bluuebunny/crossref_metadata_2025_split huggingface dataset:
AllSome Sequence Bloom Trees
Authors: Sun Chen , Harris Robert S. , Chikhi Rayan , Medvedev Paul 
Published: December 2016

AbstractThe ubiquity of next generation sequencing has transformed the size and nature of many databases, pushing the boundaries of current indexing and searching methods. One particular example is a database of 2,652 human RNA-seq experiments uploaded to the Sequence Read Archive. Recently, Solomon and Kingsford proposed the Sequence Bloom Tree data structure and demonstrated how it can be used to accurately identify SRA samples that have a transcript of interest potentially expressed. In this paper, we propose an improvement called the AllSome Sequence Bloom Tree. Results show that our new data structure significantly improves performance, reducing the tree construction time by 52.7% and query time by 39 - 85%, with a price of up to 3x memory consumption during queries. Notably, it can query a batch of 198,074 queries in under 8 hours (compared to around two days previously) and a whole set ofk-mers from a sequencing experiment (about 27 milk-mers) in under 11 minutes.
How well do RNA-Seq differential gene expression tools perform in a eukaryote with a complex transcriptome?
Authors: Froussios Kimon , Schurch Nick J. , Mackinnon Katarzyna , Gierliński Marek , Duc Céline , Simpson Gordon G. , Barton Geoffrey J. 
Published: December 2016

AbstractRNA-seq experiments are usually carried out in three or fewer replicates. In order to work well with so few samples, Differential Gene Expression (DGE) tools typically assume the form of the underlying distribution of gene expression. A recent highly replicated study revealed that RNA-seq gene expression measurements in yeast are best represented as being drawn from an underlying negative binomial distribution. In this paper, the statistical properties of gene expression in the higher eukaryoteArabidopsis thalianaare shown to be essentially identical to those from yeast despite the large increase in the size and complexity of the transcriptome: Gene expression measurements from this model plant species are consistent with being drawn from an underlying negative binomial or log-normal distribution and the false positive rate performance of nine widely used DGE tools is not strongly affected by the additional size and complexity of theA. thalianatranscriptome. For RNA-seq data, we therefore recommend the use of DGE tools that are based on the negative binomial distribution.
Climate-driven range shifts in fragmented ecosystems
Authors: Cristofari Robin , Liu Xiaoming , Bonadonna Francesco , Cherel Yves , Pistorius Pierre , Le Maho Yvon , Raybaud Virginie , Stenseth Nils Chr , Le Bohec Céline , Trucchi Emiliano 
Published: December 2016

AbstractRange shift is the primary short-term response of species to rapid climate change but it is hampered by natural or anthropogenic habitat fragmentation. Fragmented habitats expose different critical areas of a species niche to heterogeneous environmental changes resulting in uncoupled effects. Modelling species distribution under complex real-life scenarios and incorporating such uncoupled effects has not been achieved yet. Here we identify the most vulnerable areas and the potential cold refugia of a top-predator with fragmented niche range in the Southern ocean by integrating genomic, ecological and behavioural data with atmospheric and oceanographic models. Our integrative approach constitutes an indispensable example for predicting the effect of global warming on species relying on spatially and ecologically distinct areas to complete their life-cycle (e.g., migratory animals, marine pelagic organisms, central-place foragers) and, in general, on species constrained in fragmented landscapes due to continuously-growing anthropogenic pressure.
Taming the Late Quaternary phylogeography of the Eurasiatic wild ass through ancient and modern DNA
Authors: Bennett E. Andrew , Champlot Sophie , Peters Joris , Arbuckle Benjamin S. , Guimaraes Silvia , Pruvost Mélanie , Bar-David Shirli , Davis Simon S.M. , Gautier Mathieu , Kaczensky Petra , Kuehn Ralph , Mashkour Marjan , Morales-Muñiz Arturo , Pucher Erich , Tournepiche Jean-François , Uerpmann Hans-Peter , Bălăşescu Adrian , Germonpré Mietje , Gündem Can Y. , Hemami Mahmoud-Reza , Moullé Pierre-Elie , Ötzan Aliye , Uerpmann Margarete , Walzer Chris , Grange Thierry , Geigl Eva-Maria 
Published: December 2016

AbstractTaxonomic over-splitting of extinct or endangered taxa, due to an incomplete knowledge of both skeletal morphological variability and the geographical ranges of past populations, continues to confuse the link between isolated extant populations and their ancestors. This is particularly problematic with the genusEquus.To more reliably determine the evolution and phylogeographic history of the endangered Asiatic wild ass, we studied the genetic diversity and inter-relationships of both extinct and extant populations over the last 100,000 years, including samples throughout its previous range from Western Europe to Southwest and East Asia. Using 229 bp of the mitochondrial hypervariable region, an approach which allowed the inclusion of information from extremely poorly preserved ancient samples, we classify all non-African wild asses into nine clades that show a clear phylogeographic structure revealing their phylogenetic history. This study places the extinct European wild ass,E. hydruntinus, the phylogeny of which has been debated since the end of the 19thcentury, into its phylogenetic context within the Asiatic wild asses and reveals recent gene flow events between populations currently regarded as separate species. The phylogeographic organization of clades resulting from these efforts can be used not only to improve future taxonomic determination of a poorly characterized group of equids, but also to identify historic ranges, interbreeding events between various populations, and the impact of ancient climatic changes. In addition, appropriately placing extant relict populations into a broader phylogeographic and genetic context can better inform ongoing conservation strategies for this highly endangered species.
Lung epithelial cells have virus-specific and shared gene expression responses to infection by diverse respiratory viruses
Authors: VanLeuven James T. , Ridenhour Benjamin J. , Miller Craig R. , Miura Tanya A. 
Published: December 2016

AbstractThe severity and outcome of respiratory viral infections is partially determined by the cellular response mounted by infected lung epithelial cells. Disease prevention and treatment is dependent on our understanding of the shared and unique responses elicited by diverse viruses, yet few studies compare host responses to different viruses while controlling other experimental parameters. We compared changes in gene expression of murine lung epithelial cells infected individually by three respiratory viruses causing mild (rhinovirus, RV1B), moderate (coronavirus, MHV-1), and severe (influenza A virus, PR8) disease in mice. RV1B infection caused numerous gene expression changes, but the differential effect peaked at 12 hours post-infection. PR8 altered an intermediate number of genes whose expression continued to change through 24 hours. MHV-1 had comparatively few effects on host gene expression. The viruses elicited highly overlapping responses in antiviral genes, though MHV-1 induced a lower type I interferon response than the other two viruses. Signature genes were identified for each virus and included host defense genes for PR8, tissue remodeling genes for RV1B, and transcription factors for MHV-1. Our comparative approach identified universal and specific transcriptional signatures of virus infection that can be used to discover mechanisms of pathogenesis in the respiratory tract.
Summary of muscle parameters for Hill-based muscle modeling in the human lower limb
Authors: Miller Ross H. 
Published: December 2016

AbstractA summary is presented of five mechanical parameters from human lower limb skeletal muscles critical for Hill-based muscle modeling: the optimal fiber length, the fiber pennation angle, the physiological cross-sectional area (PCSA), the unloaded tendon length, and the fast-twitch fiber fraction. The data presented are drawn from a total of 29 publications including human cadaver studies,in vivoimaging studies of live humans, musculoskeletal modeling studies, and combinations of these methods. Where possible, parameter values were adjusted from the referenced data to present them with consistent definitions (normalization of measured fiber lengths to optimal sarcomere length, and calculation of PCSA as the ratio of fiber volume to fiber length). It is seen that within a specific muscle, optimal fiber lengths are fairly consistent between studies, pennation angles and PCSAs vary widely between studies, and data for unloaded tendon length are comparatively sparse. Few studies have reported fiber type fractions for a large number of muscles. Guidelines for implementing these parameter values in muscle modeling and musculoskeletal modeling are suggested.Update HistoryDecember 2, 2016: original submissionDecember 3, 2016: discussion on maximum isometric force and specific tension addedDecember 6, 2016: minor edits for typos, clarity, and missing referencesDecember 7, 2016: Tirrell et al. (2012) study added
Single-molecule sequencing of theDrosophila serratagenome
Authors: Allen Scott L. , Delaney Emily K. , Kopp Artyom , Chenoweth Stephen F. 
Published: December 2016

ABSTRACTLong read sequencing technology promises to greatly enhancede novoassembly of genomes for non-model species. While error rates have been a large stumbling block, sequencing at high coverage allows reads to be self-corrected. Here we sequence andde novoassemble the genome ofDrosophila serrata, a non-model species from themontiumsubgroup that has been well studied for clines and sexual selection. Using 11 PacBio SMRT cells, we generated 12 Gbp of raw sequence data comprising approximately 65x whole genome coverage. Read lengths averaged 8,940 bp (NRead50 12,200) with the longest read at 53 Kbp. We self-corrected reads using the PBDagCon algorithm and assembled the genome using the MHAP algorithm within the PBcR assembler. Total genome length was 198 Mbp with an N50 just under 1 Mbp. Contigs displayed a high degree of arm-level conservation withD. melanogaster. We also provide an initial annotation for this genome usingin silicogene predictions that were supported by RNA-seq data.
Long-read whole genome sequencing identifies causal structural variation in a Mendelian disease
Authors: Merker Jason D. , Wenger Aaron M. , Sneddon Tam , Grove Megan , Waggott Daryl , Utiramerur Sowmi , Hou Yanli , Lambert Christine C. , Eng Kevin S. , Hickey Luke , Korlach Jonas , Ford James , Ashley Euan A. 
Published: December 2016

AbstractCurrent clinical genomics assays primarily utilize short-read sequencing (SRS), which offers high throughput, high base accuracy, and low cost per base. SRS has, however, limited ability to evaluate tandem repeats, regions with high [GC] or [AT] content, highly polymorphic regions, highly paralogous regions, and large-scale structural variants. Long-read sequencing (LRS) has complementary strengths and offers a means to discover overlooked genetic variation in patients undiagnosed by SRS. To evaluate LRS, we selected a patient who presented with multiple neoplasia and cardiac myxomata suggestive of Carney complex for whom targeted clinical gene testing and whole genome SRS were negative. Low coverage whole genome LRS was performed on the PacBio Sequel system and structural variants were called, yielding 6,971 deletions and 6,821 insertions > 50bp. Filtering for variants that are absent in an unrelated control and that overlap a coding exon of a disease gene identified three deletions and three insertions. One of these, a heterozygous 2,184 bp deletion, overlaps the first coding exon ofPRKAR1A, which is implicated in autosomal dominant Carney complex. This variant was confirmed by Sanger sequencing and was classified as pathogenic using standard criteria for the interpretation of sequence variants. This first successful application of whole genome LRS to identify a pathogenic variant suggests that LRS has significant potential to identify disease-causing structural variation. We recommend larger studies to evaluate the diagnostic yield of LRS, and the development of a comprehensive catalog of common human structural variation to support future studies.
High-resolution tracking of microbial colonization in Fecal Microbiota Transplantation experiments via metagenome-assembled genomes
Authors: Lee Sonny TM , Kahn Stacy A. , Delmont Tom O. , Hubert Nathaniel J. , Morrison Hilary G. , Antonopoulos Dionysios A. , Rubin David T. , Eren A. Murat 
Published: December 2016

AbstractFecal microbiota transplantation (FMT) is an effective treatment for recurrentClostridium difficileinfection and shows promise for treating other medical conditions associated with intestinal dysbioses. However, we lack a sufficient understanding of which microbial populations successfully colonize the recipient gut, and the widely used approaches to study the microbial ecology of FMT experiments fail to provide enough resolution to identify populations that are likely responsible for FMT-derived benefits. Here we used shotgun metagenomics to reconstruct 97 metagenome-assembled genomes (MAGs) from fecal samples of a single donor and followed their distribution in two FMT recipients to identify microbial populations with different colonization properties. Our analysis of the occurrence and distribution patterns post-FMT revealed that 22% of the MAGs transferred from the donor to both recipients and remained abundant in their guts for at least eight weeks. Most MAGs that successfully colonized the recipient gut belonged to the order Bacteroidales. The vast majority of those that lacked evidence of colonization belonged to the order Clostridiales and colonization success was negatively correlated with the number of genes related to sporulation. Although our dataset showed a link between taxonomy and the ability of a MAG to colonize the recipient gut, we also identified MAGs with different colonization properties that belong to the same taxon, highlighting the importance of genome-resolved approaches to explore the functional basis of colonization and to identify targets for cultivation, hypothesis generation, and testing in model systems for mechanistic insights.
A Bayesian Heteroscedastic GLM with Application to fMRI Data with Motion Spikes
Authors: Eklund Anders , Lindquist Martin A. , Villani Mattias 
Published: December 2016

AbstractWe propose a voxel-wise general linear model with autoregressive noise and heteroscedastic noise innovations (GLMH) for analyzing functional magnetic resonance imaging (fMRI) data. The model is analyzed from a Bayesian perspective and has the benefit of automatically down-weighting time points close to motion spikes in a data-driven manner. We develop a highly efficient Markov Chain Monte Carlo (MCMC) algorithm that allows for Bayesian variable selection among the regressors to model both the mean (i.e., the design matrix) and variance. This makes it possible to include a broad range of explanatory variables in both the mean and variance (e.g., time trends, activation stimuli, head motion parameters and their temporal derivatives), and to compute the posterior probability of inclusion from the MCMC output. Variable selection is also applied to the lags in the autoregressive noise process, making it possible to infer the lag order from the data simultaneously with all other model parameters. We use both simulated data and real fMRI data from OpenfMRI to illustrate the importance of proper modeling of heteroscedasticity in fMRI data analysis. Our results show that the GLMH tends to detect more brain activity, compared to its homoscedastic counterpart, by allowing the variance to change over time depending on the degree of head motion.
Joint inference of demography and mutation rates from polymorphism data and pedigrees
Authors: Parat Florence , Szilágyi Sándor Miklós , Wegmann Daniel , Tellier Aurélien 
Published: December 2016

ABSTRACTInference of demography and mutation rates is of major interest but difficult because genetic data is only informative about the population mutation rate, the product of the effective population size times the mutation rate, and not about these quantities individually. Here we show that this limitation can be overcome by combining genetic data with pedigree information. To successfully use pedigree data, however, important aspects of real populations such as the presence of two sexes, unbalanced sex ratios and overlapping generations have to be taken into account. We present here an extension of the classic Wright-Fisher model accounting for these effects and show that the coalescent process under this model reduces to the classic Kingman coalescent with specific scaling parameters. We further derive the probability of a pedigree under that model and show how pedigree data can thus be used to infer demographic parameters. Finally, we present a computationally efficient inference approach combining pedigree information and genetic data summarized by the site frequency spectrum (SFS) that allows for the joint inference of the mutation rate, sex-specific population sizes and the fraction of overlapping generations. Using simulations we then show that these parameters can be accurately inferred from pedigrees spanning just a few generations, as are available for many species. We finally discuss future possible extensions of the model and inference framework necessary for applications to wild and domesticated species, namely the account for more complex demographies and the uncertainty in assigning pedigree individuals to specific generations.
Effective Cell Immunoablation in Undisrupted Developing Avian Embryos
Authors: López-Díaz Maríacruz , Buján-Varela Julia , Cadórniga-Valiño Carlos 
Published: December 2016

ABSTRACTIn birds the construction of germline chimeras by grafting exogenous primordial germ cells (PGCs) during embryonic development is feasible since they migrate to the gonads through the blood. Up to date, the efficiencies are highly variable, in part dependent on the destruction of endogenous PGCs in the recipient embryo. We show an almost complete ablation of the endogenous PGCs in stage X embryos using a baby rabbit serum (BRS), with previous cellular signaling by specific antibodies (SSEA1). The application of the treatments, either on epiblast or subgerminaly, produced the reduction of the PGCs in the embryos in a dose dependent manner. No malformations or damages were detected in the treated embryos. However, subgerminal injection of this cocktail produced a massive cellular destruction in all embryos. Therefore, sequential application is a selective and effective method to produce receptor embryos. Nevertheless, it can also be highly destructive if the mixture is applied locally, this could be useful in the treatment of malignancies.SUMMARY STATEMENTAn immunosurgery procedure is described that yields an almost complete ablation of primordial germ cells in early developing chick embryos, thus increasing the expected rates of chimerism when foreign PGCs are grafted onto these embryos
Analyses of the core eukaryotic protein subunit of telomerase support extensive adaptation to different evolutionary and life histories in the Metazoa
Authors: Lai Alvina G. , Pouchkina-Stantcheva Natalia , Di Donfrancesco Alessia , Kildisiute Gerda , Sahu Sounak , Aboobaker A. Aziz 
Published: December 2016

AbstractMost animals employ telomerase, which consists of a catalytic subunit known as the telomerase reverse transcriptase (TERT) and an RNA template, to maintain telomere ends. Given the importance of TERT and the apparent importance of telomere biology in core metazoan life history traits like ageing and the control of somatic cell proliferation, we hypothesised that TERT would have patterns of sequence and regulatory evolution reflecting adaptations to diverse evolutionary and life histories across the Animal Kingdom. To test this, we performed a complete investigation of the evolutionary history of TERT across animals. We show that although TERT is almost ubiquitous across Metazoa, it has undergone substantial sequence evolution in canonical motifs. Beyond the known canonical motifs, we also identify and compare regions that are highly variable between lineages, but for which conservation exists within phyla. Recent data have highlighted the importance of alternate splice forms of TERT in non-canonical functions in some animals. Although animals may share some conserved introns, we find that the selection of exons for alternative splicing appears to be highly variable, and regulation by alternative splicing appears to be a very dynamic feature of TERT evolution. We show that even within a closely related group of triclad flatworms, where alternative splicing of TERT was previously correlated with reproductive strategy, we observe highly diverse alternative splicing patterns. Our work establishes that the evolutionary history and structural evolution of TERT involves previously unappreciated levels of change, supporting the view that this core eukaryotic protein has adapted to the requirements of diverse animal life histories.