Hepatitis C Virus Screening Trends: Serial Cross-Sectional Analysis of the National Health Interview Survey Population, 2013-2015.
Background: Rates of hepatitis C virus (HCV) infection are markedly higher for baby boomers compared with other birth cohorts, and they are now recommended for universal one-time screening. This study examines HCV screening rates and predictors for four birth cohorts [born <1945, born 1945-1965 (baby boomers), born 1966-1985, and born >1985] of a nationally representative sample over time.Methods: We used data from the 2013-2015 National Health Interview Surveys, an annual weighted survey of the U.S. civilian noninstitutionalized population. We assessed HCV screening prevalence stratified birth cohort with bivariate and multivariable logistic regression analyses.Results: There were 15,100 participants born <1945, 28,725 baby boomers, 28,089 born 1966-1985, and 13,296 born >1985 in the final analytic sample. Screening was 11.5%-12.8% for baby boomers. The second youngest birth cohort was similar to baby boomers (13.7%-14.9%), whereas the older birth cohort was screened less. After excluding participants who typically have higher rates of HCV screening than the general population, we developed a multivariable model of the general population. In the final model for baby boomers the odds of HCV screening increased significantly with each subsequent year (OR=1.20; 95% CI=1.05-1.38 and OR=1.31; 95% CI=1.13-1.52). HCV screening was also significantly associated with age, gender, and race/ethnicity in baby boomers.Conclusions: While HCV screening is increasing over time, these increases are minimal and there is substantial room for improvement.Impact: Future research should develop interventions to increase HCV screening with special focus on groups demonstrating significantly lower screening rates, such as Hispanics and females. Cancer Epidemiol Biomarkers Prev; 27(4); 503-13. ©2018 AACR.


Computer and internet use by first year clinical and nursing students in a Nigerian teaching hospital.
The internet is an important source of up-to-date medical information. Although several studies in different countries have explored the extent to which health science students use the computer and the internet, few researches are available on this subject in Nigeria. The aim of this study was to assess the uptake of computer and internet by health science students studying in the country. One hundred and eighty three first year medical and nursing students of the University College Hospital, Ibadan, Nigeria, completed a-25 item questionnaire during routine Library Orientation Program in the medical library. The EPI-Info software was used for data analysis. The mean ages for medical students and the student nurses were 22 and 24.6 years respectively. Overall, 42.6% of the entire sample could use the computer, 57.4% could not. While more than half (58%) of the medical students are computer literate, majority (75.9%) of the student nurses are not. Slightly more than two thirds (60.7%) of the entire students had ever used the internet, 33. 9% had not. E-mail was the most popular of internet services used by the students (76.4%) and the cyber café was the common place where students had accessed these services. The students' mean scores on a 15-point perceived self-efficacy scale for internet-related tasks was 3.8 for medical and 0.7 for nursing students (p = 0.00). Students who are computer literate had superior mean scores (4.8) than those without (0.6) (p = 0.000). First year clinical and nursing students in Ibadan Nigeria have not fully utilised the opportunity that the use of computer and internet offer for medical education. Improved efforts such as inclusion of computer education in medical and nursing curricular and establishment of computer laboratories are required to increase the student's access to computers and internet.


Labeling graphene oxygen groups with europium.
Graphene-related materials contain chemically bonded oxygen atoms in the form of epoxy, hydroxy, carboxy, and carbonyl groups. It is important to determine the quantity of oxygen atoms and to understand their position on the graphene sheet. However, visualization of these groups by standard methods is a challenge. Here, we utilize europium(III) as a selective label for oxygen-containing groups. We studied three different graphene-related materials: 1) graphene oxide, 2) chemically reduced graphene oxide, and 3) thermally reduced graphene oxide (the number of oxygen containing groups decreases from material 1 to 3). We show that it is possible to efficiently use Eu as a label of oxygen-containing groups. This Eu label could be applied to determine the precise location of oxygen-containing groups on graphene sheets and also induce novel optical, electrochemical, and catalytic properties.


Validity conditions for stochastic chemical kinetics in diffusion-limited systems.
The chemical master equation (CME) and the mathematically equivalent stochastic simulation algorithm (SSA) assume that the reactant molecules in a chemically reacting system are "dilute" and "well-mixed" throughout the containing volume. Here we clarify what those two conditions mean, and we show why their satisfaction is necessary in order for bimolecular reactions to physically occur in the manner assumed by the CME and the SSA. We prove that these conditions are closely connected, in that a system will stay well-mixed if and only if it is dilute. We explore the implications of these validity conditions for the reaction-diffusion (or spatially inhomogeneous) extensions of the CME and the SSA to systems whose containing volumes are not necessarily well-mixed, but can be partitioned into cubical subvolumes (voxels) that are. We show that the validity conditions, together with an additional condition that is needed to ensure the physical validity of the diffusion-induced jump probability rates of molecules between voxels, require the voxel edge length to have a strictly positive lower bound. We prove that if the voxel edge length is steadily decreased in a way that respects that lower bound, the average rate at which bimolecular reactions occur in the reaction-diffusion CME and SSA will remain constant, while the average rate of diffusive transfer reactions will increase as the inverse square of the voxel edge length. We conclude that even though the reaction-diffusion CME and SSA are inherently approximate, and cannot be made exact by shrinking the voxel size to zero, they should nevertheless be useful in many practical situations.


Task constraints distinguish perspective inferences from perspective use during discourse interpretation in a false belief task.
Interpreting other peoples' actions relies on an understanding of their current mental states (e.g. beliefs, desires and intentions). In this paper, we distinguish between listeners' ability to infer others' perspectives and their explicit use of this knowledge to predict subsequent actions. In a visual-world study, two groups of participants (passive observers vs. active participants) watched short videos, depicting transfer events, where one character ('Jane') either held a true or false belief about an object's location. We tracked participants' eye-movements around the final visual scene, time-locked to related auditory descriptions (e.g. "Jane will look for the chocolates in the container on the left".). Results showed that active participants had already inferred the character's belief in the 1s preview period prior to auditory onset, before it was possible to use this information to predict an outcome. Moreover, they used this inference to correctly anticipate reference to the object's initial location on false belief trials at the earliest possible point (i.e. from "Jane" onwards). In contrast, passive observers only showed evidence of a belief inference from the onset of "Jane", and did not show reliable use of this inference to predict Jane's behaviour on false belief trials until much later, when the location ("left/right") was auditorily available. These results show that active engagement in a task activates earlier inferences about others' perspectives, and drives immediate use of this information to anticipate others' actions, compared to passive observers, who are susceptible to influences from egocentric or reality biases. Finally, we review evidence that using other peoples' perspectives to predict their behaviour is more cognitively effortful than simply using one's own.


Unwanted horses: The role of nonprofit equine rescue and sanctuary organizations.
Closure of US equine slaughter facilities in 2007 along with the concomitant economic recession have contributed to a sharp increase in the number of unwanted horses throughout the United States, with estimates totaling 100,000 horses per year. The objective of the study was to obtain comprehensive data regarding nonprofit organizations caring for unwanted horses, along with the characteristics and outcome of horses relinquished to these organizations. Nonprofit organizations that accept relinquished equines were contacted to participate in a 90-question survey. Responding organizations (144 of 326 eligible) in 37 states provided information on 280 cases representative of the 7,990 horses relinquished between 2007 and 2009. Data collected characterized these organizations as being in existence for 6 yr, financially supported through donations and personal funds, dedicated to the care of only 10 to 20 horses on a property of just over 30 acres, and reliant on volunteers for help. Funding was the greatest challenge to continued operation of nonprofit equine organizations, with maintenance costs for the care of a relinquished horse averaging $3,648 per year. Financial hardship, physical inability, or lack of time to care for the horses by owners were the most common reasons for relinquishment, followed by seizure through law enforcement agencies for alleged neglect or abuse. Relinquished horses consisted of mostly light horse breeds (79.3%), with Thoroughbreds and Quarter Horses as the most represented breeds. The age of relinquished horses ranged from 3 d to 42 yr old (12.4 ± 0.5 yr). About one-half of the horses entered in the survey were considered unhealthy due to illness, injury, lameness, or poor body condition. For every 4 horses relinquished to a nonprofit organization, only 3 horses were adopted or sold between 2006 and 2009, and many organizations had refused to accept additional horses for lack of resources. The estimated maximum capacity for the 326 eligible registered nonprofit equine rescue facilities of 13,400 is well below the widely published estimate of 100,000 horses that become unwanted in the United States every year. Nonprofit equine rescue and sanctuary facilities have historically played an important role in safeguarding the welfare of horses in society, but funding and capacity are limiting factors to their potential expansion in continuing to care for the current population of unwanted and neglected horses in the United States.


Assessment of vaccine herd protection in a cluster-randomised trial of Vi conjugate vaccine against typhoid fever: results of further analysis.
A cluster-randomised trial of Vi-tetanus toxoid (Vi-TT) conjugate vaccine conducted in urban Bangladeshi children found a high level of direct protection by Vi-TT but no significant vaccine herd protection. We reassessed the trial using a "fried egg" analysis to evaluate whether herd protection might have been obscured by transmission of typhoid into the clusters from the outside. A participant- and observer-blind, cluster-randomised trial was conducted between February 14, 2018 and August 12, 2019 in three wards of Mirpur, a densely populated urban area of Dhaka, Bangladesh. Children 9 months to under 16 years of age in 150 geographic clusters, which had a total of 311,289 persons present at baseline or entering during follow-up, were randomised by cluster to a single-dose of Vi-TT or Japanese encephalitis (JE) vaccine. Vi-TT protection against typhoid fever, detected at 8 treatment centres serving the study population, was compared in the original clusters for the trial, and for progressively more central subclusters ("yolks" of the "fried egg") of the cluster residents. If transmission of typhoid into the clusters had diluted observed vaccine herd protection, we hypothesised that analysis of the innermost "yolks" would reveal vaccine herd protection that was not evident in analysis of the entire clusters. The trial is registered at www.isrctn.com as ISRCTN11643110. At ≤18 months of follow-up, total vaccine effectiveness (protection of Vi-TT recipients relative to JE vaccine recipients) was 85% (95% CI: 76%, 90%); indirect effectiveness (protection of non-Vi-TT recipients in Vi-TT clusters relative to non-JE vaccine recipients in JE vaccine clusters) was 17% (95% CI: -13%, 40%); and overall effectiveness (protection of all residents in the Vi-TT clusters relative to all residents of the JE vaccine clusters) was 57% (95% CI: 44%, 66%). Analyses of subpopulations in inner 75%, 50% and 25% "yolks" of the clusters failed to reveal significant changes in any of these estimates. Our analysis did not reveal Vi-TT herd protection in the trial. Consideration should be given to exploring whether targeting adults as well as children with Vi-TT yields appreciable levels of vaccine herd protection. Bill & Melinda Gates Foundation (OPP1151153, INV-025388).


Tracking the time-course of attentional involvement in spatial working memory: an event-related potential investigation.
Spatial working memory is a cognitive brain mechanism that enables the temporary maintenance and manipulation of spatial information. Recent neuroimaging and behavioral studies have led to the proposal that directed spatial attention is the mechanism by which location information is maintained in spatial working memory. Yet it is unclear whether attentional involvement is required throughout the period of active maintenance or is only invoked during discrete task-phases such as mnemonic encoding. In the current study, we aimed to track the time-course of attentional involvement during spatial working memory by recording event-related brain potentials (ERPs) from healthy volunteers. In Experiment 1, subjects performed a delayed-recognition task. Each trial began with the presentation of a brief stimulus (S1) that indicated the relevant location that subjects were to maintain in working memory. A 4.8-5.3 sec delay interval followed during which a single task-irrelevant probe was presented. The delay interval concluded with a test item (S2) to which subjects made a response indicating whether the S2-location was the same as the S1-memory location. To determine if attention was differentially engaged during discrete phases of the trial, task-irrelevant probes were presented early (400-800 msec following S1-offset) or late (2600-3000 msec following S1-offset) during the delay interval. Sensory-evoked ERPs (P1 and N1) elicited by these irrelevant probes showed attention-like modulations with greater amplitude responses for probes occurring at the S1-memory locations in comparison to probes presented at other locations. This pattern was obtained for both early- and late-delay probes. Probe-evoked activity during delayed-recognition trials was similar to activity observed when spatial attention was explicitly focused on a location in visual space (Experiment 2). These results are consistent with a model of spatial working memory in which perceptual level selective attention is utilized throughout the entire period of active maintenance to keep relevant spatial information in mind.


Feasibility of a tobacco cessation intervention for pregnant Alaska Native women.
Among Alaska Native women residing in the Yukon-Kuskokwim (Y-K) Delta region of Western Alaska, about 79% smoke cigarettes or use smokeless tobacco during pregnancy. Treatment methods developed and evaluated among Alaska Native pregnant tobacco users do not exist. This pilot study used a randomized two-group design to assess the feasibility and acceptability of a targeted cessation intervention for Alaska Native pregnant women. Recruitment occurred over an 8-month period. Enrolled participants were randomly assigned to the control group (n = 18; brief face-to-face counseling at the first visit and written materials) or to the intervention group (n = 17) consisting of face-to-face counseling at the first visit, four telephone calls, a video highlighting personal stories, and a cessation guide. Interview-based assessments were conducted at baseline and follow-up during pregnancy (>or=60 days postrandomization). Feasibility was determined by the recruitment and retention rates. The participation rate was very low with only 12% of eligible women (35/293) enrolled. Among enrolled participants, the study retention rates were high in both the intervention (71%) and control (94%) groups. The biochemically confirmed abstinence rates at follow-up were 0% and 6% for the intervention and control groups, respectively. The low enrollment rate suggests that the program was not feasible or acceptable. Alternative approaches are needed to improve the reach and efficacy of cessation interventions for Alaska Native women.


Environmental and social influences on emerging infectious diseases: past, present and future.
During the processes of human population dispersal around the world over the past 50 000-100 000 years, along with associated cultural evolution and inter-population contact and conflict, there have been several major transitions in the relationships of Homo sapiens with the natural world, animate and inanimate. Each of these transitions has resulted in the emergence of new or unfamiliar infectious diseases. The three great historical transitions since the initial advent of agriculture and livestock herding, from ca. 10 000 years ago, occurred when: (i) early agrarian-based settlements enabled sylvatic enzootic microbes to make contact with Homo sapiens; (ii) early Eurasian civilizations (such as the Greek and Roman empires, China and south Asia) came into military and commercial contact, ca. 3000-2000 years ago, swapping their dominant infections; and (iii) European expansionism, over the past five centuries, caused the transoceanic spread of often lethal infectious diseases. This latter transition is best known in relation to the conquest of the Americas by Spanish conquistadores, when the inadvertent spread of measles, smallpox and influenza devastated the Amerindian populations.Today, we are living through the fourth of these great transitional periods. The contemporary spread and increased lability of various infectious diseases, new and old, reflect the combined and increasingly widespread impacts of demographic, environmental, behavioural, technological and other rapid changes in human ecology. Modern clinical medicine has, via blood transfusion, organ transplantation, and the use of hypodermic syringes, created new opportunities for microbes. These have contributed to the rising iatrogenic problems of hepatitis C, HIV/AIDS and several other viral infections. Meanwhile, the injudicious use of antibiotics has been a rare instance of human action actually increasing 'biodiversity'. Another aspect of this fourth transition is that modern hyper-hygienic living restricts microbial exposure in early life. This, in the 1950s, may have contributed to an epidemic of more serious, disabling, poliomyelitis, affecting older children than those affected in earlier, more endemic decades. As with previous human-microbe transitions, a new equilibrial state may lie ahead. However, it certainly will not entail a world free of infectious diseases. Any mature, sustainable, human ecology must come to terms with both the need for, and the needs of, the microbial species that help to make up the interdependent system of life on Earth. Humans and microbes are not "at war"; rather, both parties are engaged in amoral, self-interested, coevolutionary struggle. We need to understand better, and therefore anticipate, the dynamics of that process.


Intra-amygdaloid infusion of Ginkgo biloba leaf extract (EGb761) facilitates fear-potentiated startle in rats.
Ginkgo biloba extract, EGb761, is one of the most commonly used herbal supplements throughout Western society. It has been used in the treatment of various common geriatric complaints including short-term memory loss. We showed that acute systemic administration of EGb761 enhanced fear-potentiated startle (FPS) in rats. Little is known about the behavioral effects of centrally administered EGb761 on FPS. The current study was performed to evaluate the involvement of basolateral nucleus of amygdala (BLA) in the EGb761 facilitation effect on FPS. Male adult SD rats were used. EGb761 was infused into cerebroventricle or basolateral nucleus of amygdala 10 min prior to fear conditioning. Animals were then tested for FPS 24 h later. Results showed that (1) intra-cerebroventricular infusion of EGb761 (0.1, 1.0, or 3.0 microg/3.0 microl per side, bilaterally) and intra-amygdaloid infusion of EGb761 (1.0, 14.0, or 28.0 ng/microl per side, bilaterally) 30 and 10 min prior to fear conditioning, respectively, facilitated FPS in a dose-dependent manner. (2) Administration of EGb761 did not impair an animal's basal startle response or pain perception. (3) Subsequent control experiment's results indicated that the facilitation effect of EGb761 on the acquisition was not due to anxiogenic effect or non-specific effect. These results suggested that a single dose of EGb761 also has memory-enhancing effects in young animals. In addition, BLA is the central locus for EGb761 facilitation effect on FPS.


An rpsL cassette, janus, for gene replacement through negative selection in Streptococcus pneumoniae.
Natural genetic transformation offers a direct route by which synthetic gene constructs can be placed into the single circular chromosome of Streptococcus pneumoniae. However, the lack of a general negative-selection marker has hampered the introduction of constructs that do not confer a selectable phenotype. A 1.3-kb cassette was constructed comprising a kanamycin (Kn) resistance marker (kan) and a counterselectable rpsL(+) marker. The cassette conferred dominant streptomycin (Sm) sensitivity in an Sm-resistant background in S. pneumoniae. It was demonstrated that it could be used in a two-step transformation procedure to place DNA of arbitrary sequence at a chosen target site. The first transformation into an Sm-resistant strain used the cassette to tag a target gene on the chromosome by homologous recombination while conferring Kn resistance but Sm sensitivity on the recombinant. Replacement of the cassette by an arbitrary segment of DNA during a second transformation restored Sm resistance (and Kn sensitivity), allowing construction of silent mutations and deletions or other gene replacements which lack a selectable phenotype. It was also shown that gene conversion occurred between the two rpsL alleles in a process that depended on recA and that was susceptible to correction by mismatch repair.


Human AP endonuclease 1 (HAP1) protein expression in breast cancer correlates with lymph node status and angiogenesis.
Human AP endonuclease (HAP1) plays a major role in the repair of apurinic/apyrimidinic (AP) sites in cellular DNA. We used immunohistochemistry to examine the expression of HAP1 in normal breast and in 102 primary breast carcinomas. In normal breast epithelium, HAP1 had a uniformly nuclear localization. However, in lactating glandular epithelium, the expression of HAP1 was predominantly cytoplasmic. In carcinomas, both nuclear and cytoplasmic (44%), cytoplasmic (28%) or nuclear staining (24%) were observed. In four cases (4%), no HAP1 expression was detected. All patterns of expression for HAP1 were demonstrated for ductal carcinomas in situ (DCIS), although comedo-type DCIS were usually accompanied by mostly cytoplasmic staining. Similarly, the HAP1 expression in regions of invasive tumour necrosis was cytoplasmic. Pure nuclear HAP1 expression was significantly correlated with low angiogenesis (P = 0.007) and negative lymph node status (P = 0.001). In contrast, cases with cytoplasmic as well as nuclear staining were associated with poor prognostic factors, such as high angiogenesis (P = 0.03) and node positivity (P = 0.03). The pure nuclear staining may be related to better differentiation, as in normal breast, and hence better prognostic features, and cytoplasmic staining to a more metabolically active phenotype with high protein synthesis, as in lactating breast.


Consecutive aquatic jump-gliding with water-reactive fuel.
Robotic vehicles that are capable of autonomously transitioning between various terrains and fluids have received notable attention in the past decade due to their potential to navigate previously unexplored and/or unpredictable environments. Specifically, aerial-aquatic mobility will enable robots to operate in cluttered aquatic environments and carry out a variety of sensing tasks. One of the principal challenges in the development of such vehicles is that the transition from water to flight is a power-intensive process. At a small scale, this is made more difficult by the limitations of electromechanical actuation and the unfavorable scaling of the physics involved. This paper investigates the use of solid reactants as a combustion gas source for consecutive aquatic jump-gliding sequences. We present an untethered robot that is capable of multiple launches from the water surface and of transitioning from jetting to a glide. The power required for aquatic jump-gliding is obtained by reacting calcium carbide powder with the available environmental water to produce combustible acetylene gas, allowing the robot to rapidly reach flight speed from water. The 160-gram robot could achieve a flight distance of 26 meters using 0.2 gram of calcium carbide. Here, the combustion process, jetting phase, and glide were modeled numerically and compared with experimental results. Combustion pressure and inertial measurements were collected on board during flight, and the vehicle trajectory and speed were analyzed using external tracking data. The proposed propulsion approach offers a promising solution for future high-power density aerial-aquatic propulsion in robotics.


Two pathways to causal control: use and availability of information in the environment in people with and without signs of depression.
Perceiving one's causal control is important for adaptive behavior. Studying depression and other individual differences has provided insight into typical as well as pathological causal processing. We set out to study factors that have been shown to distinguish those with and without signs of depression and affect perceptions of causal control: levels of behavior, the availability of outcomes and learning about the environment or context. Two experiments were carried out in which participants, scoring low and high on the Beck Depression Inventory using established cutoffs, completed a causal control task, in which outcomes occurred with a low (.25) or high probability (.75). Behavior levels were either constrained (N1=73) or unconstrained (N2=74). Overall, findings showed that levels of behavior influenced people's experiences of the context in which events occurred. For all participants, very high behavior levels eliminated sensitivity to levels of outcomes occurring in the environment and lead to judgments that were consistent with conditional probabilities as opposed to the experimenter programmed contingency. Thus increased behavior increased perceived control via influence on context experience. This effect was also evident for those scoring high on the BDI. Overall conclusions are that behavior and context provide two important interlinked psychological pathways to perceived control. However, situations that constrain people's ability to respond freely can prevent people with signs of depression from taking control of a situation that would otherwise be uncontrollable.


Insulin in ischaemic heart disease: are associations explained by triglyceride concentrations? The Caerphilly prospective study.
To investigate the predictive value of fasting insulin concentrations for subsequent fatal or non-fatal ischaemic heart disease at five year follow up and to examine the associations between insulin and other indicators of risk. A prospective population study among 2512 men aged 45 to 59 at recruitment. A whole population sample of men resident in Caerphilly, South Wales. At recruitment fasting blood samples were taken for measurement of plasma lipids and serum insulin. Men were re-examined at a five year follow up and ischaemic heart disease events during this period were assessed from hospital notes, death certificates, and electrocardiograms. Diabetic men and those men with a fasting blood glucose of > or = 8 mmol/l were excluded from all analyses. In a univariate analysis the incidence of ischaemic heart disease increased with increasing concentration of fasting insulin, such that for men in the top 20% of the insulin distribution the odds of developing ischaemic heart disease were 1.87 relative to men in the bottom 20%. On multivariate analysis this relation disappeared on adjusting for plasma triglycerides, body mass index, and evidence of ischaemic heart disease at recruitment. In this population in South Wales there was no evidence that the fasting insulin concentration is an independent risk factor for ischaemic heart disease. The univariate association between insulin and incident disease was almost entirely explained by the association of both with triglycerides and body mass index.


Automatic Image Guidance for Assessment of Placenta Location in Ultrasound Video Sweeps.
Ultrasound-based assistive tools are aimed at reducing the high skill needed to interpret a scan by providing automatic image guidance. This may encourage uptake of ultrasound (US) clinical assessments in rural settings in low- and middle-income countries (LMICs), where well-trained sonographers can be scarce. This paper describes a new method that automatically generates an assistive video overlay to provide image guidance to a user to assess placenta location. The user captures US video by following a sweep protocol that scans a U-shape on the lower maternal abdomen. The sweep trajectory is simple and easy to learn. We initially explore a 2-D embedding of placenta shapes, mapping manually segmented placentas in US video frames to a 2-D space. We map 2013 frames from 11 videos. This provides insight into the spectrum of placenta shapes that appear when using the sweep protocol. We propose classification of the placenta shapes from three observed clusters: complex, tip and rectangular. We use this insight to design an effective automatic segmentation algorithm, combining a U-Net with a CRF-RNN module to enhance segmentation performance with respect to placenta shape. The U-Net + CRF-RNN algorithm automatically segments the placenta and maternal bladder. We assess segmentation performance using both area and shape metrics. We report results comparable to the state-of-the-art for automatic placenta segmentation on the Dice metric, achieving 0.83 ± 0.15 evaluated on 2127 frames from 10 videos. We also qualitatively evaluate 78,308 frames from 135 videos, assessing if the anatomical outline is correctly segmented. We found that addition of the CRF-RNN improves over a baseline U-Net when faced with a complex placenta shape, which we observe in our 2-D embedding, up to 14% with respect to the percentage shape error. From the segmentations, an assistive video overlay is automatically constructed that (i) highlights the placenta and bladder, (ii) determines the lower placenta edge and highlights this location as a point and (iii) labels a 2-cm clearance on the lower placenta edge. The 2-cm clearance is chosen to satisfy current clinical guidelines. We propose to assess the placenta location by comparing the 2-cm region and the bottom of the bladder, which represents a coarse localization of the cervix. Anatomically, the bladder must sit above the cervix region. We present proof-of-concept results for the video overlay.


Cathepsins L and S are not required for activation of dipeptidyl peptidase I (cathepsin C) in mice.
The cysteine protease dipeptidyl peptidase I (DPPI) activates granule-associated immune-cell serine proteases. The in vivo activator of DPPI itself is unknown; however, cathepsins L and S are candidates because they activate pro-DPPI in vitro. In this study, we tested whether cathepsins L and S activate pro-DPPI in vivo by characterizing DPPI activity and processing in cells lacking cathepsins L and S. DPPI activity, and the relative size and amounts of DPPI heavy and light chains, were identical in mast cells from wild-type and cathepsin L/S double-null mice. Furthermore, the activity of DPPI-dependent chymase was preserved in tissues of cathepsin L/S double-null mice. These results show that neither cathepsin L nor S is required for activation of DPPI and suggest that one or more additional proteases is responsible.


Pure transvaginal ventral hernia repair in humans.
Transvaginal natural orifice transluminal endoscopic surgery procedures are at the forefront of minimally invasive innovation, remarkable for shorter recovery times and decreased postoperative pain. We aim to demonstrate a novel technique of pure transvaginal laparoscopic ventral hernia repair in a series of patients performed in our institution. The patient was placed in lithotomy position and steep Trendelenburg. A 2-cm transverse colpotomy incision was made and a SILS port was introduced. One 12-mm trocar and two 5-mm trocars were placed through the SILS port and standard straight laparoscopic instruments were used. An appropriately sized round mesh was deployed within a specimen retrieval bag into the peritoneal cavity. Complete anterior circumferential fixation of the mesh was achieved using an AbsorbaTack device. The colpotomy incision was closed. There were a total of 6 pure transvaginal ventral hernia repair procedures performed in our institution between November 2010 and February 2012. The first case was converted to an open procedure after a rectal injury was recognized and repaired. Two patients had transient urinary retention that resolved after 24 hours. One patient had vaginal wound granulation noted at 2 months postoperatively. No long-term complications or recurrences were noted with a median follow-up of 9 months. The mean operative time was 107 minutes. Our initial experience with transvaginal ventral hernia repair in humans suggests that this procedure is feasible, safe, and associated with improved cosmetic results.


Differential expression and function of Arabidopsis thaliana NHX Na+/H+ antiporters in the salt stress response.
The Arabidopsis thaliana vacuolar Na+/H+ antiporter AtNHX1 is a salt tolerance determinant. Predicted amino acid sequence similarity, protein topology and the presence of functional domains conserved in AtNHX1 and prototypical mammalian NHE Na+/H+ exchangers led to the identification of five additional AtNHX genes (AtNHX2-6). The AtNHX1 and AtNHX2 mRNAs are the most prevalent transcripts among this family of genes in seedling shoots and roots. A lower-abundance AtNHX5 mRNA is present in both shoots and roots, whereas AtNHX3 transcript is expressed predominantly in roots. AtNHX4 and AtNHX6 mRNAs were detected only by RT-PCR. AtNHX1, 2 or 5 suppress, with differential efficacy, the Na+/Li+-sensitive phenotype of a yeast mutant that is deficient in the endosomal/vacuolar Na+/H+ antiporter ScNHX1. Ion accumulation data indicate that these AtNHX proteins function to facilitate Na+ ion compartmentalization and maintain intracellular K+ status. Seedling steady-state mRNA levels of AtNHX1 and AtNHX2 increase similarly after treatment with NaCl, an equi-osmolar concentration of sorbitol, or ABA, whereas AtNHX5 transcript abundance increases only in response to salt treatment. Hyper-osmotic up-regulation of AtNHX1, 2 or 5 expression is not dependent on the SOS pathway that controls ion homeostasis. However, steady-state AtNHX1, 2 and 5 transcript abundance is greater in sos1, sos2 and sos3 plants growing in medium that is not supplemented with sorbitol or NaCl, providing evidence that transcription of these genes is negatively affected by the SOS pathway in the absence of stress. AtNHX1 and AtNHX2 transcripts accumulate in response to ABA but not to NaCl in the aba2-1, mutant indicating that the osmotic responsiveness of these genes is ABA-dependent. An as yet undefined stress signal pathway that is ABA- and SOS-independent apparently controls transcriptional up-regulation of AtNHX5 expression by hyper-saline shock. Similar to AtNHX1, AtNHX2 is localized to the tonoplast of plant cells. Together, these results implicate AtNHX2 and 5, together with AtNHX1, as salt tolerance determinants, and indicate that AtNHX2 has a major function in vacuolar compartmentalization of Na+.


Vagal signaling and the somatic marker hypothesis: The effect of transcutaneous vagal nerve stimulation on delay discounting is modulated by positive mood.
Controlling impulsivity and delaying gratifications are key features of effective self-control. Delay Discounting (DD) indexes the ability to delay rewards and previous research has shown that discounting is influenced by affective states such as mood. According to the Somatic Marker Hypothesis (SMH), afferent somatic signals, such as mood, are carried by the vagus and can influence decision making. In the current study, we employed transcutaneous vagus nerve stimulation (tVNS), a novel non-invasive brain stimulation technique that stimulates the auricular branch of the afferent vagus nerve (located in the outer ear), to assess its effects on decision impulsivity, while taking into account individuals' mood and resting-state HRV as a possible confounding factor. Employing a within-subjects cross-over design, 94 participants received active or sham tVNS while performing delay discounting in two separate sessions. As compared to sham, active tVNS increased discounting, but only for individuals reporting lower positive mood, regardless of the level of negative mood reported. We evidence that the effect of tVNS on reward discounting depends on the level of positive mood. This result suggests that positive mood state might be a proxy of task-relevant arousal, likely influencing the effectiveness of afferent vagal stimulation on self-control processes, as temporal discounting.


The role of RNA conformation in RNA-protein recognition.
Interactions between protein and RNA play a key role in many biological processes in the gene expression pathway. Those interactions are mediated through a variety of RNA-binding protein domains, among them the highly abundant RNA recognition motif (RRM). Here we studied protein-RNA complexes from different RNA binding domain families solved by NMR and x-ray crystallography. Characterizing the structural properties of the RNA at the binding interfaces revealed an unexpected number of nucleotides with unusual RNA conformations, specifically found in RNA-RRM complexes. Moreover, we observed that the RNA nucleotides that are directly involved in interactions with the RRM domains, via hydrogen bonds and hydrophobic contacts, are significantly enriched with unique RNA conformations. Further examination of the sequences binding the RRM domain showed a preference for G nucleotides in syn conformation to precede or to follow U nucleotides in the anti-conformation, and U nucleotides in C2' endo conformation to precede U and G nucleotides possessing the more common C3' endo conformation. These findings imply a possible mode of RNA recognition by the RRM domains which enables the recognition of a wide variety of different RNA sequences and shapes. Overall, this study suggests an additional way by which the RRM domain recognizes its RNA target, involving a conformational readout.


Polarized but differential localization and recruitment of STIM1, Orai1 and TRPC channels in secretory cells.
Polarized Ca(2+) signals in secretory epithelial cells are determined by compartmentalized localization of Ca(2+) signaling proteins at the apical pole. Recently the ER Ca(2+) sensor STIM1 (stromal interaction molecule 1) and the Orai channels were shown to play a critical role in store-dependent Ca(2+) influx. STIM1 also gates the transient receptor potential-canonical (TRPC) channels. Here, we asked how cell stimulation affects the localization, recruitment and function of the native proteins in polarized cells. Inhibition of Orai1, STIM1, or deletion of TRPC1 reduces Ca(2+) influx and frequency of Ca(2+) oscillations. Orai1 localization is restricted to the apical pole of the lateral membrane. Surprisingly, cell stimulation does not lead to robust clustering of native Orai1, as is observed with expressed Orai1. Unexpectedly, cell stimulation causes polarized recruitment of native STIM1 to both the apical and lateral regions, thus to regions with and without Orai1. Accordingly, STIM1 and Orai1 show only 40% colocalization. Consequently, STIM1 shows higher colocalization with the basolateral membrane marker E-cadherin than does Orai1, while Orai1 showed higher colocalization with the tight junction protein ZO1. TRPC1 is expressed in both apical and basolateral regions of the plasma membrane. Co-IP of STIM1/Orai1/IP(3) receptors (IP(3) Rs)/TRPCs is enhanced by cell stimulation and disrupted by 2-aminoethoxydiphenyl borate (2APB). The polarized localization and recruitment of these proteins results in preferred Ca(2+) entry that is initiated at the apical pole. These findings reveal that in addition to Orai1, STIM1 likely regulates other Ca(2+) permeable channels, such as the TRPCs. Both channels contribute to the frequency of [Ca(2+) ] oscillations and thus impact critical cellular functions.


MicroRNA Microarray Profiling during Megakaryocyte Differentiation of Cord Blood CD133+ Hematopoietic Stem Cells.
In order to clarify the role of microRNAs (miRNA) in megakaryocyte differentiation, we ran a microRNA microarray experiment to measure the expression level of 961 human miRNA in megakaryocytes differentiated from human umbilical cord blood CD133+ cells. In this experimental study, human CD133+ hematopoietic stem cells were collected from three human umbilical cord blood (UCB) samples, and then differentiated to the megakaryocytic lineage and characterized by flow cytometry, CFU-assay and ploidy analysis. Subsequently, microarray analysis was undertaken followed by quantitative polymerase chain reaction (qPCR) to validate differentially expressed miRNA identified in the microarray analysis. A total of 10 and 14 miRNAs were upregulated (e.g. miR-1246 and miR-148-a) and down-regulated (e.g. miR- 551b and miR-10a) respectively during megakaryocyte differentiation, all of which were confirmed by qPCR. Analysis of targets of these miRNA showed that the majority of targets are transcription factors involved in megakaryopoiesis. We conclude that miRNA play an important role in megakaryocyte differentiation and may be used as targets to change the rate of differentiation and further our understanding of the biology of megakaryocyte commitment.


The association between renin angiotensin aldosterone system blockers and future osteoporotic fractures in a hypertensive population - A population-based cohort study in Taiwan.
Some cohort studies showed the possibility of renin-angiotensin-aldosterone system (RAAS) blockade in preventing future osteoporotic fractures. The study aimed to evaluate the association between angiotensin converting enzyme inhibitors (ACEIs), angiotensin II receptor blockers (ARBs), and future osteoporotic fracture in a hypertensive population. We queried the Taiwan Longitudinal Health Insurance Database between 2001 and 2012. We used propensity score matching and the total cohort was made up of 57,470 participants (28,735 matched-pairs using or not using RAAS blockers). The mean follow-up period was 6 years. The number of incident fractures was 3757. Hazard ratios (HRs) [95% confidence interval (CI)] of ACEIs and ARBs use with incident fractures were calculated. The incidence of future osteoporotic fracture was significantly lower in the ACEI and ARB user groups but not in the group using an ACEI plus ARB concomitantly, when compared with RAAS blocker nonusers. Comparing ACEI users with RAAS blocker non-users and ARB users with RAAS blocker non-users, the HRs for composite fractures were 0.70 (0.62-0.79) and 0.58 (0.51-0.65), respectively. Sensitivity analysis confirmed a lower incidence of future osteoporotic fracture in patients taking an ACEI for >55 cumulative defined daily doses (cDDDs) and those who received an ARB for >90 cDDDs. These results suggested a lower incidence of future osteoporotic fracture in a hypertensive population who were using an ACEI or ARB compared with RAAS blocker nonusers but not in the group taking an ACEI and ARB concomitantly.


Use of an Extract of Indian Sacred Plant Ocimum sanctum as an Anticariogenic Agent: An in vitro Study.
To analyze the efficacy of three different concentrations of Ocimum sanctum extract against various microorganisms, Streptococcus mutans, Streptococcus mitis, Streptococcus sanguis, Lactobacillus acidophilus. Ethanolic extract of Ocimum sanctum was prepared by the hot extraction method. The extract was diluted with an inert solvent, dimethyl sulfoxide to obtain 3 different concentrations (2.5, 5 and 10%) of the extract. 0.2% chlorhexidine was used as a positive control and dimethyl sul-foxide was used as a negative control. The extract, along with the controls, was then subjected to microbiological investigation to determine which concentration among the 3 different concentrations of extract gave a wider inhibition zone against S. mutans, S. mitis, S. sanguis, L. acidophilus. The zones of inhibition were measured in millimeters. Ocimum sanctum leaf extract demonstrated maximum antimicrobial activity against microorganisms responsible for dental caries at the 10% concentration level although 5 and 2.5% were also effective. Maximum activity was seen against S. mutans and S. sanguis with 10% extract. Ocimum sanctum leaf extract was effective against all the microorganisms. How to cite this article: Pai RK, Bhat SS, Salman A, Chandra J. Use of an Extract of Indian Sacred Plant Ocimum Sanctum as an Anticariogenic Agent: An in vitro Study. Int J Clin Pediatr Dent 2015;8(2):99-101.


The Di Bella Method (DBM) improved survival, objective response and performance status in a retrospective observational clinical study on 122 cases of breast cancer.
To increase the efficacy and reduce the toxicity of cancer therapy. The DBM with MLT (melatonin), Retinoids, vitamins E, D3, and C has a differentiating, cytostatic, antiangiogenic, immunomodulating, factorially synergic effect, at the same time reinforcing those functions that Physiology considers essential for life. With Somatostatin and/or its analogues, the DBM has an antiproliferative effect, negatively regulating the most powerful mitogenic molecule (GH), receptorially co-expressed and interactive with Prolactin, inhibited by Cabergoline and/or Bromocriptin. The negative regulation of GH extends directly to the GH-dependent growth factors. In breast cancer, the DBM entails the use of estrogen inhibitors and minimal apoptotic, non-cytotoxic and non-mutagenic doses of Cyclophosphamide or Oncocarbide, the tolerability of which is enhanced by MLT and the vitamins in the DBM. Complete and stable cure of 4 cases, and rapid regression of the tumour in another 5 cases with just the DBM (first-line therapy), without surgical intervention. No disease recurrence with the use of the DBM as adjuvant therapy. Five-year survival of 50%, of stage IV cases, considerably higher than the data reported in the literature. A more or less generalised improvement in the quality of life, without any significant and/or prolonged toxicity. The acknowledgement of the still underestimated scientific evidence, such as the multiple antitumoral mechanisms of action of MLT, the negative regulation of the interactive mitogens GH-GF (GH-dependent growth factors), Prolactin and estrogens, together with the differentiating and homeostatic action of retinoids and Vitamins E, D3, and C and MLT, made it possible to achieve these results. An essential aspect of the mechanism of action on the clinical response is the factorial synergy of the DBM components.


Space-Time Congruency Effects Using Eye Movements During Processing of Past- and Future-Related Words.
In Western cultures where people read and write from left to right, time is represented along a spatial continuum that goes from left to right (past to future), known as the mental timeline (MTL). In language, this MTL was supported by space-time congruency effects: People are faster to make lexical decisions to words conveying past or future information when left/right manual responses are compatible with the MTL. Alternatively, in cultures where people read from right to left, space-time congruency effects go in the opposite direction. Such cross-cultural differences suggest that repeated writing and reading dynamic movements are critically involved in the spatial representation of time. In most experiments on the space-time congruency effect, participants use their hand for responding, an effector that is associated to the directionality of writing. To investigate the role of the directionality of reading in the space-time congruency effect, we asked participants to make lateralized eye movements (left or right saccades) to indicate whether stimuli were real words or not (lexical decision). Eye movement responses were slower and higher in amplitude for responses incompatible with the direction of the MTL. These results reinforce the claim that repeated directional reading and writing movements promote the embodiment of time-related words.


AAV-Mediated CRISPR/Cas Gene Editing of Retinal Cells In Vivo.
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein (Cas) has recently been adapted to enable efficient editing of the mammalian genome, opening novel avenues for therapeutic intervention of inherited diseases. In seeking to disrupt yellow fluorescent protein (YFP) in a Thy1-YFP transgenic mouse, we assessed the feasibility of utilizing the adeno-associated virus 2 (AAV2) to deliver CRISPR/Cas for gene modification of retinal cells in vivo. Single guide RNA (sgRNA) plasmids were designed to target YFP, and after in vitro validation, selected guides were cloned into a dual AAV system. One AAV2 construct was used to deliver Streptococcus pyogenes Cas9 (SpCas9), and the other delivered sgRNA against YFP or LacZ (control) in the presence of mCherry. Five weeks after intravitreal injection, retinal function was determined using electroretinography, and CRISPR/Cas-mediated gene modifications were quantified in retinal flat mounts. Adeno-associated virus 2-mediated in vivo delivery of SpCas9 with sgRNA targeting YFP significantly reduced the number of YFP fluorescent cells of the inner retina of our transgenic mouse model. Overall, we found an 84.0% (95% confidence interval [CI]: 81.8-86.9) reduction of YFP-positive cells in YFP-sgRNA-infected retinal cells compared to eyes treated with LacZ-sgRNA. Electroretinography profiling found no significant alteration in retinal function following AAV2-mediated delivery of CRISPR/Cas components compared to contralateral untreated eyes. Thy1-YFP transgenic mice were used as a rapid quantifiable means to assess the efficacy of CRISPR/Cas-based retinal gene modification in vivo. We demonstrate that genomic modification of cells in the adult retina can be readily achieved by viral-mediated delivery of CRISPR/Cas.


Molecular mechanisms and the role of saturated fatty acids in the progression of non-alcoholic fatty liver disease.
The steady rise in Western obesity rates has been closely linked to significant increases in a multitude of accompanying health problems including non-alcoholic fatty liver disease (NAFLD). NAFLD severity ranges from simple steatosis to acute steatohepatitis, but the molecular mechanisms controlling progression of this disease are poorly understood. Recent literature suggests that elevated free fatty acids (FFAs), especially saturated FFAs, may play an important role in lipotoxic mechanisms, both in experimental models and in NAFLD patients. This review highlights important cellular pathways involved in hepatic lipotoxicity and how the degree of intrahepatic lipid saturation controls cell fate in response to an elevated FFA load. Relevant cellular processes that have been causally linked to lipid-induced apoptosis, known as lipoapoptosis, include endoplasmic reticulum (ER) stress, oxidative stress, mitochondrial dysfunction, and Jun N-terminal kinase (JNK) signaling. In contrast, increased triglyceride synthesis has been shown to have a protective effect against lipotoxicity, despite being one of the hallmark traits of NAFLD. Developing a more nuanced understanding of the molecular mechanisms underlying NAFLD progression will lead to more targeted and effective therapeutics for this increasingly prevalent disease, which to date has no proven pharmacologic treatment to prevent or reverse its course.


Fiber-optic sensor for handgrip-strength monitoring: conception and design.
Handgrip strength is an easy measure of skeletal muscle function as well as a powerful predictor of disability, morbidity, and mortality. In order to measure grip strength, a novel fiber-optic approach is proposed and demonstrated. The strain-dependent wavelength response of fiber Bragg gratings has been utilized to obtain the strength of individual fingers. Finite-element analysis is carried out to optimize the pressure transmission from the finger to the fiber Bragg grating. The effect of stiffness of the pressurizing media, its thickness, and the effect of contact fraction are evaluated. It is found that significant enhancement in the pressure sensitivity and wavelength-tuning range is achievable by optimizing these parameters. Also the stress-induced birefringence could be reduced to an insignificant near-zero value. The device is calibrated in terms of load to convert the wavelength shift to the strength of the grip. The time-dependent wavelength fluctuation is also studied and presented.


Therapeutic strategies evaluated by the European Society of Cutaneous Lupus Erythematosus (EUSCLE) Core Set Questionnaire in more than 1000 patients with cutaneous lupus erythematosus.
The aim of this prospective, cross-sectional, multicentre study performed by the European Society of Cutaneous Lupus Erythematosus (EUSCLE) was to investigate different therapeutic strategies and their efficacies in cutaneous lupus erythematosus (CLE) throughout Europe. Using the EUSCLE Core Set Questionnaire, topical and systemic treatment options were analysed in a total of 1002 patients (768 females and 234 males) with different CLE subtypes. The data were correlated with the Cutaneous Lupus Erythematosus Disease Area and Severity Index (CLASI) and the criteria of the American College of Rheumatology (ACR) for the classification of systemic lupus erythematosus. Sunscreens were applied by 84.0% of the study cohort and showed a high efficacy in preventing skin lesions in all disease subtypes, correlating with a lower CLASI activity score. Topical steroids were used in 81.5% of the patients, with an efficacy of 88.4%, whereas calcineurin inhibitors were applied in 16.4% of the study population and showed an efficacy of 61.7%. Systemic agents including antimalarials and several immunomodulating/-suppressive drugs, such as systemic steroids and methotrexate, were applied in 84.4% of the 1002 patients. The CLASI activity and damage score was higher in treated CLE patients compared to untreated patients, regardless of therapy with topical or systemic agents. In summary, preventive and therapeutic strategies of 1002 patients with different subtypes of CLE were analysed in this prospective, multicentre, Europe-wide study. Sunscreens were confirmed to be successful as preventive agents, and topical steroids showed a high efficacy, whereas antimalarials were used as first-line systemic treatment.


How adolescents perceive that community-based exercise improves their well-being.
To determine if adolescents perceive community-based exercise as beneficial to their well-being and in what ways. A New South Wales Police Citizens Youth Club ran a four-week fitness course. The classes involved: 1) sports including basketball and soccer, 2) non-contact boxing drills, and 3) games, both team games such as dodgeball and non-team games such as line tag. Parental consent to offer a survey at the completion of the course was requested during registration. The survey was the Warwick Edinburgh Mental Well-being Scale; it was minimally modified to measure perceived benefit to mental well-being instead of actual benefit. Thirty-one high school adolescents, ages 13-18, completed the survey. As a group, participants reported that they believed their well-being had improved after the course. The mean score for each survey item showed an improvement in every area of mental well-being for this sample of adolescents. Thirty-two per cent of adolescents reported having less energy. Survey scores indicated a statistically significant improvement in perceived well-being ( p<0.0001). The results of this study suggest that four weeks of community-based exercise improves perceived mental well-being in adolescent participants.


Infection markers as predictors of Bacteremia in an Intensive Care Unit: A prospective study.
Although several biomarkers have been evaluated for the diagnosis and prognosis of sepsis, the gold standard biomarker has not yet been found. We aimed to evaluate the diagnostic value of neutrophil-to-lymphocyte count ratio (NLCR), neopterin, pro-adrenomedullin (pro-ADM) and the other infection markers to predict bacteremia in patients with SIRS, sepsis and severe sepsis/septic shock. A prospective cohort study was conducted on septic patients in a tertiary referral hospital between December 2014- July 2015. A total of 156 patients diagnosed with SIRS, sepsis and severe sepsis/septic shock in Anesthesia intensive care unit (ICU) were included in the study. A total of 156 patients who had been diagnosed as SIRS(10.9%), sepsis (44.2%) and severe sepsis/septic shock (44.9%) were included. Positive blood cultures were obtained in 64 patients. NLCR, neopterin and pro-ADM levels were insignificant in predicting bacteremia (p>0.05). The mortality rate was significantly higher in bacteremic sepsis (43.9%) compared to non-bacteremic patients (20.8%) (p=0.001). Only procalcitonin levels were significant predictor of mortality (p<0.001). NLCR, CRP, procalcitonin, neopterin and pro-ADM levels were insignificant in diagnosis of bacteremia in critically ill patients. The gold standard method in predicting bacteremia is still blood culture positivity.


Analysis of coronary flow fields in thoracotomized dogs.
A nonlinear theory of pulsatile flow was used to investigate the detailed flow field in the left circumflex coronary artery of anesthetized open-chest dogs. Studies were carried out under a wide range of blood pressures and flow rates induced by intravenous infusions of dipyridamole. The results indicated that (1) the flow profiles, although less blunt than those in the descending aorta, are still nonparabolic, (2) the wall shear in the coronary arteries maintains a high value through diastole, and (3) during intravenous infusions of dipyridamole both coronary flow and wall shear increase. The peak value of the shear stress during these infusions, which reached 360 dynes/cm2, can approach the yield stress value of 400 dynes/cm2 reported by Fry for endothelial cells.


Plasma NfL levels and longitudinal change rates in C9orf72 and GRN-associated diseases: from tailored references to clinical applications.
Neurofilament light chain (NfL) is a promising biomarker in genetic frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). We evaluated plasma neurofilament light chain (pNfL) levels in controls, and their longitudinal trajectories in C9orf72 and GRN cohorts from presymptomatic to clinical stages. We analysed pNfL using Single Molecule Array (SiMoA) in 668 samples (352 baseline and 316 follow-up) of C9orf72 and GRN patients, presymptomatic carriers (PS) and controls aged between 21 and 83. They were longitudinally evaluated over a period of >2 years, during which four PS became prodromal/symptomatic. Associations between pNfL and clinical-genetic variables, and longitudinal NfL changes, were investigated using generalised and linear mixed-effects models. Optimal cut-offs were determined using the Youden Index. pNfL levels increased with age in controls, from ~5 to~18 pg/mL (p<0.0001), progressing over time (mean annualised rate of change (ARC): +3.9%/year, p<0.0001). Patients displayed higher levels and greater longitudinal progression (ARC: +26.7%, p<0.0001), with gene-specific trajectories. GRN patients had higher levels than C9orf72 (86.21 vs 39.49 pg/mL, p=0.014), and greater progression rates (ARC:+29.3% vs +24.7%; p=0.016). In C9orf72 patients, levels were associated with the phenotype (ALS: 71.76 pg/mL, FTD: 37.16, psychiatric: 15.3; p=0.003) and remarkably lower in slowly progressive patients (24.11, ARC: +2.5%; p=0.05). Mean ARC was +3.2% in PS and +7.3% in prodromal carriers. We proposed gene-specific cut-offs differentiating patients from controls by decades. This study highlights the importance of gene-specific and age-specific references for clinical and therapeutic trials in genetic FTD/ALS. It supports the usefulness of repeating pNfL measurements and considering ARC as a prognostic marker of disease progression. NCT02590276 and NCT04014673.


Predicting Sexual Revictimization in Childhood and Adolescence: A Longitudinal Examination Using Ecological Systems Theory.
A substantial proportion of sexual abuse victims report repeat sexual victimization within childhood or adolescence; however, there is limited understanding of factors contributing to revictimization for youth. Thus, the present study examined predictors of sexual revictimization prior to adulthood using ecological systems theory. Records of 1,915 youth presenting to a Child Advocacy Center (CAC) were reviewed to identify individual, familial, and community factors as well as initial abuse characteristics associated with risk for revictimization. Results showed that 11.1% of youth re-presented to the CAC for sexual revictimization. At the individual level, younger children, girls, ethnoracial minority youth, and those with an identified mental health problem were most likely to experience revictimization. Interpersonal factors that increased vulnerability included the presence of a noncaregiving adult in the home, being in mental health treatment, and domestic violence in the family. Community-level factors did not predict revictimization. When factors at all levels were examined in conjunction, however, only individual-level factors significantly predicted the risk for revictimization. Findings from this study provide valuable information for CACs when assessing risk for re-report of sexual abuse and add to the field's understanding of revictimization within childhood.


Target Organ Complications and Cardiovascular Events Associated With Masked Hypertension and White-Coat Hypertension: Analysis From the Dallas Heart Study.
Multiple epidemiological studies from Europe and Asia have demonstrated increased cardiovascular risks associated with isolated elevation of home blood pressure (BP) or masked hypertension (MH). Previous studies have not addressed cardiovascular outcomes associated with MH and white-coat hypertension (WCH) in the general population in the United States. The goal of this study was to determine hypertensive target organ damage and adverse cardiovascular outcomes associated with WCH (high clinic BP, ≥140/90 mm Hg; normal home BP, <135/85 mm Hg), MH (high home BP, ≥135/85 mm Hg; normal clinic BP, <140/90 mm Hg), and sustained hypertension (high home and clinic BP) in the DHS (Dallas Heart Study), a large, multiethnic, probability-based population cohort. Associations among WCH, MH, sustained hypertension, and aortic pulsed wave velocity by magnetic resonance imaging; urinary albumin-to-creatinine ratio; and cystatin C were evaluated at study baseline. Then, associations between WCH and MH with incident cardiovascular outcomes (coronary heart disease, stroke, atrial fibrillation, heart failure, and cardiovascular death) over a median follow-up period of 9 years were assessed. The study cohort comprised 3,027 subjects (50% African Americans). The sample-weighted prevalence rates of WCH and MH were 3.3% and 17.8%, respectively. Both WCH and MH were independently associated with increased aortic pulsed wave velocity, cystatin C, and urinary albumin-to-creatinine ratio. Both WCH (adjusted hazard ratio: 2.09; 95% confidence interval: 1.05 to 4.15) and MH (adjusted hazard ratio: 2.03; 95% confidence interval: 1.36 to 3.03) were independently associated with higher cardiovascular events compared with the normotensive group, even after adjustment for traditional cardiovascular risk factors. In a multiethnic U.S. population, both WCH and MH were independently associated with increased aortic stiffness, renal injury, and incident cardiovascular events. Because MH is common and associated with an adverse cardiovascular profile, home BP monitoring should be routinely performed among U.S. adults.


Implementation of Constrained DFT for Computing Charge Transfer Rates within the Projector Augmented Wave Method.
Combining constrained density function theory (cDFT) with Marcus theory is an efficient and promising way to address charge transfer reactions. Here, we present a general and robust implementation of cDFT within the projector augmented wave (PAW) framework. PAW pseudopotentials offer a reliable frozen-core electron description across the whole periodic table, with good transferability, as well as facilitate the extraction of all-electron quantities. The present implementation is applicable to two different wave function representations, atomic-centered basis sets (LCAO) and the finite-difference (FD) approximation utilizing real-space grids. LCAO can be used for large systems, molecular dynamics, or quick initialization, while more accurate calculations are achieved with the FD basis. Furthermore, the calculations can be performed with flexible boundary conditions, ranging from isolated molecules to periodic systems in one-, two-, or three-dimensions. As such, this implementation is relevant for a wide variety of applications. We also present how to extract the electronic coupling element and reorganization energy from the resulting diabatic cDFT-PAW wave functions for the parametrization of Marcus theory. Here, the combined method is applied to important test cases where practical implementations of DFT fail due to the self-interaction error, such as the dissociation of the helium dimer cation, and it is compared to other established cDFT codes. Moreover, for charge localization in a diamine cation, where it was recently shown that the commonly used generalized gradient and hybrid functionals of DFT failed to produce the localized state, cDFT produces qualitatively and quantitatively accurate results when benchmarked against self-interaction corrected DFT and high-level CCSD(T) calculations at a fraction of the computational cost.


Uncovering the Disconnect Between Nursing Workforce Policy Intentions, Implementation, and Outcomes: Lessons Learned From the Addition of a Nursing Assistant Role.
The use of nursing assistants has increased across health systems in the past 20 years, to alleviate licensed nurses' workload and to meet rising health care demands at lower costs. Evidence suggests that, when used as a substitute for licensed nurses, assistants are associated with poorer patient and nurse outcomes. Our multimethods study evaluated the impact of a policy to add nursing assistants to existing nurse staffing in Western Australia's public hospitals, on a range of outcomes. In this article, we draw the metainferences from previously published quantitative data and unpublished qualitative interview data. A longitudinal analysis of patient records found significantly higher rates adverse patient outcomes on wards that introduced nursing assistants compared with wards that did not. These findings are explained with ward-level data that show nursing assistants were added to wards with preexisting workload and staffing problems and that those problems persisted despite the additional resources. There were also problems integrating assistants into the nursing team, due to ad hoc role assignments and variability in assistants' knowledge and skills. The disconnect between policy intention and outcomes reflects a top-down approach to role implementation where assistants were presented as a solution to nurses' workload problems, without an understanding of the causes of those problems. We conclude that policy makers and managers must better understand individual care environments to ensure any new roles are properly tailored to patient and staff needs. Further, standardized training and accreditation for nursing assistant roles would reduce the supervisory burden on licensed nurses.


P300 waveform and dopamine transporter availability: a controlled EEG and SPECT study in medication-naive patients with schizophrenia and a meta-analysis.
Reduced P300 event-related potential (ERP) amplitude and latency prolongation have been reported in patients with schizophrenia compared to healthy controls. However, the influence of antipsychotics (and dopamine) on ERP measures are poorly understood and medication confounding remains a possibility. We explored ERP differences between 36 drug-naive patients with schizophrenia and 138 healthy controls and examined whether P300 performance was related to dopamine transporter (DAT) availability, both without the confounding effects of medication. We also conducted a random effects meta-analysis of the available literature, synthesizing the results of three comparable published articles and our local study. No overall significant difference was found in mean P300 ERP between patients and controls in latency or in amplitude. There was a significant gender effect, with females showing greater P300 amplitude than males. A difference between patients and controls in P300 latency was evident with ageing, with latency increasing faster in patients. No effect of DAT availability on P300 latency or amplitude was detected. The meta-analysis computed the latency pooled standardized effect size (PSES; Cohen's d) of -0.13 and the amplitude PSES (Cohen's d) of 0.48, with patients showing a significant reduction in amplitude. Our findings suggest the P300 ERP is not altered in the early stages of schizophrenia before medication is introduced, and the DAT availability does not influence the P300 ERP amplitude or latency. P300 ERP amplitude reduction could be an indicator of the progression of illness and chronicity.


Ultrashort Carbon Nanotubes That Fluoresce Brightly in the Near-Infrared.
The intrinsic near-infrared photoluminescence observed in long single-walled carbon nanotubes is known to be quenched in ultrashort nanotubes due to their tiny size as compared to the exciton diffusion length in these materials (>100 nm). Here, we show that intense photoluminescence can be created in ultrashort nanotubes (∼40 nm length) upon incorporation of exciton-trapping sp3 defect sites. Using super-resolution photoluminescence imaging at <25 nm resolution, we directly show the preferential localization of excitons at the nanotube ends, which separate by less than 40 nm and behave as independent emitters. This unexpected observation opens the possibility to synthesize fluorescent ultrashort nanotubes-a goal that has been long thought impossible-for bioimaging applications, where bright near-infrared photoluminescence and small size are highly desirable, and for quantum information science, where high quality and well-controlled near-infrared single photon emitters are needed.


Gamma-secretase activating protein is a therapeutic target for Alzheimer's disease.
Accumulation of neurotoxic amyloid-beta is a major hallmark of Alzheimer's disease. Formation of amyloid-beta is catalysed by gamma-secretase, a protease with numerous substrates. Little is known about the molecular mechanisms that confer substrate specificity on this potentially promiscuous enzyme. Knowledge of the mechanisms underlying its selectivity is critical for the development of clinically effective gamma-secretase inhibitors that can reduce amyloid-beta formation without impairing cleavage of other gamma-secretase substrates, especially Notch, which is essential for normal biological functions. Here we report the discovery of a novel gamma-secretase activating protein (GSAP) that drastically and selectively increases amyloid-beta production through a mechanism involving its interactions with both gamma-secretase and its substrate, the amyloid precursor protein carboxy-terminal fragment (APP-CTF). GSAP does not interact with Notch, nor does it affect its cleavage. Recombinant GSAP stimulates amyloid-beta production in vitro. Reducing GSAP concentrations in cell lines decreases amyloid-beta concentrations. Knockdown of GSAP in a mouse model of Alzheimer's disease reduces levels of amyloid-beta and plaque development. GSAP represents a type of gamma-secretase regulator that directs enzyme specificity by interacting with a specific substrate. We demonstrate that imatinib, an anticancer drug previously found to inhibit amyloid-beta formation without affecting Notch cleavage, achieves its amyloid-beta-lowering effect by preventing GSAP interaction with the gamma-secretase substrate, APP-CTF. Thus, GSAP can serve as an amyloid-beta-lowering therapeutic target without affecting other key functions of gamma-secretase.


A systematic review of the South African work on the well-being of young people (2000-2016).
Burgeoning research on the well-being of young people in recent years has made it difficult to identify conceptual gaps in the literature. We conducted a review of South African research in this area to better understand the use and measurement of the construct, as well as factors associated with it. The search of multiple databases identified 28 studies published in academic journals between 2000 and 2016. Within this period, studies that referred to well-being and its related subjective components varied significantly in terms of how they defined and operationalised these constructs, resulting in a fragmented body of work. The review highlights the need for a coherent research agenda in this area given the centrality of well-being research in promoting optimal outcomes in young people. Recommendations for strengthening South African research in this area are provided.


First Report of the Cucurbit Yellow Vine Disease Caused by Serratia marcescens in Watermelon and Yellow Squash in Alabama.
More than 3,000 acres of watermelon were planted in Alabama in 2010 with a production value more than $4 million (J. Kemble, personal communication). Symptoms typical of cucurbit yellow vine disease (CYVD) were observed in a 2-ha watermelon field in Crawford, AL on 8 June 2010. Watermelon, cv. Jubilee, exhibited a yellow appearance and some plants were completely wilted. Incidence of affected plants was estimated at 25%. On 24 June, plant samples were collected from a 1-ha watermelon (cv. Jubilee) field near Dadeville, AL. Approximately 30% of the plants exhibited yellowing and wilting, which is symptomatic of CYVD. Samples were also collected from a small planting of yellow crooked-neck squash at the same location. Approximately 20% of the squash plants had symptoms typical of CYVD. Cross-sections of belowground stem and primary root revealed a honey-brown phloem discoloration and a healthy appearing xylem, symptoms consistent with CYVD caused by the phloem-colonizing bacterium, Serratia marcescens Bizio (1). Isolations were made from the crown on four symptomatic watermelon and two squash plants. Approximately 2.5-mm3 tissue pieces from the phloem were excised, surface sterilized in 10% sodium hypochlorite, and ground in 1-ml PBS (phosphate buffer with saline). A 10-μl aliquot of slurry was plated onto nutrient agar (NA) (Difco, Detroit, MI) and the plates were stored at room temperature for 4 days. Individual colonies were selected and purified by serial dilution plating. Isolates from watermelon and squash were consistent with S. marcescens in colony morphology, color, and texture. Three isolates obtained from watermelon were grown on NA and suspended in sterile water at 108 cells per ml for mechanical transmission experiments on 'Lemondrop' squash. Sterile water served as a negative control. After 28 days, plants were cross-sectioned at the juncture of the root and stem and observed for phloem discoloration. Of the 56, 58, and 62 plants inoculated in three replicate studies, 78.6, 56.9, and 62.9% developed CYVD symptoms, respectively, while none of the controls were positive. Cultured bacteria from six of the symptomatic, greenhouse-inoculated plants representing the three watermelon isolates were subjected to multiplex end-point PCR using primer sets YV1/YV4, specific for the species S. marcescens, and a79F/R, which amplifies only the CYVD strains of S. marcescens (3). All six bacteria cultures along with the positive control (reference isolate W01 obtained from watermelon in Texas) were positive, while the negative PBS control was negative. Although rhizosphere-inhabiting and plant growth promoting endophytic strains of S. marcescens have been reported from Alabama (2), to our knowledge, this is the first known report of CYVD and phytopathogenic S. marcescens in Alabama cucurbits. References: (1) B. D. Bruton et al. Plant Dis. 87:937, 2004. (2) J. A. McInroy and J. W. Kloepper. Plant Soil 173:333, 1995. (3) Q. Zhang et al. Appl. Environ. Microbiol. 71:7716, 2005.


Type and intensity of FVIII exposure on inhibitor development in PUPs with haemophilia A. A patient-level meta-analysis.
The impact of treatment-related factors on inhibitor development in previously untreated patients (PUPs) with haemophilia A is still debated. We present the results of a collaborative, individual patient data meta-analytic project. Eligible data sources were published cohorts of PUPs for which patient-level data were available. The exposures of interest were factor (F)VIII type (recombinant [rFVIII] vs plasma-derived [pdFVIII]) and treatment intensity (≥ vs < 150 IU/kg/week) at first treatment. Family history of inhibitors, F8 mutations, age, treatment regimen (on-demand vs prophylaxis), secular trend and surgery were analysed as putative confounders using different statistical approaches (multivariable Cox regression, propensity score analyses, CART). Analyses accounted for the multi-centre origin of the data. We included 761 consecutive, unselected PUPs with moderate to severe haemophilia A from 10 centres in Egypt, Germany, Israel and Italy. A total of 27 % of patients developed inhibitors; 40 % and 22 % of patients treated with rFVIII and pdFVIII (unadjusted HR 2.2, 95 % CI 1.6-2.9), respectively; 51 % and 24 % of patients receiving high- and low-intensity treatment (unadjusted HR 2.9, 95 % CI 2.0-4.2), respectively. In adjusted analyses, only treatment intensity remained an independent predictor; the effect of FVIII type was largely due to confounding, but with a significant interaction between FVIII type and treatment intensity. This patient-level meta-analysis confirms, across different statistical approaches, that high-intensity treatment is a strong risk factor for inhibitor development. The possible role of FVIII type in subgroups is suggested by the test for interactions but could not be proven because of the limited subgroups sample sizes.


Curcumin suppresses the proliferation of gastric cancer cells by downregulating H19.
Curcumin, a major phytochemical in turmeric, inhibits the proliferation of many types of solid cancer cells by enhancing p53 expression. However, the long non-coding RNA H19 directly inhibits p53 activation and thus promotes gastric cancer progression. The aim of this study was to assess the role of H19 in curcumin-induced proliferative inhibition of gastric cancer. The gastric cancer cell line SGC-7901 was treated with curcumin at different concentrations and time points. The effect of curcumin on proliferation was assessed using cell counting kit-8 assays and flow cytometry with Ki67 staining. In addition, H19 expression was quantified by reverse transcription-quantitative polymerase chain reaction, and apoptosis was evaluated by flow cytometric detection of Annexin V and propidium iodide double staining. The protein expression of p53, B-cell lymphoma (Bcl)-2, Bcl-2-associated X protein (Bax) and c-Myc in curcumin-treated cells was detected by western blotting. The present study demonstrated that curcumin inhibited the proliferation of SGC7901 cells and suppressed H19 expression in a concentration-dependent manner, while p53 expression was enhanced. Ectopic expression of H19 in SGC7901 cells reversed curcumin-induced proliferative inhibition and downregulated p53 expression. Furthermore, while curcumin induced cell apoptosis and enhanced the expression ratio of Bax/Bcl-2, which are downstream molecules of p53, ectopic expression of H19 inhibited curcumin-induced cell apoptosis. In addition, curcumin decreased the expression of the c-Myc oncogene, and exogenous c-Myc protein reversed the curcumin-induced downregulation of H19 expression. These results suggested that curcumin inhibits the proliferation of gastric cancer cells by downregulating the c-Myc/H19 pathway. Therefore, curcumin may be considered a novel therapeutic strategy to inhibit gastric cancer cell growth.


Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling.
Measurement precision determines the power of any analysis to reliably identify significant signals, such as in screens for differential expression, independent of whether the experimental design incorporates replicates or not. With the compilation of large-scale RNA-Seq datasets with technical replicate samples, however, we can now, for the first time, perform a systematic analysis of the precision of expression level estimates from massively parallel sequencing technology. This then allows considerations for its improvement by computational or experimental means. We report on a comprehensive study of target identification and measurement precision, including their dependence on transcript expression levels, read depth and other parameters. In particular, an impressive recall of 84% of the estimated true transcript population could be achieved with 331 million 50 bp reads, with diminishing returns from longer read lengths and even less gains from increased sequencing depths. Most of the measurement power (75%) is spent on only 7% of the known transcriptome, however, making less strongly expressed transcripts harder to measure. Consequently, <30% of all transcripts could be quantified reliably with a relative error<20%. Based on established tools, we then introduce a new approach for mapping and analysing sequencing reads that yields substantially improved performance in gene expression profiling, increasing the number of transcripts that can reliably be quantified to over 40%. Extrapolations to higher sequencing depths highlight the need for efficient complementary steps. In discussion we outline possible experimental and computational strategies for further improvements in quantification precision. firstname.lastname@example.com


Gating kinetics of Ca2+-activated K+ channels from rat muscle incorporated into planar lipid bilayers. Evidence for two voltage-dependent Ca2+ binding reactions.
The gating kinetics of a Ca2+-activated K+ channel from adult rat muscle plasma membrane are studied in artificial planar bilayers. Analysis of single-channel fluctuations distinguishes two Ca2+- and voltage-dependent processes: (a) short-lived channel closure (less than 1 ms) events appearing in a bursting pattern; (b) opening and closing events ranging from one to several hundred milliseconds in duration. The latter process is studied independently of the first and is denoted as the primary gating mode. At constant voltage, the mean open time of the primary gating mode is a linear function of the [Ca2+], whereas the mean closed time is a linear function of the reciprocal [Ca2+]. In the limits of zero and infinite [Ca2+], the mean open and the mean closed times are, respectively, independent of voltage. These results are predicted by a kinetic scheme consisting of the following reaction steps: (a) binding of Ca2+ to a closed state; (b) channel opening; (c) binding of a second Ca2+ ion. In this scheme, the two Ca2+ binding reactions are voltage dependent, whereas the open-closed transition is voltage independent. The kinetic constant derived for this scheme gives an accurate theoretical fit to the observed equilibrium open-state probability. The results provide evidence for a novel regulatory mechanism for the activity of an ion channel: modulation by voltage of the binding of an agonist molecule, in this case, Ca2+ ion.


Promotion of lung adenocarcinoma following inhalation exposure to multi-walled carbon nanotubes.
Engineered carbon nanotubes are currently used in many consumer and industrial products such as paints, sunscreens, cosmetics, toiletries, electronic processes and industrial lubricants. Carbon nanotubes are among the more widely used nanoparticles and come in two major commercial forms, single-walled carbon nanotubes (SWCNT) and the more rigid, multi-walled carbon nanotubes (MWCNT). The low density and small size of these particles makes respiratory exposures likely. Many of the potential health hazards have not been investigated, including their potential for carcinogenicity. We, therefore, utilized a two stage initiation/promotion protocol to determine whether inhaled MWCNT act as a complete carcinogen and/or promote the growth of cells with existing DNA damage. Six week old, male, B6C3F1 mice received a single intraperitoneal (ip) injection of either the initiator methylcholanthrene(MCA, 10 μg/g BW, i.p.), or vehicle (corn oil). One week after i.p. injections, mice were exposed by inhalation to MWCNT (5 mg/m³, 5 hours/day, 5 days/week) or filtered air (controls) for a total of 15 days. At 17 months post-exposure, mice were euthanized and examined for lung tumor formation. Twenty-three percent of the filtered air controls, 26.5% of the MWCNT-exposed, and 51.9% of the MCA-exposed mice, had lung bronchiolo-alveolar adenomas and lung adenocarcinomas. The average number of tumors per mouse was 0.25, 0.81 and 0.38 respectively. By contrast, 90.5% of the mice which received MCA followed by MWCNT had bronchiolo-alveolar adenomas and adenocarcinomas with an average of 2.9 tumors per mouse 17 months after exposure. Indeed, 62% of the mice exposed to MCA followed by MWCNT had bronchiolo-alveolar adenocarcinomas compared to 13% of the mice that received filtered air, 22% of the MCA-exposed, or 14% of the MWCNT-exposed. Mice with early morbidity resulting in euthanasia had the highest rate of metastatic disease. Three mice exposed to both MCA and MWCNT that were euthanized early had lung adenocarcinoma with evidence of metastasis (5.5%). Five mice (9%) exposed to MCA and MWCNT and 1 (1.6%) exposed to MCA developed serosal tumors morphologically consistent with sarcomatous mesotheliomas, whereas mice administered MWCNT or air alone did not develop similar neoplasms. These data demonstrate that some MWCNT exposures promote the growth and neoplastic progression of initiated lung cells in B6C3F1 mice. In this study, the mouse MWCNT lung burden of 31.2 μg/mouse approximates feasible human occupational exposures. Therefore, the results of this study indicate that caution should be used to limit human exposures to MWCNT.


Computational Approaches to Detect Illicit Drug Ads and Find Vendor Communities Within Social Media Platforms.
The opioid abuse epidemic represents a major public health threat to global populations. The role social media may play in facilitating illicit drug trade is largely unknown due to limited research. However, it is known that social media use among adults in the US is widespread, there is vast capability for online promotion of illegal drugs with delayed or limited deterrence of such messaging, and further, general commercial sale applications provide safeguards for transactions; however, they do not discriminate between legal and illegal sale transactions. These characteristics of the social media environment present challenges to surveillance which is needed for advancing knowledge of online drug markets and the role they play in the drug abuse and overdose deaths. In this paper, we present a computational framework developed to automatically detect illicit drug ads and communities of vendors. The SVM- and CNN- based methods for detecting illicit drug ads, and a matrix factorization based method for discovering overlapping communities have been extensively validated on the large dataset collected from Google+, Flickr and Tumblr. Pilot test results demonstrate that our computational methods can effectively identify illicit drug ads and detect vendor-community with accuracy. These methods hold promise to advance scientific knowledge surrounding the role social media may play in perpetuating the drug abuse epidemic.


The monofunctional chorismate mutase from Bacillus subtilis. Structure determination of chorismate mutase and its complexes with a transition state analog and prephenate, and implications for the mechanism of the enzymatic reaction.
Structures have been determined for chorismate mutase from Bacillus subtilis and of complexes of this enzyme with product and an endo-oxabicyclic transition state analog using multiple isomorphous replacement plus partial structure phase combination and non-crystallographic averaging. In addition to 522 water molecules, the model includes 1380 of the 1524 amino acid residues of the four trimers (each containing 3 x 127 amino acid residues) in the asymmetric unit. Refinement to 1.9 A resolution yields 0.194 for R and r.m.s. deviations from ideal values of 0.014 A for bond lengths and 2.92 degrees for bond angles. The trimer resembles a beta-barrel structure in which a core beta-sheet is surrounded by helices. The structures of the two complexes locate the active sites which are at the interfaces of adjacent pairs of monomers in the trimer. These structures have been refined at 2.2 A to a crystallographic R value of 0.18 and show r.m.s. deviations from ideal values of 0.013 A for bond lengths and 2.84 degrees or 3.05 degrees for bond angles, respectively. The final models have 1398 amino acid residues, nine prephenate molecules and 503 water molecules in the product complex, and 1403 amino acid residues, 12 inhibitor molecules and 530 water molecules in the transition state complex. The active sites of all three of these structures are very similar and provide a structural basis for the biochemical studies that indicate a pericyclic mechanism for conversion of chorismate to prephenate. The absence of reactive catalytic residues on the enzyme, the selective binding of the single reactive conformation of chorismate, the stabilization of the polar transition state, and the possible role of the C-terminal region in "capping" the active site are factors which relate these structures to the million-fold rate enhancement of this reaction.


Peptide identification by tandem mass spectrometry with alternate fragmentation modes.
The high-throughput nature of proteomics mass spectrometry is enabled by a productive combination of data acquisition protocols and the computational tools used to interpret the resulting spectra. One of the key components in mainstream protocols is the generation of tandem mass (MS/MS) spectra by peptide fragmentation using collision induced dissociation, the approach currently used in the large majority of proteomics experiments to routinely identify hundreds to thousands of proteins from single mass spectrometry runs. Complementary to these, alternative peptide fragmentation methods such as electron capture/transfer dissociation and higher-energy collision dissociation have consistently achieved significant improvements in the identification of certain classes of peptides, proteins, and post-translational modifications. Recognizing these advantages, mass spectrometry instruments now conveniently support fine-tuned methods that automatically alternate between peptide fragmentation modes for either different types of peptides or for acquisition of multiple MS/MS spectra from each peptide. But although these developments have the potential to substantially improve peptide identification, their routine application requires corresponding adjustments to the software tools and procedures used for automated downstream processing. This review discusses the computational implications of alternative and alternate modes of MS/MS peptide fragmentation and addresses some practical aspects of using such protocols for identification of peptides and post-translational modifications.


Smooth muscle cell calcium activation mechanisms.
Smooth muscle cell (SMC) contraction is controlled by the Ca2+ and Rho kinase signalling pathways. While the SMC Rho kinase system seems to be reasonably constant, there is enormous variation with regard to the mechanisms responsible for generating Ca2+ signals. One way of dealing with this diversity is to consider how this system has been adapted to control different SMC functions. Phasic SMCs (vas deferens, uterus and bladder) rely on membrane depolarization to drive Ca2+ influx across the plasma membrane. This depolarization can be induced by neurotransmitters or through the operation of a membrane oscillator. Many tonic SMCs (vascular, airway and corpus cavernosum) are driven by a cytosolic Ca2+ oscillator that generates periodic pulses of Ca2+. A similar oscillator is present in pacemaker cells such as the interstitial cells of Cajal (ICCs) and atypical SMCs that control other tonic SMCs (gastrointestinal, urethra, ureter). The changes in membrane potential induced by these cytosolic oscillators does not drive contraction directly but it functions to couple together individual oscillators to provide the synchronization that is a characteristic feature of many tonic SMCs.


Bioinformatic and physical characterizations of genome-scale ordered RNA structure in mammalian RNA viruses.
By the analysis of thermodynamic RNA secondary structure predictions, we previously obtained evidence for evolutionarily conserved large-scale ordering of RNA virus genomes (P. Simmonds, A. Tuplin, and D. J. Evans, RNA 10:1337-1351, 2004). Genome-scale ordered RNA structure (GORS) was widely distributed in many animal and plant viruses, much greater in extent than RNA structures required for viral translation or replication, but in mammalian viruses was associated with host persistence. To substantiate the existence of large-scale RNA structure differences between viruses, a large set of alignments of mammalian RNA viruses and rRNA sequences as controls were examined by thermodynamic methods (to calculate minimum free energy differences) and by algorithmically independent RNAz and Pfold methods. These methods produced generally concordant results and identified substantial differences in the degrees of evolutionarily conserved, sequence order-dependent RNA secondary structure between virus genera and groups. A probe hybridization accessibility assay was used to investigate the physical nature of GORS. Transcripts of hepatitis C virus (HCV), hepatitis G virus/GB virus-C (HGV/GBV-C), and murine norovirus, which are predicted to be structured, were largely inaccessible to hybridization in solution, in contrast to the almost universal binding of probes to a range of unstructured virus transcripts irrespective of G+C content. Using atomic force microscopy, HCV and HGV/GBV-C RNA was visualized as tightly compacted prolate spheroids, while under the same experimental conditions the predicted unstructured poliovirus and rubella virus RNA were pleomorphic and had extensively single-stranded RNA on deposition. Bioinformatic and physical characterization methods both identified fundamental differences in the configurations of viral genomic RNA that may modify their interactions with host cell defenses and their ability to persist.


The performance of different propensity-score methods for estimating differences in proportions (risk differences or absolute risk reductions) in observational studies.
Propensity score methods are increasingly being used to estimate the effects of treatments on health outcomes using observational data. There are four methods for using the propensity score to estimate treatment effects: covariate adjustment using the propensity score, stratification on the propensity score, propensity-score matching, and inverse probability of treatment weighting (IPTW) using the propensity score. When outcomes are binary, the effect of treatment on the outcome can be described using odds ratios, relative risks, risk differences, or the number needed to treat. Several clinical commentators suggested that risk differences and numbers needed to treat are more meaningful for clinical decision making than are odds ratios or relative risks. However, there is a paucity of information about the relative performance of the different propensity-score methods for estimating risk differences. We conducted a series of Monte Carlo simulations to examine this issue. We examined bias, variance estimation, coverage of confidence intervals, mean-squared error (MSE), and type I error rates. A doubly robust version of IPTW had superior performance compared with the other propensity-score methods. It resulted in unbiased estimation of risk differences, treatment effects with the lowest standard errors, confidence intervals with the correct coverage rates, and correct type I error rates. Stratification, matching on the propensity score, and covariate adjustment using the propensity score resulted in minor to modest bias in estimating risk differences. Estimators based on IPTW had lower MSE compared with other propensity-score methods. Differences between IPTW and propensity-score matching may reflect that these two methods estimate the average treatment effect and the average treatment effect for the treated, respectively.