bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epistasis detection and modeling for genomic selection in cowpea (Vigna unguiculata. L. Walp.)
Authors: Olatoye Marcus O. , Hu Zhenbin , Aikpokpodion Peter O. 
Published: March 2019

AbstractGenetic architecture reflects the pattern of effects and interaction of genes underling phenotypic variation. Most mapping and breeding approaches generally consider the additive part of variation but offer limited knowledge on the benefits of epistasis which explains in part the variation observed in traits. In this study, the cowpea multiparent advanced generation inter-cross (MAGIC) population was used to characterize the epistatic genetic architecture of flowering time, maturity, and seed size. In addition, considerations for epistatic genetic architecture in genomic-enabled breeding (GEB) was investigated using parametric, semi-parametric, and non-parametric genomic selection (GS) models. Our results showed that large and moderate effect sized two-way epistatic interactions underlie the traits examined. Flowering time QTL colocalized with cowpea putative orthologs ofArabidopsis thalianaandGlycine maxgenes likePHYTOCLOCK1(PCL1[Vigun11g157600]) andPHYTOCHROME A(PHY A[Vigun01g205500]). Flowering time adaptation to long and short photoperiod was found to be controlled by distinct and common main and epistatic loci. Parametric and semi-parametric GS models outperformed non-parametric GS model. Using known QTL as fixed effects in GS models improved prediction accuracy when traits were controlled by both large and moderate effect QTL. In general, our study demonstrated that prior understanding the genetic architecture of a trait can help make informed decisions in GEB. This is the first report to characterize epistasis and provide insights into the underpinnings of GS versus marker assisted selection in cowpea.
Ten-year retrospective analysis ofAcinetobacter baumanniiclinical isolates reveals a proportionately large, non-nosocomial, multidrug-resistant endemic reservoir
Authors: Calix Juan J , Burnham Jason P , Feldman Mario F 
Published: March 2019

AbstractBackgroundAcinetobacter baumannii(Ab) is a global health threat notorious for causing hospital-acquired (HA) infections, though manyAbinfections are community-acquired (CA). Investigations describing contemporaneous, clinically-relevant CA and HAAbpopulations, are lacking.MethodsWe conducted a retrospective ecological analysis of 2042Abclinical isolates identified from 2007 to 2017 in the BJC HealthCare System (BJC), a multi-hospital system located in and around the greater metropolitan area in St. Louis, Missouri. We described basic clinical characteristics and antibiotic susceptibility rates of CA and HAAbisolates in comparative and longitudinal analyses.Results62.1% of allAbisolates were CA, i.e., isolated in ambulatory settings or <48 hours following hospital admission. Though HA isolates initially predominated in the largest BJC hospital, implementation of infection control efforts resulted in a disproportionate reduction in annual HA isolate occurrence. This revealed a stable, baseline occurrence of CA isolates. In all other hospitals, the annual proportion of isolates that were CA averaged 78.7% (95%CI=74.5-83.0). 42.9% and 30.4% of total CA isolates were from skin and soft tissue/musculoskeletal (SST/MSK) and urinary sources, respectively, while HA isolates were primarily respiratory (55.6%). Rates of carbapenem resistance, a surrogate for multidrug resistant (MDR) phenotypes, were higher among respiratory and HA cases (∼60%) compared to contemporaneous non-respiratory CA counterparts (∼40%).ConclusionsMDRAbreservoirs associated with SST/MSK and urinary niches persist outside of hospital environments in a large U.S. healthcare system, even after the implementation of effective hospital infection control measures.SummaryWe compared hospital-acquired and community-acquiredAcinetobacter baumanniiin a large U.S. healthcare system through a ten-year retrospective ecological analysis. Community-acquired isolates composed over 60% of totalA. baumanniiisolates, were primarily from non-respiratory sources and exhibited carbapenem resistance rates of 35-40%.
Sex-specific population dynamics and demography of capercaillie (Tetrao urogallus L.) in a patchy environment
Authors: Augustine Ben C. , Kéry Marc , Marin Juanita Olano , Mollet Pierre , Pasinelli Gilberto , Sutherland Chris 
Published: March 2019

AbstractModeling the population dynamics of patchily distributed species is a challenge, particularly when inference must be based on incomplete and small data sets such as those from most species of conservation concern. Open population spatial capture-recapture (SCR) models are ideally suited to quantify population trends, but have seen only limited use since their introduction.To investigate population trend and sex-specific population dynamics, we applied an open SCR model to a capercaillie (Tetrao urogallus) population in Switzerland living in eight distinct forest patches totalling 22 km2 within a region of 908 km2. The population was surveyed using genetic sampling of scat in 2009, 2012 and 2015. We fit an open SCR model with sex-specific detection and population dynamics parameters while accounting for the patchy distribution of habitat and the uncertainty introduced by observing the population in three years only.Between 2009 and 2015, a total of 143 males, 112 females and 4 individuals of uncertain sex were detected. The annual per capita recruitment rate was estimated at 0.115 (SE 0.0144) for males and 0.127 (0.0168) for females. The estimated annual survival probability for males was 0.758 (0.0241) and 0.707 (0.0356) for females. The population trajectory implied by these survival and recruitment estimates was a decline of 2% per year; however, the sex specificity of the model revealed a decline in the male population only, with no evidence of decline in the female population. Further, the population decline observed in males was explained by the demography of just two of the eight patches.Using a customized open population SCR model, we determined that the endangered capercaillie in our Swiss study area had a stable female population and a declining male population, with the male decline due to population dynamics in a subset of the study area. Our study highlights the flexibility of open population SCR models for assessing population trajectories through time and across space and emphasizes the desirability of estimating sex-stratified population trends especially in species of conservation concern.
Stress-Induced Transcriptional Memory Accelerates Promoter-Proximal Pause-Release and Decelerates Termination over Mitotic Divisions
Authors: Vihervaara Anniina , Mahat Dig Bijay , Himanen Samu V. , Blom Malin A.H. , Lis John T. , Sistonen Lea 
Published: March 2019

SummaryHeat shock triggers an instant reprogramming of gene and enhancer transcription, but whether cells encode a memory to stress, at the level of nascent transcription, has remained unknown. Here, we measured transcriptional response to acute heat stress in unconditioned cells and in daughters of cells that had been exposed to a single or multiple heat shocks. Tracking RNA Polymerase II (Pol II) genome-wide at nucleotide-resolution revealed that cells precisely remember their transcriptional identity throughout stress, restoring Pol II distribution at gene bodies and enhancers upon recovery. However, single heat shock primed faster gene-induction in the daughter cells by increasing promoter-proximal Pol II pausing, and accelerating the pause-release. In repeatedly stressed cells, both basal and inducible transcription was refined, and pre-mRNA processing decelerated, which retained transcripts on chromatin and reduced recycling of the transcription machinery. These results mechanistically uncovered how the steps of pause-release and termination maintain transcriptional memory over mitosis.Highlights-Cell type-specific transcription precisely recovers after heat-induced reprogramming-Single heat shock primes genes for accelerated induction over mitotic divisionsviaincreased promoter-proximal Pol II pausing and faster pause-release-Multiple heat shocks refine basal and inducible transcription over mitotic divisions to support survival of the daughter cells-Decelerated termination at active genes reduces recycling of Pol II to heat-activated promoters and enhancers-HSF1 increases the rate of promoter-proximal pause-releaseviadistal and proximal regulatory elements
Rapid invariant encoding of scene layout in human OPA
Authors: Henriksson Linda , Mur Marieke , Kriegeskorte Nikolaus 
Published: March 2019

SUMMARYSuccessful visual navigation requires a sense of the geometry of the local environment. How do our brains extract this information from retinal images? Here we visually presented scenes with all possible combinations of five scene-bounding elements (left, right and back wall, ceiling, floor) to human subjects during functional magnetic resonance imaging (fMRI) and magnetoencephalography (MEG). The fMRI response patterns in the scene-responsive occipital place area (OPA) reflected scene layout with invariance to changes in surface texture. This result contrasted sharply with the primary visual cortex (V1), which reflected low-level image features of the stimuli, and parahippocampal place area (PPA), which showed better texture than layout decoding. MEG indicated that the texture-invariant scene-layout representation is computed from visual input within ~100 ms, suggesting a rapid computational mechanism. Taken together, these results suggest that the cortical representation underlying our instant sense of the environmental geometry is located in OPA.
Low marine food levels mitigate high migration costs in anadromous populations
Authors: Chaparro-Pedraza P. Catalina , de Roos André M. 
Published: March 2019

AbstractMigratory fish populations, like salmon, have dramatically declined for decades. Because of their extensive and energetically costly breeding travel anadromous fish are sensitive to a variety of environmental threats, in particular infrastructure building in freshwater streams and food declines in the ocean. Here, we analyze the effects of these two threats combined. Unexpectedly, we find that low marine food availabilities favor, as opposed to threaten, the ecological success of endangered populations. This counterintuitive effect results from an aspect of individual energetics that individuals switching to higher food levels reach larger sizes with concomitant larger migration costs but have lower energy densities. Surprisingly, the decline of food levels in the ocean after the completion of dams may thus mitigate the risk of extinction of migratory fish populations. This highlights the need of a mechanistic understanding integrating individual energetics, life history, and population dynamics to accurately assess biological consequences of environmental change.
Identifying the most influential features of neural population responses for information encoding and behavior
Authors: Nogueira Ramon , Peltier Nicole E. , Anzai Akiyuki , DeAngelis Gregory C. , Martínez-Trujillo Julio , Moreno-Bote Rubén 
Published: March 2019

SummaryIdentifying the features of population responses that are relevant to the amount of information encoded by neuronal populations is a crucial step toward understanding the neural code. Statistical features such as tuning properties, individual and shared response variability, and global activity modulations could all affect the amount of information encoded and modulate behavioral performance. We show that two features in particular affect information: the modulation of population responses across conditions and the projection of the inverse population variability along the modulation axis. We demonstrate that fluctuations of these two quantities are correlated with fluctuations of behavioral performance in various tasks and brain regions. In contrast, fluctuations in mean correlations among neurons and global activity have negligible or inconsistent effects on the amount of information encoded and behavioral performance. Our results are consistent with predictions of a model that optimally decodes population responses, which suggests that in our behavioral tasks the readout of information is near-optimal.
Differential effects of two HDAC inhibitors with distinct concomitant DNA hypermethylation or hypomethylation in breast cancer cells
Authors: Kalle Arunasree M. , Wang Zhibin 
Published: March 2019

AbstractDNA methylation and histone acetylation are the two important epigenetic phenomena that control the status of X-chromosome inactivation (XCI), a process of dosage compensation in mammals resulting in active X chromosome (Xa) and inactive X chromosome (Xi) in females. While DNA methyltransferases (DNMTs) are known to maintain the DNA hypermethylation of Xi, it remains to be determined how one or a few of 18 known histone deacetylases (HDACs) contribute(s) to Xi maintenance. Herein we found that HDAC1/2/4/6 were overexpressed in breast cancer cells, MDA-MB-231, with Xa/Xa status compared to normal breast epithelial cells, MCF10A, with Xa/Xi status. Inhibition of these overexpressed HDACs with two different drugs, sodium butyrate (SB) and Trichostatin A (TSA), caused surprisingly distinct effects on global DNA methylation: hypermethylation and hypomethylation, respectively, as well as distinct effects on a repressing histone mark H3K27me3 for heterochromatin and an active mark H3K56ac for DNA damage. Surveying three DNMTs through immunoblot analyses for insights revealed the up- or down-regulation of DNMT3A upon drug treatments in a concentration-dependent manner. These results correlated with the decreased XIST and increased TSIX expression in MDA-MB 231 as a possible mechanism of Xi loss and were reversed with SB treatment. Further RNA-seq analysis indicated differential gene expression correlating with the promoter methylation status of a few genes. Collectively, our results demonstrate a crosstalk between HDACs and DNMTs and the novel involvement of HDACs in skewed Xi in breast cancer.
Biological age is a universal marker of aging, stress, and frailty
Authors: Pyrkov Timothy V. , Fedichev Peter O. 
Published: March 2019

SummaryWe carried out a systematic investigation of supervised learning techniques for biological age modeling. The biological aging acceleration is associated with the remaining health- and life-span. Artificial Deep Neural Networks (DNN) could be used to reduce the error of chronological age predictors, though often at the expense of the ability to distinguish health conditions. Mortality and morbidity hazards models based on survival follow-up data showed the best performance. Alternatively, logistic regression trained to identify chronic diseases was shown to be a good approximation of hazards models when data on survival follow-up times were unavailable. In all models, the biological aging acceleration was associated with disease burden in persons with diagnosed chronic age-related conditions. For healthy individuals, the same quantity was associated with molecular markers of inflammation (such as C-reactive protein), smoking, current physical, and mental health (including sleeping troubles, feeling tired or little interest in doing things). The biological age thus emerged as a universal biomarker of age, frailty and stress for applications involving large scale studies of the effects of longevity drugs on risks of diseases and quality of life.To be published as Chapter 2 in “Biomarkers of aging”, ed. A. Moskalev, Springer, 2019.
Nanoparticles migration near liquid-liquid interfaces using diffuse interface model
Authors: Daher Ali , Ammar Amine , Hijazi Abbas 
Published: March 2019

Purpose
The purpose of this paper is to develop a numerical model for the simulation of the dynamics of nanoparticles (NPs) at liquid–liquid interfaces. Two cases have been studied, NPs smaller than the interfacial thickness, and NPs greater than the interfacial thickness.

Design/methodology/approach
The model is based on the molecular dynamics (MD) simulation in addition to phase field (PF) method, through which the discrete model of particles motion is superimposed on the continuum model of fluids which is a new ide a in numerical modeling. The liquid–liquid interface is modeled using the diffuse interface model.

Findings
For NPs smaller than the interfacial thickness, the results obtained show that the concentration gradient of one fluid in the other gives rise to a hydrodynamic drag force that drives the NPs to agglomerate at the interface. Whereas, for spherical NPs greater than the interfacial thickness, the results show that such NPs oscillate at the interface which agrees with some experimental studies.

Practical implications
The results are important in the field of numerical modeling, especially that the model is general and can be used to study different systems. This will be of great interest in the field of studying the behavior of NPs inside fluids and near interfaces, which enters in many industrial applications.

Originality/value
The idea of superimposing the molecular dynamic method on the PF method is a new idea in numerical modeling.
Parallel fast-neighbor-searching and communication strategy for particle-based methods
Authors: Fu Lin , Ji Zhe , Hu Xiangyu Y. , Adams Nikolaus A. 
Published: March 2019

Purpose
This paper aims to develop a parallel fast neighbor search method and communication strategy for particle-based methods with adaptive smoothing-length on distributed-memory computing systems.

Design/methodology/approach
With a multi-resolution-based hierarchical data structure, the parallel neighbor search method is developed to detect and construct ghost buffer particles, i.e. neighboring particles on remote processor nodes. To migrate ghost buffer particles among processor nodes, an undirected graph is established to characterize the sparse data communication relation and is dynamically recomposed. By the introduction of an edge coloring algorithm from graph theory, the complex sparse data exchange can be accomplished within optimized frequency. For each communication substep, only efficient nonblocking point-to-point communication is involved.

Findings
Two demonstration scenarios are considered: fluid dynamics based on smoothed-particle hydrodynamics with adaptive smoothing-length and a recently proposed physics-motivated partitioning method [Fu et al., JCP 341 (2017): 447-473]. Several new concepts are introduced to recast the partitioning method into a parallel version. A set of numerical experiments is conducted to demonstrate the performance and potential of the proposed parallel algorithms.

Originality/value
The proposed methods are simple to implement in large-scale parallel environment and can handle particle simulations with arbitrarily varying smoothing-lengths. The implemented smoothed-particle hydrodynamics solver has good parallel performance, suggesting the potential for other scientific applications.
The disclosure of financial forward-looking information
Authors: Bravo Francisco , Alcaide-Ruiz Maria Dolores 
Published: March 2019

PurposeThe purpose of this paper is to examine the association between the financial expertise (accounting and non-accounting) of female directors in the audit committee and the voluntary disclosure of financial forward-looking information.Design/methodology/approachThe sample is composed of companies belonging to the Standard and Poor`s 100 Index in 2016. Content analysis techniques are used to analyze both information disclosed in annual reports and the financial expertise of female directors.FindingsThe results fail to find an association between the presence of women in the audit committee and the disclosure of financial forward-looking information. However, the disclosure of this information is associated with the presence of female audit committee members with financial expertise, especially accounting expertise.Research implicationsThe academic implications are related with the need for a consideration of the personal attributes of female directors to understand their role in the boardroom or on subcommittees.Practical implicationsGiven the importance of financial forward-looking information in the capital markets, these findings will also help policymakers and managers to implement effective corporate governance structures and will have significant implications for the selection of female audit committee members.Originality/valueThis paper is the first to examine whether the specific expertise of female directors, beyond mere gender, makes a difference in financial forward-looking disclosure strategies.
The emission trading system, risk management committee and voluntary corporate response to climate change – a CDP study
Authors: Hossain Mohammed , Farooque Omar 
Published: March 2019

PurposeThe purpose of this study is to examine the impact of emission trading system, board risk management committee and firm age on firms’ responsiveness to climate change in Carbon Disclosure Project (CDP) 2011. More specifically, this study investigates whether global corporation’s responses on carbon-related disclosure are influenced by some specific attributes.Design/methodology/approachThe study covers a sample of 500 companies in 38 countries in 12 geographical locations. It uses the carbon disclosure scores in the CDP 2011 as the dependent variable. The authors estimate the OLS regression model to investigate the hypotheses.FindingsThe findings demonstrate that the presence of an emission trading system, a board risk management committee and the firm age have a significant positive relationship with carbon disclosure scores (i.e. CDP scores). However, the impacts of the board risk management committee and firm age on CDP scores are not moderated by the emission trading system at the firm level, suggesting that they have an independent and substitutive effect on climate change-related risk disclosure.Originality/valueThe study may be of relevance to investors and other stakeholders in evaluating the accountability of companies in relation to strategies for managing climate risk.
An intelligent computational framework for the definition and identification of the womenswear silhouettes
Authors: Fu Bailu , Liu Xiaogang 
Published: March 2019

Purpose
The current studies on the clothing silhouette are very limited. The purpose of this paper is to propose an innovative framework to intelligently identify the womenswear silhouette with the latest computer technologies. To clearly define the womenswear silhouette, an accurate numerical definition is proposed.

Design/methodology/approach
The study first processes and segments the useful parts on the static catwalk image data files following existing graphic extraction approaches. Six basic alphabetical womenswear silhouette types are selected and numerically defined. Then, the proposed framework automatically classifies the six basic womenswear silhouettes considering the different slopes between three main clothing parts. Six clothing situations are discovered according to different designs and the detailed cases are systematically categorized. In addition, aspects influencing the judgment of the clothing silhouettes such as the skin, the background, the drastic change points are also considered. The proposed silhouette definition and identification framework is novel and proved accurate.

Findings
The proposed definition and identification framework of womenswear silhouettes have been proved a viable approach that is fully compatible with the current computer technologies. The validation study shows that the presented identification procedure has a desirable accuracy over 90 percent.

Originality/value
The proposed methodology develops brand new standards to numerically define and identify the womenswear silhouette, which was not available in the past. Besides, the measurement, the identification and the classification procedures are fully validated by the image data collected from 14 world famous brands over 11 consecutive seasons. It is shown that the proposed numerical framework of the womenswear silhouettes is a robust one, considering all of the observed design variabilities.