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Matthew A Psioda, Joseph G Ibrahim
We consider the problem of Bayesian sample size determination for a clinical trial in the presence of historical data that inform the treatment effect. Our broadly applicable, simulation-based methodology provides a framework for calibrating the informativeness of a prior while simultaneously identifying the minimum sample size required for a new trial such that the overall design has appropriate power to detect a non-null treatment effect and reasonable type I error control. We develop a comprehensive strategy for eliciting null and alternative sampling prior distributions which are used to define Bayesian generalizations of the traditional notions of type I error control and power...
March 14, 2018: Biostatistics
Clément Niel, Christine Sinoquet, Christian Dina, Ghislain Rocheleau
Motivation: Large scale genome-wide association studies (GWAS) are tools of choice for discovering associations between genotypes and phenotypes. To date, many studies rely on univariate statistical tests for association between the phenotype and each assayed single nucleotide polymorphism (SNP). However, interaction between SNPs, namely epistasis, must be considered when tackling the complexity of underlying biological mechanisms. Epistasis analysis at large scale entails a prohibitive computational burden when addressing the detection of more than two interacting SNPs...
March 14, 2018: Bioinformatics
Robert T Keys, Anina N Rich, Regine Zopf
Tracking one's own body is essential for environmental interaction, and involves integrating multisensory cues with stored information about the body's typical features. Exactly how multisensory information is integrated in own-body perception is still unclear. For example, Ide and Hidaka (Exp Brain Res 228:43-50, 2013) found that participants made less precise visuo-tactile temporal order judgments (TOJ) when viewing hands in a plausible orientation (upright; typical for one's own hand) compared to an implausible orientation (rotated 180°)...
March 15, 2018: Experimental Brain Research. Experimentelle Hirnforschung. Expérimentation Cérébrale
Neshat Golikhajeh, Bahram Naseri, Jabraeil Razmjou, Reza Hosseini, Marzieh Asadi Aghbolaghi
In order to understand the population genetic diversity and structure of Spodoptera exigua (Hübner) (Lepidoptera: Noctuidae), a serious pest of sugar beet in Iran and the world, we genotyped 133 individuals from seven regions in Iran using four microsatellite loci. Significant difference was seen between the observed and expected heterozygosity in all loci. A lower observed heterozygosity than expected heterozygosity indicated a low heterozygosity in these populations. The value of F showed a high genetic differentiation, so that the mean of Fst was 0...
March 13, 2018: Journal of Economic Entomology
Marco Helbich, Derek de Beurs, Mei-Po Kwan, Rory C O'Connor, Peter P Groenewegen
Background: Natural outdoor environments, such as green spaces (ie, grass, forests, or parks), blue spaces (ie, visible bodies of fresh or salt water), and coastal proximity, have been increasingly shown to promote mental health. However, little is known about how and the extent to which these natural environments are associated with suicide mortality. Our aim was to investigate whether the availability of green space and blue space within people's living environments and living next to the coast are protective against suicide mortality...
March 2018: Lancet. Planetary Health
Guoqi Li, Lei Deng, Gaoxi Xiao, Pei Tang, Changyun Wen, Wuhua Hu, Jing Pei, Luping Shi, H Eugene Stanley
Complex networks characterize the nature of internal/external interactions in real-world systems including social, economic, biological, ecological, and technological networks. Two issues keep as obstacles to fulfilling control of large-scale networks: structural controllability which describes the ability to guide a dynamical system from any initial state to any desired final state in finite time, with a suitable choice of inputs; and optimal control, which is a typical control approach to minimize the cost for driving the network to a predefined state with a given number of control inputs...
March 15, 2018: Scientific Reports
Hythem Sidky, Jonathan K Whitmer
Existing adaptive bias techniques, which seek to estimate free energies and physical properties from molecular simulations, are limited by their reliance on fixed kernels or basis sets which hinder their ability to efficiently conform to varied free energy landscapes. Further, user-specified parameters are in general non-intuitive yet significantly affect the convergence rate and accuracy of the free energy estimate. Here we propose a novel method, wherein artificial neural networks (ANNs) are used to develop an adaptive biasing potential which learns free energy landscapes...
March 14, 2018: Journal of Chemical Physics
Núria Folguera-Blasco, Elisabet Cuyàs, Javier A Menéndez, Tomás Alarcón
Understanding the control of epigenetic regulation is key to explain and modify the aging process. Because histone-modifying enzymes are sensitive to shifts in availability of cofactors (e.g. metabolites), cellular epigenetic states may be tied to changing conditions associated with cofactor variability. The aim of this study is to analyse the relationships between cofactor fluctuations, epigenetic landscapes, and cell state transitions. Using Approximate Bayesian Computation, we generate an ensemble of epigenetic regulation (ER) systems whose heterogeneity reflects variability in cofactor pools used by histone modifiers...
March 15, 2018: PLoS Computational Biology
Stephen S Curran, Eric E Pulis, Michael J Andres, Robin M Oversteet
Two cryptic species of haploporid digeneans belonging in Saccocoelioides are described from Costa Rica; one from a poeciliid fish Poecilia gillii and the other from a characid fish, Astyanx aeneus. Traditional morphological features are examined and found to be largely inefficient for differentiate among new species and 20 New World congeners. Comparison of ribosomal DNA sequences among the 2 new species, 2 North American, 4 Middle American, and 3 South American species of Saccocoelioides, including the type-species Saccocoelioides nanii from Argentina and Saccocoelioides sogandaresi from Texas, is effective for differentiating among these species...
March 16, 2018: Journal of Parasitology
Zachary H Marion, James A Fordyce, Benjamin M Fitzpatrick
Recently there have been major theoretical advances in the quantification and partitioning of diversity within and among communities, regions, and ecosystems. However, applying those advances to real data remains a challenge. Ecologists often end up describing their samples rather than estimating the diversity components of an underlying study system, and existing approaches do not easily provide statistical frameworks for testing ecological questions. Here we offer one avenue to do all of the above using a hierarchical Bayesian approach...
March 15, 2018: Ecology
Teresa Fernández-Crespo, Rick J Schulting, Javier Ordoño, Andreas Duering, Francisco Etxeberria, Lourdes Herrasti, Ángel Armendariz, José I Vegas, Christopher Bronk Ramsey
OBJECTIVES: San Juan ante Portam Latinam is one of a small number of European Neolithic sites meeting many of the archaeological criteria expected for a mass grave, and furthermore presents evidence for violent conflict. This study aims to differentiate between what is potentially a single episode of deposition, versus deposition over some centuries, or, alternatively, that resulting from a combination of catastrophic and attritional mortality. The criteria developed are intended to have wider applicability to other such proposed events...
March 15, 2018: American Journal of Physical Anthropology
Peter A Nigrovic, Timothy Beukelman, George Tomlinson, Brian M Feldman, Laura E Schanberg, Yukiko Kimura
BACKGROUND: Systemic juvenile idiopathic arthritis is a rare febrile arthritis of childhood characterized by a potentially severe course, including prolonged glucocorticoid exposure, growth failure, destructive arthritis, and life-threatening macrophage activation syndrome. Early cytokine-blocking biologic therapy may improve long-term outcomes, although some systemic juvenile idiopathic arthritis patients respond well to non-biologic treatment, leaving optimal management undefined. Consequently, treatment of new-onset systemic juvenile idiopathic arthritis by expert clinicians varies widely...
March 1, 2018: Clinical Trials: Journal of the Society for Clinical Trials
Yulun Liu, Stacia M DeSantis, Yong Chen
Many randomized controlled trials (RCTs) report more than one primary outcome. As a result, multivariate meta-analytic methods for the assimilation of treatment effects in systematic reviews of RCTs have received increasing attention in the literature. These methods show promise with respect to bias reduction and efficiency gain compared to univariate meta-analysis. However, most methods for multivariate meta-analysis have focused on pairwise treatment comparisons (i.e., when the number of treatments is two)...
January 2018: Journal of the Royal Statistical Society. Series C, Applied Statistics
Tatsuya Yamada, Makoto Nishiyama, Shigeyuki Oba, Henri Claver Jimbo, Kazushi Ikeda, Shin Ishii, Kyonsoo Hong, Yuichi Sakumura
Biological cells express intracellular biomolecular information to the extracellular environment as various physical responses. We show a novel computational approach to estimate intracellular biomolecular pathways from growth cone electrophysiological responses. Previously, it was shown that cGMP signaling regulates membrane potential (MP) shifts that control the growth cone turning direction during neuronal development. We present here an integrated deterministic mathematical model and Bayesian reversed-engineering framework that enables estimation of the molecular signaling pathway from electrical recordings and considers both the system uncertainty and cell-to-cell variability...
March 14, 2018: Scientific Reports
Xue-Yan Liu, Keisuke Koba, Lina A Koyama, Sarah E Hobbie, Marissa S Weiss, Yoshiyuki Inagaki, Gaius R Shaver, Anne E Giblin, Satoru Hobara, Knute J Nadelhoffer, Martin Sommerkorn, Edward B Rastetter, George W Kling, James A Laundre, Yuriko Yano, Akiko Makabe, Midori Yano, Cong-Qiang Liu
Plant nitrogen (N) use is a key component of the N cycle in terrestrial ecosystems. The supply of N to plants affects community species composition and ecosystem processes such as photosynthesis and carbon (C) accumulation. However, the availabilities and relative importance of different N forms to plants are not well understood. While nitrate (NO3 - ) is a major N form used by plants worldwide, it is discounted as a N source for Arctic tundra plants because of extremely low NO3 - concentrations in Arctic tundra soils, undetectable soil nitrification, and plant-tissue NO3 - that is typically below detection limits...
March 14, 2018: Proceedings of the National Academy of Sciences of the United States of America
Michael A Irvine, Bernhard P Konrad, Warren Michelow, Robert Balshaw, Mark Gilbert, Daniel Coombs
Increasing HIV testing rates among high-risk groups should lead to increased numbers of cases being detected. Coupled with effective treatment and behavioural change among individuals with detected infection, increased testing should also reduce onward incidence of HIV in the population. However, it can be difficult to predict the strengths of these effects and thus the overall impact of testing. We construct a mathematical model of an ongoing HIV epidemic in a population of gay, bisexual and other men who have sex with men...
March 2018: Journal of the Royal Society, Interface
Christian Herrmann, Penelope Vounatsou, Beat Thürlimann, Nicole Probst-Hensch, Christian Rothermundt, Silvia Ess
INTRODUCTION: In the past decades, mortality due to breast cancer has declined considerably in Switzerland and other developed countries. The reasons for this decline remain controversial as several factors occurred almost simultaneously, including important advances in treatment approaches, breast cancer awareness and the introduction of mammography screening programmes in many European countries. In Switzerland, mammography screening programmes (MSPs) have existed in some regions for over 20 years but do not yet exist in others...
March 14, 2018: BMJ Open
Mingsheng Yang, Lu Song, Jianhang Mao, Yuxia Shi, Changjing Wu, Yunxia Zhang, Li Huang, Weifeng Peng, Xiaomeng Liu
Complete mitochondrial genome (mitogenome) of the Omiodes indicata was sequenced and characterized. The circular mitogenome is 15,367 bp long, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an A + T-rich region. Nucleotide composition is highly biased toward A + T nucleotides (81.6%). All 13 PCGs initiate with canonical start codon (ATN), except for cox1 that initiates with CGA. All tRNAs have a typical clover-leaf structure, except for trnS1 (AGN) in which the base pairs of the dihydrouridine (DHU) arm are reduced...
March 11, 2018: International Journal of Biological Macromolecules
Yang Bai, Hannelore Bové, Tim S Nawrot, Benoit Nemery
BACKGROUND: Carbon load in airway macrophages (AM) has been proposed as an internal marker to assess long-term exposure to combustion-derived pollutant particles. However, it is not known how this biomarker is affected by changes in exposure. We studied the clearance kinetics of black carbon (BC) in AM, obtained by sputum induction, in a one-year panel study. METHODS: AM BC was measured 8 times with 6 weeks intervals in healthy young subjects: 15 long-term residents in Leuven, Belgium (BE, mean annual PM10 20-30 μg/m3 ) and 30 newcomers having arrived recently (< 3 weeks) in Leuven from highly polluted cities (mean annual PM10  > 50 μg/m3 ) in low and middle-income countries (LMIC, n = 15), or from low to moderately polluted cities in high-income countries (HIC, n = 15)...
March 14, 2018: Particle and Fibre Toxicology
Alexander Trumpp, Johannes Lohr, Daniel Wedekind, Martin Schmidt, Matthias Burghardt, Axel R Heller, Hagen Malberg, Sebastian Zaunseder
BACKGROUND: Camera-based photoplethysmography (cbPPG) is a measurement technique which enables remote vital sign monitoring by using cameras. To obtain valid plethysmograms, proper regions of interest (ROIs) have to be selected in the video data. Most automated selection methods rely on specific spatial or temporal features limiting a broader application. In this work, we present a new method which overcomes those drawbacks and, therefore, allows cbPPG to be applied in an intraoperative environment...
March 14, 2018: Biomedical Engineering Online
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