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https://www.readbyqxmd.com/read/29149300/the-effect-of-non-reversibility-on-inferring-rooted-phylogenies
#1
Svetlana Cherlin, Sarah E Heaps, Tom M W Nye, Richard J Boys, Tom A Williams, T Martin Embley
Most phylogenetic models assume that the evolutionary process is stationary and reversible. In addition to being biologically improbable, these assumptions also impair inference by generating models under which the likelihood does not depend on the position of the root. Consequently, the root of the tree cannot be inferred as part of the analysis. Yet identifying the root position is a key component of phylogenetic inference because it provides a point of reference for polarising ancestor/descendant relationships and therefore interpreting the tree...
November 15, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29148070/growth-factors-for-diabetic-foot-ulcers-mixed-treatment-comparison-analysis-of-randomized-clinical-trials
#2
Kannan Sridharan, Gowri Sivaramakrishnan
AIMS: Topical growth factors accelerate wound healing in patients with diabetic foot ulcers (DFU). Due to the absence of head to head comparisons, we carried out Bayesian network meta-analysis to compare the efficacy and safety of growth factors. METHODS: Using an appropriate search strategy, randomized controlled trials on topical growth factors compared with standard of care in patients with DFU, were included. Proportion of patients with complete healing was the primary outcome...
November 17, 2017: British Journal of Clinical Pharmacology
https://www.readbyqxmd.com/read/29147578/modelling-historical-changes-in-the-force-of-infection-of-chagas-disease-to-inform-control-and-elimination-programmes-application-in-colombia
#3
Zulma M Cucunubá, Pierre Nouvellet, Lesong Conteh, Mauricio Javier Vera, Victor Manuel Angulo, Juan Carlos Dib, Gabriel Jaime Parra-Henao, María Gloria Basáñez
Background: WHO's 2020 milestones for Chagas disease include having all endemic Latin American countries certified with no intradomiciliary Trypanosoma cruzi transmission, and infected patients under care. Evaluating the variation in historical exposure to infection is crucial for assessing progress and for understanding the priorities to achieve these milestones. Methods: Focusing on Colombia, all the available age-structured serological surveys (undertaken between 1995 and 2014) were searched and compiled...
2017: BMJ Global Health
https://www.readbyqxmd.com/read/29146528/hierarchical-bayesian-models-for-the-autonomic-based-concealed-information-test
#4
Yusuke Shibuya, Kensuke Okada, Tokihiro Ogawa, Izumi Matsuda, Michiko Tsuneoka
The concealed information test (CIT) is a psychophysiological memory detection technique for examining whether an examinee recognizes crime-relevant information. In current statistical analysis practice, the autonomic responses are usually transformed into Z scores within individuals to remove inter- and intra-individual variability. However, this conventional procedure leads to overestimation of the effect size, specifically the standardized mean difference of the autonomic responses between the crime-relevant information and the crime-irrelevant information...
November 13, 2017: Biological Psychology
https://www.readbyqxmd.com/read/29145086/active-learning-for-classifying-data-streams-with-unknown-number-of-classes
#5
Saad Mohamad, Moamar Sayed-Mouchaweh, Abdelhamid Bouchachia
The classification of data streams is an interesting but also a challenging problem. A data stream may grow infinitely making it impractical for storage prior to processing and classification. Due to its dynamic nature, the underlying distribution of the data stream may change over time resulting in the so-called concept drift or the possible emergence and fading of classes, known as concept evolution. In addition, acquiring labels of data samples in a stream is admittedly expensive if not infeasible at all...
October 27, 2017: Neural Networks: the Official Journal of the International Neural Network Society
https://www.readbyqxmd.com/read/29143611/one-or-two-serological-assay-testing-strategy-for-diagnosis-of-hbv-and-hcv-infection-the-use-of-predictive-modelling
#6
John V Parry, Philippa Easterbrook, Anita R Sands
BACKGROUND: Initial serological testing for chronic hepatitis B virus (HBV) and hepatitis C virus (HCV) infection is conducted using either rapid diagnostic tests (RDT) or laboratory-based enzyme immunoassays (EIA)s for detection of hepatitis B surface antigen (HBsAg) or antibodies to HCV (anti-HCV), typically on serum or plasma specimens and, for certain RDTs, capillary whole blood. WHO recommends the use of standardized testing strategies - defined as a sequence of one or more assays to maximize testing accuracy while simplifying the testing process and ideally minimizing cost...
November 1, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/29142017/modelling-the-effects-of-phylogeny-and-body-size-on-within-host-pathogen-replication-and-immune-response
#7
Soumya Banerjee, Alan S Perelson, Melanie Moses
Understanding how quickly pathogens replicate and how quickly the immune system responds is important for predicting the epidemic spread of emerging pathogens. Host body size, through its correlation with metabolic rates, is theoretically predicted to impact pathogen replication rates and immune system response rates. Here, we use mathematical models of viral time courses from multiple species of birds infected by a generalist pathogen (West Nile Virus; WNV) to test more thoroughly how disease progression and immune response depend on mass and host phylogeny...
November 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29141579/a-missense-variant-in-the-coil1a-domain-of-the-keratin-25-gene-is-associated-with-the-dominant-curly-hair-coat-trait-crd-in-horse
#8
Caroline Morgenthaler, Mathieu Diribarne, Aurélien Capitan, Rachel Legendre, Romain Saintilan, Maïlys Gilles, Diane Esquerré, Rytis Juras, Anas Khanshour, Laurent Schibler, Gus Cothran
BACKGROUND: Curly horses present a variety of curl phenotypes that are associated with various degrees of curliness of coat, mane, tail and ear hairs. Their origin is still a matter of debate and several genetic hypotheses have been formulated to explain the diversity in phenotype, including the combination of autosomal dominant and recessive alleles. Our purpose was to map the autosomal dominant curly hair locus and identify the causal variant using genome-wide association study (GWAS) and whole-genome sequencing approaches...
November 15, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29140792/a-bayesian-hierarchical-model-for-identifying-significant-polygenic-effects-while-controlling-for-confounding-and-repeated-measures
#9
Christopher McMahan, James Baurley, William Bridges, Chase Joyner, Muhamad Fitra Kacamarga, Robert Lund, Carissa Pardamean, Bens Pardamean
Genomic studies of plants often seek to identify genetic factors associated with desirable traits. The process of evaluating genetic markers one by one (i.e. a marginal analysis) may not identify important polygenic and environmental effects. Further, confounding due to growing conditions/factors and genetic similarities among plant varieties may influence conclusions. When developing new plant varieties to optimize yield or thrive in future adverse conditions (e.g. flood, drought), scientists seek a complete understanding of how the factors influence desirable traits...
November 15, 2017: Statistical Applications in Genetics and Molecular Biology
https://www.readbyqxmd.com/read/29140482/estimating-autoantibody-signatures-to-detect-autoimmune-disease-patient-subsets
#10
Zhenke Wu, Livia Casciola-Rosen, Ami A Shah, Antony Rosen, Scott L Zeger
Autoimmune diseases are characterized by highly specific immune responses against molecules in self-tissues. Different autoimmune diseases are characterized by distinct immune responses, making autoantibodies useful for diagnosis and prediction. In many diseases, the targets of autoantibodies are incompletely defined. Although the technologies for autoantibody discovery have advanced dramatically over the past decade, each of these techniques generates hundreds of possibilities, which are onerous and expensive to validate...
November 13, 2017: Biostatistics
https://www.readbyqxmd.com/read/29139606/two-stage-model-for-multivariate-longitudinal-and-survival-data-with-application-to-nephrology-research
#11
Ipek Guler, Christel Faes, Carmen Cadarso-Suárez, Laetitia Teixeira, Anabela Rodrigues, Denisa Mendonça
In many follow-up studies different types of outcomes are collected including longitudinal measurements and time-to-event outcomes. Commonly, it is of interest to study the association between them. Joint modeling approaches of a single longitudinal outcome and survival process have recently gained increasing attention from both frequentist and Bayesian perspective. However, in many studies several longitudinal biomarkers are of interest and instead of selecting one single biomarker, the relationships between all these outcomes and their association with survival needs to be investigated...
November 2017: Biometrical Journal. Biometrische Zeitschrift
https://www.readbyqxmd.com/read/29138952/age-estimation-by-assessment-of-pulp-chamber-volume-a-bayesian-network-for-the-evaluation-of-dental-evidence
#12
Emanuele Sironi, Franco Taroni, Claudio Baldinotti, Cosimo Nardi, Gian-Aristide Norelli, Matteo Gallidabino, Vilma Pinchi
PURPOSE: The present study aimed to investigate the performance of a Bayesian method in the evaluation of dental age-related evidence collected by means of a geometrical approximation procedure of the pulp chamber volume. Measurement of this volume was based on three-dimensional cone beam computed tomography images. METHODS: The Bayesian method was applied by means of a probabilistic graphical model, namely a Bayesian network. Performance of that method was investigated in terms of accuracy and bias of the decisional outcomes...
November 14, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/29138300/high-zika-virus-seroprevalence-in-salvador-northeastern-brazil-limits-the-potential-for-further-outbreaks
#13
Eduardo Martins Netto, Andres Moreira-Soto, Celia Pedroso, Christoph Höser, Sebastian Funk, Adam J Kucharski, Alexandra Rockstroh, Beate M Kümmerer, Gilmara Souza Sampaio, Estela Luz, Sara Nunes Vaz, Juarez Pereira Dias, Fernanda Anjos Bastos, Renata Cabral, Thomas Kistemann, Sebastian Ulbert, Xavier de Lamballerie, Thomas Jaenisch, Oliver J Brady, Christian Drosten, Manoel Sarno, Carlos Brites, Jan Felix Drexler
During 2015 to 2016, Brazil reported more Zika virus (ZIKV) cases than any other country, yet population exposure remains unknown. Serological studies of ZIKV are hampered by cross-reactive immune responses against heterologous viruses. We conducted serosurveys for ZIKV, dengue virus (DENV), and Chikungunya virus (CHIKV) in 633 individuals prospectively sampled during 2015 to 2016, including microcephaly and non-microcephaly pregnancies, HIV-infected patients, tuberculosis patients, and university staff in Salvador in northeastern Brazil using enzyme-linked immunosorbent assays (ELISAs) and plaque reduction neutralization tests...
November 14, 2017: MBio
https://www.readbyqxmd.com/read/29137194/integrated-display-and-simulation-for-automatic-dependent-surveillance-broadcast-and-traffic-collision-avoidance-system-data-fusion
#14
Yanran Wang, Gang Xiao, Zhouyun Dai
Automatic Dependent Surveillance-Broadcast (ADS-B) is the direction of airspace surveillance development. Research analyzing the benefits of Traffic Collision Avoidance System (TCAS) and ADS-B data fusion is almost absent. The paper proposes an ADS-B minimum system from ADS-B In and ADS-B Out. In ADS-B In, a fusion model with a variable sampling Variational Bayesian-Interacting Multiple Model (VSVB-IMM) algorithm is proposed for integrated display and an airspace traffic situation display is developed by using ADS-B information...
November 13, 2017: Sensors
https://www.readbyqxmd.com/read/29136595/modeling-the-temporal-dynamics-of-intertidal-benthic-infauna-biomass-with-environmental-factors-impact-assessment-of-land-reclamation
#15
Ye Yang, Ting Fong May Chui, Ping Ping Shen, Yang Yang, Ji Dong Gu
Anthropogenic activities such as land reclamation are threatening tidal marshes worldwide. This study's hypothesis is that land reclamation in a semi-enclosed bay alters the seasonal dynamics of intertidal benthic infauna, which is a key component in the tidal marsh ecosystem. Mai Po Tidal Marsh, Deep Bay, Pearl River Estuary, China was used as a case study to evaluate the hypothesis. Ecological models that simulate benthic biomass dynamics with governing environmental factors were developed, and various scenario experiments were conducted to evaluate the impact of reclamations...
November 11, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29136231/characterisation-of-the-ptb-thermal-neutron-calibration-facility-with-the-bonner-sphere-spectrometer-nemus
#16
M Zboril, M Luszik-Bhadra, D Radeck, M Reginatto, A Zimbal
The neutron field of the PTB Thermal Neutron Calibration Facility was characterised with the help of the Bonner sphere spectrometer of PTB, NEutron MUltisphere Spectrometer (NEMUS). For the analysis of the Bonner sphere data an analytical model of the neutron energy distribution was used. The unfolding of neutron spectra was performed via the method of Bayesian parameter estimation. Comparison of the results of thermal neutron fluence and thermal ambient dose equivalent with the results of the reference method of gold activation showed a very good agreement...
November 10, 2017: Radiation Protection Dosimetry
https://www.readbyqxmd.com/read/29136211/p3-phylogenetic-posterior-prediction-in-revbayes
#17
Sebastian Höhna, Lyndon M Coghill, Genevieve G Mount, Robert C Thomson, Jeremy M Brown
Tests of absolute model fit are crucial in model-based inference because poorly structured models can lead to biased parameter estimates. In Bayesian inference, posterior predictive simulations can be used to test absolute model fit. However such tests have not been commonly practiced in phylogenetic inference due to a lack of convenient and flexible software. Here we describe our newly implemented tests of model fit using posterior predictive testing, based on both data- and inference-based test statistics, in the phylogenetics software RevBayes...
November 10, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29136145/a-two-step-method-for-variable-selection-in-the-analysis-of-a-case-cohort-study
#18
P J Newcombe, S Connolly, S Seaman, S Richardson, S J Sharp
Background: Accurate detection and estimation of true exposure-outcome associations is important in aetiological analysis; when there are multiple potential exposure variables of interest, methods for detecting the subset of variables most likely to have true associations with the outcome of interest are required. Case-cohort studies often collect data on a large number of variables which have not been measured in the entire cohort (e.g. panels of biomarkers). There is a lack of guidance on methods for variable selection in case-cohort studies...
November 10, 2017: International Journal of Epidemiology
https://www.readbyqxmd.com/read/29134543/bayesian-inference-for-psychology-part-iii-parameter-estimation-in-nonstandard-models
#19
Dora Matzke, Udo Boehm, Joachim Vandekerckhove
We demonstrate the use of three popular Bayesian software packages that enable researchers to estimate parameters in a broad class of models that are commonly used in psychological research. We focus on WinBUGS, JAGS, and Stan, and show how they can be interfaced from R and MATLAB. We illustrate the use of the packages through two fully worked examples; the examples involve a simple univariate linear regression and fitting a multinomial processing tree model to data from a classic false-memory experiment. We conclude with a comparison of the strengths and weaknesses of the packages...
November 13, 2017: Psychonomic Bulletin & Review
https://www.readbyqxmd.com/read/29134086/multiple-optimality-criteria-support-ornithoscelida
#20
Luke A Parry, Matthew G Baron, Jakob Vinther
A recent study of early dinosaur evolution using equal-weights parsimony recovered a scheme of dinosaur interrelationships and classification that differed from historical consensus in a single, but significant, respect; Ornithischia and Saurischia were not recovered as monophyletic sister-taxa, but rather Ornithischia and Theropoda formed a novel clade named Ornithoscelida. However, these analyses only used maximum parsimony, and numerous recent simulation studies have questioned the accuracy of parsimony under equal weights...
October 2017: Royal Society Open Science
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