bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Genomic Signature of Influenza Infection Shows Potential for Presymptomatic Detection, Guiding Early Therapy, and Monitoring Clinical Responses
Authors: McClain Micah T. , Nicholson Bradly P. , Park Lawrence P. , Liu Tzu-Yu , Hero Alfred O. , Tsalik Ephraim L. , Zaas Aimee K. , Veldman Timothy , Hudson Lori L. , Lambkin-Williams Robert , Gilbert Anthony , Burke Thomas , Nichols Marshall , Ginsburg Geoffrey S. , Woods Christopher W. 
Published: January 2016

Abstract
Early, presymptomatic intervention with oseltamivir (corresponding to the onset of a published host-based genomic signature of influenza infection) resulted in decreased overall influenza symptoms (aggregate symptom scores of 23.5 vs 46.3), more rapid resolution of clinical disease (20 hours earlier), reduced viral shedding (total median tissue culture infectious dose [TCID50] 7.4 vs 9.7), and significantly reduced expression of several inflammatory cytokines (interferon-γ, tumor necrosis factor-α, interleukin-6, and others). The host genomic response to influenza infection is robust and may provide the means for early detection, more timely therapeutic interventions, a meaningful reduction in clinical disease, and an effective molecular means to track response to therapy.
Temperature regimes impact coral assemblages along environmental gradients on lagoonal reefs in Belize
Authors: Baumann Justin H. , Townsend Joseph E. , Courtney Travis A. , Aichelman Hannah E. , Davies Sarah W. , Lima Fernando P. , Castillo Karl D. 
Published: January 2016

AbstractCoral reefs are increasingly threatened by global and local anthropogenic stressors such as rising seawater temperature, nutrient enrichment, sedimentation, and overfishing. Although many studies have investigated the impacts of local and global stressors on coral reefs, we still do not fully understand how these stressors influence coral community structure, particularly across environmental gradients on a reef system. Here, we investigate coral community composition across three different temperature and productivity regimes along a nearshore-offshore gradient on lagoonal reefs of the Belize Mesoamerican Barrier Reef System (MBRS). A novel metric was developed using ultra-high-resolution satellite-derived estimates of sea surface temperatures (SST) to classify reefs as exposed to low (lowTP), moderate (modTP), or high (highTP) temperature parameters over 10 years (2003 to 2012). Coral species richness, abundance, diversity, density, and percent cover were lower at highTPsites relative to lowTPand modTPsites, but these coral community traits did not differ significantly between lowTPand modTPsites. Analysis of coral life history strategies revealed that highTPsites were dominated by hardy stress tolerant and fast-growing weedy coral species, while lowTPand modTPsites consisted of competitive, generalist, weedy, and stress-tolerant coral species. Satellite-derived estimates ofChlorophyll-a (chl-a)were obtained for 13-years (2003-2015) as a proxy for primary production.Chl-aconcentrations were highest at highTPsites, medial at modTPsites, and lowest at lowTPsites. Notably, thermal parameters correlated better with coral community traits between site types than productivity, suggesting that temperature (specifically number of days above the thermal bleaching threshold) played a greater role in defining coral community structure than productivity on the MBRS. Dominance of weedy and stress-tolerant genera at highTPsites suggests that corals utilizing these two life history strategies may be better suited to cope with warmer oceans and thus may warrant protective status under climate change.
Evolution of corticosteroid specificity for human, chicken, alligator and frog glucocorticoid receptors
Authors: Katsu Yoshinao , Kohno Satomi , Oka Kaori , Baker Michael E. 
Published: January 2016

AbstractWe investigated the evolution of the response of human, chicken, alligator and frog glucocorticoid receptors (GRs) to dexamethasone, cortisol, corticosterone, 11-deoxycorticosterone, 11-deoxycortisol and aldosterone. We find significant differences among these vertebrates in the transcriptional activation of their full length GRs by these steroids, indicating that there were changes in the specificity of the GR for steroids during the evolution of terrestrial vertebrates. To begin to study the role of interactions between different domains on the GR in steroid sensitivity and specificity for terrestrial GRs, we investigated transcriptional activation of truncated GRs containing their hinge domain and ligand binding domain (LBD) fused to a GAL4 DNA binding domain (GAL4 DBD). Compared to corresponding full length GRs, transcriptional activation of GAL4 DBD-GR hinge/LBD constructs required higher steroid concentrations and displayed altered steroid specificity, indicating that interactions between the hinge/LBD and other domains are important in glucocorticoid activation of these terrestrial GRs.
Searching more genomic sequence with less memory for fast and accurate metagenomic profiling
Authors: Gardner Shea N. , Ames Sasha K. , Gokhale Maya B. , Slezak Tom R. , Allen Jonathan E. 
Published: January 2016

AbstractSoftware for rapid, accurate, and comprehensive microbial profiling of metagenomic sequence data on a desktop will play an important role in large scale clinical use of metagenomic data. Here we describe LMAT-ML (Livermore Metagenomics Analysis Toolkit-Marker Library) which can be run with 24 GB of DRAM memory, an amount available on many clusters, or with 16 GB DRAM plus a 24 GB low cost commodity flash drive (NVRAM), a cost effective alternative for desktop or laptop users. We compared results from LMAT with five other rapid, low-memory tools for metagenome analysis for 131 Human Microbiome Project samples, and assessed discordant calls with BLAST. All the tools except LMAT-ML reported overly specific or incorrect species and strain resolution of reads that were in fact much more widely conserved across species, genera, and even families. Several of the tools misclassified reads from synthetic or vector sequence as microbial or human reads as viral. We attribute the high numbers of false positive and false negative calls to a limited reference database with inadequate representation of known diversity. Our comparisons with real world samples show that LMAT-ML is the only tool tested that classifies the majority of reads, and does so with high accuracy.
Structural variation detection with read pair information — An improved null-hypothesis reduces bias
Authors: Sahlin Kristoffer , Frånberg Mattias , Arvestad Lars 
Published: January 2016

AbstractReads from paired-end and mate-pair libraries are often utilized to find structural variation in genomes, and one common approach is to use their fragment length for detection. After aligning read-pairs to the reference, read-pair distances are analyzed for statistically significant deviations. However, previously proposed methods are based on a simplified model of observed fragment lengths that does not agree with data. We show how this model limits statistical analysis of identifying variants and propose a new model, by adapting a model we have previously introduced for contig scaffolding, which agrees with data. From this model we derive an improved improved null hypothesis that, when applied in the variant caller CLEVER, reduces the number of false positives and corrects a bias that contributes to more deletion calls than insertion calls. A reference implementation is freely available athttps://github.com/ksahlin/GetDistr.
Fast and accurate single-cell RNA-Seq analysis by clustering of transcript-compatibility counts
Authors: Ntranos Vasilis , Kamath Govinda M. , Zhang Jesse , Pachter Lior , Tse David N. 
Published: January 2016

AbstractCurrent approaches to single-cell transcriptomic analysis are computationally intensive and require assay-specific modeling which limit their scope and generality. We propose a novel method that departs from standard analysis pipelines, comparing and clustering cells based not on their transcript or gene quantifications but on their transcript-compatibility read counts. In re-analysis of two landmark yet disparate single-cell RNA-Seq datasets, we show that our method is up to two orders of magnitude faster than previous approaches, provides accurate and in some cases improved results, and is directly applicable to data from a wide variety of assays.
Changes in attractor dynamics predict altered perceptual decision making with dorsolateral prefrontal tDCS
Authors: Bonaiuto James J. , de Berker Archy , Bestmann Sven 
Published: January 2016

AbstractThe left dorsolateral prefrontal cortex (dlPFC) has been linked to the accumulation and comparison of perceptual evidence for decision making independent of sensory and response modalities. We investigated the possible neural dynamics underlying the role of dlPFC in perceptual decision making, through a combination of noninvasive neurostimulation in humans and computational modeling. First, we used an established and biophysically realistic model of a decision making network that employs competition between neural populations. Simulation of depolarizing noninvasive brain stimulation in this model decreased decision time, while hyperpolarizing stimulation increased it. This behavioral effect was caused by an increase in the rate of neural activity integration via recurrent connections, as well as changes in the susceptibility of the network to noisy background inputs which modulated population firing rate differences prior to the onset of the stimulus. These pre-stimulus differences biased the response to one or the other option, thus speeding or slowing decisions.We then tested these model predictions in healthy participants performing a perceptual decision making task while receiving transcranial direct current stimulation (tDCS) over the left dlPFC, analogous to our simulated network stimulation. We found a striking match between model predictions and experimental results: depolarizing (inward) currents reduced and hyperpolarizing (outward) currents increased response times, but accuracy remained unaffected. Our results provide interventional evidence for the role of left dlPFC in perceptual decision making, and suggest that this region integrates and compares sensory evidence through competitive interactions between pyramidal cell populations which are selective for each response option. Mechanistically, our model suggests that stimulation of this region changes the rate at which evidence can be accumulated through recurrent activity and its susceptibility to background noise. More generally, our approach demonstrates that a linkage between computational modeling and noninvasive brain stimulation allows mechanistic accounts of brain function to be causally tested.
Genetic regulation of transcriptional variation in naturalArabidopsis thalianaaccessions
Authors: Zan Yanjun , Shen Xia , Forsberg Simon K. G. , Carlborg Örjan 
Published: January 2016

AbstractAn increased knowledge of the genetic regulation of expression inArabidopsis thalianais likely to provide important insights about the basis of the plant’s extensive phenotypic variation. Here, we reanalysed two publicly available datasets with genome-wide data on genetic and transcript variation in large collections of naturalA. thalianaaccessions. Transcripts from more than half of all genes were detected in the leaf of all accessions, and from nearly all annotated genes in at least one accession. Thousands of genes had high transcript levels in some accessions but no transcripts at all in others and this pattern was correlated with the genome-wide genotype. In total, 2,669 eQTL were mapped in the largest population, and 717 of them were replicated in the other population. 646 cis-eQTLs regulated genes that lacked detectable transcripts in some accessions, and for 159 of these we identified one, or several, common structural variants in the populations that were shown to be likely contributors to the lack of detectable RNA-transcripts for these genes. This study thus provides new insights on the overall genetic regulation of global gene-expression diversity in the leaf of naturalA. thalianaaccessions. Further, it also shows that strong cis-acting polymorphisms, many of which are likely to be structural variations, make important contributions to the transcriptional variation in the worldwideA. thalianapopulation.
Fine-scale crossover rate variation on theC. elegansX chromosome
Authors: Bernstein Max R. , Rockman Matthew V. 
Published: January 2016

AbstractMeiotic recombination creates genotypic diversity within species. Recombination rates vary substantially across taxa and the distribution of crossovers can differ significantly among populations and between sexes. Crossover locations within species have been found to vary by chromosome and by position within chromosomes, where most crossover events occur in small regions known as recombination hotspots. However, several species appear to lack hotspots despite significant crossover heterogeneity. The nematodeCaenorhabditis eleganswas previously found to have the least fine-scale variation in crossover distribution among organisms studied to date. It is unclear whether this pattern extends to the X chromosome given its unique compaction through the pachytene stage of meiotic prophase in hermaphrodites. We generated 798 recombinant nested near-isogenic lines (NILs) with crossovers in a 1.41 Mb region on the left arm of the X chromosome to determine if its recombination landscape is similar to that of the autosomes. We find that the fine-scale variation in crossover rate is lower than that of other model species and is inconsistent with hotspots. The relationship of genomic features to crossover rate is dependent on scale, with GC content, histone modifications, and nucleosome occupancy being negatively associated with crossovers. We also find that the abundances of 4-6 base pair DNA motifs significantly explain crossover density. These results are consistent with recombination occurring at unevenly distributed sites of open chromatin.
Integrating ISSM into TAM to enhance digital library services
Authors: Chen Jung-Fang , Chang Jui-Fang , Kao Cheng-Wan , Huang Yueh-Min 
Published: January 2016

PurposeThis study aims to propose a new model by incorporating information system success model (ISSM) into technology acceptance model (TAM) with an “attitude toward using” as the connection variable. The new model is then adopted to analyse and investigate empirical data and develop relevant factors, which affect the personal usage behaviour and net benefits for National Central Library in Taiwan to enhance digital library services. The research results can benefit future establishment and design of library information system or improvement of website service procedures.Design/methodology/approachThis study selected National Central Library Taiwan Digital Meta-Library as the research theme, and used stratified convenience sampling to perform interviews in various colleges and universities in the southern Taiwan. A total of 264 valid questionnaires were returned, and this study used structural equation modelling (SEM) to perform analyses.FindingsThe results reveal that attitude toward using is significantly and positively affected by perceived usefulness, perceived ease of use and user satisfaction. However, service quality of information system and personal net benefits do not have a significant and positive effect on attitude toward using, while they have an indirect and significant effect on attitude toward using through user satisfaction. Based on the results above, “user satisfaction” is the critical factor affecting the attitude toward using. Therefore, to strengthen users’ positive attitude toward using, the factor of user satisfaction is a key for enhancing digital library service.Originality/valueThis study constructed the “New Technology Information Assessment Model” as the reference for improving practical assessment. Moreover, this study also proposed the suggestions concerning digital library information services.
Two complimentary duties under corporate social responsibility
Authors: Nwoke Uchechukwu 
Published: January 2016

Purpose– The purpose of this paper is to critically examine the concept of corporate social responsibility (CSR) in Nigeria’s Delta region and draw a distinction between philanthropic CSR (positive affirmative CSR) and the more demanding duty not to harm the ecosystem (negative injunction CSR). It suggests that for CSR to contribute to sustainable development, oil multinational corporations (MNCs) need to perform the more demanding duties and not only philanthropy.Design/methodology/approach– The method applied is a critical evaluation of the nature and categories of CSR. It thoroughly reviews existing literature on CSR and uses them to identify and separate for analytical purposes, the different obligations arising from the concept.Findings– The paper highlights the inability of oil MNCs in Nigeria to differentiate between philanthropic CSR and the more demanding duty to care for the host communities and their environment. It suggests that this failure, arguably attributable to the “shareholder value” model of corporate governance, appears to lie at the heart of the unrest in the region.Practical– By performing only the positive CSR duties, while neglecting the negative injunction obligations, oil MNCs continue to attract hostility from the host communities who feel that their survival is at stake.Originality/value– The paper extends the knowledge of the CSR practices of MNCs in Nigeria, by clearly delineating the two CSR duties and by linking the failure of MNCs to perform the negative injunctions to the shareholder value model of corporate governance.
Universal learning: findings from an analysis of serious case review executive summaries
Authors: Aylett Jay 
Published: January 2016

Purpose
– The purpose of this paper is to report and discuss the findings of a thematic analysis from a survey of 114 serious case review (SCR) executive summaries in adult safeguarding. The Care Act 2014 (Section 44) makes the establishment of Safeguarding Adults Boards a statutory requirement. One of their responsibilities/functions is to undertake Safeguarding Adults Reviews (SAR-previously known as SCRs). They must also publish an annual report which includes the recommendations and actions from these SAR’s. This paper draws attention to the potential of SCR as national learning materials, and offers recommendations for strengthening the scope for interpretation in practice.

Design/methodology/approach
– This paper maps the findings and recommendations from 114 SCRs undertaken in England and Wales between 2000 and 2012. It then identifies the dominant themes and universal lessons to emerge, and makes suggestions for the improvement of learning.

Findings
– The demographic profile of SCRs bore some correlation to UK prevalence reports on perpetrator characteristics, but there was variance in relation to victim characteristics, where people with mental illness were the subject of SCRs with a level of frequency that does not mirror the prevalence of mental illness in reported abuse in the UK. The thematic analysis of conclusions and recommendations identified that these could be categorised as either idiosyncratic or bureaucratic.

Research limitations/implications
– The quality and quantity of information contained within the various SCR executive summary reports collated evidenced the lack of consistency/standardisation. Consequently, the analysis of demographic characteristics from these reports was compromised by incomplete data. In order to strengthen the scope of interpretation and understanding from future SARs to inform wider learning within the safeguarding community some national collation and standardisation is necessary.

Originality/value
– This paper offers an analysis of the demographic profile and common themes emerging from an examination of the largest survey of SCR executive summaries reported on in the UK so far.
Fundamental Islamic perspective of work ethics
Authors: Aldulaimi Saeed Hameed 
Published: January 2016

Purpose– This paper debates the Islamic perspective on the work ethics employed in an organization. It aims to discuss the issues of assumptions involving the Islamic Work Ethic (IWE). Therefore, this paper addresses the gap in the management literature and suggests a group of dimensions from fundamentals of Islam.Design/methodology/approach– The paper reviews the foundations of IWE and investigates various empirical studies conducted in several countries. Then, briefly presents a short historical and conceptual review of the work ethic construct, suggests a general conceptual definition of work ethic, and offers multidimensional model including a series of constructs which can enable researchers to evaluate and measure work ethic in Islamic societies.Findings– The study reveals that there is an evidence of ethics formulation depending on Islamic literature which constructs Islamic values for work. This paper proposes new perspective about the right ethics of work in Islam. Further, multidimensional model including 18 dimensions has been developed to evaluate work ethic in Islamic societies.Research limitations/implications– This field needs to reconsider the constructs of IWEs where it is far from reflecting Islamic theory. This paper presents new dimensions which can be utilized to enrich this area.Originality/value– This is one of the few attempts to suggest the appropriate constructs of IWE in the management literature. It provides 18 elements responsible and have the promise to strengthen individual transparency and morally which eventually enhance economic progress in Islamic world.
TOPSIS method for intuitionistic fuzzy multiple-criteria decision making and its application to investment selection
Authors: Zeng Shouzhen , Xiao Yao 
Published: January 2016

Purpose
– The purpose of this paper is to present a hybrid intuitionistic fuzzy technique for order preference by similarity to ideal solution (TOPSIS) method, called intuitionistic fuzzy ordered weighted averaging weighted averaging (OWAWA) distance TOPSIS (IFOWAWAD-TOPSIS) method for intuitionistic fuzzy multiple-criteria decision making (MCDM) problems.

Design/methodology/approach
– Based on the OWAWA operator, the authors develop the intuitionistic fuzzy OWAWA distance measure, then the IFOWAWAD-TOPSIS method is obtained by using the IFOWAWAD and traditional TOPSIS.

Findings
– The developed IFOWAWAD-TOPSIS method can overcome the drawback of traditional TOPSIS method that cannot consider both the subjective information of attributes and the attitudinal character of decision maker.

Research limitations/implications
– Clearly, this paper is devoted to the OWA operator, MCDM and intuitionistic fuzzy theory.

Practical implications
– The developed method is applicable in a wide range of situations such as decision-making, statistics, engineering and economics. A numerical example concerning investment selection is given to illustrate the practicability and usefulness of the proposed approach.

Originality/value
– This paper fulfils an identified need to study how to make a decision considering both the subjective information of attribute and the attitudinal character of decision maker in intuitionistic fuzzy environment.