bluuebunny/crossref_metadata_2025_split huggingface dataset:
HyDe: a Python Package for Genome-Scale Hybridization Detection
Authors: Blischak Paul D. , Chifman Julia , Wolfe Andrea D. , Kubatko Laura S. 
Published: September 2017

AbstractThe analysis of hybridization and gene flow among closely related taxa is a common goal for researchers studying speciation and phylogeography. Many methods for hybridization detection use simple site pattern frequencies from observed genomic data and compare them to null models that predict an absence of gene flow. The theory underlying the detection of hybridization using these site pattern probabilities exploits the relationship between the coalescent process for gene trees within population trees and the process of mutation along the branches of the gene trees. For certain models, site patterns are predicted to occur in equal frequency (i.e., their difference is 0), producing a set of functions calledphylogenetic invariants. In this paper we introduce HyDe, a software package for detecting hybridization using phylogenetic invariants arising under the coalescent model with hybridization. HyDe is written in Python, and can be used interactively or through the command line using pre-packaged scripts. We demonstrate the use of HyDe on simulated data, as well as on two empirical data sets from the literature. We focus in particular on identifying individual hybrids within population samples and on distinguishing between hybrid speciation and gene flow. HyDe is freely available as an open source Python package under the GNU GPL v3 on both GitHub (https://github.com/pblischak/HyDe) and the Python Package Index (PyPI:https://pypi.python.org/pypi/phyde).
The PAGE Study: How Genetic Diversity Improves Our Understanding of the Architecture of Complex Traits
Authors: Wojcik Genevieve L , Graff Mariaelisa , Nishimura Katherine K , Tao Ran , Haessler Jeffrey , Gignoux Christopher R , Highland Heather M , Patel Yesha M , Sorokin Elena P , Avery Christy L , Belbin Gillian M , Bien Stephanie A , Cheng Iona , Cullina Sinead , Hodonsky Chani J , Hu Yao , Huckins Laura M , Jeff Janina , Justice Anne E , Kocarnik Jonathan M , Lim Unhee , Lin Bridget M , Lu Yingchang , Nelson Sarah C , Park Sung-Shim L , Poisner Hannah , Preuss Michael H , Richard Melissa A , Schurmann Claudia , Setiawan Veronica W , Sockell Alexandra , Vahi Karan , Vishnu Abhishek , Verbanck Marie , Walker Ryan , Young Kristin L , Zubair Niha , Acuna-Alonso Victor , Ambite Jose Luis , Barnes Kathleen C , Boerwinkle Eric , Bottinger Erwin , Bustamante Carlos D , Caberto Christian , Canizales-Quinteroes Samuel , Conomos Matthew P , Deelman Ewa , Do Ron , Doheny Kimberly , Fernandez-Rhodes Lindsay , Fornage Myriam , Heiss Gerardo , Henn Brenna , Hindorff Lucia A , Jackson Rebecca D , Hailu Benyam , Laurie Cecelia A , Laurie Cathy C , Li Yuqing , Lin Dan-Yu , Moreno-Estrada Andres , Nadkarni Girish , Norman Paul , Pooler Loreall C , Reiner Alexander P , Romm Jane , Sabati Chiara , Sandoval Karla , Sheng Xin , Stahl Eli A , Stram Daniel O , Thornton Timothy A , Wassel Christina L , Wilkens Lynne R , Winkler Cheryl A , Yoneyama Sachi , Buyske Steven , Haiman Chris , Kooperberg Charles , Marchand Loic Le , Loos Ruth JF , Matise Tara C , North Kari E , Peters Ulrike , Kenny Eimear E , Carlson Christopher S 
Published: September 2017

Summary/AbstractGenome-wide association studies (GWAS) have laid the foundation for investigations into the biology of complex traits, drug development, and clinical guidelines. However, the dominance of European-ancestry populations in GWAS creates a biased view of the role of human variation in disease, and hinders the equitable translation of genetic associations into clinical and public health applications. The Population Architecture using Genomics and Epidemiology (PAGE) study conducted a GWAS of 26 clinical and behavioral phenotypes in 49,839 non-European individuals. Using strategies designed for analysis of multi-ethnic and admixed populations, we confirm 574 GWAS catalog variants across these traits, and find 38 secondary signals in known loci and 27 novel loci. Our data shows strong evidence of effect-size heterogeneity across ancestries for published GWAS associations, substantial benefits for fine-mapping using diverse cohorts, and insights into clinical implications. We strongly advocate for continued, large genome-wide efforts in diverse populations to reduce health disparities.
The cost of heat waves and droughts for global crop production
Authors: Mehrabi Zia , Ramankutty Navin 
Published: September 2017

AbstractHeat waves and droughts are a key risk to global crop production and quantifying the extent of this risk is essential for insurance assessment and disaster risk reduction. Here we estimate the cumulative production losses of six major commodity groups under both extreme heat and drought events, across 131 countries, over the time period of 1961-2014. Our results show substantial variation in national disaster risks that have hitherto gone unrecognised in regional and global average estimates. The most severe losses are represented by cereal losses in Angola (4.1%), Botswana (5.7%), USA (4.4%) and Australia (4.4%), oilcrop losses in Paraguay (5.5%), pulse losses in Angola (4.7%) and Nigeria (4.8%), and root and tuber losses in Thailand (3.2%). In monetary terms we estimate the global production loss over this period to be $237 billion US Dollars (2004-2006 baseline). The nations that incurred the largest financial hits were the USA ($116 billion), the former Soviet Union ($37 billion), India ($28 billion), China ($10.7 billion) and Australia ($8.5 billion USD). Our analysis closes an important gap in our understanding of the impacts of extreme weather events on global crop production and provides the basis for country relevant disaster risk reduction.
Selenzyme: Enzyme selection tool for pathway design
Authors: Carbonell Pablo , Wong Jerry , Swainston Neil , Takano Eriko , Turner Nicholas J. , Scrutton Nigel S. , Kell Douglas B. , Breitling Rainer , Faulon Jean-Loup 
Published: September 2017

AbstractSynthetic biology applies the principles of engineering to biology in order to create biological functionalities not seen before in nature. One of the most exciting applications of synthetic biology is the design of new organisms with the ability to produce valuable chemicals including pharmaceuticals and biomaterials in a greener; sustainable fashion. Selecting the right enzymes to catalyze each reaction step in order to produce a desired target compound is, however, not trivial. Here, we present Selenzyme, a free online enzyme selection tool for metabolic pathway design. The user is guided through several decision steps in order to shortlist the best candidates for a given pathway step. The tool graphically presents key information about enzymes based on existing databases and tools such as: similarity of sequences and of catalyzed reactions; phylogenetic distance between source organism and intended host species; multiple alignment highlighting conserved regions, predicted catalytic site, and active regions; and relevant properties such as predicted solubility and transmembrane regions. Selenzyme provides bespoke sequence selection for automated workflows in biofoundries. The tool is integrated as part of the pathway design stage into the design-build-test-learn SYNBIOCHEM pipeline. The Selenzyme web server is available athttp://selenzyme.synbiochem.co.uk.
The Microbiomes of Pancreatic Tissue in Pancreatic Cancer and Non-Cancer Subjects
Authors: del Castillo Erika , Meier Richard , Koestler Devin C. , Chen Tsute , Paster Bruce J. , Charpentier Kevin P. , Kelsey Karl T. , Izard Jacques , Michaud Dominique S. 
Published: September 2017

AbstractObjectiveTo determine whether bacteria are present in the pancreas of pancreatic cancer and non-cancer subjects and examine whether bacterial profiles vary by site and disease phenotype.Design77 patients requiring surgery for pancreatic diseases, or diseases of the foregut, at the Rhode Island Hospital (RIH) were recruited into this study between 2014 and 2016. In addition, 36 whole pancreas were obtained from the National Disease Research Interchange (NDRI) from subjects who were of similar age as the RIH patients and had not died of cancer. The primary exposure of interest was the measurement of the relative abundance of bacterial taxa in all tissue specimens using 16S rRNA gene sequencing.ResultsNumber of bacterial reads per sample varied substantially across sample type and patients, but all demonstrated the presence of diverse gastrointestinal bacteria, including bacterial taxa typically identified in the oral cavity. Bacterial profiles were noted to be more similar within individuals across sites in the pancreas, than between individuals by site, suggesting that the pancreas as a whole has its own microbiome. Comparing the mean relative abundance of bacterial taxa in pancreatic cancer patients to those without cancer revealed differences in bacterial taxa previously linked to periodontal disease, includingPorphyromonas.ConclusionsBacterial taxa known to inhabit the oral cavity, as well as the intestine, were identified in pancreatic tissue of cancer and non-cancer subjects. Whether any of these bacteria play a causal role in pancreatic carcinogenesis, or are simply opportunistic in nature, needs to be further examined.
On information metrics for spatial coding
Authors: Souza Bryan C. , Pavão Rodrigo , Belchior Hindiael , Tort Adriano B.L. 
Published: September 2017

AbstractThe hippocampal formation is involved in navigation, and its neuronal activity exhibits a variety of spatial correlates (e.g., place cells, grid cells). The quantification of the information encoded by spikes has been standard procedure to identify which cells have spatial correlates. For place cells, most of the established metrics derive from Shannon’s mutual information (Shannon, 1948), and convey information rate in bits/sec or bits/spike (Skaggs et al., 1993; Skaggs et al., 1996). Despite their widespread use, the performance of these metrics in relation to the original mutual information metric has never been investigated. In this work, using simulated and real data, we find that the current information metrics correlate less with the accuracy of spatial decoding than the original mutual information metric. We also find that the top informative cells may differ among metrics, and show a surrogate-based normalization that yields comparable spatial information estimates. Since different information metrics may identify different neuronal populations, we discuss current and alternative definitions of spatially informative cells, which affect the metric choice.
SnapperDB: A database solution for routine sequencing analysis of bacterial isolates
Authors: Dallman Timothy , Ashton Philip , Schafer Ulf , Jironkin Aleksey , Painset Anais , Shaaban Sharif , Hartman Hassan , Myers Richard , Underwood Anthony , Jenkins Claire , Grant Kathie 
Published: September 2017

AbstractReal-time surveillance of infectious disease using whole genome sequencing data poses challenges in both result generation and communication. SnapperDB represents a set of tools to store bacterial variant data and facilitate reproducible and scalable analysis of bacterial populations. We also introduce the ‘SNP address’ nomenclature to describe the relationship between isolates in a population to the single nucleotide resolution.SummaryWe announce the release of SnapperDB v1.0 a program for scalable routine SNP analysis and storage of microbial populations.AvailabilitySnapperDB is implemented as a python application under the open source BSD license. All code and user guides are available athttps://github.com/phe-bioinformatics/snapperdb.Contacttim.dallman@phe.gov.ukSupplementary informationSupplementary data are available at Bioinformatics online.
SodaPop: A computational suite for simulating the dynamics of asexual populations
Authors: Gauthier Louis , Di Franco Rémicia , Serohijos Adrian W.R. 
Published: September 2017

AbstractMotivationSimulating protein evolution with realistic constraints from population genetics is essential in addressing problems in molecular evolution, from understanding the forces shaping the evolutionary landscape to the clinical challenges of antibiotic resistance, viral evolution and cancer.ResultsTo address this need, we present SodaPop, a new forward-time simulator of large asexual populations aimed at studying their structure, dynamics and the distribution of fitness effects with flexible assumptions on the fitness landscape. SodaPop integrates biochemical and biophysical properties in a cell-based, object-oriented framework and provides an efficient, open-source toolkit for performing large-scale simulations of protein evolution.Availability and implementationSource code and binaries are freely available athttps://github.com/louisgt/SodaPopunder the GNU GPLv3 license. The software is implemented in C++ and supported on Linux, Mac OS/X and Windows.Contactadrian.serohijos@umontreal.caSupplementary informationSupplementary information is available on the Github project page.
Real-time DNA barcoding in a remote rainforest using nanopore sequencing
Authors: Pomerantz Aaron , Peñafiel Nicolás , Arteaga Alejandro , Bustamante Lucas , Pichardo Frank , Coloma Luis A. , Barrio-Amorós César L. , Salazar-Valenzuela David , Prost Stefan 
Published: September 2017

AbstractAdvancements in portable scientific instruments provide promising avenues to expedite field work in order to understand the diverse array of organisms that inhabit our planet. Here we tested the feasibility forin situmolecular analyses of endemic fauna using a portable laboratory fitting within a single backpack, in one of the world’s most imperiled biodiversity hotspots: the Ecuadorian Chocó rainforest. We utilized portable equipment, including the MinION DNA sequencer (Oxford Nanopore Technologies) and miniPCR (miniPCR), to perform DNA extraction, PCR amplification and real-time DNA barcode sequencing of reptile specimens in the field. We demonstrate that nanopore sequencing can be implemented in a remote tropical forest to quickly and accurately identify species using DNA barcoding, as we generated consensus sequences for species resolution with an accuracy of >99% in less than 24 hours after collecting specimens. In addition, we generated sequence information at Universidad Tecnológica Indoamérica in Quito for the recently re-discovered Jambato toadAtelopus ignescens, which was thought to be extinct for 28 years, a rare species of blind snakeTrilepida guayaquilensis, and two undescribed species ofDipsassnakes. In this study we establish how mobile laboratories and nanopore sequencing can help to accelerate species identification in remote areas (especially for species that are difficult to diagnose based on characters of external morphology), be applied to local research facilities in developing countries, and rapidly generate information for species that are rare, endangered and undescribed, which can potentially aid in conservation efforts.
fingertipsR: an R package for accessing population health information in England
Authors: Fox Sebastian , Flowers Julian , Thelwall Simon , Flint Daniel , Hain Doris 
Published: September 2017

AbstractFingertips is a major public repository of population and public health indicators for England, built and maintained by Public Health England (PHE). The indicators are arranged in thematic or topical profiles covering a wide range of health issues including:broad Health Profilesspecific topics such as liver disease and end of liferisk factors including alcohol, smoking, physical activitypopulation healthcare health services data for general practices, cancer, mental healthhealth protection data on general health protection, TB, antimicrobial resistancelifecourse profiles for younger and older peoplemortality and morbidity.Fingertips makes data available for more than 1,500 indicators spread across more than 70 profiles. The data can be accessed fromhttps://fingertips.phe.org.ukwhere the data are visualised in variety of ways including heatmaps, choropleth maps, line charts for trends, “spine” charts (graphs which compare multiple indicators for a single geographic area), scatter plots and so on. Data can be obtained as downloads or figures which can be exported or cut and paste into reports and slides.A recent addition to the Fingertips platform was an Automated Programming Interface (API) to enable developers to re-use the data. To facilitate access to Fingertips data we have designed anRpackage -fingertipsR- enabling rapid and easy access to the data by analysts and data scientists. The package is available from the Comprehensive R Archive Network (CRAN).This paper describes thefingertipsRpackage which provides tools accessing a wide range of public health data for England from the Fingertips website using its API.
Deep learning of the splicing (epi)genetic code reveals a novel candidate mechanism linking histone modifications to ESC fate decision
Authors: Xu Yungang , Wang Yongcui , Luo Jiesi , Zhao Weiling , Zhou Xiaobo 
Published: September 2017

ABSTRACTAlternative splicing (AS) is a genetically and epigenetically regulated pre-mRNA processing to increase transcriptome and proteome diversity. Comprehensively decoding these regulatory mechanisms holds promise in getting deeper insights into a variety of biological contexts involving in AS, such as development and diseases. We assembled splicing (epi)genetic code, DeepCode, for human embryonic stem cell (hESC) differentiation by integrating heterogeneous features of genomic sequences, 16 histone modifications with a multi-label deep neural network. With the advantages of epigenetic features, DeepCode significantly improves the performance in predicting the splicing patterns and their changes during hESC differentiation. Meanwhile, DeepCode reveals the superiority of epigenomic features and their dominant roles in decoding AS patterns, highlighting the necessity of including the epigenetic properties when assembling a more comprehensive splicing code. Moreover, DeepCode allows the robust predictions across cell lineages and datasets. Especially, we identified a putative H3K36me3-regulated AS event leading to a nonsense-mediated mRNA decay of BARD1. Reduced BARD1 expression results in the attenuation of ATM/ATR signalling activities and further the hESC differentiation. These results suggest a novel candidate mechanism linking histone modifications to hESC fate decision. In addition, when trained in different contexts, DeepCode can be expanded to a variety of biological and biomedical fields.
A novel mechanism for volitional locomotion in larval zebrafish
Authors: Ehrlich David E. , Schoppik David 
Published: September 2017

AbstractTo locomote stably, animals must coordinate volitional actions that change posture with opposing reflexes that hold posture constant [1–8]. These conflicting actions are thought to necessitate integrated control, in which reflexes are modulated to permit or even produce volitional movements [9–14]. Here we report that larval zebrafish (Danio rerio) utilize a simpler control scheme featuring independent volitional and reflexive movements. We present behavioral evidence that larvae swim in depth by appending destabilizing trunk rotations to steer with independent rotations to balance. When we manipulated buoyancy to deflect fish up or down, they redirected steering without coordinated changes to their balance reflex. As balance developed and increasingly opposed destabilization-mediated steering, larvae acquired compensatory use of their pectoral fins to steer. Removing the pectoral fins from older larvae impaired steering but preserved the strong balance reflex. Consequentially, older larvae without fins were strikingly less maneuverable — unable to revert to destabilization-mediated steering — revealing a rigidity inherent within the framework of independent volitional and reflexive control. Larval zebrafish therefore produce effective but inflexible locomotion by sequencing independent volitional and reflexive movements. These results reveal a simple control scheme, applicable for robotic design, that solves the general problem of coordinating volitional movements with the vital reflexes that oppose them.
Time-conditional properties of branches in coalescent gene trees
Authors: Platt Alexander 
Published: September 2017

ABSTRACTCoalescent gene trees have proven to be a powerful framework for formulating and solving problems in population genetics both in theory and practice. Using them, geneticists have been able to generate expectations for many attributes of a random sample of genotypes from a population given a model of the history of the population. This paper derives three new properties of coalescent gene trees that will help characterize the present-day impacts of historical events. Considering a single branch sampled at a given timetsin the past, it presents distributions describing 1) the length of time a branch sampledtsgenerations in the past had existed at the time of sampling, 2) the length of time that branch continues from timetstowards the present, and3) the the probability that the branch is ancestral toxindividuals in a modern sample.
Repeated performance in problem-solving tasks attenuates human cortical responses
Authors: Meshulam Meir , Golan Tal , Harel Michal , Groppe David , Keller Corey J. , Mégevand Pierre , Mehta Ashesh , Malach Rafael 
Published: September 2017

AbstractA ubiquitous characteristic of human cortical networks is their tendency to rapidly change their response properties upon repetition. While this phenomenon has been amply documented using simple sensory-motor tasks, it is still unclear to what extent brain activations change on a short time scale when we are engaged in high level, complex tasks. Here, we examined this question using three types of high-level visual problems. We analyzed data from intracranial recordings performed in eight patients, focusing on the location and type of changes and on their relationship to overt behavior. Our results show significant repetition effects, manifested as signal decrease with repetition, in three different groups of electrodes:Visualsites, which increased their activity during stimuli presentation;Processing Positivesites, which demonstrated increased activity throughout the experimental trial; andProcessing Negativesites, which demonstrated suppression of activity during the trial as compared to baseline. Interestingly, despite these significant repetition effects, response time remained unchanged with repetition. These findings bear directly upon our ability to interpret results aggregated across multiple repetitions of the same complex task.
Telomere repeats induce domains of H3K27 methylation in Neurospora
Authors: Jamieson Kirsty , McNaught Kevin J. , Ormsby Tereza , Leggett Neena A. , Honda Shinji , Selker Eric U. 
Published: September 2017

ABSTRACTDevelopment in higher organisms requires selective gene silencing, directed in part by di-/tri-methylation of lysine 27 on histone H3 (H3K27me2/3). Knowledge of the cues that control formation of such repressive Polycomb domains is extremely limited. We exploited natural and engineered chromosomal rearrangements in the fungusNeurospora crassato elucidate the control of H3K27me2/3. Analyses of H3K27me2/3 in strains bearing chromosomal rearrangements revealed both position-dependent and position-independent facultative heterochromatin. We found that proximity to chromosome ends is necessary to maintain, and sufficient to induce, transcriptionally repressive, subtelomeric H3K27me2/3. We ascertained that such telomere-proximal facultative heterochromatin requires native telomere repeats and found that a short array of ectopic telomere repeats, (TTAGGG)17, can induce a large domain (∼225 kb) of H3K27me2/3. This provides an example of acis-acting sequence that directs H3K27 methylation. Our findings provide new insight into the relationship between genome organization and control of heterochromatin formation.