bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Automated Approach to the Quantitation of Vocalizations and Vocal Learning in the Songbird
Authors: Mets David G. , Brainard Michael S. 
Published: July 2017

AbstractStudies of learning mechanisms critically depend on the ability to accurately assess learning outcomes. This assessment can be impeded by the often complex, multidimensional nature of behavior. We present a novel, automated approach to evaluating imitative learning that is founded in information theory. Conceptually, our approach estimates the amount of information present in a reference behavior that is absent from the learned behavior. We validate our approach through examination of songbird vocalizations, complex learned behaviors the study of which has provided many insights into sensory-motor learning in general and vocal learning in particular. Historically, learning has been holistically assessed by human inspection or through comparison of specific song features selected by experimenters (e.g. fundamental frequency, spectral entropy). In contrast, our approach relies on statistical models that broadly capture the structure of each song, and then uses these models to estimate the amount of information in the reference song but absent from the learned song. We show that our information theoretic measure of song learning (contrast entropy) is well correlated with human evaluation of song learning. We then expand the analysis beyond song learning and show that contrast entropy also detects the typical song deterioration that occurs following deafening. More broadly, this approach potentially provides a framework for assessing learning across a broad range of similarly structured behaviors.Author SummaryMeasuring learning outcomes is a critical objective of research into the neural, molecular, and behavioral mechanisms that support learning. Demonstration that a given manipulation results in better or worse learning outcomes requires an accurate and consistent measurement of learning quality. However, many behaviors (e.g. speech, walking, and reading) are complex and multidimensional, confounding the assessment of learning. One behavior subject to such confounds, vocal learning in Estrildid finches, has emerged as a vital model for sensory motor learning broadly and human speech learning in particular. Here, we demonstrate a new approach, founded in information theory, to the assessment of learning for complex high dimensional behaviors. Conceptually, we determine the amount of information (across many dimensions) present in a reference behavior and then assess how much of that information is present in the resultant learned behavior. We show that this measure provides an accurate, holistic, and automated assessment of vocal learning in Estrildid finches. Potentially, this same approach could be deployed to assess shared content in any multidimensional data, behavioral or otherwise.
Two Chinese medicine species constants and the accurate identification of Chinese medicines
Authors: zou Huabin 
Published: July 2017

AbstractSince the ancient times, all over the world, the identification of herbal medicines have to be based on empirical knowledge. In this article two species constants of traditional Chinese medicines(TCM) were discovered relying on the maximum information states of Dual index information theory equation, or common heredity and variation information theory. The two species constants, common peak ratiosPg= 61% andPg= 70%, which corresponding to symmetry and asymmetry variation states, respectively, were used as two absolute quantitative criteria to identify complex biology systems-TCM. Considered the influences of many other factors on components and experiment processes, the practical theoretical identification standards should be establishedPg≧58~64% andPg≧67~73%, within the relativeerror within −3% and + 3% of information value around the maximum information states. Combining the maximum number of effective sample optimum method with this two theoretical standards, the optimized classification of a TCM sample set can be carried out correctly. 42 samples belonging to four species of combination Chinese medicines were tested. The infrared (IR) fingerprint spectra (FPS) of their powder were measured and analyzed by means of the approach provided above. Among the six pairs of four Chinese medicine species, five of them follow the species constantPg=61%, one of them obeys thePg= 70%. The correct recognition ratio of samples was 95.2%, and that of species was 100%.
SOD1A4Vaggregation alters ubiquitin homeostasis in a cell model of ALS
Authors: Farrawell Natalie E. , Lambert-Smith Isabella , Mitchell Kristen , McKenna Jessie , McAlary Luke , Ciryam Prajwal , Vine Kara L. , Saunders Darren N. , Yerbury Justin J. 
Published: July 2017

AbstractAmyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease involving the selective death of upper and lower motor neurons in the primary motor cortex and spinal cord. A hallmark of ALS pathology is the accumulation of ubiquitinated protein inclusions within motor neurons. Previous studies suggest the sequestration of ubiquitin (Ub) into inclusions reduces the availability of free Ub, which is essential for cellular function and survival. However, the dynamics of the Ub landscape in ALS have not yet been described. Here we show that Ub homeostasis is altered in a SOD1 cell model of ALS. Utilising fluorescently tagged Ub, we followed the distribution of Ub in living cells expressing SOD1 and show that Ub is present at the earliest stages of SOD1 aggregation. We also report that cells containing aggregates of mutant SOD1 have greater ubiquitin-proteasome system (UPS) dysfunction as measured by the accumulation of the fluorescent proteasome reporter tdTomatoCL1. Furthermore, SOD1 aggregation is associated with the redistribution of Ub and depletion of the free Ub pool. Ubiquitomics analysis indicates that mutant SOD1 is associated with a shift of Ub to a pool of supersaturated proteins including those associated with oxidative phosphorylation and metabolism, corresponding with altered mitochondrial morphology and function. Taken together, these results suggest misfolded SOD1 contributes to UPS dysfunction and that Ub homeostasis is an important target for monitoring pathological changes in ALS.
A geography aware reconciliation method to investigate diversification patterns in host/parasite interactions
Authors: Berry V. , Chevenet F. , Doyon J-P. , Jousselin E. 
Published: July 2017

ABSTRACTCospeciation studies aim at investigating whether hosts and symbionts speciate simultaneously or whether the associations diversify through host shifts. This problem is often tackled through reconciliation analyses that map the symbiont phylogeny onto the host phylogeny by mixing different types of diversification events. These reconciliations can be difficult to interpret and not always biologically realistic. Researchers have underlined that the biogeographic histories of both hosts and symbionts influence the probability of cospeciation and host switches, but up to now no reconciliation software integrates geographic data. We present a new functionality in theMowglisoftware that bridges this gap. The user can provide geographic information on both the host and symbiont extant and ancestral taxa. Constraints in the reconciliation algorithm have been implemented to generate biologically realistic codiversification scenarios. We apply our method to the fig/fig wasp association and infer diversification scenarios that differ from reconciliations ignoring geographic information. In addition, we updated the reconciliation viewerSylvXin order to visualize ancestral character states on the phylogenetic trees and highlight zones that are geographically inconsistent in reconciliations computed without geographic constraints. We suggest that the comparison of reconciliations obtained with and without constraints can help solving ambiguities in the biogeographic histories of the partners. With the development of robust methods in historical biogeography and the advent of next-generation sequencing that leads to better-resolved trees, a geography aware reconciliation method represents a substantial advance that is likely to be useful to researchers studying the evolution of biotic interactions and biogeography.
GDSCTools for Mining Pharmacogenomic Interactions in Cancer
Authors: Cokelaer Thomas , Chen Elisabeth , Iorio Francesco , Menden Michael P. , Lightfoot Howard , Saez-Rodriguez Julio , Garnett Mathew J. 
Published: July 2017

AbstractMotivationLarge pharmacogenomic screenings integrate heterogeneous cancer genomic data sets as well as anti-cancer drug responses on thousand human cancer cell lines. Mining this data to identify new therapies for cancer sub-populations would benefit from common data structures, modular computational biology tools and user-friendly interfaces.ResultsWe have developed GDSCTools: a software aimed at the identification of clinically relevant genomic markers of drug response. The Genomics of Drug Sensitivity in Cancer (GDSC) database (www.cancerRxgene.org) integrates heterogeneous cancer genomic data sets as well as anti-cancer drug responses on a thousand cancer cell lines. Including statistical tools (ANOVA) and predictive methods (Elastic Net), as well as common data structures, GDSCTools allows users to reproduce published results from GDSC, to analyse their own drug responses or genomic datasets, and to implement new analytical methods.Contactthomas.cokelaer@pasteur.fr
Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization
Authors: Kojic Aleksandar , Cuadrado Ana , Koninck Magali De , Rodríguez-Corsino Miriam , Gómez-López Gonzalo , Le Dily François , Marti-Renom Marc A. , Losada Ana 
Published: July 2017

AbstractIn addition to mediating sister chromatid cohesion, cohesin plays a central role in DNA looping and segmentation of the genome into contact domains (TADs). Two variant cohesin complexes that contain either STAG/SA1 or SA2 are present in all cell types. Here we addressed their specific contribution to genome architecture in non-transformed human cells. We found that cohesin-SA1 drives stacking of cohesin rings at CTCF-bound sites and thereby contributes to the stabilization and preservation of TAD boundaries. In contrast, a more dynamic cohesin-SA2 promotes cell type-specific contacts between enhancers and promoters within TADs independently of CTCF. SA2 loss, a condition frequently observed in cancer cells, results in increased intra-TAD interactions, likely altering the expression of key cell identity genes.
Genome-wide genetic data on ~500,000 UK Biobank participants
Authors: Bycroft Clare , Freeman Colin , Petkova Desislava , Band Gavin , Elliott Lloyd T. , Sharp Kevin , Motyer Allan , Vukcevic Damjan , Delaneau Olivier , O’Connell Jared , Cortes Adrian , Welsh Samantha , McVean Gil , Leslie Stephen , Donnelly Peter , Marchini Jonathan 
Published: July 2017

AbstractThe UK Biobank project is a large prospective cohort study of ~500,000 individuals from across the United Kingdom, aged between 40-69 at recruitment. A rich variety of phenotypic and health-related information is available on each participant, making the resource unprecedented in its size and scope. Here we describe the genome-wide genotype data (~805,000 markers) collected on all individuals in the cohort and its quality control procedures. Genotype data on this scale offers novel opportunities for assessing quality issues, although the wide range of ancestries of the individuals in the cohort also creates particular challenges. We also conducted a set of analyses that reveal properties of the genetic data – such as population structure and relatedness – that can be important for downstream analyses. In addition, we phased and imputed genotypes into the dataset, using computationally efficient methods combined with the Haplotype Reference Consortium (HRC) and UK10K haplotype resource. This increases the number of testable variants by over 100-fold to ~96 million variants. We also imputed classical allelic variation at 11 human leukocyte antigen (HLA) genes, and as a quality control check of this imputation, we replicate signals of known associations between HLA alleles and many common diseases. We describe tools that allow efficient genome-wide association studies (GWAS) of multiple traits and fast phenome-wide association studies (PheWAS), which work together with a new compressed file format that has been used to distribute the dataset. As a further check of the genotyped and imputed datasets, we performed a test-case genome-wide association scan on a well-studied human trait, standing height.
Vermont: a multi-perspective visual interactive platform for mutational analysis
Authors: Fassio Alexandre V , Martins Pedro M , Guimarães Samuel da S , Junior Sócrates S A , Ribeiro Vagner S , de Melo-Minardi Raquel C , de A Silveira Sabrina 
Published: July 2017

AbstractBackgroundA huge amount of data about genomes and sequence variation is available and continues to grow on a large scale, which makes experimentally characterizing these mutations infeasible regarding disease association and effects on protein structure and function. Therefore, reliable computational approaches are needed to support the understanding of mutations and their impacts. Here, we present VERMONT 2.0, a visual interactive platform that combines sequence and structural parameters with interactive visualizations to make the impact of protein point mutations more understandable.ResultsWe aimed to contribute a novel visual analytics oriented method to analyze and gain insight on the impact of protein point mutations. To assess the ability of VERMONT to do this, we visually examined a set of mutations that were experimentally characterized to determine if VERMONT could identify damaging mutations and why they can be considered so.ConclusionsVERMONT allowed us to understand mutations by interpreting position-specific structural and physicochemical properties. Additionally, we note some specific positions we believe have an impact on protein function/structure in the case of mutation.
Use of a Sibling Subtraction Method (SSM) for Identifying Causal Mutations inC. elegansby Whole-Genome Sequencing
Authors: Joseph Braveen B. , Blouin Nicolas A. , Fay David S. 
Published: July 2017

AbstractWhole-genome sequencing (WGS) has become an indispensible tool for identifying causal mutations obtained from genetic screens. To reduce the number of causal mutation candidates typically uncovered by WGS,C. elegansresearchers have developed several strategies. One involves crossing N2-background mutants to the polymorphic strain CB4856, which can be used to simultaneously identify mutant-strain variants and obtain high-density mapping information. This approach, however, is not well suited for uncovering mutations in complex genetic backgrounds, and CB4856 polymorphisms can alter phenotypes. Several other approaches make use of DNA variants introduced by mutagenesis. This information is used to implicate genomic regions with high densities of DNA lesions that persist after mutant backcrossing, but these methods provide lower mapping resolution than use of CB4856. To identify suppressor mutations using WGS, we developed a new approach termed the Sibling Subtraction Method (SSM). This method works by eliminating variants present in both mutants and their non-mutant siblings, thus greatly reducing the number of candidates. We used this method here with two members of theC. elegansNimA-related kinase family,nekl-2andnekl-3. Combining weak aphenotypic alleles ofnekl-2andnekl-3leads to penetrant molting defects and larval arrest. We isolated ~50 suppressors ofnekl-2; nekl-3synthetic lethality using F1-clonal screening methods and a toxin-based counter-selection strategy. When applied to five of the identified suppressors, SSM led to only one to four suppressor candidates per strain. Thus SSM is a powerful approach for identifying causal mutations in any genetic background and provides an alternative to current methods.
Common neural responses to narrative speech in disorders of consciousness
Authors: Iotzov Ivan , Fidali Brian C , Petroni Agustin , Conte Mary M , Schiff Nicholas D , Parra Lucas C 
Published: July 2017

AbstractObjectiveClinical assessment of auditory attention in patients with disorders of consciousness is often limited by motor impairment. Here, we employ inter-subject correlations among electroencephalography responses to naturalistic speech in order to assay auditory attention among patients and healthy controls.MethodsElectroencephalographic data were recorded from 20 subjects with disorders of consciousness and 14 healthy controls during of two narrative audio stimuli, presented both forwards and time-reversed. Inter-subject correlation of evoked electroencephalography signals were calculated, comparing responses of both groups to those of the healthy control subjects. This analysis was performed blinded and subsequently compared to the diagnostic status of each patient based on the Coma Recovery Scale-Revised.ResultsSubjects with disorders of consciousness exhibit significantly lower inter-subject correlation than healthy controls during narrative speech. Additionally, while healthy subjects had higher inter-subject correlation values in forward vs. backwards presentation, neural responses did not vary significantly with the direction of playback in subjects with disorders of consciousness. Increased inter-subject correlation values in the backward speech condition were noted with improving disorder of consciousness diagnosis, both in cross-sectional analysis and in a subset of patients with longitudinal data.InterpretationInter-subject correlation of neural responses to narrative speech audition differentiates healthy controls from patients and appears to index clinical diagnoses in disorders of consciousness.
Language evolution to revolution: the leap from rich-vocabulary non-recursive communication system to recursive language 70,000 years ago was associated with acquisition of a novel component of imagination, called Prefrontal Synthesis, enabled by a mutation that slowed down the prefrontal cortex maturation simultaneously in two or more children – the Romulus and Remus hypothesis
Authors: Vyshedskiy Andrey 
Published: July 2017

AbstractThere is an overwhelming archeological and genetic evidence that modern speech apparatus was acquired by hominins by 600,000 years ago1. On the other hand, artifacts signifying modern imagination, such as (1) composite figurative arts, (2) bone needles with an eye, (3) construction of dwellings, and (4) elaborate burials arose not earlier than 70,000 years ago2. It remains unclear (1) why there was a long gap between acquisition of modern speech apparatus and modern imagination, (2) what triggered the acquisition of modern imagination 70,000 years ago, and (3) what role language might have played in this process. Our research into evolutionary origin of modern imagination has been driven by the observation of a temporal limit for the development of a particular component of imagination. Modern children not exposed to recursive language in early childhood never acquire the type of active constructive imagination called Prefrontal Synthesis (PFS). Unlike vocabulary and grammar acquisition, which can be learned throughout one’s lifetime, there is a strong critical period for the development of PFS and individuals not exposed to recursive language in early childhood can never acquire PFS as adults. Their language will always lack understanding of spatial prepositions and recursion that depend on the PFS ability. In a similar manner, early hominins would not have been able to learn recursive language as adults and, therefore, would not be able to teach recursive language to their children. Thus, the existence of a strong critical period for PFS acquisition creates an evolutionary barrier for behavioral modernity. An evolutionary mathematical model suggests that a synergistic confluence of three events (1) a genetic mutation that extended the critical period by slowing down the prefrontal cortex development simultaneously in two or more children, (2) invention of recursive elements of language, such as spatial prepositions, by these children and (3) their dialogic communications using these recursive elements, resulted in concurrent conversion of a non-recursive communication system of their parents to recursive language and acquisition of PFS around 70,000 years ago.
Genome-wide divergence among invasive populations ofAedes aegyptiin California
Authors: Lee Yoosook , Schmidt Hanno , Collier Travis C. , Conner William R. , Hanemaaijer Mark J. , Slatkin Montgomery , Marshall John M. , Chiu Joanna C. , Smartt Chelsea T. , Lanzaro Gregory C. , Mulligan F. Steve , Cornel Anthony J. 
Published: July 2017

AbstractIn the summer of 2013,Aedes aegyptiLinnaeus was first detected in three cities in central California (Clovis, Madera and Menlo Park). It has now been detected in multiple locations in central and southern CA as far south as San Diego and Imperial Counties. A number of published reports suggest that CA populations have been established from multiple independent introductions. Here we report the first population genomics analyses ofAe. aegyptibased on individual, field collected whole genome sequences. We analyzed 46Ae. aegyptigenomes to establish genetic relationships among populations from sites in California, Florida and South Africa. We identified 3 major genetic clusters within California; one that includes all sample sites in the southern part of the state (South of Tehachapi mountain range) plus the town of Exeter in central California and two additional clusters in central California. A lack of concordance between mitochondrial and nuclear genealogies suggests that the three founding populations were polymorphic for two main mitochondrial haplotypes prior to being introduced to California. One of these has been lost in the Clovis populations, possibly by a founder effect. Genome-wide comparisons indicate extensive differentiation between genetic clusters. Our observations support recent introductions ofAe. aegyptiinto California from multiple, genetically diverged source populations. Our data reveal signs of hybridization among diverged populations within CA. Genetic markers identified in this study will be of great value in pursuing classical population genetic studies which require larger sample sizes.