Fast fitting to low resolution density maps: elucidating large-scale motions of the ribosome.
Determining the conformational rearrangements of large macromolecules is challenging experimentally and computationally. Case in point is the ribosome; it has been observed by high-resolution crystallography in several states, but many others are known only from low-resolution methods including cryo-electron microscopy. Combining these data into dynamical trajectories that may aid understanding of its largest-scale conformational changes has so far remained out of reach of computational methods. Most existing methods either model all atoms explicitly, resulting in often prohibitive cost, or use approximations that lose interesting structural and dynamical detail. In this work, I introduce Internal Coordinate Flexible Fitting, which uses full atomic forces and flexibility in limited regions of a model, capturing extensive conformational rearrangements at low cost. I use it to turn multiple low-resolution density maps, crystallographic structures and biochemical information into unified all-atoms trajectories of ribosomal translocation. Internal Coordinate Flexible Fitting is three orders of magnitude faster than the most comparable existing method.


Responses of retinal rods to single photons.
1. A suction electrode was used to record the membrane current of single rod outer segments in pieces of toad retina. During dim illumination the membrane current showed pronounced fluctuations. 2. Amplitude histograms of responses to dim flashes of fixed intensity exhibited two discrete peaks, one at 0 pA and one near 1 pA, suggesting that the response was quantized. By setting a criterion amplitude level, flash responses could be classed as 'failures' (no response) or as 'successes' (at least one quantal event). 3. The variation of fraction of successes with flash intensity was consistent with the hypothesis that each quantal electrical event resulted from a single photoisomerization. 4. The quantal event had a mean amplitude of about 1 pA (5% of the standing dark current) and a standard deviation of 0.2 pA. Dispersion in the event amplitude prevented identification of histogram peaks corresponding to two or more photoisomerizations. 5. Individual quantal responses exhibited a smooth shape very similar to that of the average quantal response. This suggests that a single photoisomerization releases many particles of transmitter and that radial diffusion of internal transmitter is not a major source of delay in the light response. 6. The 'quantum efficiency' with which an absorbed photon generated an electrical event was measured as 0.5 +/- 0.1 (S.E. of mean, n = 4). This is slightly lower than the quantum efficiency of photoisomerization obtained previously for rhodopsin in solution. 7. At wavelengths between 420 and 700 nm the quantal event was invariant in size, although the cell's sensitivity varied over a range of 10(5). 8. The power spectrum of the fluctuations in dim steady light was predicted by assuming that a random series of quantal events occurred independently. 9. In brighter light the fluctuations were faster, and the response to an incremental flash was reduced in size and duration. The power spectrum could be predicted by assuming random superposition of events with the shape of the incremental flash response.


Broadband converging plasmon resonance at a conical nanotip.
We propose an analytical theory which predicts that Converging Plasmon Resonance (CPR) at conical nanotips exhibits a red-shifted and continuous band of resonant frequencies and suggests potential application of conical nanotips in various fields, such as plasmonic solar cells, photothermal therapy, tip-enhanced Raman and other spectroscopies. The CPR modes exhibit superior confinement and ten times broader scattering bandwidth over the entire solar spectrum than smooth nano-structures. The theory also explicitly connects the optimal angles and resonant optical frequencies to the material permittivities, with a specific optimum half angle that depends only on the real permittivity for high-permittivity and low-loss materials.


Stratified cancer screening: the practicalities of implementation.
Improving understanding of the genetic basis of disease susceptibility enables us to estimate individuals' risk of developing cancer and offer them disease prevention, including screening, stratified to reflect that risk. Little attention has so far been given to the implementation of stratified screening. This article reviews the issues that would arise in delivering such tailored approaches to prevention in practice. Issues analysed include the organisational context within which implementation of stratified prevention would occur, how the offer of screening would be made, making sure consent is adequately informed, how individuals' risk would be assessed, the age at which risk estimation should occur, and the potential use of genetic data for other purposes. The review also considers how management might differ depending on individuals' risk, how their results would be communicated and their follow-up arranged, and the different issues raised by modification of an existing screening programme, such as that for breast cancer, and the establishment of a new one, for example for prostate cancer. Stratified screening based on genetic testing is a radically new approach to prevention. Various organisational issues would need to be considered before it could be introduced, and a number of questions require further research.


FOXO genes in channel catfish and their response after bacterial infection.
FOXO proteins are a subgroup of the forkhead family of transcription factors that play crucial roles in lifespan regulation. In addition, FOXO proteins are also involved in immune responses. After a systematic study of FOXO genes in channel catfish, Ictalurus punctatus, seven FOXO genes were identified and characterized, including FOXO1a, FOXO1b, FOXO3a, FOXO3b, FOXO4, FOXO6a and FOXO6b. Through phylogenetic and syntenic analyses, it was found that FOXO1, FOXO3 and FOXO6 were duplicated in the catfish genome, as in the zebrafish genome. Analysis of the relative rates of nonsynonymous (dN) and synonymous (dS) substitutions revealed that the FOXO genes were globally strongly constrained by negative selection. Differential expression patterns were observed in the majority of FOXO genes after Edwardsiella ictaluri and Flavobacterium columnare infections. After E. ictaluri infection, four FOXO genes with orthologs in mammal species were significantly upregulated, where FOXO6b was the most dramatically upregulated. However, after F. columnare infection, the expression levels of almost all FOXO genes were not significantly affected. These results suggested that either a pathogenesis-specific pattern or tissue-specific pattern existed in catfish after these two bacterial infections. Taken together, these findings indicated that FOXO genes may play important roles in immune responses to bacterial infections in catfish.


The role of ventilator graphics when setting dual-control modes.
Dual-control ventilation modes were introduced with the goal of combining the advantages of volume-control ventilation (constant minute ventilation) and pressure-control ventilation (rapid, variable flow). Dual-control ventilation modes have gained popularity despite little evidence to support routine use. The individual operation and response of the dual-control modes must be understood by the clinician to allow safe and effective use. Graphic displays of pressure, volume, and flow can aid the clinician in detecting inappropriate use of dual-control modes and adjusting settings accordingly. Inspecting the waveforms will lead clinicians to the realization that dual-control does not guarantee a set tidal volume and that variability in delivered tidal volume is greater with dual-control than with pressure control. These realizations have important implications for low-tidal volume strategies.


Towards a gold standard: regarding quality in public domain chemistry databases and approaches to improving the situation.
In recent years there has been a dramatic increase in the number of freely accessible online databases serving the chemistry community. The internet provides chemistry data that can be used for data-mining, for computer models, and integration into systems to aid drug discovery. There is however a responsibility to ensure that the data are high quality to ensure that time is not wasted in erroneous searches, that models are underpinned by accurate data and that improved discoverability of online resources is not marred by incorrect data. In this article we provide an overview of some of the experiences of the authors using online chemical compound databases, critique the approaches taken to assemble data and we suggest approaches to deliver definitive reference data sources.


Changes in bacterial and eukaryotic community structure after mass lysis of filamentous cyanobacteria associated with viruses.
During an experiment in two laboratory-scale enclosures filled with lake water (130 liters each) we noticed the almost-complete lysis of the cyanobacterial population. Based on electron microscopic observations of viral particles inside cyanobacterial filaments and counts of virus-like particles, we concluded that a viral lysis of the filamentous cyanobacteria had taken place. Denaturing gradient gel electrophoresis (DGGE) of 16S ribosomal DNA fragments qualitatively monitored the removal of the cyanobacterial species from the community and the appearance of newly emerging bacterial species. The majority of these bacteria were related to the Cytophagales and actinomycetes, bacterial divisions known to contain species capable of degrading complex organic molecules. A few days after the cyanobacteria started to lyse, a rotifer species became dominant in the DGGE profile of the eukaryotic community. Since rotifers play an important role in the carbon transfer between the microbial loop and higher trophic levels, these observations confirm the role of viruses in channeling carbon through food webs. Multidimensional scaling analysis of the DGGE profiles showed large changes in the structures of both the bacterial and eukaryotic communities at the time of lysis. These changes were remarkably similar in the two enclosures, indicating that such community structure changes are not random but occur according to a fixed pattern. Our findings strongly support the idea that viruses can structure microbial communities.


Comparison of T-matrix calculation methods for scattering by cylinders in optical tweezers.
The T-matrix method, or the T-matrix formulation of scattering, is a framework for mathematically describing the scattering properties of an object as a linear relationship between expansion coefficients of the incident and scattering fields in a basis of vector spherical wave functions (VSWFs). A variety of methods can be used to calculate the T-matrix. We explore the applicability of the extended boundary condition method (EBCM) and point matching (PM) method to calculate the T-matrix for scattering by cylinders in optical tweezers and hence the optical force acting on them. We compare both methods with the discrete-dipole approximation (DDA) to measure their accuracy for different sizes and aspect ratios (ARs) for Rayleigh and wavelength-size cylinders. We determine range of sizes and ARs giving errors below 1% and 10%. These results can help researchers choose the most efficient method to calculate the T-matrix for nonspherical particles with acceptable accuracy.


Applying phylogenomics to understand the emergence of Shiga-toxin-producing Escherichia coli O157:H7 strains causing severe human disease in the UK.
Shiga-toxin-producing Escherichia coli (STEC) O157:H7 is a recently emerged zoonotic pathogen with considerable morbidity. Since the emergence of this serotype in the 1980s, research has focussed on unravelling the evolutionary events from the E. coli O55:H7 ancestor to the contemporaneous globally dispersed strains observed today. In this study, the genomes of over 1000 isolates from both human clinical cases and cattle, spanning the history of STEC O157:H7 in the UK, were sequenced. Phylogenetic analysis revealed the ancestry, key acquisition events and global context of the strains. Dated phylogenies estimated the time to evolution of the most recent common ancestor of the current circulating global clone to be 175 years ago. This event was followed by rapid diversification. We show the acquisition of specific virulence determinates has occurred relatively recently and coincides with its recent detection in the human population. We used clinical outcome data from 493 cases of STEC O157:H7 to assess the relative risk of severe disease including haemolytic uraemic syndrome from each of the defined clades in the population and show the dramatic effect Shiga toxin repertoire has on virulence. We describe two strain replacement events that have occurred in the cattle population in the UK over the last 30 years, one resulting in a highly virulent strain that has accounted for the majority of clinical cases in the UK over the last decade. There is a need to understand the selection pressures maintaining Shiga-toxin-encoding bacteriophages in the ruminant reservoir and the study affirms the requirement for close surveillance of this pathogen in both ruminant and human populations.


Coral reefs under rapid climate change and ocean acidification.
Atmospheric carbon dioxide concentration is expected to exceed 500 parts per million and global temperatures to rise by at least 2 degrees C by 2050 to 2100, values that significantly exceed those of at least the past 420,000 years during which most extant marine organisms evolved. Under conditions expected in the 21st century, global warming and ocean acidification will compromise carbonate accretion, with corals becoming increasingly rare on reef systems. The result will be less diverse reef communities and carbonate reef structures that fail to be maintained. Climate change also exacerbates local stresses from declining water quality and overexploitation of key species, driving reefs increasingly toward the tipping point for functional collapse. This review presents future scenarios for coral reefs that predict increasingly serious consequences for reef-associated fisheries, tourism, coastal protection, and people. As the International Year of the Reef 2008 begins, scaled-up management intervention and decisive action on global emissions are required if the loss of coral-dominated ecosystems is to be avoided.


Nutrition and the developing brain: nutrient priorities and measurement.
Nutrients and growth factors regulate brain development during fetal and early postnatal life. The rapidly developing brain is more vulnerable to nutrient insufficiency yet also demonstrates its greatest degree of plasticity. Certain nutrients have greater effects on brain development than do others. These include protein, energy, certain fats, iron, zinc, copper, iodine, selenium, vitamin A, choline, and folate. The effect of any nutrient deficiency or overabundance on brain development will be governed by the principle of timing, dose, and duration. The ability to detect the specific effects of nutrient deficiencies is dependent on knowing which area of the brain is preferentially affected and on having neurologic assessments that tap into the functions of those specific areas. As examples, protein-energy malnutrition causes both global deficits, which are testable by general developmental testing, and area-specific effects on the hippocampus and the cortex. Iron deficiency alters myelination, monoamine neurotransmitter synthesis, and hippocampal energy metabolism in the neonatal period. Assessments of these effects could include tests for speed of processing (myelination), changes in motor and affect (monoamines), and recognition memory (hippocampus). Zinc deficiency alters autonomic nervous system regulation and hippocampal and cerebellar development. Long-chain polyunsaturated fatty acids are important for synaptogenesis, membrane function, and, potentially, myelination. Overall, circuit-specific behavioral and neuroimaging tests are being developed for use in progressively younger infants to more accurately assess the effect of nutrient deficits both while the subject is deficient and after recovery from the deficiency.


Isolation of Drosophila egg chambers for imaging.
The fruit fly Drosophila melanogaster is an important model for basic research into the molecular mechanisms underlying cell function and development, as well as a major biomedical research tool. A significant advantage of Drosophila is the ability to apply live cell imaging to a variety of living tissues that can be dissected and imaged in vivo, ex vivo, or in vitro. Drosophila egg chambers, for example, have proven to be a useful model system for studying border cell migration, Golgi unit transport, the rapid movement of mRNA and protein particles, and the role of microtubules in meiosis and oocyte differentiation. A crucial first step before imaging is preparation of the experimental material to ensure physiological relevance and to achieve the best conditions for image quality. Early- to mid-stage egg chambers cannot be mounted in an aqueous-based medium, because this causes a change in microtubule organization and follicle cell morphology. Such egg chambers survive better in Halocarbon oil, which allows free diffusion of oxygen, has low viscosity, and thus prevents dehydration and hypoxia. With a refractive index similar to glycerol, Halocarbon oil also has good optical properties for imaging. It also provides a good environment for injection and is particularly useful for long-term imaging of embryos. However, unlike with aqueous solutions, changes in the medium are not possible. This protocol describes the isolation of Drosophila egg chambers.


CerbB2 status in breast cancer: pathologic issues.
CerbB2 status determination in breast cancer is currently performed for predictive and prognostic information. However, much has yet to be learned about the accuracy, reproducibility and clinical correlation of the different testing methods available today. This is a review of the testing methods commonly in use and their applications in the management of breast cancer. A Medline search for review articles with keywords cerbB2, Her2 testing, immunohistochemistry (IHC), fluorescence in situ hybridisation (FISH) and breast cancer was done. Manual cross-referencing from the afore-mentioned articles and perusal of the package inserts, recommendations and manuals from the manufacturers of various commercially available test kits were also performed. The 2 main methods of testing in use in most routine laboratories are IHC and FISH on formalin fixed, paraffin embedded, breast cancer tissue. There is no single, universally accepted method and the plethora of testing and interpretative protocols has confounded the issue of clinical correlation of cerbB2 status with outcome and patient selection for therapy. The current consensus in the literature is leaning towards FISH; however, as pointed out in this paper, the use of FISH as a routine test in most diagnostic laboratories is not yet a reality mainly due to cost, technical and manpower constraints. In this regard, IHC is by default the preferred choice in many routine laboratories. Universal standardisation of testing methods for cerbB2 status determination, together with further clinical studies on the correlation of each method with outcome and response to therapy, will aid in the identification of the ideal method for stratifying patients with breast cancer into prognostic and optimal therapeutic groups.


Treatment and Survival of Medicare Beneficiaries with Colorectal Cancer: A Comparative Analysis Between a Rural State Cancer Registry and National Data.
The aim was to examine and compare with "national" estimates, receipt of colorectal cancer (CRC) treatment in the initial phase of care and survival following a CRC diagnosis in rural Medicare beneficiaries. A retrospective study was conducted on fee-for-service Medicare beneficiaries diagnosed with CRC in 2003-2006, identified from West Virginia Cancer Registry (WVCR)-Medicare linked database (N = 2119). A comparative cohort was identified from Surveillance, Epidemiology, and End Results (SEER)-Medicare (N = 38,168). CRC treatment received was ascertained from beneficiaries' Medicare claims in the 12 months post CRC diagnosis or until death, whichever happened first. Receipt of minimally appropriate CRC treatment (MACT) was defined using recommended CRC treatment guidelines. All-cause and CRC-specific mortality in the 36-month period post CRC diagnosis were examined. Differences in usage of CRC surgery, chemotherapy, and radiation were observed between the 2 populations, with those from WVCR-Medicare being less likely to receive any type of CRC surgery (adjusted odds ratio [AOR] = 0.82; 95% confidence interval [CI] = [0.73-0.93]). Overall, those from WVCR-Medicare had a lower likelihood of receiving MACT, (AOR = 0.85; 95% CI = [0.76-0.96]) compared to their national counterparts. Higher hazard of CRC mortality was observed in the WVCR-Medicare cohort (adjusted hazard ratio = 1.26; 95% CI = [1.20-1.32]) compared to the SEER-Medicare cohort. Although more beneficiaries from WVCR-Medicare were diagnosed in early-stage CRC compared to their SEER-Medicare counterparts, they had a lower likelihood of receiving MACT and a higher hazard of CRC mortality. This study highlights the need for an increased focus on improving access to care at every phase of the CRC care continuum, especially for those from rural settings.


Somatic mutation and gain of copy number of PIK3CA in human breast cancer.
Phosphatidylinositol 3-kinases (PI3Ks) are a group of lipid kinases that regulate signaling pathways involved in cell proliferation, adhesion, survival, and motility. Even though PIK3CA amplification and somatic mutation have been reported previously in various kinds of human cancers, the genetic change in PIK3CA in human breast cancer has not been clearly identified. Fifteen breast cancer cell lines and 92 primary breast tumors (33 with matched normal tissue) were used to check somatic mutation and gene copy number of PIK3CA. For the somatic mutation study, we specifically checked exons 1, 9, and 20, which have been reported to be hot spots in colon cancer. For the analysis of the gene copy number, we used quantitative real-time PCR and fluorescence in situ hybridization. We also treated several breast cancer cells with the PIK3CA inhibitor LY294002 and compared the apoptosis status in cells with and without PIK3CA mutation. We identified a 20.6% (19 of 92) and 33.3% (5 of 15) PIK3CA somatic mutation frequency in primary breast tumors and cell lines, respectively. We also found that 8.7% (8 of 92) of the tumors harbored a gain of PIK3CA gene copy number. Only four cases in this study contained both an increase in the gene copy number and a somatic mutation. In addition, mutation of PIK3CA correlated with the status of Akt phosphorylation in some breast cancer cells and inhibition of PIK3CA-induced increased apoptosis in breast cancer cells with PIK3CA mutation. Somatic mutation rather than a gain of gene copy number of PIK3CA is the frequent genetic alteration that contributes to human breast cancer progression. The frequent and clustered mutations within PIK3CA make it an attractive molecular marker for early detection and a promising therapeutic target in breast cancer.


Identifying inhibitory compounds in lignocellulosic biomass hydrolysates using an exometabolomics approach.
Inhibitors are formed that reduce the fermentation performance of fermenting yeast during the pretreatment process of lignocellulosic biomass. An exometabolomics approach was applied to systematically identify inhibitors in lignocellulosic biomass hydrolysates. We studied the composition and fermentability of 24 different biomass hydrolysates. To create diversity, the 24 hydrolysates were prepared from six different biomass types, namely sugar cane bagasse, corn stover, wheat straw, barley straw, willow wood chips and oak sawdust, and with four different pretreatment methods, i.e. dilute acid, mild alkaline, alkaline/peracetic acid and concentrated acid. Their composition and that of fermentation samples generated with these hydrolysates were analyzed with two GC-MS methods. Either ethyl acetate extraction or ethyl chloroformate derivatization was used before conducting GC-MS to prevent sugars are overloaded in the chromatograms, which obscure the detection of less abundant compounds. Using multivariate PLS-2CV and nPLS-2CV data analysis models, potential inhibitors were identified through establishing relationship between fermentability and composition of the hydrolysates. These identified compounds were tested for their effects on the growth of the model yeast, Saccharomyces. cerevisiae CEN.PK 113-7D, confirming that the majority of the identified compounds were indeed inhibitors. Inhibitory compounds in lignocellulosic biomass hydrolysates were successfully identified using a non-targeted systematic approach: metabolomics. The identified inhibitors include both known ones, such as furfural, HMF and vanillin, and novel inhibitors, namely sorbic acid and phenylacetaldehyde.


Toward Quantitative Measurements of Enzyme Kinetics by Dissolution Dynamic Nuclear Polarization.
Dissolution dynamic nuclear polarization (D-DNP) experiments enabled us to study the kinetics of the enzymatic phosphorylation reaction of glucose to form glucose-6-phosphate (G6P) by hexokinase (HK), with or without the presence of an excess of G6P, which is known to be an inhibitor of the enzyme. Against all expectations, our observations demonstrate that the phosphorylation of both α and β glucose anomers occurs with comparable kinetics. The catalytic constant of the reaction was estimated based on a simple kinetic model tailored for hyperpolarized systems.


Observation of terahertz-radiation-induced ionization in a single nano island.
Terahertz (THz) electromagnetic wave has been widely used as a spectroscopic probe to detect the collective vibrational mode in vast molecular systems and investigate dielectric properties of various materials. Recent technological advances in generating intense THz radiation and the emergence of THz plasmonics operating with nanoscale structures have opened up new pathways toward THz applications. Here, we present a new opportunity in engineering the state of matter at the atomic scale using THz wave and a metallic nanostructure. We show that a medium strength THz radiation of 22 kV/cm can induce ionization of ambient carbon atoms through interaction with a metallic nanostructure. The prepared structure, made of a nano slot antenna and a nano island located at the center, acts as a nanogap capacitor and enhances the local electric field by two orders of magnitudes thereby causing the ionization of ambient carbon atoms. Ionization and accumulation of carbon atoms are also observed through the change of the resonant condition of the nano slot antenna and the shift of the characteristic mode in the spectrum of the transmitted THz waves.


Genetic Diversity of Crimean Congo Hemorrhagic Fever Virus Strains from Iran.
Crimean Congo hemorrhagic fever virus (CCHFV) is a member of the Bunyaviridae family and Nairovirus genus. It has a negative-sense, single stranded RNA genome approximately 19.2 kb, containing the Small, Medium, and Large segments. CCHFVs are relatively divergent in their genome sequence and grouped in seven distinct clades based on S-segment sequence analysis and six clades based on M-segment sequences. Our aim was to obtain new insights into the molecular epidemiology of CCHFV in Iran. We analyzed partial and complete nucleotide sequences of the S and M segments derived from 50 Iranian patients. The extracted RNA was amplified using one-step RT-PCR and then sequenced. The sequences were analyzed using Mega5 software. Phylogenetic analysis of partial S segment sequences demonstrated that clade IV-(Asia 1), clade IV-(Asia 2) and clade V-(Europe) accounted for 80 %, 4 % and 14 % of the circulating genomic variants of CCHFV in Iran respectively. However, one of the Iranian strains (Iran-Kerman/22) was associated with none of other sequences and formed a new clade (VII). The phylogenetic analysis of complete S-segment nucleotide sequences from selected Iranian CCHFV strains complemented with representative strains from GenBank revealed similar topology as partial sequences with eight major clusters. A partial M segment phylogeny positioned the Iranian strains in either association with clade III (Asia-Africa) or clade V (Europe). The phylogenetic analysis revealed subtle links between distant geographic locations, which we propose might originate either from international livestock trade or from long-distance carriage of CCHFV by infected ticks via bird migration.


A continuous-time persistent random walk model for flocking.
A classical random walker is characterized by a random position and velocity. This sort of random walk was originally proposed by Einstein to model Brownian motion and to demonstrate the existence of atoms and molecules. Such a walker represents an inanimate particle driven by environmental fluctuations. On the other hand, there are many examples of so-called "persistent random walkers," including self-propelled particles that are able to move with almost constant speed while randomly changing their direction of motion. Examples include living entities (ranging from flagellated unicellular organisms to complex animals such as birds and fish), as well as synthetic materials. Here we discuss such persistent non-interacting random walkers as a model for active particles. We also present a model that includes interactions among particles, leading to a transition to flocking, that is, to a net flux where the majority of the particles move in the same direction. Moreover, the model exhibits secondary transitions that lead to clustering and more complex spatially structured states of flocking. We analyze all these transitions in terms of bifurcations using a number of mean field strategies (all to all interaction and advection-reaction equations for the spatially structured states), and compare these results with direct numerical simulations of ensembles of these interacting active particles.


Reduced vaginal elasticity, reduced lubrication, and deep and superficial dyspareunia in irradiated gynecological cancer survivors.
The purpose of this study was to examine whether or not vaginal elasticity or lack of lubrication is associated with deep or superficial dyspareunia. We investigated gynecological cancer survivors treated with radiation therapy. In a population-based study with 616 women answering a questionnaire (participation rate 78%) and who were treated with radiotherapy for gynecological cancer, we analyzed information from 243 women (39%) who reported that they had had intercourse during the previous six months. Analyses included log-binomial regression (relative risks) and multiple imputations by chained equations in combination with Bayesian Model Averaging, yielding a posterior probability value. Age range of this cancer recurrent-free group of women was 29-80. Dyspareunia affected 164 of 243 of the women (67%). One hundred thirty-four women (55%) reported superficial pain, 97 women (40%) reported deep pain, and 87 women (36%) reported both types of dyspareunia. The relative risk (RR) of deep dyspareunia was 1.87 (CI 1.41-2.49) with impaired vaginal elasticity compared to normal vaginal elasticity. Age and lower abdominal swelling were separate risk factors for deep dyspareunia. However, effects remain after adjusting for these factors. The relative risk of deep dyspareunia was almost twice as high with impaired vaginal elasticity compared to normal vaginal elasticity. If we wish to treat or even prevent deep dyspareunia in women with gynecological cancer, we may use our knowledge of the pathophysiology of deep dyspareunia and increasingly provide dilators together with instructions on how to use them for stretching exercises in order to retain vaginal elasticity. Results highlight the need for studies with more precise questions distinguishing superficial from deep dyspareunia so that in the future we may be able to primarily try to avoid reduced vaginal elasticity and secondarily reduce the symptoms.


A systematic review of tests predicting ovarian reserve and IVF outcome.
The age-related decline of the success in IVF is largely attributable to a progressive decline of ovarian oocyte quality and quantity. Over the past two decades, a number of so-called ovarian reserve tests (ORTs) have been designed to determine oocyte reserve and quality and have been evaluated for their ability to predict the outcome of IVF in terms of oocyte yield and occurrence of pregnancy. Many of these tests have become part of the routine diagnostic procedure for infertility patients who undergo assisted reproductive techniques. The unifying goals are traditionally to find out how a patient will respond to stimulation and what are their chances of pregnancy. Evidence-based medicine has progressively developed as the standard approach for many diagnostic procedures and treatment options in the field of reproductive medicine. We here provide the first comprehensive systematic literature review, including an a priori protocolized information retrieval on all currently available and applied tests, namely early-follicular-phase blood values of FSH, estradiol, inhibin B and anti-Müllerian hormone (AMH), the antral follicle count (AFC), the ovarian volume (OVVOL) and the ovarian blood flow, and furthermore the Clomiphene Citrate Challenge Test (CCCT), the exogenous FSH ORT (EFORT) and the gonadotrophin agonist stimulation test (GAST), all as measures to predict ovarian response and chance of pregnancy. We provide, where possible, an integrated receiver operating characteristic (ROC) analysis and curve of all individual evaluated published papers of each test, as well as a formal judgement upon the clinical value. Our analysis shows that the ORTs known to date have only modest-to-poor predictive properties and are therefore far from suitable for relevant clinical use. Accuracy of testing for the occurrence of poor ovarian response to hyperstimulation appears to be modest. Whether the a priori identification of actual poor responders in the first IVF cycle has any prognostic value for their chances of conception in the course of a series of IVF cycles remains to be established. The accuracy of predicting the occurrence of pregnancy is very limited. If a high threshold is used, to prevent couples from wrongly being refused IVF, a very small minority of IVF-indicated cases (approximately 3%) are identified as having unfavourable prospects in an IVF treatment cycle. Although mostly inexpensive and not very demanding, the use of any ORT for outcome prediction cannot be supported. As poor ovarian response will provide some information on OR status, especially if the stimulation is maximal, entering the first cycle of IVF without any prior testing seems to be the preferable strategy.


Automated measurement of the refractive index of fluids.
A method for automating refractive-index measurements of fluids has been developed. An encoded rotation stage and position-sensitive detector enable automated reading of angles typically acquired by visual means. Two tunable lasers are used to obtain index measurements at ten discrete wavelengths across the visible spectrum. This method has been implemented on a Hilger-Chance refractometer from which the bulk refractive-index values for various transparent fluids have been measured. An index measurement accuracy of better than one part in the fourth decimal place for distilled water and a few parts in the fourth decimal place for higher index fluids is obtained.


Cyber-workstation for computational neuroscience.
A Cyber-Workstation (CW) to study in vivo, real-time interactions between computational models and large-scale brain subsystems during behavioral experiments has been designed and implemented. The design philosophy seeks to directly link the in vivo neurophysiology laboratory with scalable computing resources to enable more sophisticated computational neuroscience investigation. The architecture designed here allows scientists to develop new models and integrate them with existing models (e.g. recursive least-squares regressor) by specifying appropriate connections in a block-diagram. Then, adaptive middleware transparently implements these user specifications using the full power of remote grid-computing hardware. In effect, the middleware deploys an on-demand and flexible neuroscience research test-bed to provide the neurophysiology laboratory extensive computational power from an outside source. The CW consolidates distributed software and hardware resources to support time-critical and/or resource-demanding computing during data collection from behaving animals. This power and flexibility is important as experimental and theoretical neuroscience evolves based on insights gained from data-intensive experiments, new technologies and engineering methodologies. This paper describes briefly the computational infrastructure and its most relevant components. Each component is discussed within a systematic process of setting up an in vivo, neuroscience experiment. Furthermore, a co-adaptive brain machine interface is implemented on the CW to illustrate how this integrated computational and experimental platform can be used to study systems neurophysiology and learning in a behavior task. We believe this implementation is also the first remote execution and adaptation of a brain-machine interface.


Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants.
RNA Polymerase II (Pol II) regulatory cascades involving transcription factors (TFs) and their targets orchestrate the genetic circuitry of every eukaryotic organism. In order to understand how these cascades function, they can be dissected into small genetic networks, each containing just a few Pol II transcribed genes, that generate specific signal-processing outcomes. Small RNA regulatory circuits involve direct regulation of a small RNA by a TF and/or direct regulation of a TF by a small RNA and have been shown to play unique roles in many organisms. Here, we will focus on small RNA regulatory circuits containing Pol II transcribed microRNAs (miRNAs). While the role of miRNA-containing regulatory circuits as modular building blocks for the function of complex networks has long been on the forefront of studies in the animal kingdom, plant studies are poised to take a lead role in this area because of their advantages in probing transcriptional and posttranscriptional control of Pol II genes. The relative simplicity of tissue- and cell-type organization, miRNA targeting, and genomic structure make the Arabidopsis thaliana plant model uniquely amenable for small RNA regulatory circuit studies in a multicellular organism. In this Review, we cover analysis, tools, and validation methods for probing the component interactions in miRNA-containing regulatory circuits. We then review the important roles that plant miRNAs are playing in these circuits and summarize methods for the identification of small genetic circuits that strongly influence plant function. We conclude by noting areas of opportunity where new plant studies are imminently needed.


Effect of activated protein C in second intention healing of equine distal limb wounds: a preliminary study.
To investigate the effect of activated protein C (APC) on second intention healing of distal limb wounds in horses. In this experimental study of eight Standardbred geldings, six full-thickness skin wounds (2 × 1.5 cm) were created on one metacarpus (biopsy limb) and five similar wounds were created on the contralateral metacarpus (photographed limb). Three wounds on the biopsy limb were treated topically with 190 µg APC on days 1, 3, 6 and 9, while the remaining three wounds were untreated (control). One treated and one control wound were biopsied on days 4, 7 and 11 for histopathology. Wounds on the photographed limb were treated with either 66% Manuka honey gel, a commercial antibiotic ointment (bacitracin-neomycin-polymixin B ointment; BNP) or petrolatum daily throughout healing, treated on days 1,3,6 and 9 with 190 µg APC or left untreated. These wounds were digitally photographed and the wound area measured on day 1, then weekly until day 49. Overall time to healing was recorded. There was no effect of APC on wound size, the rate of healing or the overall time to heal. However, compared with control wounds, histological scoring demonstrated enhanced epithelialisation (day 4) and angiogenesis (day 11). Wound healing variables for wounds treated with APC, Manuka honey gel and control wounds were not different and the variables for wounds treated with BNP and petrolatum demonstrated delayed healing. The improvements in histological scores in APC-treated wounds suggest further study into the effect of APC on second intention wound healing in horses is warranted.


Development and Use of Natural Language Processing for Identification of Distant Cancer Recurrence and Sites of Distant Recurrence Using Unstructured Electronic Health Record Data.
Large-scale analysis of real-world evidence is often limited to structured data fields that do not contain reliable information on recurrence status and disease sites. In this report, we describe a natural language processing (NLP) framework that uses data from free-text, unstructured reports to classify recurrence status and sites of recurrence for patients with breast and hepatocellular carcinomas (HCC). Using two cohorts of breast cancer and HCC cases, we validated the ability of a previously developed NLP model to distinguish between no recurrence, local recurrence, and distant recurrence, based on clinician notes, radiology reports, and pathology reports compared with manual curation. A second NLP model was trained and validated to identify sites of recurrence. We compared the ability of each NLP model to identify the presence, timing, and site of recurrence, when compared against manual chart review and International Classification of Diseases coding. A total of 1,273 patients were included in the development and validation of the two models. The NLP model for recurrence detects distant recurrence with an area under the curve of 0.98 (95% CI, 0.96 to 0.99) and 0.95 (95% CI, 0.88 to 0.98) in breast and HCC cohorts, respectively. The mean accuracy of the NLP model for detecting any site of distant recurrence was 0.9 for breast cancer and 0.83 for HCC. The NLP model for recurrence identified a larger proportion of patients with distant recurrence in a breast cancer database (11.1%) compared with International Classification of Diseases coding (2.31%). We developed two NLP models to identify distant cancer recurrence, timing of recurrence, and sites of recurrence based on unstructured electronic health record data. These models can be used to perform large-scale retrospective studies in oncology.


Impact of Changing Treatment Strategies on Outcomes in Pediatric Ulcerative Colitis.
In recent years, treatment strategies for ulcerative colitis have evolved with an early step-up approach, the availability of biologicals, and therapeutic drug monitoring.We carried out this study to evaluate the effect of these changes on disease outcomes. In this retrospective review, 2 time periods were defined: Group 1 (2005-2010) and Group 2 (2011-2016). Baseline demographic, endoscopic parameters, and medication use were compared. Overall colectomy rate, number of disease flares per year, and number of hospital admissions per year were compared between the 2 groups. Group 1 had 71 children, and in children in Group 2. The use of 5-ASA increased in Group 2 (Group 2, 99.2% vs. Group 1, 84.5%, P = 0.0007). In addition, infliximab and thiopurines were introduced earlier in the disease course.The 2-year cumulative probability of colectomy decreased from 14% to 3% (P = 0.02) between the 2 periods. No change in median number of flares per year [Group 1, 0.41 (IQR 0.6) vs. Group 2, 0.62 (IQR 0.91), P = 0.28] or median number of hospital admissions per year [Group 1, 0.30 (IQR 0.77) vs. Group 2, 0.21 (IQR 0.75), P = 0.52] was seen.Thereafter, we proceeded to identify the changes in treatment strategies that were responsible for the reduction in colectomy and we found that the use of infliximab OR 3.7 (95% CI 1.1-11.7), P = 0.02, was independently associated with it. A reduction in 2-year colectomy rates has been observed in patients with pediatric ulcerative colitis since biologics have become available for its treatment. The numbers of disease-flares rates and hospital admissions remain unchanged.


Innovation, imitation, and problem-solving in a networked group.
We implemented a problem-solving task in which groups of participants simultaneously played a simple innovation game in a complex problem space, with score feedback provided after each of a number of rounds. Each participant in a group was allowed to view and imitate the guesses of others during the game. The results showed the use of social learning strategies previously studied in other species, and demonstrated benefits of social learning and nonlinear effects of group size on strategy and performance. Rather than simply encouraging conformity, groups provided information to each individual about the distribution of useful innovations in the problem space. Imitation facilitated innovation rather than displacing it, because the former allowed good solutions to be propagated and preserved for further cumulative innovations in the group. Participants generally improved their solutions through the use of fairly conservative strategies, such as changing only a small portion of one's solution at a time, and tending to imitate solutions similar to one's own. Changes in these strategies over time had the effect of making solutions increasingly entrenched, both at individual and group levels. These results showed evidence of nonlinear dynamics in the decentralization of innovation, the emergence of group phenomena from complex interactions of individual efforts, stigmergy in the use of social information, and dynamic tradeoffs between exploration and exploitation of solutions. These results also support the idea that innovation and creativity can be recognized at the group level even when group members are generally cautious and imitative.


Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination.
A key challenge when imaging living cells is how to noninvasively extract the most spatiotemporal information possible. Unlike popular wide-field and confocal methods, plane-illumination microscopy limits excitation to the information-rich vicinity of the focal plane, providing effective optical sectioning and high speed while minimizing out-of-focus background and premature photobleaching. Here we used scanned Bessel beams in conjunction with structured illumination and/or two-photon excitation to create thinner light sheets (<0.5 μm) better suited to three-dimensional (3D) subcellular imaging. As demonstrated by imaging the dynamics of mitochondria, filopodia, membrane ruffles, intracellular vesicles and mitotic chromosomes in live cells, the microscope currently offers 3D isotropic resolution down to ∼0.3 μm, speeds up to nearly 200 image planes per second and the ability to noninvasively acquire hundreds of 3D data volumes from single living cells encompassing tens of thousands of image frames.


Residual antimicrobial effect of chlorhexidine digluconate and octenidine dihydrochloride on reconstructed human epidermis.
The objective of the present investigation was to examine the residual antimicrobial activity after a topical exposure of reconstructed human epidermis (RHE) to equimolar solutions of either chlorhexidine digluconate (CHG, 0.144% w/v) or octenidine dihydrochloride (OCT, 0.1% w/v) for 15 min. RHE-associated antiseptic agents were more effective on Staphylococcus aureus than on Pseudomonas aeruginosa. S. aureus was not detected after 24 h of contact, which demonstrated a microbicidal efficacy of greater than 5-log10 reduction. In contrast, P. aeruginosa was reduced by approximately 2 log10 at the same incubation time, which parallels the growth of the initial inoculum. This result could be interpreted either as a microbiostatic effect or as an adherence of P. aeruginosa to a low positively charged surface. Small amounts of CHG and OCT can penetrate the stratum corneum. Using these antiseptic agents, the viability of keratinocytes was reduced to 65-75% of that of the untreated RHE control following 24 h incubation in the presence of test microorganisms. With consideration of antimicrobial activity and cytotoxic effect, OCT corresponds better to a biocompatible antiseptic agent than CHG.


Targeted enrichment: maximizing orthologous gene comparisons across deep evolutionary time.
Estimated phylogenies of evolutionarily diverse taxa will be well supported and more likely to be historically accurate when the analysis contains large amounts of data-many genes sequenced across many taxa. Inferring such phylogenies for non-model organisms is challenging given limited resources for whole-genome sequencing. We take advantage of genomic data from a single species to test the limits of hybridization-based enrichment of hundreds of exons across frog species that diverged up to 250 million years ago. Enrichment success for a given species depends greatly on the divergence time between it and the reference species, and the resulting alignment contains a significant proportion of missing data. However, our alignment generates a well-supported phylogeny of frogs, suggesting that this technique is a practical solution towards resolving relationships across deep evolutionary time.


A Functionally Conserved Gene Regulatory Network Module Governing Olfactory Neuron Diversity.
Sensory neuron diversity is required for organisms to decipher complex environmental cues. In Drosophila, the olfactory environment is detected by 50 different olfactory receptor neuron (ORN) classes that are clustered in combinations within distinct sensilla subtypes. Each sensilla subtype houses stereotypically clustered 1-4 ORN identities that arise through asymmetric divisions from a single multipotent sensory organ precursor (SOP). How each class of SOPs acquires a unique differentiation potential that accounts for ORN diversity is unknown. Previously, we reported a critical component of SOP diversification program, Rotund (Rn), increases ORN diversity by generating novel developmental trajectories from existing precursors within each independent sensilla type lineages. Here, we show that Rn, along with BarH1/H2 (Bar), Bric-à-brac (Bab), Apterous (Ap) and Dachshund (Dac), constitutes a transcription factor (TF) network that patterns the developing olfactory tissue. This network was previously shown to pattern the segmentation of the leg, which suggests that this network is functionally conserved. In antennal imaginal discs, precursors with diverse ORN differentiation potentials are selected from concentric rings defined by unique combinations of these TFs along the proximodistal axis of the developing antennal disc. The combinatorial code that demarcates each precursor field is set up by cross-regulatory interactions among different factors within the network. Modifications of this network lead to predictable changes in the diversity of sensilla subtypes and ORN pools. In light of our data, we propose a molecular map that defines each unique SOP fate. Our results highlight the importance of the early prepatterning gene regulatory network as a modulator of SOP and terminally differentiated ORN diversity. Finally, our model illustrates how conserved developmental strategies are used to generate neuronal diversity.


Anaphase-promoting complex/cyclosome-CDH1-mediated proteolysis of the forkhead box M1 transcription factor is critical for regulated entry into S phase.
The forkhead box M1 (FoxM1) transcription factor is overexpressed in many cancers, and in mouse models it is required for tumor progression. FoxM1 activates expression of the cell cycle genes required for both S and M phase progression. Here we demonstrate that FoxM1 is degraded in late mitosis and early G(1) phase by the anaphase-promoting complex/cyclosome (APC/C) E3 ubiquitin ligase. FoxM1 interacts with the APC/C complex and its adaptor, Cdh1. Expression of Cdh1 stimulated degradation of the FoxM1 protein, and depletion of Cdh1 resulted in stabilization of the FoxM1 protein in late mitosis and in early G(1) phase of the cell cycle. Cdh1 has been implicated in regulating S phase entry. We show that codepletion of FoxM1 inhibits early S phase entry observed in Cdh1-depleted cells. The N-terminal region of FoxM1 contains both destruction box (D box) and KEN box sequences that are required for targeting by Cdh1. Mutation of either the D box sequence or the KEN box sequence stabilized FoxM1 and blocked Cdh1-induced proteolysis. Cells expressing a nondegradable form of FoxM1 entered S phase rapidly following release from M phase arrest. Together, our observations show that FoxM1 is one of the targets of Cdh1 in late M or early G(1) phase and that its proteolysis is important for regulated entry into S phase.


How to Handle Lymphadenectomy Specimens to Identify Metastasis More Accurately in Gynecologic Pathology.
To identify the value of processing multiple sections to detect metastasis in lymph nodes (LNs) dissected during gynecologic cancer surgery, and to evaluate the sizes of metastatic LNs in each region to compare with the largest one. This retrospective study included 362 patients who had gynecologic cancer with at least one metastatic LN. Slides of 627 metastatic LN specimens were categorized according to the processing technique into single and more than one section (MOS) groups. In the MOS group, the LNs were cut into 2 or 3 parallel slices because their greatest dimensions exceeded 0.5 cm. Sizes of LN metastatic foci (MF) were measured and defined as follows: MF ⩽2 mm as micrometastasis and MF >2 mm as macrometastasis. The largest LN diameters among the metastatic LNs and the largest LNs in those regions were measured. Groups were compared using the Kruskal-Wallis test. Sixty-five (10.3%) of the metastatic LNs included in this study had micrometastases and 40 (6.3%) of them had MF ⩽1 mm. The rate of micrometastasis was higher in the MOS group than in the single-section group (11.8% vs 8.5%, respectively). Twenty-eight percent (n = 175) of metastatic LNs were not the largest, and 55.5% of those were less than 1 cm in diameter. Methods of LN processing and macroscopic evaluation are not standardized, and processing single sections from LNs may overlook micrometastases. The detection rate of micrometastases can be improved by processing multiple sections from LNs.


Phonological reduction in maternal speech in northern Australian English: change over time.
Segmental variation in maternal speech to children changes over time. This study investigated variation in non-citation speech processes in a longitudinal, 26-hour corpus of maternal northern Australian English. Recordings were naturalistic parent-child interactions when children (N=4) were 1;6, 2;0, and 2;6. The mothers' speech was phonetically transcribed and analyzed. Based on previous sociophonetic research showing proportional changes in speech variants in maternal speech as children get older, it was predicted that deletion of word-initial /h/ and word-final /v/, processes common in non-citation speech, would increase over time. Instead results showed a non-linear change in deletion within a stable set of lexical items. Deletion proportionately increased between 1;6 and 2;0 and decreased between 2;0 and 2;6. Further analysis indicated increased deletion was not accounted for by changes in speech rate, which only marginally increased over time. Findings suggest mothers fine-tune differentially over time as children's receptive and productive language knowledge develops.


Control of breathing in patients with chronic obstructive lung disease.
1. Using the mouth occlusion pressure technique, we have studied the control of breathing in seven hypercapnic and eight non-hypercapnic patients with chronic obstructive lung disease. 2. When breathing room air, pulmonary ventilation, mean inspiratory flow and P0.1 (mouth occlusion pressure developed 0.1 s after the onset of occluded inspiration at functional residual capacity) were not significantly different between the two groups of patients. Tidal volume, however, was significantly lower in the hypercapnic than in the non-hypercapnic patients, as a result of a significantly lower duration of inspiration. 3. The lower tidal volume in the hypercapnic patients leads to decreased alveolar ventilation, and appears to be the main cause of retention of carbon dioxide.


Filamentation without intensity clamping.
We present measurements of the supercontinuum emission (SCE) from ultrashort Ti:Saph laser pulse filamentation in air in a tightly focused geometry. The spectral broadening of SCE indicates that peak intensities exceed the clamping value of a few 10(13) W/cm(2) obtained for filamentation in a loose focusing geometry by at least one order of magnitude. We provide an interpretation for this regime of filamenation without intensity clamping.


Effects of whole-body vibration after eccentric exercise on muscle soreness and muscle strength recovery.
[Purpose] The aim of this study was to investigate whether or not a single whole-body vibration treatment after eccentric exercise can reduce muscle soreness and enhance muscle recovery. [Subjects and Methods] Twenty untrained participants were randomly assigned to two groups: a vibration group (n=10) and control group (n=10). Participants performed eccentric quadriceps training of 4 sets of 5 repetitions at 120% 1RM, with 4 min rest between sets. After that, the vibration group received 3 sets of 1 min whole body vibration (12 Hz, 4 mm) with 30 s of passive recovery between sets. Serum creatine kinase, blood urea nitrogen, muscle soreness (visual analog scale) and muscle strength (peak isometric torque) were assessed. [Results] Creatine kinase was lower in the vibration group than in the control group at 24 h (200.2 ± 8.2 vs. 300.5 ± 26.1 U/L) and at 48 h (175.2 ± 12.5 vs. 285.2 ± 19.7 U/L) post-exercise. Muscle soreness decreased in vibration group compared to control group at 48 h post-exercise (34.1 ± 11.4 vs. 65.2 ± 13.2 mm). [Conclusion] Single whole-body vibration treatment after eccentric exercise reduced delayed onset muscle soreness but it did not affect muscle strength recovery.


Properties of a normal mouse cell DNA sequence (sarc) homologous to the src sequence of Moloney sarcoma virus.
A 15.0-kilobase (kb) Eco RI DNA fragment from normal mouse Balb/c genomic DNA that contains sequences (sarc) homologous to the acquired cell sequences (src) of Moloney sarcoma virus (MSV) has been cloned in phage lambda. The sarc region (1.2 to 1.3 kb) of the 15.0-kb cell fragment is indistinguishable from the src region of two isolates of MSV as judged by heteroduplex and restriction endonuclease analyses. The cellular sequences flanking sarc show no homology to other MSV sequences. Whereas cloned subgenomic portions of MSV that contain src transformed NIH-3T3 cells in vitro, the cloned sarc fragment is inactive.


Peroxisome Proliferator-activated receptor γ activation by ligands and dephosphorylation induces proprotein convertase subtilisin kexin type 9 and low density lipoprotein receptor expression.
Proprotein convertase subtilisin kexin type 9 (PCSK9) plays an important role in cholesterol homeostasis by enhancing the degradation of LDL receptor (LDLR) protein. Peroxisome proliferator-activated receptor γ (PPARγ) has been shown to be atheroprotective. PPARγ can be activated by ligands and/or dephosphorylation with ERK1/2 inhibitors. The effect of PPARγ on PCSK9 and LDLR expression remains unknown. In this study, we investigated the effects of PPARγ on PCSK9 and LDLR expression. At the cellular levels, PPARγ ligands induced PCSK9 mRNA and protein expression in HepG2 cells. PCSK9 expression was induced by inhibition of ERK1/2 activity but inhibited by ERK1/2 activation. The mutagenic study and promoter activity assay suggested that the induction of PCSK9 expression by ERK1/2 inhibitors was tightly linked to PPARγ dephosphorylation. However, PPARγ activation by ligands or ERK1/2 inhibitors induced hepatic LDLR expression. The promoter assay indicated that the induction of LDLR expression by PPARγ was sterol regulatory element-dependent because PPARγ enhanced sterol regulatory element-binding protein 2 (SREBP2) processing. In vivo, administration of pioglitazone or U0126 alone increased PCSK9 expression in mouse liver but had little effect on PCSK9 secretion. However, the co-treatment of pioglitazone and U0126 enhanced both PCSK9 expression and secretion. Similar to in vitro, the increased PCSK9 expression by pioglitazone and/or U0126 did not result in decreased LDLR expression and function. In contrast, pioglitazone and/or U0126 increased LDLR protein expression and membrane translocation, SREBP2 processing, and CYP7A1 expression in the liver, which led to decreased total and LDL cholesterol levels in serum. Our results indicate that although PPARγ activation increased PCSK9 expression, PPARγ activation induced LDLR and CYP7A1 expression that enhanced LDL cholesterol metabolism.


Mesenchymal stromal cell density is increased in higher grade myelodysplastic syndromes and independently predicts survival.
We retrospectively tested the prognostic and diagnostic significance of CD271+ mesenchymal stromal cell (MSC) density in cytopenic patients who underwent bone marrow biopsy to evaluate for myelodysplastic syndromes (MDS). CD271+ MSC density was quantitated by automated image analysis of tissue microarray cores in 125 cytopenic patients: 40 lower grade MDS (<5% marrow blasts), 24 higher grade MDS, and 61 benign. CD271+ MSC density was increased in higher grade MDS compared with benign (P = .006) and lower grade MDS (P = .02). CD271+ MSC density was predictive of survival among patients with MDS independent of Revised International Prognostic Scoring System (IPSS-R), history of transfusion, therapy-related MDS, and fibrosis (hazard ratio, 3.4; P < .001). Among low or intermediate IPSS-R patients, median survival was significantly shorter in the high CD271+ MSC density group (47 vs 18 months, P < .02). High CD271+ MSC density is characteristic of higher grade MDS and is associated with poor risk independent of known prognostic factors.


Comparative analysis of methods for representing and searching for transcription factor binding sites.
An important step in unravelling the transcriptional regulatory network of an organism is to identify, for each transcription factor, all of its DNA binding sites. Several approaches are commonly used in searching for a transcription factor's binding sites, including consensus sequences and position-specific scoring matrices. In addition, methods that compute the average number of nucleotide matches between a putative site and all known sites can be employed. Such basic approaches can all be naturally extended by incorporating pairwise nucleotide dependencies and per-position information content. In this paper, we evaluate the effectiveness of these basic approaches and their extensions in finding binding sites for a transcription factor of interest without erroneously identifying other genomic sequences. In cross-validation testing on a dataset of Escherichia coli transcription factors and their binding sites, we show that there are statistically significant differences in how well various methods identify transcription factor binding sites. The use of per-position information content improves the performance of all basic approaches. Furthermore, including local pairwise nucleotide dependencies within binding site models results in statistically significant performance improvements for approaches based on nucleotide matches. Based on our analysis, the best results when searching for DNA binding sites of a particular transcription factor are obtained by methods that incorporate both information content and local pairwise correlations. The software is available at http://compbio.cs.princeton.edu/bindsites.


Role of group velocity in tracking field energy in linear dielectrics.
A new context for the group delay function (valid for pulses of arbitrary bandwidth) is presented for electromagnetic pulses propagating in a uniform linear dielectric medium. The traditional formulation of group velocity is recovered by taking a narrowband limit of this generalized context. The arrival time of a light pulse at a point in space is defined using a time expectation integral over the Poynting vector. The delay between pulse arrival times at two distinct points consists of two parts: a spectral superposition of group delays and a delay due to spectral reshaping via absorption or amplification. The use of the new context is illustrated for pulses propagating both superluminally and subluminally. The inevitable transition to subluminal behavior for any initially superluminal pulse is also demonstrated.


Prognostic factors for mature natural killer (NK) cell neoplasms: aggressive NK cell leukemia and extranodal NK cell lymphoma, nasal type.
Patients with natural killer (NK) cell neoplasms, aggressive NK cell leukemia (ANKL) and extranodal NK cell lymphoma, nasal type (ENKL), have poor outcome. Both diseases show a spectrum and the boundary of them remains unclear. The purpose of this study is to draw a prognostic model of total NK cell neoplasms. We retrospectively analyzed 172 patients (22 with ANKL and 150 with ENKL). The ENKLs consisted of 123 nasal and 27 extranasal (16 cutaneous, 9 hepatosplenic, 1 intestinal and 1 nodal) lymphomas. Complete remission rate for ENKL was 73% in stage I, but 15% in stage IV, which was consistent with that for ANKL (18%). The prognosis of ENKL was better than that of ANKL (median survival 10 versus 1.9 months, P < 0.0001) but was comparable when restricted to stage IV cases (4.0 months, P = 0.16). Multivariate analysis showed that four factors (non-nasal type, stage, performance status and numbers of extranodal involvement) were significant prognostic factors. Using these four variables, an NK prognostic index was successfully constructed. Four-year overall survival of patients with zero, one, two and three or four adverse factors were 55%, 33%, 15% and 6%, respectively. The current prognostic model successfully stratified patients with NK cell neoplasms with different outcomes.


Evidence for cell cycle suppression and microRNA regulation of cyclin D1 during anoxia exposure in turtles.
The red-eared slider turtle (Trachemys scripta elegans) has a well-developed natural tolerance for oxygen deprivation that derives from biochemical adaptations, including anoxia-induced suppression of metabolic rate. We hypothesized that mechanisms that suppress ATP-expensive cell cycle activity would contribute significantly to establishing the hypometabolic state during anaerobiosis. Cyclin D1 is a critical regulator of the G 1 phase of the cell cycle and is regarded as key to initiating cell proliferation. The relative protein expression of cyclin D1 was analyzed in both whole-cell and nuclear fractions of liver, kidney and skeletal muscle from turtles exposed to 5 or 20 h of submergence anoxia. Expression of cyclin D1 in both total and nuclear fractions decreased significantly under anoxia in liver and kidney as compared with aerobic controls, but no significant change occurred in muscle. The relative phosphorylation state of cyclin D1 (threonine 286) was also unchanged during anoxia in all tissues. Since phosphorylation of threonine 286 is necessary for proteasomal degradation of cyclin D1, this implies that an alternative mechanism is responsible for cyclin D1 suppression in anoxia. Levels of cyclin D1 mRNA transcripts did not change under anoxia in any tissue, so a post-transcriptional method of regulation was implicated. Analysis of the 3'UTR of cyclin D1 showed the presence of both an AU-rich region and a conserved binding site for microRNA-16-1 and microRNA-15a. Levels of both microRNAs increased in liver and kidney (but not in muscle) under anoxic conditions, implicating microRNA inhibition of mRNA translation as the mechanism underlying the suppression of cyclin D1 protein levels in the anoxic turtle.


Open globe injuries in Nigerian children: epidemiological characteristics, etiological factors, and visual outcome.
To evaluate the epidemiological characteristics, the etiological factors, the type and severity of injury, visual outcome, and prognostic factors of open globe injuries in children. This was a retrospective non-comparative case study. A chart review was performed of patients aged 16 years or younger presented at the Eye Unit of the Federal Medical Centre Makurdi, Nigeria, between January 2001 and December 2006. Data were collected on patient demographics, geographic locale of injury, type of ocular injury and vision. Statistical significance was indicated by P < 0.05. The study sample comprised 78 children. A statistically significantly greater number of males (n = 51) sustained injury compared to females (n = 27; P < 0.05). The mean age of the study sample was 9.7 ± 2.40 years (range, 1 year 2 months to 15 years 8 months). The age-group that sustained injury most commonly was 6 years to 10 years. Left eyes were more likely to be affected, accounting for 53 (68.0%) cases. There were 54% (n = 42) of patients injured at home and 51.0% (n = 40) were injured while playing. The most common injury was corneoscleral laceration, (67.9% [n = 24] eyes). Only 30.0% (n = 23) patients presented within the first 24 hours of the injury, 38.5% (n = 30) of patients were visually impaired and 25.6% (n = 20) patients were blind on presentation. Visual acuity at last follow up indicated that 39.7% (n = 31) patients were visually impaired and 39.7% (n = 31) were blind. More public health efforts should be geared towards preventing potential causes of ocular injury at home and at playgrounds.


Cardioversion of atrial fibrillation. State of the art, 1995.
Since it was introduced in the late 1950s, direct-current cardioversion has been the standard procedure used to transfer patients with chronic atrial fibrillation to sinus rhythm. This review gives an overview of technical aspects of cardioversion, its risk and complications together with some clinical aspects, including factors of importance for a successful result. The haemodynamic benefits of sinus rhythm versus atrial fibrillation are also briefly emphasised, as are risk factors for thromboembolic events related to cardioversion. This review provides easily available information to those utilising this technology. A programme for cardioversion may be implemented on the basis of this.


Increasing trends of anaphylaxis-related events: an analysis of anaphylaxis using nationwide data in Taiwan, 2001-2013.
Anaphylaxis is a severe, potentially fatal, and systemic allergic reaction. Previous studies document increasing trends in incidence rates of anaphylaxis-related events in Western countries, yet little is known about the incidence and trend of anaphylaxis in Asia. In this study, we aimed to determine time trends in incidence rates of anaphylaxis-related events in Taiwan from 2001 through 2013. We utilized medical claims data from the National Health Insurance Research Databases in Taiwan. We identified anaphylaxis-related events (ICD-9-CM-codes: 995.0, 995.60-995.69, 999.41-999.42, and 999.49) and calculated incidence rates. Poisson regression models were applied to examine trends and incidence rates. A total of 2496 patients (mean age, 45.11 years; 56% male) with first-time anaphylaxis were identified during 34,430,000 person-years of observation time. The overall incidence of anaphylaxis was 7.25 (95% confidence interval (CI) = 6.97-7.53) per 100,000 person-years, increasing from 4.79 in 2001 to 8.20 in 2013, with an incidence rate ratio (IRR) of 1.05 (95%CI = 1.04-1.06). Over the 13-year period, the increasing trends were found in incident diagnosis of anaphylaxis-related outpatient or emergency department visits (IRR = 1.06, 95%CI = 1.05-1.08) and admissions to intensive care units (IRR = 1.06, 95%CI = 1.03-1.10), whereas the trends in incidence of anaphylaxis-related hospitalizations remained steady. The proportion of patients requiring hospitalizations among all patients with anaphylaxis (p _trend = 0.01), as well as the proportion requiring intensive care treatment among patients who were hospitalized (p _trend = 0.01), both increased with age. The incidence rate of anaphylaxis in Taiwan has increased at an average rate of 5% annually since 2001, paralleling the rising trends in several Western countries.


NGS catalog: A database of next generation sequencing studies in humans.
Next generation sequencing (NGS) technologies have been rapidly applied in biomedical and biological research since its advent only a few years ago, and they are expected to advance at an unprecedented pace in the following years. To provide the research community with a comprehensive NGS resource, we have developed the database Next Generation Sequencing Catalog (NGS Catalog, http://bioinfo.mc.vanderbilt.edu/NGS/index.html), a continually updated database that collects, curates and manages available human NGS data obtained from published literature. NGS Catalog deposits publication information of NGS studies and their mutation characteristics (SNVs, small insertions/deletions, copy number variations, and structural variants), as well as mutated genes and gene fusions detected by NGS. Other functions include user data upload, NGS general analysis pipelines, and NGS software. NGS Catalog is particularly useful for investigators who are new to NGS but would like to take advantage of these powerful technologies for their own research. Finally, based on the data deposited in NGS Catalog, we summarized features and findings from whole exome sequencing, whole genome sequencing, and transcriptome sequencing studies for human diseases or traits.


Value-Based Caching in Information-Centric Wireless Body Area Networks.
We propose a resilient cache replacement approach based on a Value of sensed Information (VoI) policy. To resolve and fetch content when the origin is not available due to isolated in-network nodes (fragmentation) and harsh operational conditions, we exploit a content caching approach. Our approach depends on four functional parameters in sensory Wireless Body Area Networks (WBANs). These four parameters are: age of data based on periodic request, popularity of on-demand requests, communication interference cost, and the duration for which the sensor node is required to operate in active mode to capture the sensed readings. These parameters are considered together to assign a value to the cached data to retain the most valuable information in the cache for prolonged time periods. The higher the value, the longer the duration for which the data will be retained in the cache. This caching strategy provides significant availability for most valuable and difficult to retrieve data in the WBANs. Extensive simulations are performed to compare the proposed scheme against other significant caching schemes in the literature while varying critical aspects in WBANs (e.g., data popularity, cache size, publisher load, connectivity-degree, and severe probabilities of node failures). These simulation results indicate that the proposed VoI-based approach is a valid tool for the retrieval of cached content in disruptive and challenging scenarios, such as the one experienced in WBANs, since it allows the retrieval of content for a long period even while experiencing severe in-network node failures.


Identification of a universal Group B streptococcus vaccine by multiple genome screen.
Group B Streptococcus (GBS) is a multiserotype bacterial pathogen representing a major cause of life-threatening infections in newborns. To develop a broadly protective vaccine, we analyzed the genome sequences of eight GBS isolates and cloned and tested 312 surface proteins as vaccines. Four proteins elicited protection in mice, and their combination proved highly protective against a large panel of strains, including all circulating serotypes. Protection also correlated with antigen accessibility on the bacterial surface and with the induction of opsonophagocytic antibodies. Multigenome analysis and screening described here represent a powerful strategy for identifying potential vaccine candidates against highly variable pathogens.


Genome-wide analysis reveals novel genes essential for heme homeostasis in Caenorhabditis elegans.
Heme is a cofactor in proteins that function in almost all sub-cellular compartments and in many diverse biological processes. Heme is produced by a conserved biosynthetic pathway that is highly regulated to prevent the accumulation of heme--a cytotoxic, hydrophobic tetrapyrrole. Caenorhabditis elegans and related parasitic nematodes do not synthesize heme, but instead require environmental heme to grow and develop. Heme homeostasis in these auxotrophs is, therefore, regulated in accordance with available dietary heme. We have capitalized on this auxotrophy in C. elegans to study gene expression changes associated with precisely controlled dietary heme concentrations. RNA was isolated from cultures containing 4, 20, or 500 microM heme; derived cDNA probes were hybridized to Affymetrix C. elegans expression arrays. We identified 288 heme-responsive genes (hrgs) that were differentially expressed under these conditions. Of these genes, 42% had putative homologs in humans, while genomes of medically relevant heme auxotrophs revealed homologs for 12% in both Trypanosoma and Leishmania and 24% in parasitic nematodes. Depletion of each of the 288 hrgs by RNA-mediated interference (RNAi) in a transgenic heme-sensor worm strain identified six genes that regulated heme homeostasis. In addition, seven membrane-spanning transporters involved in heme uptake were identified by RNAi knockdown studies using a toxic heme analog. Comparison of genes that were positive in both of the RNAi screens resulted in the identification of three genes in common that were vital for organismal heme homeostasis in C. elegans. Collectively, our results provide a catalog of genes that are essential for metazoan heme homeostasis and demonstrate the power of C. elegans as a genetic animal model to dissect the regulatory circuits which mediate heme trafficking in both vertebrate hosts and their parasites, which depend on environmental heme for survival.


Preferences and choices for care and health insurance.
Legislation that came into effect in 2006 has dramatically altered the health insurance system in the Netherlands, placing greater emphasis on consumer choice and competition among insurers. The potential for such competition depends largely on consumer preferences for price and quality of service by insurers and quality of affiliated providers. This study provides initial evidence on the preferences of Dutch consumers and how they view trade-offs between various aspects of health insurance product design. A key feature of the analysis is that we compare the responses of high and low risk individuals, where risk is defined by the presence of a costly chronic condition. This contrast is critically important for understanding incentives facing insurers and for identifying potential unanticipated consequences of market competition. The results from our conjoint analysis suggest that not only high risk but also low risk individuals are willing to pay substantially more for insurance products that can be shown to provide better health outcomes. This suggests that insurance products that are more expensive and provide better quality of care may also attract low risk individuals. Therefore, development and dissemination of good, reliable and understandable health plan performance indicators may effectively reduce the problem of adverse selection.


Metatranscriptomic Analyses of Diel Metabolic Functions During a Microcystis Bloom in Western Lake Erie (United States).
This study examined diel shifts in metabolic functions of Microcystis spp. during a 48-h Lagrangian survey of a toxin-producing cyanobacterial bloom in western Lake Erie in the aftermath of the 2014 Toledo Water Crisis. Transcripts mapped to the genomes of recently sequenced lower Great Lakes Microcystis isolates showed distinct patterns of gene expression between samples collected across day (10:00 h, 16:00 h) and night (22:00 h, 04:00 h). Daytime transcripts were enriched in functions related to Photosystem II (e.g., psbA), nitrogen and phosphate acquisition, cell division (ftsHZ), heat shock response (dnaK, groEL), and uptake of inorganic carbon (rbc, bicA). Genes transcribed during nighttime included those involved in phycobilisome protein synthesis and Photosystem I core subunits. Hierarchical clustering and principal component analysis (PCA) showed a tightly clustered group of nighttime expressed genes, whereas daytime transcripts were separated from each other over the 48-h duration. Lack of uniform clustering within the daytime transcripts suggested that the partitioning of gene expression in Microcystis is dependent on both circadian regulation and physicochemical changes within the environment.


Smoking cessation and survival among people diagnosed with non-metastatic cancer.
We aimed to estimate the effects of smoking cessation on survival among people diagnosed with cancer. We used data from a Comprehensive Community Cancer Program that is part of a large urban safety-net hospital system. Eligible patients were diagnosed with primary invasive solid tumors between 2013 and 2015, and were current smokers at time of diagnosis. Our exposure of interest was initiation of smoking cessation within 6 months of cancer diagnosis. We estimated inverse probability weighted restricted mean survival time (RMST) differences and risk ratio (RR) for all cause 3-year mortality. Our study population comprised 369 patients, of whom 42% were aged < 55 years, 59% were male, 44% were racial/ethnic minorities, and 59% were uninsured. The 3-year RMST was 1.8 (95% CL: - 1.5, 5.1) months longer for individuals who initiated smoking cessation within 6 months of cancer diagnosis. The point estimate for risk of 3-year mortality was lower for initiation of smoking cessation within 6 months of diagnosis compared with no initiation within 6 months (RR = 0.72, 95% CL: 0.37, 1.4). Our point estimates suggest longer 3-year survival, but the results are compatible with 1.5 month shorter or 5.1 longer 3-year overall survival after smoking cessation within 6 months of cancer diagnosis. Future studies with larger sample sizes that test the comparative effectiveness of different smoking cessation strategies are needed for more detailed evidence to inform decision-making about the effect of smoking cessation on survival among cancer patients. The benefits of smoking cessation after cancer diagnosis may include longer survival, but the magnitude of benefit is unclear.


Ultra-wideband optical leaky-wave slot antennas.
We propose and investigate an ultra-wideband leaky-wave antenna that operates at optical frequencies for the purpose of efficient energy coupling between localized nanoscale optical circuits and the far-field. The antenna consists of an optically narrow aluminum slot on a silicon substrate. We analyze its far-field radiation pattern in the spectral region centered around 1550 nm with a 50% bandwidth ranging from 2000 nm to 1200 nm. This plasmonic leaky-wave slot produces a maximum far-field radiation angle at 32° and a 3 dB beamwidth of 24° at its center wavelength. The radiation pattern is preserved within the 50% bandwidth suffering only insignificant changes in both the radiation angle and the beamwidth. This wide-band performance is quite unique when compared to other optical antenna designs. Furthermore, the antenna effective length for radiating 90% and 99.9% of the input power is only 0.5λ(0) and 1.5λ(0) respectively at 1550 nm. The versatility and simplicity of the proposed design along with its small footprint makes it extremely attractive for integration with nano-optical components using existing technologies.


Association between TERT promoter polymorphisms and acute myeloid leukemia risk and prognosis.
Telomerase reverse transcriptase gene (TERT) promoter mutations are identified in many malignancies but not in hematological malignancies. Here we analyzed TERT and protection of telomeres 1 gene (POT1) mutations, and four different TERT SNVs in 226 acute myeloid leukemia (AML) patients and 806 healthy individuals in a case referent design, where also overall survival was assessed. A significant association for increased risk of AML was found for TERT SNVs, rs2853669 (OR = 2.45, p = 0.00015) and rs2736100 (OR = 1.5, p = 0.03). The overall survival for patients with CC genotype of rs2853669 was significantly shorter compared to those with TT or TC genotypes (p = 0.036 and 0.029 respectively). The influence of TERT rs2853669 CC on survival was confirmed in multivariable Cox regression analysis as an independent risk biomarker in addition to high risk group, higher age and treatment. No hot spot TERT promoter mutations at -228C > T or -250C > T or POT1 mutations could be identified in this AML cohort. We show that rs2853669 CC may be a risk factor for the development of AML that may also be used as a prognostic marker to identify high risk normal karyotype-AML (NK-AML) patients, for treatment guidance.


Active hematopoietic hubs in Drosophila adults generate hemocytes and contribute to immune response.
Blood cell development in Drosophila shares significant similarities with vertebrate. The conservation ranges from biphasic mode of hematopoiesis to signaling molecules crucial for progenitor cell formation, maintenance, and differentiation. Primitive hematopoiesis in Drosophila ensues in embryonic head mesoderm, whereas definitive hematopoiesis happens in larval hematopoietic organ, the lymph gland. This organ, with the onset of pupation, ruptures to release hemocytes into circulation. It is believed that the adult lacks a hematopoietic organ and survives on the contribution of both embryonic and larval hematopoiesis. However, our studies revealed a surge of blood cell development in the dorsal abdominal hemocyte clusters of adult fly. These active hematopoietic hubs are capable of blood cell specification and can respond to bacterial challenges. The presence of progenitors and differentiated hemocytes embedded in a functional network of Laminin A and Pericardin within this hematopoietic hub projects it as a simple version of the vertebrate bone marrow.


Vibration measurement by the time-averaged electronic speckle pattern interferometry methods.
Three different image-processing methods based on the time-averaged technique were compared by the electronic speckle pattern interferometry (ESPI) technique for vibration measurement. The three methods are the video-signal-addition method, the video-signal-subtraction method, and the amplitude-fluctuation method. Also, errors introduced by using the zero-order Bessel function directly into the analysis of the fringe pattern were investigated. The video-signal-addition method has been the most generally used ESPI technique for vibration measurement. However, without additional image and/or signal-processing procedures, the fringe pattern obtained directly by the video-signal-addition method is rather difficult to observe. The reason for poor visibility of the experimentally obtained fringe pattern with this method is explained. To increase the fringe pattern's visibility without additional image and/or signal processes, we tried two video-signal-subtraction methods. One of the two methods is the video-signal-subtraction method that has normally been used in the static applications. The other method, called the amplitude-fluctuation method, and its associated theory are reported here.


Structure formation in diindenoperylene thin films on copper(111).
First-principles calculations were combined with scanning tunneling microscopy (STM) measurements to analyze the adsorption of diindenoperylene (DIP) molecules on Cu(111) surfaces. The influence of the substrate on the geometry of single adsorbed molecules, their diffusion barriers, as well as the role of step-edges and intermolecular interactions for molecular self-assembly and structure growth are studied. Long-range ordered arrangements of DIP molecules are found to be most favorable irrespective of the terrace width. Energetically less favored short-range order structures, however, are observed as well.


Fluctuating optimum and temporally variable selection on breeding date in birds and mammals.
Temporal variation in natural selection is predicted to strongly impact the evolution and demography of natural populations, with consequences for the rate of adaptation, evolution of plasticity, and extinction risk. Most of the theory underlying these predictions assumes a moving optimum phenotype, with predictions expressed in terms of the temporal variance and autocorrelation of this optimum. However, empirical studies seldom estimate patterns of fluctuations of an optimum phenotype, precluding further progress in connecting theory with observations. To bridge this gap, we assess the evidence for temporal variation in selection on breeding date by modeling a fitness function with a fluctuating optimum, across 39 populations of 21 wild animals, one of the largest compilations of long-term datasets with individual measurements of trait and fitness components. We find compelling evidence for fluctuations in the fitness function, causing temporal variation in the magnitude, but not the direction of selection. However, fluctuations of the optimum phenotype need not directly translate into variation in selection gradients, because their impact can be buffered by partial tracking of the optimum by the mean phenotype. Analyzing individuals that reproduce in consecutive years, we find that plastic changes track movements of the optimum phenotype across years, especially in bird species, reducing temporal variation in directional selection. This suggests that phenological plasticity has evolved to cope with fluctuations in the optimum, despite their currently modest contribution to variation in selection.


Compensatory load redistribution of horses with induced weightbearing hindlimb lameness trotting on a treadmill.
The compensatory mechanisms of horses with weightbearing hindlimb lameness are still not fully understood. That weightbearing, unilateral hindlimb lameness would not only alter stride characteristics to diminish structural stress in the affected limb but also induce compensatory load adjustments in the other supporting limbs. To document the load and time shifting mechanisms of horses with unilateral weightbearing hindlimb lameness. Reversible lameness was induced in 8 clinically sound horses by applying a solar pressure model. Three degrees of lameness (subtle, mild and moderate) were induced and compared with the nonlame (sound) control measurement. Vertical ground reaction forces were recorded for all 4 limbs simultaneously on an instrumented treadmill. Compared to the sound situation, moderate hindlimb hoof lameness induced a decrease in stride duration (-3.3%) and stride impulse (-3.1%). Diagonal impulse decreased selectively in the lame diagonal stance (-7.7%). Within the diagonal limb pair, vertical impulse was shifted to the forelimb during the lame diagonal stance (+6.5%) and to the hindlimb during the sound diagonal stance (+3.2%). Peak vertical force and vertical impulse decreased in the lame limb (-15%), but only vertical impulse increased in the contralateral hindlimb (+5.7%). Stance duration was prolonged in both hindlimbs (+2.5%). Suspension duration was reduced to a greater extent after push-off of the lame diagonal limb pair (-21%) than after the sound diagonal limb pair (-9.2%). Four compensatory mechanisms could be identified that served to reduce structural stress, i.e. peak vertical force on the affected limb: 1) reduction of the total vertical impulse per stride; 2) diagonal impulse decreased selectively in the lame diagonal; 3) impulse was shifted within the lame diagonal to the forelimb and in the sound diagonal to the hindlimb; and 4) the rate of loading and peak forces were reduced by prolonging the stance duration. Load shifting mechanisms are not only effective in diminishing peak forces in the affected limb, but also suppress compensatory overload in other limbs. Selected force and time parameters allow the unequivocal identification of the lame limb. Future studies have to examine how far these compensatory mechanisms may be generalised for other defined orthopaedic problems in the hindlimb.


Loop-Mediated Isothermal Amplification Test for Trypanosoma gambiense Group 1 with Stem Primers: A Molecular Xenomonitoring Test for Sleeping Sickness.
The World Health Organization has targeted Human African Trypanosomiasis (HAT) for elimination by 2020 with zero incidence by 2030. To achieve and sustain this goal, accurate and easy-to-deploy diagnostic tests for Gambian trypanosomiasis which accounts for over 98% of reported cases will play a crucial role. Most needed will be tools for surveillance of pathogen in vectors (xenomonitoring) since population screening tests are readily available. The development of new tests is expensive and takes a long time while incremental improvement of existing technologies that have potential for xenomonitoring may offer a shorter pathway to tools for HAT surveillance. We have investigated the effect of including a second set of reaction accelerating primers (stem primers) to the standard T. brucei gambiense LAMP test format. The new test format was analyzed with and without outer primers. Amplification was carried out using Rotorgene 6000 and the portable ESE Quant amplification unit capable of real-time data output. The stem LAMP formats indicated shorter time to results (~8 min), were 10-100-fold more sensitive, and indicated higher diagnostic sensitivity and accuracy compared to the standard LAMP test. It was possible to confirm the predicted product using ESE melt curves demonstrating the potential of combining LAMP and real-time technologies as possible tool for HAT molecular xenomonitoring.


Induction of neutralizing antibodies against human immunodeficiency virus type 1 primary isolates by Gag-Env pseudovirion immunization.
A major challenge for the development of an effective HIV vaccine is to elicit neutralizing antibodies against a broad array of primary isolates. Monomeric gp120-based vaccine approaches have not been successful in inducing this type of response, prompting a number of approaches designed to recreate the native glycoprotein complex that exists on the viral membrane. Gag-Env pseudovirions are noninfectious viruslike particles that recreate the native envelope glycoprotein structure and have the potential to generate neutralizing antibody responses against primary isolates. In this study, an inducible cell line was created in order to generate Gag-Env pseudovirions for examination of neutralizing antibody responses in guinea pigs. Unadjuvanted pseudovirions generated relatively weak anti-gp120 responses, while the use of a block copolymer water-in-oil emulsion or aluminum hydroxide combined with CpG oligodeoxynucleotides resulted in high levels of antibodies that bind to gp120. Sera from immunized animals neutralized a panel of human immunodeficiency virus (HIV) type 1 primary isolate viruses at titers that were significantly higher than that of the corresponding monomeric gp120 protein. Interpretation of these results was complicated by the occurrence of neutralizing antibodies directed against cellular (non-envelope protein) components of the pseudovirion. However, a major component of the pseudovirion-elicited antibody response was directed specifically against the HIV envelope. These results provide support for the role of pseudovirion-based vaccines in generating neutralizing antibodies against primary isolates of HIV and highlight the potential confounding role of antibodies directed at non-envelope cell surface components.


Beyond active learning: a case study of teaching practices in an occupation-centered curriculum.
Although occupation-centered curricula are highly promoted, the teaching processes that convey such designs remain unclear. This case study elucidated occupation-centered teaching practices. Interview and observational data were collected over 8 weeks, and analysis involved coding transcriptions, data matrices, concept maps, journaling, and writing. Participants augmented active learning strategies with strategies that linked course topics to the subject of occupation. The use of linking strategies suggested that: (a) course content was treated as two-tiered; (b) neither content nor instructional processes were inherently occupation-centered; and (c) subject-centered education strengthens social learning theories. Although curricula may appear occupation-centered based on a curriculum description and course content, ultimately "linking opportunities" in the classroom constitute an essential feature that demarcates a program as occupation-centered.


Occult pulmonary haemorrhage in leukaemia.
Through gleeding into the lung parenchyma is responsible for morbidity and mortality in patients with leukaemia pulmonary haemorrhage is seldom diagnosed during life. We diagnosed occult pulmonary haemorrhage in five leukaemic patients with unexplained infiltrates on chest roetgenograms by examining alveolar macrophages retrieved by bronchopulmonary lavage. Macrophage haemosiderin content was greatly increased in the patients with pulmonary haemorrhage as compared to normal and thrombocytopenic control subjects. Haemoglobin and intact erythrocytes in alveolar macrophages were taken as evidence of recent haemorrhage. Intrapulmonary bleeding may occur often in patients with leukaemia, and bronchopulmonary lavage offers a safe approach to diagnosis and allows for concomitant identification of pulmonary infection.