y
Quantitative analysis of terahertz spectra for illicit drugs using adaptive-range micro-genetic algorithm
NASA Astrophysics Data System (ADS)
In the field of anti-illicit drug applications, many suspicious mixture samples might consist of various drug components--for example, a mixture of methamphetamine, heroin, and amoxicillin--which makes spectral identification very difficult. A terahertz spectroscopic quantitative analysis method using an adaptive range micro-genetic algorithm with a variable internal population (ARVIP??GA) has been proposed. Five mixture cases are discussed using ARVIP eh?GA driven quantitative terahertz spectroscopic analysis in this paper. The devised simulation results show agreement with the previous experimental results, which suggested that the proposed technique has potential applications for terahertz spectral identifications of drug mixture components. The results show agreement with the results obtained using other experimental and numerical techniques.
Chen, Yi; Ma, Yong; Lu, Zheng; Peng, Bei; Chen, Qin