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Matthews Brett A BA School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332, - - 2014
This paper details a novel probabilistic method for automatic neural spike sorting which uses stochastic point process models of neural spike trains and parameterized action potential waveforms. A novel likelihood model for observed firing times as the aggregation of hidden neural spike trains is derived, as well as an iterative ...
Song Yunke Y Biomedical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of - - 2014
Adapter ligation is a critical first step in many microRNA analysis methods including microarray, qPCR, and sequencing. Previous studies have shown that ligation bias can have dramatic effects on both the fidelity of expression profiles and reproducibility across samples. We have developed a method for high efficiency and low bias ...
Ericsson Aaron C AC Mutant Mouse Regional Resource Center (MMRRC), Rat Resource and Research Center (RRRC), Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, USA. - - 2014
Segmented filamentous bacteria (SFB) are commensal bacteria that were first identified in the ilea of mice and rats. Morphologically similar bacteria occur in a broad range of host species, but all strains have been refractory to in vitro culture thus far. Although SFB were once considered innocuous members of the ...
Ryu Ehri E Department of Psychology, Boston College Chestnut Hill, MA, - - 2014
Assessing goodness of model fit is one of the key questions in structural equation modeling (SEM). Goodness of fit is the extent to which the hypothesized model reproduces the multivariate structure underlying the set of variables. During the earlier development of multilevel structural equation models, the "standard" approach was to ...
Schermelleh-Engel Karin K Department of Psychology, Goethe University Frankfurt, - - 2014
Evaluating model fit in nonlinear multilevel structural equation models (MSEM) presents a challenge as no adequate test statistic is available. Nevertheless, using a product indicator approach a likelihood ratio test for linear models is provided which may also be useful for nonlinear MSEM. The main problem with nonlinear models is ...
Banon-Maneus E E Comprehensive Pneumology Center, University Hospital Großhadern, Ludwig-Maximilians-University, 81337 Munich, Germany ; Fundació Clínic, Laboratori Experimental de Nefrologia i Transplantament (LENIT), CELLEX 2B, C/Casanova 143, 08036 Barcelona, - - 2014
Progression of chronic kidney disease (CKD) is characterized by deposition of extracellular matrix. This is an irreversible process that leads to tubulointerstitial fibrosis and finally loss of kidney function. Wnt/ β -catenin pathway was reported to be aberrantly activated in the progressive damage associated with chronic organ failure. Extensive renal ...
Liao Bo B Key Laboratory for Embedded and Network Computing of Hunan Province, the College of Information Science and Engineering, Hunan University, Changsha Hunan, - - 2014
Sparse representation classification (SRC) is one of the most promising classification methods for supervised learning. This method can effectively exploit discriminating information by introducing a [Formula: see text] regularization terms to the data. With the desirable property of sparisty, SRC is robust to both noise and outliers. In this study, ...
Kalinowska Barbara B Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Krakow, Poland; Faculty of Physics, Astronomy and Applied Computer Science - Jagiellonian University, Krakow, - - 2014
This work discusses the role of unstructured polypeptide chain fragments in shaping the protein's hydrophobic core. Based on the "fuzzy oil drop" model, which assumes an idealized distribution of hydrophobicity density described by the 3D Gaussian, we can determine which fragments make up the core and pinpoint residues whose location ...
Boughammoura Sondès S Faculty of Sciences of Monastir, UR Electrolytes, University of Monastir, 5000 Monastir, - - 2014
We have proved in details that the dielectric friction remains the principal frictional effect for a stretched polyion modeled as a chain of charged spheres, whereas, in the case of Manning's model (infinite thread with a continuous distribution of charge), this friction effect is nonexistent. According to this chain model, ...
Zhang H M HM Maize Research Institute, Shanxi Academy of Agricultural Sciences, Xinzhou City, - - 2014
Maize (Zea mays L.) is one of the most important crops in the world. In this study, 13 agronomic traits of a recombinant inbred line population that was derived from the cross between Mo17 and Huangzao4 were investigated in maize: ear diameter, ear length, ear axis diameter, ear weight, plant ...
Peterlík Igor I Institut Hospitalo-Universitaire, Strasbourg, - - 2014
Accurate biomechanical modeling of liver is of paramount interest in pre-operative planning or computer-aided per-operative guidance. Since the liver is an organ composed of three different components (parenchyma, vascularization and Glisson's capsule), an efficient and realistic simulation of its behaviour is a challenging task. In this paper we propose a ...
Rassoli Aisa A Biological Fluid Mechanics Research Laboratory, Biomedical Engineering Faculty, Amirkabir University of Technology (Tehran Polytechnic), Tehran, - - 2014
Purpose: The Mechanical properties of the ureteral wall may be altered by certain diseases&nbsp;such as megaureter. Ureter compliance and wall tension alterations can occur, leading to&nbsp;some abnormalities such as reflex mechanisms. Familiarizing with the mechanical properties&nbsp;of the ureter can help us advance in the understanding of urinary tract diseases. Materials ...
Matsuda Eiko E Department of Arts and Sciences, The University of Tokyo, Tokyo, Japan; School of Informatics and Engineering, University of Sussex, Brighton, United Kingdom; Japan Society for the Promotion of Science, Tokyo, - - 2014
Vicarious trial-and-error (VTE) is a behavior observed in rat experiments that seems to suggest self-conflict. This behavior is seen mainly when the rats are uncertain about making a decision. The presence of VTE is regarded as an indicator of a deliberative decision-making process, that is, searching, predicting, and evaluating outcomes. ...
Gusenleitner Daniel D Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America; Department of Computational Biomedicine, Boston University Medical Campus, Boston, Massachusetts, United States of - - 2014
Despite an overall decrease in incidence of and mortality from cancer, about 40% of Americans will be diagnosed with the disease in their lifetime, and around 20% will die of it. Current approaches to test carcinogenic chemicals adopt the 2-year rodent bioassay, which is costly and time-consuming. As a result, ...
Godsey Brian - - 2014
[This corrects the article on p. e68358 in vol. 8.].
Badhan Raj K Singh RK Manchester Pharmacy School, the University of Manchester, Oxford Road, Manchester, M13 9PT, UK. - - 2014
Central nervous system (CNS) drug disposition is dictated by a drug's physicochemical properties and its ability to permeate physiological barriers. The blood-brain barrier (BBB), blood-cerebrospinal fluid barrier and centrally located drug transporter proteins influence drug disposition within the central nervous system. Attainment of adequate brain-to-plasma and cerebrospinal fluid-to-plasma partitioning is ...
Oh S R SR Department of Food Science and Technology, Chung-Ang University, 72-1 Nae-ri, Daeduk-myun, Ansung, Gyunggido 456-756, Republic of - - 2014
The inhibitory effect of chlorine (50, 100, and 200 mg/kg) was investigated with and without UV radiation (300 mW·s/cm(2)) for the growth of Listeria monocytogenes in chicken breast meat. Using a polynomial model, predictive growth models were also developed as a function of chlorine concentration, UV exposure, and storage temperature ...
Liu Yang Y 0000-0002-1187-6388 School of Transportation Science and Engineering, Harbin Institute of Technology, Harbin 150090, China ; Postdoctoral Station of Civil Engineering, Harbin Institute of Technology, Harbin 150090, - - 2014
Updating the structural model of complex structures is time-consuming due to the large size of the finite element model (FEM). Using conventional methods for these cases is computationally expensive or even impossible. A two-level method, which combined the Kriging predictor and the component mode synthesis (CMS) technique, was proposed to ...
Huang Qiongyu Q Department of Geographical Sciences, University of Maryland, College Park, Maryland, United States of - - 2014
Avian diversity is under increasing pressures. It is thus critical to understand the ecological variables that contribute to large scale spatial distribution of avian species diversity. Traditionally, studies have relied primarily on two-dimensional habitat structure to model broad scale species richness. Vegetation vertical structure is increasingly used at local scales. ...
Terashi Genki G School of Pharmacy, Kitasato - - 2014
In the absence of experimentally determined three dimensional (3D) structures of proteins, the prediction of protein structures using computational methods is a standard alternative approach in bioinformatics. When using the predicted protein models to compute the native structure of an unknown target protein, estimating the actual quality of the protein ...
Zoratto Francesca F 0000-0002-3626-8928 Section of Behavioural Neuroscience, Department of Cell Biology and Neurosciences, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy ; Bambino Gesù Children's Hospital IRCCS, Rome, - - 2014
Interest is rising for animal modeling of pathological gambling. Using the operant probabilistic-delivery task (PDT), gambling proneness can be evaluated in laboratory animals. Drawing a comparison with rats, this study evaluated the common marmoset (Callithrix jacchus) using a PDT. By nose- or hand-poking, subjects learnt to prefer a large (LLL, ...
Tedford Stephanie E SE Department of Pharmacology, Center for Compulsive Behavior and Addiction, Rush University Medical Center Chicago, IL, USA ; Department of Pharmacology, Rush University Medical Center Chicago, IL, - - 2014
Pathological gambling is one manifestation of impulse control disorders. The biological underpinnings of these disorders remain elusive and treatment is far from ideal. Animal models of impulse control disorders are a critical research tool for understanding this condition and for medication development. Modeling such complex behaviors is daunting, but by ...
Tétard-Jones Catherine C Molecular Agriculture Group, Nafferton Ecological Farming Group, School of Agriculture, Food and Rural Development, Newcastle University, Newcastle-Upon-Tyne, United - - 2014
'Omics analysis (transcriptomics, proteomics) quantifies changes in gene/protein expression, providing a snapshot of changes in biochemical pathways over time. Although tools such as modelling that are needed to investigate the relationships between genes/proteins already exist, they are rarely utilised. We consider the potential for using Structural Equation Modelling to investigate ...
Fang Keyan K Key Laboratory of Humid Subtropical Eco-Geographical Process (Ministry of Education), College of Geographical Sciences, Fujian Normal University, Fuzhou, Fujian Province, China ; Key Laboratory of Western China's Environmental Systems (Ministry of Education), Research School of Arid Environment and Climate Change, Lanzhou University, Lanzhou, Gansu Province, China ; Department of Geosciences and Geography, University of Helsinki, Helsinki City, Helsinki, - - 2014
Traditional detrending methods assign equal mean value to all tree-ring series for chronology developments, despite that the mean annual growth changes in different time periods. We find that the strength of a tree-ring model can be improved by giving more weights to tree-ring series that have a stronger climate signal ...
Bekara Mohammed El Amine ME University Paris Est, Anses, Laboratory of Animal Health, Epidemiology Unit, Maisons-Alfort, - - 2014
Epidemiological models are key tools for designing and evaluating detection and control strategies against animal infectious diseases. In France, after decades of decrease of bovine tuberculosis (bTB) incidence, the disease keeps circulating. Increasing prevalence levels are observed in several areas, where the detection and control strategy could be adapted. The ...
Krivitsky Pavel N PN Pennsylvania State University, University Park, - - 2014
Models of dynamic networks - networks that evolve over time - have manifold applications. We develop a discrete-time generative model for social network evolution that inherits the richness and flexibility of the class of exponential-family random graph models. The model - a Separable Temporal ERGM (STERGM) - facilitates separable modeling ...
Salewski Volker V Michael-Otto-Institut im NABU, Bergenhusen, - - 2014
Changes in morphology have been postulated as one of the responses of animals to global warming, with increasing ambient temperatures leading to decreasing body size. However, the results of previous studies are inconsistent. Problems related to the analyses of trends in body size may be related to the short-term nature ...
Li Quanfeng - - 2014
The nutrient composition of corn is variable. To prevent unforeseen reductions in growth performance, grading and analytical methods are used to minimize nutrient variability between calculated and analyzed values. This experiment was carried out to define the sources of variation in the energy content of corn and to develop a ...
Moseby Katherine E KE The University of Adelaide, North Terrace, Adelaide, Australia; Arid Recovery, Roxby Downs, - - 2014
Reintroduction programs for threatened species often include elaborate release strategies designed to improve success, but their advantages are rarely tested scientifically. We used a set of four experiments to demonstrate that the influence of release strategies on short-term reintroduction outcomes is related to both intrinsic and extrinsic factors. We compared ...
Baumann Jenny J IUF-Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany; Both authors contributed equally to this - - 2014
The developing nervous system is highly vulnerable to the adverse effects of chemical agents. Currently, there is an increasing need for testing and regulating chemical compounds in general use and, due to the lack of available data, to identify those which are developmental neurotoxicants. In this context, alternative testing strategies ...
Ebrahimi Mansour M Department of Biology, School of Basic Sciences, University of Qom, Qom, - - 2014
The evolution of the influenza A virus to increase its host range is a major concern worldwide. Molecular mechanisms of increasing host range are largely unknown. Influenza surface proteins play determining roles in reorganization of host-sialic acid receptors and host range. In an attempt to uncover the physic-chemical attributes which ...
Polade Suraj D SD Climate, Atmospheric Science and Physical Oceanography (CASPO), Scripps Institution of Oceanography, La Jolla, CA, - - 2014
Future changes in the number of dry days per year can either reinforce or counteract projected increases in daily precipitation intensity as the climate warms. We analyze climate model projected changes in the number of dry days using 28 coupled global climate models from the Coupled Model Intercomparison Project, version ...
Thomsen Kim K Department of Clinical Microbiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, - - 2014
Medical biofilms have attracted substantial attention especially in the past decade. Animal models are contributing significantly to understand the pathogenesis of medical biofilms. In addition, animal models are an essential tool in testing the hypothesis generated from clinical observations in patients and preclinical testing of agents showing in vitro antibiofilm ...
Schvartzman M Sol MS Food Safety Department, Teagasc Food Research Centre Moorepark, Fermoy, Ireland ; Biosystems Engineering, School of Agriculture, Food Science and Veterinary Medicine, University College Dublin Dublin, - - 2014
Surface-ripened cheeses are matured by means of manual or mechanical technologies posing a risk of cross-contamination, if any cheeses are contaminated with Listeria monocytogenes. In predictive microbiology, primary models are used to describe microbial responses, such as growth rate over time and secondary models explain how those responses change with ...
Yan Chang-An CA State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China ; Key Laboratory of Digital Earth Science, Institute of Remote Sensing and Digital Earth (RADI), Chinese Academy of Sciences (CAS), Beijing 100094, - - 2014
A watershed hydrological model, hydrological simulation program-Fortran (HSPF), was applied to simulate the spatial and temporal variation of hydrological processes in the Jiaoyi watershed of Huaihe River Basin, the heaviest shortage of water resources and polluted area in China. The model was calibrated using the years 2001-2004 and validated with ...
Ares Manuel M - - 2014
Quality control must be maintained at every step of a microarray experiment, from RNA isolation through statistical evaluation. Here we provide suggestions for analyzing microarray data. Because the utility of the results depends directly on the design of the experiment, the first critical step is to ensure that the experiment ...
Meyer Carl G CG Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Honolulu, Hawai'i, United States of - - 2014
Tiger sharks (Galecerdo cuvier) are apex predators characterized by their broad diet, large size and rapid growth. Tiger shark maximum size is typically between 380 & 450 cm Total Length (TL), with a few individuals reaching 550 cm TL, but the maximum size of tiger sharks in Hawaii waters remains ...
Buyel Johannes Felix JF Institute for Molecular Biotechnology, RWTH Aachen - - 2014
Plants provide multiple benefits for the production of biopharmaceuticals including low costs, scalability, and safety. Transient expression offers the additional advantage of short development and production times, but expression levels can vary significantly between batches thus giving rise to regulatory concerns in the context of good manufacturing practice. We used ...
Delellis Pietro P 1] Department of Electrical Engineering and Information Technology, University of Naples Federico II, Naples 80125, Italy [2] Department of Mechanical and Aerospace Engineering, Polytechnic School of Engineering, New York University, Brooklyn, New York 11201, - - 2014
We posit a new geometric perspective to define, detect, and classify inherent patterns of collective behaviour across a variety of animal species. We show that machine learning techniques, and specifically the isometric mapping algorithm, allow the identification and interpretation of different types of collective behaviour in five social animal species. ...
Gentile Lori F LF Departments of Surgery, University of Florida College of Medicine, Gainesville, Florida, United States of - - 2014
Animal models for the study of sepsis are being increasingly scrutinized, despite their essential role for early translational research. In particular, recent studies have suggested that at the level of the leukocyte transcriptome, murine models of burns, trauma and endotoxemia markedly differ from their human equivalents, and are only weakly ...
Shangguan Wei W 0000-0001-7622-8210 College of Global Change and Earth System Science, Beijing Normal University, No. 19, Xinjiekouwai Street, Beijing 100875, - - 2014
We investigated eleven particle-size distribution (PSD) models to determine the appropriate models for describing the PSDs of 16349 Chinese soil samples. These data are based on three soil texture classification schemes, including one ISSS (International Society of Soil Science) scheme with four data points and two Katschinski's schemes with five ...
- - 2014
[This corrects the article DOI: 10.1371/journal.pone.0095000.].
Rocha Bruno Alves BA Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901 Ribeirão Preto, SP, - - 2014
Monensin A is a commercially important natural product isolated from Streptomyces cinnamonensins that is primarily employed to treat coccidiosis. Monensin A selectively complexes and transports sodium cations across lipid membranes and displays a variety of biological properties. In this study, we evaluated the Jacobsen catalyst as a cytochrome P450 biomimetic ...
Bhargava Kiran K Department of Pharmacology and Therapeutics, King George's Medical University Erstwhile CSMMU, Lucknow 226003, - - 2014
In this work, 3D model of D2 dopamine receptor was determined by comparative homology modeling program MODELLER. The computed model's energy was minimized and validated using PROCHECK and Errat tool to obtain a stable model structure and was submitted in Protein Model Database (PMDB-ID: PM0079251). Stable model was used for ...
Talluri Rajesh R The University of Texas MD Anderson Cancer Center, Houston, TX, - - 2014
We propose Bayesian methods for Gaussian graphical models that lead to sparse and adaptively shrunk estimators of the precision (inverse covariance) matrix. Our methods are based on lasso-type regularization priors leading to parsimonious parameterization of the precision matrix, which is essential in several applications involving learning relationships among the variables. ...
Galli Corrado Lodovico CL Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano, - - 2014
Our research is aimed at devising and assessing a computational approach to evaluate the affinity of endocrine active substances (EASs) and their metabolites towards the ligand binding domain (LBD) of the androgen receptor (AR) in three distantly related species: human, rat, and zebrafish. We computed the affinity for all the ...
Zhang Jun J Department of Chemistry, Rutgers University, Camden, New Jersey, United States of America; The Rutgers Center for Computational and Integrative Biology, Camden, New Jersey, United States of - - 2014
In vitro bioassays have been developed and are currently being evaluated as potential alternatives to traditional animal toxicity models. Already, the progress of high throughput screening techniques has resulted in an enormous amount of publicly available bioassay data having been generated for a large collection of compounds. When a compound ...
Mukherjee Sayak - - 2014
[This corrects the article on p. e73937 in vol. 8.].
Weir Scott M SM The Institute of Environmental and Human Health, Department of Environmental Toxicology, Texas Tech University, Lubbock, Texas, United States of - - 2014
Despite widespread recognition of significant data deficiencies, reptiles remain a relatively understudied taxon in ecotoxicology. To conduct ecological risk assessments on reptiles frequently requires using surrogate taxa such as birds, but recent research suggests that reptiles have significantly different exposure profiles and toxicant sensitivity. We exposed western fence lizards, Sceloporus ...
Smith Aaron D AD Department of Biological Sciences, Northern Arizona University, PO Box 5640, Flagstaff, AZ, 86011-5640, - - 2014
Darkling beetle larvae (Coleoptera, Tenebrionidae) are collectively referred to as false wireworms. Larvae from several species in the genus Eleodes are considered to be agricultural pests, though relatively little work has been done to associate larvae with adults of the same species and only a handful of species have been ...
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