bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating Error Models for Whole Genome Sequencing Using Mixtures of Dirichlet-Multinomial Distributions
Authors: Wu Steven H. , Schwartz Rachel S. , Winter David J. , Conrad Donald F. , Cartwright Reed A. 
Published: November 2015

AbstractMotivationAccurate identification of genotypes is critical in identifying de novo mutations, linking mutations with disease, and determining mutation rates. Because de novo mutations are rare, even low levels of genotyping error can cause a large fraction of false positive de novo mutations. Biological and technical processes that adversely affect genotyping include copy-number-variation, paralogous sequences, library preparation, sequencing error, and reference-mapping biases, among others.ResultsWe modeled the read depth for all data as a mixture of Dirichlet-multinomial distributions, resulting in significant improvements over previously used models. In most cases the best model was comprised of two distributions. The major-component distribution is similar to a binomial distribution with low error and low reference bias. The minor-component distribution is overdispersed with higher error and reference bias. We also found that sites fitting the minor component are enriched for copy number variants and low complexity region. We expect that this approach to modeling the distribution of NGS data, will lead to improved genotyping. For example, this approach provides an expected distribution of reads that can be incorporated into a model to estimate de novo mutations using reads across a pedigree.AvailabilityMethods and data files are available athttps://github.com/CartwrightLab/WuEtAl2016/.Contactcartwright@asu.edu
A short remark on Ontogenetic model and its analytical solution
Authors: Li Ya , He Ji-Huan 
Published: November 2015

AbstractThe ontogenetic growth modeling has been of conspicuously scientific interest, as well as its practical importance in many industrial activities for optimal design. Much work has been done recently to understand the growth mechanism of living organism with a nonlinear time dependence. Some quantitative metabolic models which have been provided to describe organism growth curves are in comparison with what for ontogenetic growth represented by G.B. West et al. (West et al., 2001) in his basic formulations used to discuss the application on different growth patterns. Herein the analytical solution is also involved. In this paper we re-analyzed the assumptions underlying them to find whether the basic relation of organism growth estimated can inosculate with the equation we have proposed.
Natural selection reduces linked neutral divergence between distantly related species
Authors: Phung Tanya N. , Huber Christian D. , Lohmueller Kirk E. 
Published: November 2015

ABSTRACTMuch work has been devoted to understanding the evolutionary processes shaping genetic variation across genomes. Studies have found neutral polymorphism is reduced close to genes and in regions of low recombination, suggesting the effects of natural selection. However, the effect of selection on neutral sequence divergence between species remains ambiguous. While studies have reported correlations between divergence and recombination, theoretical arguments suggest selection may not affect divergence at linked neutral sites. Here we address these outstanding issues by examining how natural selection has affected divergence between distantly related species. We show that neutral divergence is negatively correlated with functional content and positively correlated with estimates of background selection from primates. These patterns persist even when comparing humans and mice, species that split 75 million years ago. Further, neutral divergence is positively correlated with recombination rate. The correlation increases when focusing on genic regions, and biased gene conversion cannot explain all of this correlation. These signatures suggest that natural selection has affected linked divergence between distantly related species. Coalescent models indicate that background selection can generate these patterns. Even when the contribution of ancestral polymorphism to divergence is small, background selection in the ancestral population can still explain a large proportion of the variance in divergence across the genome. Thus, the view that selection does not affect divergence at linked neutral sites needs to be reconsidered. Our work has important implications for understanding evolution of genomes and interpreting patterns of genetic variation.
An integrated metagenomics pipeline for strain profiling reveals novel patterns of transmission and global biogeography of bacteria
Authors: Nayfach Stephen , Rodriguez-Mueller Beltran , Garud Nandita , Pollard Katherine S. 
Published: November 2015

AbstractWe present theMetagenomic Intra-species Diversity Analysis System (MIDAS), which is an integrated computational pipeline for quantifying bacterial species abundance and strain-level genomic variation, including gene content and single nucleotide polymorphisms, from shotgun metagenomes. Our method leverages a database of >30,000 bacterial reference genomes which we clustered into species groups. These cover the majority of abundant species in the human microbiome but only a small proportion of microbes in other environments, including soil and seawater. We appliedMIDASto stool metagenomes from 98 Swedish mothers and their infants over one year and used rare single nucleotide variants to reveal extensive vertical transmission of strains at birth but colonization with strains unlikely to derive from the mother at later time points. This pattern was missed with species-level analysis, because the infant gut microbiome composition converges towards that of an adult over time. We also appliedMIDASto 198 globally distributed marine metagenomes and used gene content to show that many prevalent bacterial species have population structure that correlates with geographic location. Strain-level genetic variants present in metagenomes clearly reveal extensive structure and dynamics that are obscured when data is analyzed at a higher taxonomic resolution.
Cortical state and natural movie responses in cat visual cortex
Authors: Spacek Martin A. , Swindale Nicholas V. 
Published: November 2015

AbstractHow does cortical state affect neural responses to naturalistic stimuli, and is it analogous between anesthetized and awake animals? We recorded spikes and local field potential (LFP) from all layers of isoflurane-anesthetized cat primary visual cortex (V1) while repeatedly presenting wide-field natural scene movie clips. Spiking responses of single units were remarkably precise, reliable and sparse, with lognormally distributed mean firing rates. Many units had distinct barcode-like firing patterns, with features as little as 10 ms wide. LFP-derived cortical state switched spontaneously between synchronized (1/f) and desynchronized (broadband). Surprisingly, responses were more precise, reliable and sparse during the synchronized than desynchronized state. Because the desynchronized state under anesthesia is thought to correspond to attending periods in awake animals, during which responses are enhanced, our results complicate the analogy between cortical states in anesthetized and awake animals. The presenceof orientation maps in cat V1 may explain contrary reports in anesthetized rodents, and predicts a similar result in anesthetized ferret and primate V1.Significance StatementGlobal brain activity changes spontaneously over time and can be characterized along a spectrum from slow synchronized activity, to fast desynchronized activity. This spectrum is similar in awake, asleep and anesthetized animals, but is its effect on neural responses the same in all cases? Here we show that neural responses to natural movies in anesthetized cat visual cortex are more precise during synchronized activity. This is contrary to reports in anesthetized rodents, which we suggest may be due to greater columnar organization in cat visual cortex. Since this is also contrary to enhanced responses and behavioural performance during attention, when activity is desynchronized, our results suggest that similar brain states in awake and anesthetized animals may not be functionally analogous.
Biomechanics of shear-sensitive adhesion in climbing animals: peeling, pre-tension and sliding-induced changes in interface strength
Authors: Labonte David , Federle Walter 
Published: November 2015

AbstractRapid control of adhesive forces is one of the key benchmarks where footpads of climbing animals outperform conventional adhesives, promising novel bio-inspired attachment systems. All climbing animals use shear forces to switch rapidly between firm attachment and easy detachment, but the detailed mechanisms underlying ‘shear-sensitive adhesion’ have remained unclear. Here, we show that attachment forces of stick insects follow classic peeling theory when shear forces are small, but strongly exceed predictions as soon as their pads start to slide due to high shear forces. Pad sliding dramatically increases the critical peel forceviaa combination of two distinct mechanisms. First, partial sliding will pre-stretch the pads, so that they are effectively stiffer upon detachment and peel increasingly like inextensible tape. We demonstrate how this effect can be directly related to peeling theories which account for frictional dissipation. Second, pad sliding reduces the thickness of the secretion layer in the contact zone, thereby decreasing the interfacial mobility, and increasing the stress levels required for peeling. The approximately linear increase of adhesion with friction results in a sharp increase of adhesion at peel angles less than ca. 30°, allowing rapid switching between attachment and detachment during locomotion. Our results may apply to diverse climbing animals independent of pad morphology and adhesive mechanism, and highlight that control of adhesion is not solely achieved by direction-dependence and morphological anisotropy, suggesting promising new routes for the development of bio-inspired adhesives.
Hybrid dysgenesis inDrosophila simulansassociated with a rapid invasion of theP-element
Authors: Hill Tom , Schlötterer Christian , Betancourt Andrea J. 
Published: November 2015

AbstractIn a classic example of the invasion of a species by a selfish genetic element, theP-element was horizontally transferred from a distantly related species intoDrosophila melanogaster. Despite causing ‘hybrid dysgenesis’, a syndrome of abnormal phenotypes that include sterility, theP-element spread globally in the course of a few decades inD. melanogaster. Until recently, its sister species, includingD. simulans, remainedP-element free. Here, we find a hybrid dysgenesis-like phenotype in the offspring of crosses betweenD. simulansstrains collected in different years; a survey of 181 strains shows that around 20% of strains induce hybrid dysgenesis. Using genomic and transcriptomic data, we show that this dysgenesis-inducing phenotype is associated with the invasion of theP-element. To characterize this invasion temporally and geographically, we survey 631D. simulansstrains collected on three continents and over 27 years for the presence of theP-element. We find that theD. simulans P-element invasion occurred rapidly and nearly simultaneously in the regions surveyed, with strains containingP-elements being rare in 2006 and common by 2014. Importantly, as evidenced by their resistance to the hybrid dysgenesis phenotype, strains collected from the latter phase of this invasion have adapted to suppress the worst effects of theP-element.Author SummarySome genes perform necessary organismal functions, others hijack the cellular machinery to replicate themselves, potentially harming the host in the process. These ‘selfish genes’ can spread through genomes and species; as a result, eukaryotic genomes are typically saddled with large amounts of parasitic DNA. Here, we chronicle the surprisingly rapid global spread of a selfish transposable element through a close relative of the genetic model,Drosophila melanogaster. We see that, as it spreads, the transposable element is associated with damaging effects, including sterility, but that the flies quickly adapt to the negative consequences of the transposable element.
Hyper-variability in Circulating Insulin Levels and Physiological Outcomes to High Fat Feeding in MaleIns1−/−:Ins2+/−Mice in a Specific Pathogen-free Facility
Authors: Templeman Nicole M. , Mehran Arya E. , Johnson James D. 
Published: November 2015

AbstractInsulin is an essential hormone with key roles in energy homeostasis and body composition. Mice and rats, unlike other mammals, have two insulin genes: the rodent-specificIns1gene and the ancestralIns2gene. The relationships between insulin gene dosage and obesity has previously been explored in male and femaleIns2−/−mice with full or reducedIns1dosage, as well as in femaleIns1−/−mice with full or partialIns2dosage. We report herein unexpected hyper-variability in circulating insulin and physiological responses to high fat feeding in maleIns1−/−:Ins2+/−mice. Two large cohorts ofIns1−/−:Ins2+/−mice and theirIns1−/−:Ins2+/+littermates were fed chow diet or high fat diet (HFD) from weaning and housed in specific pathogen-free (SPF) conditions. Cohort A and cohort B were studied one year apart. Contrary to female mice from the same litters, inactivating oneIns2allele on the completeIns1-null background did not cause a consistent reduction of circulating insulin in male mice. In cohort A, HFD-fed males showed an equivalent degree of insulin hypersecretion and weight gain, regardless ofIns2dosage. In cohort B,Ins1−/−:Ins2+/−males showed decreased insulin levels and body mass, compared toIns1−/−:Ins2+/+littermates. While experimental conditions were held consistent between cohorts, we found that HFD-fedIns1−/−:Ins2+/−mice with lower insulin levels had increased corticosterone. Collectively, these observations highlight the hyper-variability and range of phenotypic characteristics modulated byIns2gene dosage, specifically in male mice.
pong: fast analysis and visualization of latent clusters in population genetic data
Authors: Behr Aaron A. , Liu Katherine Z. , Liu-Fang Gracie , Nakka Priyanka , Ramachandran Sohini 
Published: November 2015

Abstract1MotivationA series of methods in population genetics use multilocus genotype data to assign individuals membership in latent clusters. These methods belong to a broad class of mixed-membership models, such as latent Dirichlet allocation used to analyze text corpora. Inference from mixed-membership models can produce different output matrices when repeatedly applied to the same inputs, and the number of latent clusters is a parameter that is often varied in the analysis pipeline. For these reasons, quantifying, visualizing, and annotating the output from mixed-membership models are bottlenecks for investigators across multiple disciplines from ecology to text data mining.2ResultsWe introducepong, a network-graphical approach for analyzing and visualizing membership in latent clusters with a native D3.js interactive visualization.pongleverages efficient algorithms for solving the Assignment Problem to dramatically reduce runtime while increasing accuracy compared to other methods that process output from mixed-membership models. We applypongto 225,705 unlinked genome-wide single-nucleotide variants from 2,426 unrelated individuals in the 1000 Genomes Project, and identify previously overlooked aspects of global human population structure. We show thatpongoutpaces current solutions by more than an order of magnitude in runtime while providing a customizable and interactive visualization of population structure that is more accurate than those produced by current tools.3Availabilitypongis freely available and can be installed using the Python package management systempip.pong’s source code is available athttps://github.com/abehr/pong.4Contactaaron_behr@alumni.brown.edu,sramachandran@brown.edu
Detecting Heterogeneity in Population Structure Across the Genome in Admixed Populations
Authors: McHugh Caitlin , Brown Lisa , Thornton Timothy A. 
Published: November 2015

ABSTRACTThe genetic structure of human populations is often characterized by aggregating measures of ancestry across the autosomal chromosomes. While it may be reasonable to assume that population structure patterns are similar genome-wide in relatively homogeneous populations, this assumption may not be appropriate for admixed populations, such as Hispanics and African Americans, with recent ancestry from two or more continents. Recent studies have suggested that systematic ancestry differences can arise at genomic locations in admixed populations as a result of selection and non-random mating. Here, we propose a method, which we refer to as the chromosomal ancestry differences (CAnD) test, for detecting heterogeneity in population structure across the genome. CAnD uses local ancestry inferred from SNP genotype data to identify chromosomes harboring genomic regions with ancestry contributions that are significantly different than expected. In simulation studies with real genotype data from Phase III of the HapMap Project, we demonstrate the validity and power of CAnD. We apply CAnD to the HapMap Mexican American (MXL) and African American (ASW) population samples; in this analysis the software RFMix is used to infer local ancestry at genomic regions assuming admixing from Europeans, West Africans, and Native Americans. The CAnD test provides strong evidence of heterogeneity in population structure across the genome in the MXL sample(p = 4e −05), which is largely driven by elevated Native American ancestry and deficit of European ancestry on the X chromosomes. Among the ASW, all chromosomes are largely African derived and no heterogeneity in population structure is detected in this sample.
Spatial selection and local adaptation jointly shape life-history evolution during range expansion
Authors: Van Petegem Katrien , Boeye J. , Stoks R. , Bonte D. 
Published: November 2015

AbstractIn the context of climate change and species invasions, range shifts increasingly gain attention because the rates at which they occur in the Anthropocene induce fast shifts in biological assemblages. During such range shifts, species experience multiple selection pressures. Especially for poleward expansions, a straightforward interpretation of the observed evolutionary dynamics is hampered because of the joint action of evolutionary processes related to spatial selection and to adaptation towards local climatic conditions. To disentangle the effects of these two processes, we integrated stochastic modeling and empirical approaches, using the spider miteTetranychus urticaeas a model species. We demonstrate considerable latitudinal quantitative genetic divergence in life-history traits inT. urticae, that was shaped by both spatial selection and local adaptation. The former mainly affected dispersal behavior, while development was mainly shaped by adaptation to the local climate. Divergence in life-history traits in species shifting their range poleward can consequently be jointly determined by fast local adaptation to the environmental gradient and contemporary evolutionary dynamics resulting from spatial selection. The integration of modeling with common garden experiments provides a powerful tool to study the contribution of these two evolutionary processes on life-history evolution during range expansion.
GeTFIRST: ontology-based keyword search towards semantic disambiguation
Authors: Nguyen Hoang-Minh , Nguyen Hong-Quang , Tran Khoi-Nguyen , Vo Xuan-Vinh 
Published: November 2015

Purpose
– This paper aims to improve the semantic-disambiguation capability of an information-retrieval system by taking advantages of a well-crafted classification tree. The unstructured nature and sheer volume of information accessible over networks have made it drastically difficult for users to seek relevant information. Many information-retrieval methods have been developed to address this problem, and keyword-based approach is amongst the most common approach. Such an approach is often inadequate to cope with the conceptualization associated with user needs and contents. This brings about the problem of semantic ambiguation that refers to the disagreement in meaning of terms between involving parties of a communication due to polysemy, leading to increased complexity and lesser accuracy in information integration, migration, retrieval and other related activities.

Design/methodology/approach
– A novel ontology-based search approach, named GeTFIRST (short for Graph-embedded Tree Fostering Information Retrieval SysTem), is proposed to disambiguate keywords semantically. The contribution is twofold. First, a search strategy is proposed to prune irrelevant concepts for accuracy improvement using our Graph-embedded Tree (GeT)-based ontology. Second, a path-based ranking algorithm is proposed to incorporate and reward the content specificity.

Findings
– An empirical evaluation was performed on United States Patent And Trademark Office (USPTO) patent datasets to compare our approach with full-text patent search approaches. The results showed that GeTFIRST handled the ambiguous keywords with higher keyword-disambiguation accuracy than traditional search approaches.

Originality/value
– The search approach of this paper copes with the semantic ambiguation by using our proposed GeT-based ontology and a path-based ranking algorithm.
Banks’ stability-efficiency within dual banking system: a stochastic frontier analysis
Authors: Louati Salma , Boujelbene Younes 
Published: November 2015

Purpose
– The purpose of this paper is to examine and compare the market power and the efficiency-stability of Islamic and conventional banks in the MENA zone and South East Asia during the 2005-2012 period.

Design/methodology/approach
– The author applied an empirical approach in two steps. First, the author estimates the Lerner indicator, which is a measure of competition. Then, this measure is regressed and other explanatory variables on the banking “stability-efficiency” are derived simultaneously from the estimation of a stability stochastic frontier.

Findings
– The author concludes that increased competition in the Islamic banking sector promotes the overall banking stability. Besides, whether there is a low or high competitiveness, the size of an Islamic bank is positively related to financial stability. However, large conventional banks operating in market with limited competitiveness become more involved in the risk behavior. The author concludes that capitalization has a positive effect on stability only in case of low competitiveness.

Originality/value
– The originality of this research lies in the application of the stochastic frontier approach (SFA) on the Z-score indicator. This methodology enables to take into account the differences between the current and the optimum stability that each bank can achieve, thus creating a new measure of financial stability called “efficiency-stability”.