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Auriane Virgili, Matthieu Authier, Pascal Monestiez, Vincent Ridoux
Despite large efforts, datasets with few sightings are often available for rare species of marine megafauna that typically live at low densities. This paucity of data makes modelling the habitat of these taxa particularly challenging. We tested the predictive performance of different types of species distribution models fitted to decreasing numbers of sightings. Generalised additive models (GAMs) with three different residual distributions and the presence only model MaxEnt were tested on two megafauna case studies differing in both the number of sightings and ecological niches...
2018: PloS One
Jessica M Skeie, Benjamin T Aldrich, Andrew S Goldstein, Gregory A Schmidt, Cynthia R Reed, Mark A Greiner
The objective of this study was to characterize the proteome of the corneal endothelial cell layer and its basement membrane (Descemet membrane) in humans with various severities of type II diabetes mellitus compared to controls, and identify differentially expressed proteins across a range of diabetic disease severities that may influence corneal endothelial cell health. Endothelium-Descemet membrane complex tissues were peeled from transplant suitable donor corneas. Protein fractions were isolated from each sample and subjected to multidimensional liquid chromatography and tandem mass spectrometry...
2018: PloS One
Nikoleta S Kolovos, Jeff Gill, Peter H Michelson, Allan Doctor, Mary E Hartman
OBJECTIVE: To evaluate the effectiveness of a physician-led rapid response team program on morbidity and mortality following unplanned admission to the PICU. DESIGN: Before-after study. SETTING: Single-center quaternary-referral PICU. PATIENTS: All unplanned PICU admissions from the ward from 2005 to 2011. INTERVENTIONS: The dataset was divided into pre- and post-rapid response team groups for comparison...
March 9, 2018: Pediatric Critical Care Medicine
Sangeeta Taneja, Amarnath Jena, Rajesh Taneja, Aru Singh, Aashim Ahuja
OBJECTIVE: The purpose of this study is to assess whether temporal changes in68 Ga-prostate-specific membrane antigen (PSMA)-HBED-CC uptake and multiparametric MRI parameters derived using PET/MRI can aid in characterization of benign and malignant prostate lesions. MATERIALS AND METHODS: Thirty-five men with 29 malignant and six benign prostate lesions undergoing complete clinical workup including histologic analysis were enrolled for this retrospective study. All had undergone simultaneous whole-body68 Ga-PSMAHBED-CC PET/MRI...
March 12, 2018: AJR. American Journal of Roentgenology
Erika E Scott, Nicole Krupa, Paul L Jenkins
This article provides an estimate for the economic costs of agricultural injuries sustained in the states of Maine and New Hampshire between the years 2008 and 2010. The authors used a novel dataset of 562 agriculturally related occupational injuries, and cost estimates were generated using the CDC's Web-based Injury Statistics Query and Reporting System (WISQARS). Individual cases from the dataset that did not match the query options for WISQARS were excluded. Of the 562 agricultural injuries identified in the dataset, 361 met the WISQARS criteria...
January 29, 2018: Journal of Agricultural Safety and Health
D M Liebe, R R White
The objective of this study was to quantitatively summarize literature reporting endophyte-infected (Neotyphodium coenophialum) tall fescue (Festuca arundinacea) effects on cattle ADG. This meta-analysis evaluated endophyte infection level, climate, and forage yield using a literature dataset of 138 treatments from 20 articles. Three infection level measurements were tested: endophyte infection as a percentage of infected tillers (E%); ergovaline concentration in ppb ([E]); and total ergot alkaloid concentration ([TEA])...
March 8, 2018: Journal of Animal Science
Xiao He, Lukas Folkman, Karsten Borgwardt
Motivation: Large-scale screenings of cancer cell lines with detailed molecular profiles against libraries of pharmacological compounds are currently being performed in order to gain a better understanding of the genetic component of drug response and to enhance our ability to recommend therapies given a patient's molecular profile. These comprehensive screens differ from the clinical setting in which (1) medical records only contain the response of a patient to very few drugs, (2) drugs are recommended by doctors based on their expert judgment, and (3) selecting the most promising therapy is often more important than accurately predicting the sensitivity to all potential drugs...
March 8, 2018: Bioinformatics
Ryuichiro Nakato, Katsuhiko Shirahige
Motivation: Chromatin immunoprecipitation followed by sequencing (ChIP-seq) can detect read-enriched DNA loci for point-source (e.g., transcription factor binding) and broad-source factors (e.g., various histone modifications). Although numerous quality metrics for ChIP-seq data have been developed, the 'peaks' thus obtained are still difficult to assess with respect to signal-to-noise ratio (S/N) and the percentage of false positives. Results: We developed a quality-assessment tool for ChIP-seq data, SSP (strand-shift profile), that quantifies S/N and peak reliability without peak calling...
March 8, 2018: Bioinformatics
Katie L Hill, Roger L Breton, Gillian E Manning, R Scott Teed, Marie Capdevielle, Brian Slezak
Triclosan is an antibacterial and antifungal chemical used in a variety of consumer products including soaps, detergents, moisturizers, and cosmetics. Aquatic ecosystems may be exposed to triclosan following the release of remaining residues in wastewater effluents and biosolids. In December of 2017, Environment and Climate Change Canada (ECCC) released a Federal Environmental Quality Guideline (FEQG) report that contained a Federal Water Quality Guideline (FWQG) for triclosan. This guideline will be used as an adjunct to the risk assessment and risk management of priority chemicals identified under the Government of Canada's Chemicals Management Plan (CMP)...
March 12, 2018: Integrated Environmental Assessment and Management
Andrew Spriggs, Steven T Henderson, Melanie L Hand, Susan D Johnson, Jennifer M Taylor, Anna Koltunow
Cowpea ( Vigna unguiculata (L.) Walp) is an important legume crop for food security in areas of low-input and smallholder farming throughout Africa and Asia. Genetic improvements are required to increase yield and resilience to biotic and abiotic stress and to enhance cowpea crop performance. An integrated cowpea genomic and gene expression data resource has the potential to greatly accelerate breeding and the delivery of novel genetic traits for cowpea. Extensive genomic resources for cowpea have been absent from the public domain; however, a recent early release reference genome for IT97K-499-35 ( Vigna unguiculata  v1...
February 9, 2018: Gates Open Res
Emma Slaymaker, Estelle McLean, Alison Wringe, Clara Calvert, Milly Marston, Georges Reniers, Chodziwadziwa Whiteson Kabudula, Amelia Crampin, Alison Price, Denna Michael, Mark Urassa, Daniel Kwaro, Maquins Sewe, Jeffrey W Eaton, Rebecca Rhead, Jessica Nakiyingi-Miiro, Tom Lutalo, Dorean Nabukalu, Kobus Herbst, Victoria Hosegood, Basia Zaba
Timely progression of people living with HIV (PLHIV) from the point of infection through the pathway from diagnosis to treatment is important in ensuring effective care and treatment of HIV and preventing HIV-related deaths and onwards transmission of infection.  Reliable, population-based estimates of new infections are difficult to obtain for the generalised epidemics in sub-Saharan Africa.  Mortality data indicate disease burden and, if disaggregated along the continuum from diagnosis to treatment, can also reflect the coverage and quality of different HIV services...
November 6, 2017: Gates Open Res
Yue Yan, Jinzhong Yang, Sam Beddar, Geoffrey S Ibbott, Zhifei Wen, Laurence E Court, Ken-Pin Hwang, Mo Kadbi, Sunil Krishnan, Clifton Fuller, Steven J Frank, James N Yang, Peter A Balter, Rajat J Kudchadker, Jihong Wang
We developed a novel technique to study the impact of geometric distortion of magnetic resonance imaging (MRI) on intensity-modulated radiation therapy treatment planning.
 The measured 3D datasets of residual geometric distortion (a 1.5-T MRI component of an MRI linear accelerator system) was fitted with a second-order polynomial model to map the spatial dependence of geometric distortions. Then the geometric distortion model was applied to computed tomography (CT) image and structure data to simulate the distortion of MRI data and structures...
March 12, 2018: Physics in Medicine and Biology
Séverine Bord, Christèle Bioche, Pierre Druilhet
We consider the problem of estimating a population size by removal sampling when the sampling rate is unknown. Bayesian methods are now widespread and allow to include prior knowledge in the analysis. However, we show that Bayes estimates based on default improper priors lead to improper posteriors or infinite estimates. Similarly, weakly informative priors give unstable estimators that are sensitive to the choice of hyperparameters. By examining the likelihood, we show that population size estimates can be stabilized by penalizing small values of the sampling rate or large value of the population size...
March 12, 2018: Biometrical Journal. Biometrische Zeitschrift
Yijun Lin, Dimitrios Stripelis, Yao-Yi Chiang, José Luis Ambite, Rima Habre, Fan Pan, Sandrah P Eckel
Air quality models are important for studying the impact of air pollutant on health conditions at a fine spatiotemporal scale. Existing work typically relies on area-specific, expert-selected attributes of pollution emissions (e,g., transportation) and dispersion (e.g., meteorology) for building the model for each combination of study areas, pollutant types, and spatiotemporal scales. In this paper, we present a data mining approach that utilizes publicly available OpenStreetMap (OSM) data to automatically generate an air quality model for the concentrations of fine particulate matter less than 2...
November 2017: Proceedings of the ... ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems: ACM GIS
Terril L Verplaetse, Kelly E Moore, Brian P Pittman, Walter Roberts, Lindsay M Oberleitner, Philip H Smith, Kelly P Cosgrove, Sherry A McKee
Background: Stress contributes to the development and maintenance of substance use disorders (SUD), with some research suggesting that the impact of stress on SUD is greater in women. However, this has yet to be evaluated in a national dataset, across major substances of abuse. Methods: Using data from the newly available U.S. National Epidemiologic Survey on Alcohol and Related Conditions (NESARC; Wave 3; n =36,309) we evaluated relationships among past year stressful life events (0 or 1 vs...
January 2018: Chronic Stress
D J McFarland, J R Wolpaw
Brain-Computer Interfaces (BCIs) are real-time computer-based systems that translate brain signals into useful commands. To date most applications have been demonstrations of proof-of-principle; widespread use by people who could benefit from this technology requires further development. Improvements in current EEG recording technology are needed. Better sensors would be easier to apply, more confortable for the user, and produce higher quality and more stable signals. Although considerable effort has been devoted to evaluating classifiers using public datasets, more attention to real-time signal processing issues and to optimizing the mutually adaptive interaction between the brain and the BCI are essential for improving BCI performance...
December 2017: Current Opinion in Biomedical Engineering
Jens C Hegg, Jonathan Middleton, Ben Luca Robertson, Brian P Kennedy
The migration of Pacific salmon is an important part of functioning freshwater ecosystems, but as populations have decreased and ecological conditions have changed, so have migration patterns. Understanding how the environment, and human impacts, change salmon migration behavior requires observing migration at small temporal and spatial scales across large geographic areas. Studying these detailed fish movements is particularly important for one threatened population of Chinook salmon in the Snake River of Idaho whose juvenile behavior may be rapidly evolving in response to dams and anthropogenic impacts...
February 2018: Heliyon
Michael G Dwyer, Jesper Hagemeier, Niels Bergsland, Dana Horakova, Jonathan R Korn, Nasreen Khan, Tomas Uher, Jennie Medin, Diego Silva, Manuela Vaneckova, Eva Kubala Havrdova, Robert Zivadinov
Background: A percent brain volume change (PBVC) cut-off of -0.4% per year has been proposed to distinguish between pathological and physiological changes in multiple sclerosis (MS). Unfortunately, standardized PBVC measurement is not always feasible on scans acquired outside research studies or academic centers. Percent lateral ventricular volume change (PLVVC) is a strong surrogate measure of PBVC, and may be more feasible for atrophy assessment on real-world scans. However, the PLVVC rate corresponding to the established PBVC cut-off of -0...
2018: NeuroImage: Clinical
Ryu-Ichiro Hashimoto, Takashi Itahashi, Rieko Okada, Sayaka Hasegawa, Masayuki Tani, Nobumasa Kato, Masaru Mimura
Abnormalities in functional brain networks in schizophrenia have been studied by examining intrinsic and extrinsic brain activity under various experimental paradigms. However, the identified patterns of abnormal functional connectivity (FC) vary depending on the adopted paradigms. Thus, it is unclear whether and how these patterns are inter-related. In order to assess relationships between abnormal patterns of FC during intrinsic activity and those during extrinsic activity, we adopted a data-fusion approach and applied partial least square (PLS) analyses to FC datasets from 25 patients with chronic schizophrenia and 25 age- and sex-matched normal controls...
2018: NeuroImage: Clinical
Sanuji Gajamange, David Raffelt, Thijs Dhollander, Elaine Lui, Anneke van der Walt, Trevor Kilpatrick, Joanne Fielding, Alan Connelly, Scott Kolbe
Long term irreversible disability in multiple sclerosis (MS) is thought to be primarily driven by axonal degeneration. Axonal degeneration leads to degenerative atrophy, therefore early markers of axonal degeneration are required to predict clinical disability and treatment efficacy. Given that additional pathologies such as inflammation, demyelination and oedema are also present in MS, it is essential to develop axonal markers that are not confounded by these processes. The present study investigated a novel method for measuring axonal degeneration in MS based on high angular resolution diffusion magnetic resonance imaging...
2018: NeuroImage: Clinical
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