bluuebunny/crossref_metadata_2025_split huggingface dataset:
In vivo measurement of hemodynamic information in stenosed rat blood vessels using X-ray PIV
Authors: Park Hanwook , Park Jun Hong , Lee Sang Joon 
Published: November 2016

AbstractMeasurements of the hemodynamic information of blood flows, especially wall shear stress (WSS), in animal models with circulatory vascular diseases (CVDs) are important to understand the pathological mechanism of CVDs. In this study, X-ray particle image velocimetry (PIV) with high spatial resolution was applied to obtain velocity field information in stenosed blood vessels with high WSS. 3D clips fabricated with a 3D printer were applied to the abdominal aorta of a rat cadaver to induce artificial stenosis in the real blood vessel of an animal model. The velocity and WSS information of blood flows in the stenosed vessel were obtained and compared at various stenosis severities. In vivo measurement was also conducted by fastening a stenotic clip on a live rat model through surgical intervention to reduce the flow rate to match the limited temporal resolution of the present X-ray PIV system. Further improvement of the temporal resolution of the system might be able to provide in vivo measurements of hemodynamic information from animal disease models under physiological conditions. The present results would be helpful for understanding the relation between hemodynamic characteristics and the pathological mechanism in animal CVD models.
Chemotypic variation in terpenes emitted from storage pools influences early aphid colonisation on tansy
Authors: Clancy Mary V. , Zytynska Sharon E. , Senft Matthias , Weisser Wolfgang W. , Schnitzler Jörg-Peter 
Published: November 2016

AbstractTansy plants (Tanacetum vulgare L.) exhibit high chemical variation, particularly in mono- and sesquiterpenes that are stored in specialised glands on the plant surface. In the present work we investigated the effects of terpene chemotypes on Metopeurum fuscoviride, an aphid species specialised on tansy, and their tending ants, at the field scale. Previous studies have chemotyped tansy by assessing dominant compounds; here we propose a method of chemotyping using all volatile compounds that are likely emitted from the storage glands. The analysis is based on two extraction methods: GC-MS analysis of leaf hexane extracts and SBSE analysis of headspace emissions. In an initial screening we identified the subset of compounds present in both chemical patterns, labelled as ‘compounds likely emitted from storage’. In a large field survey we could show that the putative chemotypic emission pattern from storage pools significantly affected the early aphid colonisation of tansy. Moreover, the statistical analyses revealed that minor compounds exerted a stronger influence on aphid and tending-ant presence than dominant compounds. Overall we demonstrated that within the enormous chemotypic variation of terpenes in tansy plants, chemical signatures of volatile terpenes can be related to the occurrence of insects on individual plants in the field.
Exploring the transfer of self-efficacy: academic self-efficacy predicts exercise and nutrition self-efficacy / Una exploración de la transferencia de la autoeficacia: la autoeficacia académica predice la autoeficacia nutritiva y del ejercicio físico
Authors: Massar Karlijn , Malmberg Roos 
Published: November 2016

In this research, we investigated the transfer of self-efficacy (SE) beliefs from one domain to another. Specifically, we explored whether academic SE beliefs might be able to predict exercise (Study 1) and nutrition (Study 2) SE. Additionally, to explore the underlying mechanisms, participants reported on domain confidence, perceived similarity and domain importance. Specifically, in Study 1, undergraduate students reported on their academic SE beliefs, confidence in the academic and exercise domains and their exercise SE beliefs ( n = 50). In Study 2, participants reported on their academic SE beliefs, confidence in the academic and nutrition domains and their nutrition SE beliefs ( n = 71). Moreover, in both studies, the perceived importance and the perceived similarity between domains were measured. Multiple regression analyses revealed that academic SE beliefs, academic confidence and exercise confidence were significant predictors of exercise SE beliefs (Study 1); for Study 2 nutrition SE was predicted by academic SE, academic confidence, nutrition confidence and nutrition importance diet. Additionally, we found a partial suppression effect in both studies: academic confidence strengthened the relationship between academic SE and exercise SE in Study 1, and between academic SE and nutrition SE in Study 2. Discussion focuses on the similarities and differences between the studies’ results and the implications for the literature.
Fishery-Independent Surveys of the Queen Conch Stock in Western Puerto Rico, with an Assessment of Historical Trends and Management Effectiveness
Authors: Baker Nicole , Appeldoorn Richard S. , Torres-Saavedra Pedro A. 
Published: November 2016

Abstract
The queen conch Lobatus gigas continues to support a commercial fishery in Puerto Rico despite a history of overfishing and low population densities. The goals of this study were to generate density estimates for the queen conch, to assess temporal trends, and to evaluate hypotheses of management interest using generalized linear models. Density data were supplemented by size- and age-class data. Total mean density was 14.1/ha (adults = 7.3/ha; juveniles = 6.6/ha). Year plus habitat and depth (associated effects) were significant factors influencing adult and juvenile density. Lower densities of both juvenile and adult queen conchs were observed in 1997 and 2001 than in 2013, but there have been no differences since 2006. This indicates an improvement in the population, though not recently. A location effect compared sites within the U.S. Exclusive Economic Zone (EEZ), which is closed to fishing, with those in local waters, which are open to fishing. The location term was significant for adults, with lower densities inshore regardless of year. For juveniles, both the location and year × location terms were significant; the EEZ had a higher juvenile density and a proportionally greater density increase (from 2.3/h to 10.0/ha) from 1997 to 2013. Length-frequency diagrams showed an increase in the proportion of adult conchs of 16–20-cm shell length in 2013 relative to 1997. This suggests an effect of the 22.86-cm minimum size limit implemented in 2004. Juveniles comprised 50% of the population in 2013, compared with 70% in 1997, and adults were found in the oldest age-class during the 2013 survey. This suggests an overall decrease in fishing mortality since 1997. Changes in survey methodology are recommended, including but not limited to shortening transects to increase the number of sites, utilizing a two-stage design, not utilizing scooters, standardizing the areas surveyed, and stratifying by depth and habitat.
Received November 30, 2015; accepted July 12, 2016
The Image Data Resource: A Scalable Platform for Biological Image Data Access, Integration, and Dissemination
Authors: Williams Eleanor , Moore Josh , Li Simon W. , Rustici Gabriella , Tarkowska Aleksandra , Chessel Anatole , Leo Simone , Antal Bálint , Ferguson Richard K. , Sarkans Ugis , Brazma Alvis , Carazo Salas Rafael E. , Swedlow Jason R. 
Published: November 2016

AbstractAccess to primary research data is vital for the advancement of science. To extend the data types supported by community repositories, we built a prototype Image Data Resource (IDR) that collects and integrates imaging data acquired across many different imaging modalities. IDR links high-content screening, super-resolution microscopy, time-lapse and digital pathology imaging experiments to public genetic or chemical databases, and to cell and tissue phenotypes expressed using controlled ontologies. Using this integration, IDR facilitates the analysis of gene networks and reveals functional interactions that are inaccessible to individual studies. To enable re-analysis, we also established a computational resource based on IPython notebooks that allows remote access to the entire IDR. IDR is also an open source platform that others can use to publish their own image data. Thus IDR provides both a novel on-line resource and a software infrastructure that promotes and extends publication and re-analysis of scientific image data.
Prestimulus alpha-band power biases visual discrimination confidence, but not accuracy
Authors: Samaha Jason , Iemi Luca , Postle Bradley R. 
Published: November 2016

AbstractOscillations in the alpha-band (8-13 Hz) of human electroencephalographic (EEG) recordings are thought to reflect cortical excitability. As such, the magnitude of alpha power prior to the onset of a near threshold visual stimulus has been shown to predict stimulus detectability. Mechanistically, however, non-specific increases in visual-cortical excitability should result in amplified signal as well as amplified noise, leaving actual discriminability unchanged. Using a two-choice orientation discrimination task with equally probable stimuli, we found that discrimination accuracy was unaffected by fluctuations in prestimulus alpha-band power. Decision confidence, on the other hand, was strongly negatively correlated with prestimulus alpha power. This finding constitutes a clear dissociation between objective and subjective measures of visual perception as a function of prestimulus cortical excitability. This dissociation is predicted by models of perceptual confidence under which the balance of evidence in favor of each choice drives objective performance but only the magnitude of evidence in favor of the chosen stimulus drives subjective reports, suggesting that human perceptual confidence can be suboptimal.
DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding
Authors: Ma Wenxiu , Yang Lin , Rohs Remo , Stafford Noble William 
Published: November 2016

AbstractMotivationTranscription factors (TFs) bind to specific DNA sequence motifs. Several lines of evidence suggest that TF-DNA binding is mediated in part by properties of the local DNA shape: the width of the minor groove, the relative orientations of adjacent base pairs, etc. Several methods have been developed to jointly account for DNA sequence and shape properties in predicting TF binding affinity. However, a limitation of these methods is that they typically require a training set of aligned TF binding sites.ResultsWe describe a sequence+shape kernel that leverages DNA sequence and shape information to better understand protein-DNA binding preference and affinity. This kernel extends an existing class ofk-mer based sequence kernels, based on the recently described di-mismatch kernel. Using threein vitrobenchmark datasets, derived from universal protein binding microarrays (uPBMs), genomic context PBMs (gcPBMs) and SELEX-seq data, we demonstrate that incorporating DNA shape information improves our ability to predict protein-DNA binding affinity. In particular, we observe that (1) thek-spectrum+shape model performs better than the classicalk-spectrum kernel, particularly for smallkvalues; (2) the di-mismatch kernel performs better than thek-mer kernel, for largerk; and (3) the di-mismatch+shape kernel performs better than the di-mismatch kernel for intermediatekvalues.AvailabilityThe software is available athttps://bitbucket.org/wenxiu/sequence-shape.gitContactrohs@usc.edu,william-noble@uw.eduSupplementary informationSupplementary data are available atBioinformaticsonline.
Tracing the biogeographical origin of South Asian populations using DNA SatNav
Authors: Das Ranajit , Upadhyai Priyanka 
Published: November 2016

AbstractThe Indian subcontinent includes India, Bangladesh, Pakistan, Nepal, Bhutan, and Sri Lanka that collectively share common anthropological and cultural roots. Given the enigmatic population structure, complex history and genetic heterogeneity of populations from this region, their biogeographical origin and history remain a fascinating question. In this study we carried out an in-depth genetic comparison of the five South Asian populations available in the 1000 Genomes Project, namely Gujarati Indians from Houston, Texas (GIH), Punjabis from Lahore (PJL), Indian Telugus from UK (ITU), Sri Lankan Tamils from UK (STU) and Bengalis from Bangladesh (BEB), tracing their putative biogeographical origin using a DNA SatNav algorithm - Geographical Population Structure (GPS). GPS positioned >70% of GIH and PJL genomes in North India and >80% of ITU and STU samples in South India. All South Asian genomes appeared to be assigned with reasonable accuracy, along trade routes that thrived in the ancient Mauryan Empire, which had played a significant role in unifying the Indian subcontinent and in the process brought the ancient North and South Indian populations in close proximity, promoting admixture between them, ~2300 years before present (YBP). Our findings suggest that the genetic admixture between ancient North and South Indian populations likely first occurred along the Godavari and Krishna river basin in Central-South India. Finally our biogeographical analyses provide critical insights into the population history and sociocultural forces driving migration patterns that may have been instrumental in shaping the population structure of the Indian subcontinent.
Coordinate Based Random Effect Size meta-analysis of neuroimaging studies
Authors: Tench CR , Tanasescu Radu , Cottam WJ , Constantinescu CS , Auer DP 
Published: November 2016

1AbstractLow power in neuroimaging studies can make them difficult to interpret, and Coordinate based meta‐ analysis (CBMA) may go some way to mitigating this issue. CBMA has been used in many analyses to detect where published functional MRI or voxel-based morphometry studies testing similar hypotheses report significant summary results (coordinates) consistently. Only the reported coordinates and possiblytstatistics are analysed, and statistical significance of clusters is determined by coordinate density.Here a method of performing coordinate based random effect size meta-analysis and meta-regression is introduced. The algorithm (ClusterZ) analyses both coordinates and reportedtstatistic orZscore, standardised by the number of subjects. Statistical significance is determined not by coordinate density, but by a random effects meta-analyses of reported effects performed cluster-wise using standard statistical methods and taking account of censoring inherent in the published summary results. Type 1 error control is achieved using the false cluster discovery rate (FCDR), which is based on the false discovery rate. This controls both the family wise error rate under the null hypothesis that coordinates are randomly drawn from a standard stereotaxic space, and the proportion of significant clusters that are expected under the null. Such control is vital to avoid propagating and even amplifying the very issues motivating the meta-analysis in the first place. ClusterZ is demonstrated on both numerically simulated data and on real data from reports of grey matter loss in multiple sclerosis (MS) and syndromes suggestive of MS, and of painful stimulus in healthy controls. The software implementation is available to download and use freely.
Towards new cholera prophylactics and treatment: Crystal structures of bacterial enterotoxins in complex with GM1 mimics
Authors: Heggelund Julie E. , Mackenzie Alasdair , Martinsen Tobias , Cheshev Pavel , Bernardi Anna , Krengel Ute 
Published: November 2016

AbstractCholera is a life-threatening disease in many countries, and new drugs are clearly needed.C-glycosidic antagonists may serve such a purpose. Atomic resolution crystal structures of these compounds in complexes with the cholera toxin give unprecedented atomic details of the molecular interactions, and show how the inhibitors efficiently block the GM1 binding site. These molecules are well suited for development into low-cost prophylactic drugs, due to their relatively easy syntheses and their resistance to glycolytic enzymes. One of the compounds links two toxin B-pentamers in the crystal structure, which may yield improved inhibition through the formation of toxin aggregates. These structures can spark the improved design of GM1 mimics, either alone or as multivalent inhibitors connecting multiple GM1-binding sites. Future developments may further include compounds that link the primary and secondary binding sites. Serving as decoys, receptor mimics may lessen symptoms while avoiding the use of antibiotics.
Electrical Stimulus Artifact Cancellation and Neural Spike Detection on Large Multi-Electrode Arrays
Authors: Mena Gonzalo E. , Grosberg Lauren E. , Madugula Sasidhar , Hottowy Paweł , Litke Alan , Cunningham John , Chichilnisky E.J. , Paninski Liam 
Published: November 2016

AbstractSimultaneous electrical stimulation and recording using multi-electrode arrays can provide a valuable technique for studying circuit connectivity and engineering neural interfaces. However, interpreting these measurements is challenging because the spike sorting process (identifying and segregating action potentials arising from different neurons) is greatly complicated by electrical stimulation artifacts across the array, which can exhibit complex and nonlinear waveforms, and overlap temporarily with evoked spikes. Here we develop a scalable algorithm based on a structured Gaussian Process model to estimate the artifact and identify evoked spikes. The effectiveness of our methods is demonstrated in both real and simulated 512-electrode recordings in the peripheral primate retina with single-electrode and several types of multi-electrode stimulation. We establish small error rates in the identification of evoked spikes, with a computational complexity that is compatible with real-time data analysis. This technology may be helpful in the design of future high-resolution sensory prostheses based on tailored stimulation (e.g., retinal prostheses), and for closed-loop neural stimulation at a much larger scale than currently possible.Author SummarySimultaneous electrical stimulation and recording using multi-electrode arrays can provide a valuable technique for studying circuit connectivity and engineering neural interfaces. However, interpreting these recordings is challenging because the spike sorting process (identifying and segregating action potentials arising from different neurons) is largely stymied by electrical stimulation artifacts across the array, which are typically larger than the signals of interest. We develop a novel computational framework to estimate and subtract away this contaminating artifact, enabling the large-scale analysis of responses of possibly hundreds of cells to tailored stimulation. Importantly, we suggest that this technology may also be helpful for the development of future high-resolution neural prosthetic devices (e.g., retinal prostheses).
cAMP signaling mediates behavioral flexibility and consolidation of social status inDrosophilaaggression
Authors: Chouhan Nitin Singh , Mohan Krithika , Ghose Aurnab 
Published: November 2016

ABSTRACTSocial rituals, like male-male aggression inDrosophila, are often stereotyped and the component behavioral patterns modular. The likelihood of transition from one behavioral pattern to another is malleable by experience and confers flexibility to the behavioral repertoire. Experience-dependent modification of innate aggressive behavior in flies alters fighting strategies during fights and establishes dominant-subordinate relationships. Dominance hierarchies resulting from agonistic encounters are consolidated to longer lasting social status-dependent behavioral modifications resulting in a robust loser effect.We show that cyclic adenosine monophosphate (cAMP) dynamics regulated by the calcium/calmodulin-dependent adenylyl cyclase, Rut and the cAMP phosphodiesterase, Dnc but not the Amn gene product, in specific neuronal groups of the mushroom body and central complex, mediate behavioral plasticity necessary to establish dominant- subordinate relationships.rutanddncmutant flies are unable to alter fighting strategies and establish dominance relationships during agonistic interactions. This real-time flexibility during a fight is independent of changes in aggression levels. Longer-term consolidation of social status in the form of a loser effect, however, requires additionalAmn-dependent inputs to cAMP signaling and involves a circuit-level association between the α/β and γ neurons of the mushroom body.Our findings implicate cAMP signaling in mediating plasticity of behavioral patterns in aggressive behavior and in the generation of a temporally stable memory trace that manifests as a loser effect.SUMMARY STATEMENTPhasic recruitment of different cAMP signaling modalities in specific neuronal groups lead to the formation of temporally distinct components of learning and memory in fly aggression.
Strategies of social media use in disaster management
Authors: Kim Kyungwoo , Jung Kyujin , Chilton Kenneth 
Published: November 2016

PurposeThe purpose of this paper is to understand the effects of social media use on the resilience of organizations involved in emergency response. While social media has been utilized as a critical tool in the field of emergency management, few researchers have systemically examined its effect on organizations’ capacity to bounce back from catastrophic events. From the dimensional approach to social media use, this research focuses on the following three functions: providing information to local communities, transmitting information to local communities, and responding to the emotions of local communities.Design/methodology/approachThe authors used survey data gleaned from 79 key organizations involved in emergency management to investigate the impact of social media use on resilience after a tragic flood in Seoul, South Korea in 2013. The authors also conducted interviews with ten emergency management officials to understand what administrative challenges they confront in using social media for their tasks.FindingsThe authors found that the provision of disaster information on social media such as Facebook, Twitter, and YouTube has a positive effect on the perceived level of organizational resilience. In addition, social media use correlates positively with community emotional responses.Research limitations/implicationsGiven the focus on the emergency response to a natural disaster in urban areas, the results might not be generalizable to smaller cities or rural areas. The survey items that measure the perceptions of emergency managers may not represent the physical aspects of disaster recovery, such as the restoration of housing stock.Practical implicationsThe findings suggest that public and nonprofit organizations can use social media to communicate with other organizations and the public in ways that demonstrate resilience. Emergency managers should address administrative challenges, such as trustworthiness of information delivered via social media and lack of personnel.Originality/valueThis paper provides systematic understandings of the effects of social media use on the resilience of the organizations that respond to a disaster.