bluuebunny/crossref_metadata_2025_split huggingface dataset:
Drivers of variation in species impacts for a multi-host fungal disease of bats
Authors: Langwig Kate E. , Frick Winifred F. , Hoyt Joseph R. , Parise Katy L. , Drees Kevin P. , Kunz Thomas H. , Foster Jeffrey T. , Kilpatrick A. Marm 
Published: October 2016

Disease can play an important role in structuring species communities because the effects of disease vary among hosts; some species are driven towards extinction, while others suffer relatively little impact. Why disease impacts vary among host species remains poorly understood for most multi-host pathogens, and factors allowing less-susceptible species to persist could be useful in conserving highly affected species. White-nose syndrome (WNS), an emerging fungal disease of bats, has decimated some species while sympatric and closely related species have experienced little effect. We analysed data on infection prevalence, fungal loads and environmental factors to determine how variation in infection among sympatric host species influenced the severity of WNS population impacts. Intense transmission resulted in almost uniformly high prevalence in all species. By contrast, fungal loads varied over 3 orders of magnitude among species, and explained 98% of the variation among species in disease impacts. Fungal loads increased with hibernating roosting temperatures, with bats roosting at warmer temperatures having higher fungal loads and suffering greater WNS impacts. We also found evidence of a threshold fungal load, above which the probability of mortality may increase sharply, and this threshold was similar for multiple species. This study demonstrates how differences in behavioural traits among species—in this case microclimate preferences—that may have been previously adaptive can be deleterious after the introduction of a new pathogen. Management to reduce pathogen loads rather than exposure may be an effective way of reducing disease impact and preventing species extinctions.
This article is part of the themed issue ‘Tackling emerging fungal threats to animal health, food security and ecosystem resilience’.
An agent-based model of dengue virus transmission shows how multiple uncertainties about vaccine efficacy influence public health impact projections
Authors: Perkins T. Alex , Reiner Robert C. , España Guido , ten Bosch Quirine A. , Verma Amit , Liebman Kelly A. , Paz-Soldan Valerie A. , Elder John P. , Morrison Amy C. , Stoddard Steven T. , Kitron Uriel , Vazquez-Prokopec Gonzalo M. , Scott Thomas W. , Smith David L. 
Published: October 2016

ABSTRACTGiven the limited effectiveness of strategies based solely on vector control to reduce dengue virus (DENV) transmission, it is expected that an effective vaccine could play a pivotal role in reducing the global disease burden of dengue. Of several dengue vaccines under development, Dengvaxia®from Sanofi Pasteur recently became the first to become licensed in select countries and to achieve WHO recommendation for use in certain settings, despite the fact that a number of uncertainties about its profile complicate projections of its public health impact. We used a stochastic, agent-based model for DENV transmission to perform simulations of the public health impact of dengue vaccines in light of two key uncertainties: (1) “statistical uncertainty” about the numerical value of the vaccine’s efficacy against disease, and (2) “biological uncertainty” about the extent to which its efficacy against disease derives from the amelioration of symptoms, blocking of DENV infection, or some combination thereof. Simulations of a generic dengue vaccine showed that the proportion of disease episodes averted following 20 years of routine vaccination of nine-year olds at 80% coverage was sensitive to both the numerical value of vaccine efficacy and to the extent to which efficacy derives from blocking of DENV infection. Simulations of a vaccine resembling Dengvaxia®took into account that vaccine trial results substantially reduced statistical uncertainty but did not address biological uncertainty, resulting in the proportion of disease episodes averted being more sensitive to biological uncertainty than to statistical uncertainty. Taken together, our results indicate limitations associated with the use of symptomatic disease as the primary endpoint of dengue vaccine trials and highlight the importance of considering multiple forms of uncertainty in projections of a vaccine’s public health impact.
GSKB: A gene set database for pathway analysis in mouse
Authors: Lai Liming , Hennessey Jason , Bares Valerie , Son Eun Woo , Ban Yuguang , Wang Wei , Qi Jianli , Jiang Gaixin , Liberzon Arthur , Xijin Ge Steven 
Published: October 2016

ABSTRACTInterpretation of high-throughput genomics data based on biological pathways constitutes a constant challenge, partly because of the lack of supporting pathway database. In this study, we created a functional genomics knowledgebase in mouse, which includes 33,261 pathways and gene sets compiled from 40 sources such as Gene Ontology, KEGG, GeneSetDB, PANTHER, microRNA and transcription factor target genes,etc. In addition, we also manually collected and curated 8,747 lists of differentially expressed genes from 2,526 published gene expression studies to enable the detection of similarity to previously reported gene expression signatures. These two types of data constitute a Gene Set Knowledgebase (GSKB), which can be readily used by various pathway analysis software such as gene set enrichment analysis (GSEA). Using our knowledgebase, we were able to detect the correct microRNA (miR-29) pathway that was suppressed using antisense oligonucleotides and confirmed its role in inhibiting fibrogenesis, which might involve upregulation of transcription factor SMAD3. The knowledgebase can be queried as a source of published gene lists for further meta-analysis. Through meta-analysis of 56 published gene lists related to retina cells, we revealed two fundamentally different types of gene expression changes. One is related to stress and inflammatory response blamed for causing blindness in many diseases; the other associated with visual perception by normal retina cells. GSKB is available online athttp://ge-lab.org/gs/, and also as a Bioconductor package (gskb,https://bioconductor.org/packages/gskb/). This database enables in-depth interpretation of mouse genomics data both in terms of known pathways and the context of thousands of published expression signatures.
LR-DNase: Predicting TF binding from DNase-seq data
Authors: van der Velde Arjan , Purcaro Michael , Noble William Stafford , Weng Zhiping 
Published: October 2016

ABSTRACTTranscription factors play a key role in the regulation of gene expression. Hypersensitivity to DNase I cleavage has long been used to gauge the accessibility of genomic DNA for transcription factor binding and as an indicator of regulatory genomic locations. An increasing amount of ChIP-seq data on a large number of TFs is being generated, mostly in a small number of cell types. DNase-seq data are being produced for hundreds of cell types. We aimed to develop a computational method that could combine ChIP-seq and DNase-seq data to predict TF binding sites in a wide variety of cell types. We trained and tested a logistic regression model, called LR-DNase, to predict binding sites for a specific TF using seven features derived from DNase-seq and genomic sequence. We calculated the area under the precision-recall curve at a false discovery rate cutoff of 0.5 for the LR-DNase model, a number of logistic regression models with fewer features, and several existing state-of-the-art TF binding prediction methods. The LR-DNase model outperformed existing unsupervised and supervised methods. Additionally, for many TFs, a model that uses only two features, DNase-seq reads and motif score, was sufficient to match the performance of the best existing methods.
Structure and origin of theWhite Caplocus and its role in evolution of grain color in maize
Authors: Tan Bao-Cai , Guan Jiahn-Chou , Ding Shuo , Wu Shan , Saunders Jonathan W. , Koch Karen E. , McCarty Donald R. 
Published: October 2016

AbstractSelection for yellow and white grain types has been central to post-domestication improvement of maize. While genetic control of carotenoid biosynthesis in endosperm is attributed primarily to theYellow1(Y1) phytoene synthase gene, less is known about the role of the dominant white endosperm factorWhite Cap(Wc). We show that theWclocus contains multiple, tandem copies of aCarotenoid cleavage dioxygenase 1(Ccd1) gene that encodes a carotenoid-degrading enzyme. A survey of 111 maize inbreds and landraces, together with 21 teosinte accessions reveals thatWcis exclusive to maize, where it is prevalent in white-grain (y1) varieties. Moreover,Ccd1copy number varies extensively amongWcalleles (from 1 to 23 copies), and confers a proportional range ofCcd1expression in diverse organs. We propose that this dynamic source of quantitative variation inCcd1expression was created in maize shortly after domestication by a two-step,Tam3Ltransposon-mediated process. First, a chromosome segment containingCcd1and several nearby genes duplicated at a position 1.9 Mb proximal to the progenitorCcd1rlocus on chromosome 9. Second, a subsequent interaction ofTam3Ltransposons at the new locus created a 28-kb tandem duplication, setting up expansion ofCcd1copy number by unequal crossing over. In this way, transposon-mediated variation in copy number at theWclocus created phenotypic variation that provided a foundation for breeding and selection of white grain color in maize.
CASTOR: A machine learning platform for reproducible viral genome classification
Authors: Remita Mohamed Amine , Halioui Ahmed , Diouara Abou Abdallah Malick , Daigle Bruno , Kiani Golrokh , Diallo Abdoulaye Baniré 
Published: October 2016

AbstractMotivationAdvances in cloning and sequencing technology yielded a massive number of genome of virus strains. The classification and annotation of these genomes constitute important assets in the discovery of genomic variability, taxonomic characteristics and disease mechanisms. Existing classification methods are often designed for a well-studied virus. Thus, the viral comparative genomic studies could benefit from more generic, fast and accurate tools for classifying and typing newly sequenced strains of diverse virus families.ResultsHere, we introduce a fast, accurate and generic virus classification platform, CASTOR, based on a machine learning approach. CASTOR is inspired by a well-known technique in molecular biology: Restriction Fragment Length Polymorphism (RFLP). It simulates the restriction digestion of genomic material by different enzymes into fragments in-silico. It uses two metrics to construct feature vectors for machine learning algorithms in the classification step. We benchmark CASTOR for the classification of distinct datasets of Human Papillomaviruses (HPV), Hepatitis B Viruses (HBV) and Human Immunodeficiency viruses (HIV). Results reveal true positive rates of 99%, 99% and 98% for HPV Alpha species, HBV genotyping and HIV M group subtyping respectively. Furthermore, CASTOR shows a competitive performance compare to well-known HIV-specific classifier REGA and COMET on whole genome andpolfragments. With such prediction rates, genericity and robustness, as well as rapidity, such approach could constitute a reference in large-scale virus studies. Finally, we developed the CASTOR web platform for open access and reproducible viral machine learning classifiers.Availabilityhttp://castor.bioinfo.uqam.caContactdiallo.abdoulaye@uqam.ca
Towards an ontology-based recommender system for relevant bioinformatics workflows
Authors: Halioui Ahmed , Valtchev Petko , Diallo Abdoulaye Baniré 
Published: October 2016

AbstractBackgroundWith the large and diverse type of biological data, bioinformatic solutions are being more complex and computationally intensive. New specialized data skills need to be acquired by researchers in order to follow this development. Workflow Management Systems rise as an efficient way to automate tasks through abstract models in order to assist users during their problem solving tasks. However, current solutions could have several problems in reusing the developed models for given tasks. The large amount of heterogenous data and the lack of knowledge in using bioinformatics tools could mislead the users during their analyses. To tackle this issue, we propose an ontology-based workflow-mining framework generating semantic models of bioinformatic best practices in order to assist scientists. To this end, concrete workflows are extracted from scientific articles and then mined using a rich domain ontology.ResultsIn this study, we explore the specific topics of phylogenetic analyses. We annotated more than 300 recent articles using different ontological concepts and relations. Relative supports (frequencies) of discovered workflow components in texts show interesting results of relevant resources currently used in the different phylogenetic analysis steps. Mining concrete workflows from texts lead us to discover abstract but relevant patterns of the best combinations of tools, parameters and input data for specific phylogenetic problems.ConclusionsExtracted patterns would make workflows more intuitive and easy to be reused in similar situations. This could provide a stepping-stone into the identification of best practices and pave the road to a recommender system.
Concerted action of neuroepithelial basal shrinkage and active epithelial migration ensures efficient optic cup morphogenesis
Authors: Sidhaye Jaydeep , Norden Caren 
Published: October 2016

AbstractOrgan formation is a multi-scale event that involves changes at the intracellular, cellular and tissue level. Organogenesis often starts with the formation of characteristically shaped organ precursors. However, the cellular mechanisms driving organ precursor formation are often not clear. Here, using zebrafish, we investigate the epithelial rearrangements responsible for the development of the hemispherical retinal neuroepithelium (RNE), a part of the optic cup. We show that in addition to basal shrinkage of RNE cells, active migration of connected epithelial cells into the RNE is a crucial player in its formation. This cellular movement is driven by progressive cell-matrix contacts and actively translocates prospective RNE cells to their correct location before they adopt neuroepithelial fate. Failure of this migration during neuroepithelium formation leads to ectopic determination of RNE cells and consequently impairs optic cup formation. Overall, this study illustrates how spatiotemporal coordination between morphogenic movements and fate determination critically influences organogenesis.
Compromised External Validity: Federally ProducedCannabisDoes Not Reflect Legal Markets
Authors: Vergara Daniela , Bidwell L. Cinnamon , Gaudino Reggie , Torres Anthony , Du Gary , Ruthenburg Travis C. , deCesare Kymron , Land Donald P. , Hutchison Kent E. , Kane Nolan C. 
Published: October 2016

AbstractAs the most widely used illicit drug, the basis of the fastest growing major industry in the US, and as a source of numerous under-studied psychoactive compounds, understanding the psychological and physiological effects ofCannabisis essential. The National Institute on Drug Abuse (NIDA) is designated as the sole legal producer ofCannabisfor use in US research studies. We sought to compare the chemical profiles ofCannabisvarieties that are available to consumers in states that have state-legalized useversuswhat is available to researchers interested in studying the plant and its effects. Our results demonstrate that the federally producedCannabishas significantly less variety and lower concentrations of cannabinoids. Current research, which has focused on material that is far less diverse and less potent than that used by the public, limits our understanding of the plant’s chemical, biological, psychological, medical, and pharmacological properties. Investigation is urgently needed on the diverse forms ofCannabisused by the public in state-legal markets.
Fractal Features of Proto-Plant’s Origin and their Possible Consequences
Authors: Galitskii V.V. 
Published: October 2016

AbstractThe extension of the sectional model of the spruce crown’s dynamics into diapason (0, 1) of the fractal parameter μ has demonstrated the existence of green biomass on branches of three orders in form of photosynthesizing (green) points. We investigated the growth of point sets on an interval as a model of the origin of proto-plants, which are formed due to endosymbiosis of cyanobacteria and protists. The fractal properties of the sets of evenly placed points and group sets were studied using the box-counting method. For the group sets, the character of dependence μ on the growing total number of points changes radically differently depending on whether the number of the points per group or the number of groups was fixed. As the host does not have the initial infrastructure needed for an increase in cyanobacteria per group, the first path is implemented and μ decreases from 1 to 0.25 when groups consist of two points per group. If and when the host develops necessary anatomical features (infrastructure), the second pathway is realized and μ grows to 1. The combined trajectory of μ initially demonstrates a slow growth of the size of the photosynthetic system and then an exponential growth after the development of the host’s infrastructure. Similar fractal peculiarity also characterizes trees and is an innate property of plants. Assumptions on the morphological recapitulation of proto-plant in higher plants’ ontogenesis (embryogenesis and seed germination) and also a possibility to fix the number of cyanobacteria per group are discussed.
Phenotype-specific information improves prediction of functional impact for noncoding variants
Authors: Bodea Corneliu A. , Mitchell Adele A. , Bloemendal Alex , Day-Williams Aaron G. , Runz Heiko , Sunyaev Shamil R. 
Published: October 2016

AbstractFunctional characterization of the noncoding genome is essential for the biological understanding of gene regulation and disease. Here, we introduce the computational framework PINES (Phenotype-Informed Noncoding Element Scoring) which predicts the functional impact of noncoding variants by integrating epigenetic annotations in a phenotype-dependent manner. A unique feature of PINES is that analyses may be customized towards genomic annotations from cell types of the highest relevance given the phenotype of interest. We illustrate that PINES identifies functional noncoding variation more accurately than methods that do not use phenotype-weighted knowledge, while at the same time being flexible and easy to use via a dedicated web portal.
Metafounders are Fst fixation indices and reduce bias in single step genomic evaluations
Authors: Garcia-Baccino Carolina Andrea , Legarra Andres , Christensen Ole F , Misztal Ignacy , Pocrnic Ivan , Vitezica Zulma G , Cantet Rodolfo J.C. 
Published: October 2016

ABSTRACTBACKGROUNDMetafounders are pseudo-individuals that condense the genetic heterozygosity and relationships within and across base pedigree populations, i.e. ancestral populations. This work addresses estimation and usefulness of metafounder relationships in Single Step GBLUP.RESULTSWe show that the ancestral relationship parameters are proportional to standardized covariances of base allelic frequencies across populations, like Fst fixation indexes. These covariances of base allelic frequencies can be estimated from marker genotypes of related recent individuals, and pedigree. Simple methods for estimation include naïve computation of allele frequencies from marker genotypes or a method of moments equating average pedigree-based and marker-based relationships. Complex methods include generalized least squares or maximum likelihood based on pedigree relationships. To our knowledge, methods to infer Fstcoefficients and Fstdifferentiation have not been developed for related populations.A compatible genomic relationship matrix constructed as a crossproduct of {−1,0,1} codes, and equivalent (up to scale factors) to an identity by state relationship matrix at the markers, is derived. Using a simulation with a single population under selection, in which only males and youngest animals were genotyped, we observed that generalized least squares or maximum likelihood gave accurate and unbiased estimates of the ancestral relationship parameter (true value: 0.40) whereas the other two (naïve and method of moments) were biased (estimates of 0.43 and 0.35). We also observed that genomic evaluation by Single Step GBLUP using metafounders was less biased in terms of accurate genetic trend (0.01 instead of 0.12 bias), slightly overdispersed (0.94 instead of 0.99) and as accurate (0.74) than the regular Single Step GBLUP. Single Step GBLUP using metafounders also provided consistent estimates of heritability.CONCLUSIONSEstimation of metafounder relationship can be achieved using BLUP-like methods with pedigree and markers. Inclusion of metafounder relationships improves bias of genomic predictions with no loss in accuracy.
Touching on transparency in city local law making
Authors: Leshinsky Rebecca 
Published: October 2016

Purpose
The purpose for this paper is to share jurisdictional knowledge on local law-making theory and praxis, an area of law not well represented in the literature despite its involvement in day-to-day life.

Design/methodology/approach
The paper not only shares knowledge about the local law-making process in Melbourne, Australia, but also explores attitudes to local law-making gathered through semi-structured interviews from a sample of relevant stakeholders.

Findings
The paper reports on findings from a study undertaken in Melbourne, Australia. Stakeholder perceptions and attitudes were canvassed regarding local law-making in the areas of land use planning and waste management. Overall, stakeholders were satisfied that Melbourne is a robust jurisdiction offering a fair and transparent local law-making system, but they see scope for more public participation.

Research limitations/implications
The findings suggest that even though the state of Victoria offers a fair and transparent system of local law-making, there is still significant scope for more meaningful involvement from the community, as well as space for more effective enforcement of local laws. The stage is set for greater cross-jurisdictional reciprocal learning about local law-making between cities.

Originality/value
This paper offers meaningful and utilitarian insight for policy and law makers, academics and built environment professionals from relevant stakeholders on the operation and transparency of local law-making.
Open supply? On the future of document supply in the world of open science
Authors: Schöpfel Joachim 
Published: October 2016

Purpose
The purpose of this paper is to propose a personal viewpoint on the development of document supply in the context of the recent European Union (EU) decisions on open science.

Design/methodology/approach
The paper provides some elements to the usual questions of service development, about business, customers, added value, environment and objectives.

Findings
The EU goal for open science is 100 per cent available research results in 2020. To meet the challenge, document supply must change, include more and other content, serve different targets groups, apply innovative technology and provide knowledge. If not, document supply will become a marginalized library service.

Originality/value
Basically, open science is not library-friendly, and it does not offer a solution for the actual problems of document supply. But it may provide an opportunity for document supply to become a modern service able to deal with new forms of unequal access and digital divide.