bluuebunny/crossref_metadata_2025_split huggingface dataset:
GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions
Authors: Gundersen Gregory W. , Jones Matthew R. , Rouillard Andrew D. , Kou Yan , Monteiro Caroline D. , Feldmann Axel S. , Hu Kevin S. , Ma’ayan Avi 
Published: May 2015

Abstract
Motivation: Identification of differentially expressed genes is an important step in extracting knowledge from gene expression profiling studies. The raw expression data from microarray and other high-throughput technologies is deposited into the Gene Expression Omnibus (GEO) and served as Simple Omnibus Format in Text (SOFT) files. However, to extract and analyze differentially expressed genes from GEO requires significant computational skills.
Results: Here we introduce GEO2Enrichr, a browser extension for extracting differentially expressed gene sets from GEO and analyzing those sets with Enrichr, an independent gene set enrichment analysis tool containing over 70 000 annotated gene sets organized into 75 gene-set libraries. GEO2Enrichr adds JavaScript code to GEO web-pages; this code scrapes user selected accession numbers and metadata, and then, with one click, users can submit this information to a web-server application that downloads the SOFT files, parses, cleans and normalizes the data, identifies the differentially expressed genes, and then pipes the resulting gene lists to Enrichr for downstream functional analysis. GEO2Enrichr opens a new avenue for adding functionality to major bioinformatics resources such GEO by integrating tools and resources without the need for a plug-in architecture. Importantly, GEO2Enrichr helps researchers to quickly explore hypotheses with little technical overhead, lowering the barrier of entry for biologists by automating data processing steps needed for knowledge extraction from the major repository GEO.
Availability and implementation: GEO2Enrichr is an open source tool, freely available for installation as browser extensions at the Chrome Web Store and FireFox Add-ons. Documentation and a browser independent web application can be found at http://amp.pharm.mssm.edu/g2e/.
Contact: avi.maayan@mssm.edu
Fast parametric time warping of peak lists
Authors: Wehrens Ron , Bloemberg Tom G. , Eilers Paul H.C. 
Published: May 2015

Abstract
Summary: Alignment of peaks across samples is a difficult but unavoidable step in the data analysis for all analytical techniques containing a separation step like chromatography. Important application examples are the fields of metabolomics and proteomics. Parametric time warping (PTW) has already shown to be very useful in these fields because of the highly restricted form of the warping functions, avoiding overfitting. Here, we describe a new formulation of PTW, working on peak-picked features rather than on complete profiles. Not only does this allow for a much more smooth integration in existing pipelines, it also speeds up the (already among the fastest) algorithm by orders of magnitude. Using two publicly available datasets we show the potential of the new approach. The first set is a LC–DAD dataset of grape samples, and the second an LC–MS dataset of apple extracts.
Availability and implementation: Parametric time warping of peak lists is implemented in the ptw package, version 1.9.1 and onwards, available from Github (https://github.com/rwehrens/ptw) and CRAN (http://cran.r-project.org). The package also contains a vignette, providing more theoretical details and scripts to reproduce the results below.
Contact: ron.wehrens@wur.nl
Exploring relation types for literature-based discovery
Authors: Preiss Judita , Stevenson Mark , Gaizauskas Robert 
Published: May 2015

AbstractObjective Literature-based discovery (LBD) aims to identify “hidden knowledge” in the medical literature by: (1) analyzing documents to identify pairs of explicitly related concepts (terms), then (2) hypothesizing novel relations between pairs of unrelated concepts that are implicitly related via a shared concept to which both are explicitly related. Many LBD approaches use simple techniques to identify semantically weak relations between concepts, for example, document co-occurrence. These generate huge numbers of hypotheses, difficult for humans to assess. More complex techniques rely on linguistic analysis, for example, shallow parsing, to identify semantically stronger relations. Such approaches generate fewer hypotheses, but may miss hidden knowledge. The authors investigate this trade-off in detail, comparing techniques for identifying related concepts to discover which are most suitable for LBD.Materials and methods A generic LBD system that can utilize a range of relation types was developed. Experiments were carried out comparing a number of techniques for identifying relations. Two approaches were used for evaluation: replication of existing discoveries and the “time slicing” approach.1Results Previous LBD discoveries could be replicated using relations based either on document co-occurrence or linguistic analysis. Using relations based on linguistic analysis generated many fewer hypotheses, but a significantly greater proportion of them were candidates for hidden knowledge.Discussion and Conclusion The use of linguistic analysis-based relations improves accuracy of LBD without overly damaging coverage. LBD systems often generate huge numbers of hypotheses, which are infeasible to manually review. Improving their accuracy has the potential to make these systems significantly more usable.
Photon underproduction crisis: Are QSOs sufficient to resolve it?
Authors: Khaire Vikram , Srianand Raghunathan 
Published: May 2015

Abstract
We investigate the recent claim of ‘photon underproduction crisis’ by Kollmeier et al. which suggests that the known sources of ultraviolet (UV) radiation may not be sufficient to generate the inferred H i photoionization rate ($\Gamma _{\rm H\,\small {i}}$) in the low-redshift intergalactic medium. Using the updated QSO emissivities from the recent studies and our cosmological radiative transfer code developed to estimate the UV background, we show that the QSO contributions to $\Gamma _{\rm H\,\small {i}}$ is higher by a factor ∼2 as compared to the previous estimates. Using self-consistently computed combinations of star formation rate density and dust attenuation, we show that a typical UV escape fraction of 4 per cent from star-forming galaxies should be sufficient to explain the inferred $\Gamma _{\rm H\,\small {i}}$ by Kollmeier et al. Interestingly, we find that the contribution from QSOs alone can explain the recently inferred $\Gamma _{\rm H\,\small {i}}$ by Shull et al. which used the same observational data but different simulation. Therefore, we conclude that the crisis is not as severe as it was perceived before and there seems no need to look for alternate explanations such as low luminosity hidden QSOs or decaying dark matter particles.
Cortical microcircuit determination through global perturbation and sparse sampling in grid cells
Authors: Widloski John , Fiete Ila R. 
Published: May 2015

AbstractUnder modern interrogation, famously well-studied neural circuits such as that for orientation tuning in V1 are steadily giving up their secrets, but quite basic questions about connectivity and dynamics, including whether most computation is done by lateral processing or by selective feedforward summation, remain unresolved. We show here that grid cells offer a particularly rich opportunity for dissecting the mechanistic underpinnings of a cortical circuit, through a strategy based on global circuit perturbation combined with sparse neural recordings. The strategy is based on the theoretical insight that small perturbations of circuit activity will result in characteristic quantal shifts in the spatial tuning relationships between grid cells, which should be observable from multisingle unit recordings of a small subsample of the population. The predicted shifts differ qualitatively across candidate recurrent network mechanisms, and also distinguish between recurrent versus feedforward mechanisms. More generally, the proposed strategy demonstrates how sparse neural recordings coupled with global perturbation in the grid cell system can reveal much more about circuit mechanism as it relates to function than can full knowledge of network activity or of the synaptic connectivity matrix.
Ecological and evolutionary adaptations shape the gut microbiome of BaAka African rainforest hunter-gatherers
Authors: Gomez Andres , Petrzelkova Klara , Yeoman Carl J. , Burns Michael B. , Amato Katherine R. , Vlckova Klara , Modry David , Todd Angelique , Jost Robinson Carolyn A. , Remis Melissa J. , Torralba Manolito , Nelson Karen E. , Carbonero Franck , Rex Gaskins H. , Wilson Brenda , Stumpf Rebecca M. , White Bryan A. , Leigh Steven R. , Blekhman Ran 
Published: May 2015

AbstractThe gut microbiome provides access to otherwise unavailable metabolic and immune functions, likely affecting mammalian fitness and evolution. To investigate how this microbial ecosystem impacts evolutionary adaptation of humans to particular habitats, we explore the gut microbiome and metabolome of the BaAka rainforest hunter-gatherers from Central Africa. The data demonstrate that the BaAka harbor a colonic ecosystem dominated by Prevotellaceae and other taxa likely related to an increased capacity to metabolize plant structural polysaccharides, phenolics, and lipids. A comparative analysis shows that the BaAka gut microbiome shares similar patterns with that of the Hadza, another hunter-gatherer population from Tanzania. Nevertheless, the BaAka harbor significantly higher bacterial diversity and pathogen load compared to the Hadza, as well as other Western populations. We show that the traits unique to the BaAka microbiome and metabolome likely reflect adaptations to hunter-gatherer lifestyles and particular subsistence patterns. We hypothesize that the observed increase in microbial diversity and potential pathogenicity in the BaAka microbiome has been facilitated by evolutionary adaptations in immunity genes, resulting in a more tolerant immune system.SignificanceHuman ecological adaptation requires changes at the genomic level. However, the gut microbiome, the collection of microbes inhabiting the gastrointestinal tract and their functions, also responds significantly to ecological challenge. To determine how the gut microbiome responds to evolutionary adaptations in the host, we profiled gut bacterial communities of the BaAka, rainforest hunter-gatherers from Central Africa. The gut microbiome of the BaAka shows adaptations to metabolize foods rich in fiber, tannins and fats. Similarly, higher bacterial diversity and abundance of pathogenic bacteria, compared to other hunter-gatherers and western populations, suggest that the BaAka immune system evolved to coexist with increased pathogen threats. Accordingly, these results show how the gut microbiome contributes to human ecological plasticity, impacting host adaptation and evolution.
Molecular Fossils from Microorganisms Preserved in Glacial Ice
Authors: Buford Price P. , Jeffrey Morris J. , Bay Ryan C. , Adhikari Ajeeth , Giovannoni Stephen J. , Vergin Kevin L. 
Published: May 2015

ABSTRACTThe study of microbial evolution is hindered by the fact that microbial populations leave few fossils. We hypothesized that bacterial cells preserved in ancient ice could be used as a molecular fossil record if their DNA could be extracted and sequenced. Channels formed along triple junctions of ice crystals contain liquid “veins” in which microbial cells may be preserved intact. Since vertical motion through the ice matrix is impossible, microbes found in ice cores are representative of microbes present at the time the ice was formed. We detected chlorophyll fluorescence in intact ice cores taken from Greenland and Antarctica. Flow cytometric analysis localized at least some of this fluorescence to particles < 1 μm in diameter. Metagenomic analysis of meltwater indeed revealed sequences similar to modern strains of the picocyanobacterial generaSynechococcusandProchlorococcus, and some of these sequences were distinct from any sequences known from modern oceans or glacial environments. Our study is a first proof-of-concept of the use of ice cores as records of microbial evolution, and we suggest that future genetic studies with higher vertical resolution in the cores might shed light on the pace and character of evolution of these ecologically important cells.
FIQT: a simple, powerful method to accurately estimate effect sizes in genome scans
Authors: Bigdeli Tim B. , Lee Donghyung , Riley Brien P. , Vladimirov Vladimir , Fanous Ayman H. , Kendler Kenneth S. , Bacanu Silviu-Alin 
Published: May 2015

AbstractGenome scans, including both genome-wide association studies and deep sequencing, continue to discover a growing number of significant association signals for various traits. However, often variants meeting genome-wide significance criteria explain far less of the overall trait variance than “sub-threshold” association signals. To extract these sub-threshold signals, there is a need for methods which accurately estimate the mean of all (normally-distributed) test-statistics from a genome scan (i.e., Z-scores). This is currently achieved by the difficult procedures of adjusting all Z-scorestatistics for “winner’s curse” (multiple testing). Given that multiple testing adjustments are much simpler for p-values, we propose a method for estimating Z-scores means by i) first adjusting their p-values for multiple testing and then ii) transforming the adjusted p-values to upper tail Z-scores with the sign of the original statistics. Because a False Discovery Rate (FDR) procedure is used for multiple testing adjustment, we denote this methodFDRInverseQuantile Transformation (FIQT). When compared to competitors, e.g. Empirical Bayes (including proposed improvements), FIQT is more i) accurate and ii) computationally efficient by orders of magnitude. Its accuracy advantage is substantial at larger sample sizes and/or moderate numbers of association signals. Practical application of FIQT to Z-scores from the first Psychiatric Genetic Consortium (PGC) schizophrenia predicts a non-trivial fraction of the significant signal regions from the subsequent published PGC schizophrenia studies. Finally, we suggest that FIQT might be i) used to improve subject level risk prediction and ii) further improved by modelling the noncentrality ofstatistics.
The Multi-allelic Genetic Architecture of a Variance-heterogeneity Locus for Molybdenum Accumulation Acts as a Source of Unexplained Additive Genetic Variance
Authors: Forsberg Simon K.G. , Andreatta Matthew E. , Huang Xin-Yuan , Danku John , Salt David E. , Carlborg Örjan 
Published: May 2015

AbstractMost biological traits are regulated by both genetic and environmental factors. Individual loci contributing to the phenotypic diversity in a population are generally identified by their contributions to the trait mean. Genome-wide association (GWA) analyses can also detect loci based on variance differences between genotypes and several hypotheses have been proposed regarding the possible genetic mechanisms leading to such signals. Little is, however, known about what causes them and whether this genetic variance-heterogeneity reflects mechanisms of importance in natural populations. Previously, we identified a variance-heterogeneity GWA (vGWA) signal for leaf molybdenum concentrations inArabidopsis thaliana. Here, fine-mapping of this association to a ∼78 kb Linkage Disequilibrium (LD)-block reveals that it emerges from the independent effects of three genetic polymorphisms on the high-variance associated version of this LD-block. By revealing the genetic architecture underlying this vGWA signal, we uncovered the molecular source of a significant amount of hidden additive genetic variation (“missing heritability”). Two of the three polymorphisms on the high-variance LD-block are promoter variants for Molybdate transporter 1 (MOT1), and the third a variant located ∼25 kb downstream of this gene. A fourth independent association was also detected ∼600 kb upstream of the LD-block. Testing of T-DNA knockout alleles for genes in the associated regions suggestAT2G25660(unknown function) andAT2G26975(Copper Transporter 6; COPT6) as the strongest candidates for the associations outsideMOT1. Our results show that multi-allelic genetic architectures within a single LD-block can lead to a variance-heterogeneity between genotypes in natural populations. Further they provide novel insights into the genetic regulation of ion homeostasis inA. thaliana, and empirically confirm that variance-heterogeneity based GWA methods are a valuable tool to detect novel associations of biological importance in natural populations.
Time management profiles of Cypriot school principals: a mixed-methods approach
Authors: Kouali Georgia , Pashiardis Petros 
Published: May 2015

Purpose
– The purpose of this paper is to present the results of a piece of research concerning the time management of Cypriot primary school principals. Time management refers to the interrelation of five independent variables: the various tasks principals perform, their frequency, the degree of accomplishment of those tasks, the use of time management techniques and time management style (from monochronic to polychronic).

Design/methodology/approach
– Quantitative methods were used (questionnaire) together with qualitative methods (observation, interviews, collection of artifacts), in order to obtain richer, deeper data and view multiple angles of the same phenomenon.

Findings
– The results of cluster analysis indicated three different time management profiles/types of principals: The Centralized Monochrons, the Procrastinative Managers and the Decentralized Polychrons. One basic conclusion is that the principals who adopt the practices of the Decentralized Polychrons manage better their time.

Practical implications
– The three time management profiles of principals are described, analysed, and discussed in order to reach conclusions about the selection, training, and placement of school principals. Through the description of the everyday practice of Cypriot principals useful information concerning school leadership and management are also provided. Finally, the conclusions of this research may prove useful for principals, because they are provided with the opportunity to rethink and evaluate their own time management and effectiveness of their daily practices.

Originality/value
– The creation and description of the three time management profiles is the main contribution of this piece of research, since there are not any time management types-profiles registered in the bibliography, which were produced with the use of scientific instruments and procedures.
An analysis of intensive mode pedagogy in management education in India
Authors: Mishra Sita , Nargundkar Rajendra 
Published: May 2015

Purpose– Management education is at its peak in India. But pedagogy and modes of delivery are not always innovative compared to top international Business Schools. It is through experimentation that the paper may be able to discover what works best in our context. The purpose of this paper is to determine the effectiveness of intensive mode of delivery vs traditional semester-wide teaching of management courses among MBA students of a leading Business School, through one such experiment.Design/methodology/approach– A total of 19 dimensions were used in this study. The questionnaire was tested on two different groups. An independent samplet-test was conducted for each dimension, to find out if the group that was subjected to this experiment had opinions different from the group that did not undergo the accelerated version.Findings– The results indicated perceptions on most of the dimensions disconcerting, barring increase in commitment, engagement, focus, and concentration with intensive mode. Further, this negative perception augmented towards intensive delivery mode, after experiencing traditional delivery.Practical implications– The literature does appear to show controversial outcomes related to intensive mode but more studies are in support of intensive modes of delivery format. The issue of whether students learn better in a semester/trimester of traditional length or with a compressed schedule is a key concern to the innovations in higher education scheduling today. Findings of this study pose a serious threat to all those management institutions which are planning to attempt to speed up the delivery of programmes and courses within them in order to reduce cost or other reasons.Originality/value– In education literature, significant amount of research has been carried out using a time compressed in developed countries. This study is one of the first studies, which focuses on determining the effectiveness of intensive teaching against traditional trimester/semester wide teaching among MBA education in India.
Impact of writing proficiency and writing center participation on academic performance
Authors: Bielinska-Kwapisz Agnieszka 
Published: May 2015

Purpose– Given that there exists in the literature relatively little research into the effectiveness of writing centers at universities, the purpose of this paper is to show the impact of university writing centers on first-year business seminar student writing.Design/methodology/approach– This quantitative study involved 315 first-year undergraduate business students. Logistic and quantile regression analysis was used to test two hypotheses.Findings– Results indicate that student intrinsic and extrinsic motivational factors positively influenced the likelihood that a student visits the center. Student grades on writing assignments were significantly higher for students who visited the writing center but only for students who scored in the top 40th percentile of the grade distribution.Practical implications– Writing centers should try to reach all students not only those who are naturally motivated. Most importantly, centers should find ways to help students in the lower portion of grade distribution since these students presumably require sustained help.Originality/value– This paper suggests that writing centers helped only students at the top of the grades distribution which may be valuable to universities in assessing impact of writing centers and help in the efforts to improve student writing. However, this effect can only be uncovered using quantile regression. Therefore, this research has demonstrated the potential usefulness of quantile regression as a predictive and explanatory tool in assessment.