bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of residue pairing in interacting β-strands from a predicted residue contact map
Authors: Mao Wenzhi , Wang Tong , Zhang Wenxuan , Gong Haipeng 
Published: November 2017

AbstractDespite the rapid progress of protein residue contact prediction, predicted residue contact maps frequently contain many errors. However, information of residue pairing in β strands could be extracted from a noisy contact map, due to the presence of characteristic contact patterns in β-β interactions. This information may benefit the tertiary structure prediction of mainly β proteins. In this work, we introduce a novel ridge-detection-based β-β contact predictor, RDb2C, to identify residue pairing in β strands from any predicted residue contact map. The algorithm adopts ridge detection, a well-developed technique in computer image processing, to capture consecutive residue contacts, and then utilizes a novel multi-stage random forest framework to integrate the ridge information and additional features for prediction. Starting from the predicted contact map of CCMpred, RDb2C remarkably outperforms all state-of-the-art methods on two conventional test sets of β proteins (BetaSheet916 and BetaSheet1452), and achieves F1-scores of ~62% and ~76% at the residue level and strand level, respectively. Taking the prediction of the more advanced RaptorX-Contact as input, RDb2C achieves impressively higher performance, with F1-scores reaching ~76% and ~86% at the residue level and strand level, respectively. According to our tests on 61 mainly β proteins, improvement in the β-β contact prediction can further ameliorate the structural prediction.Availability: All source data and codes are available athttp://166.111.152.91/Downloads.htmlor at the GitHub address ofhttps://github.com/wzmao/RDb2C.Author summaryDue to the topological complexity, mainly β proteins are challenging targets in protein structure prediction. Knowledge of the pairing between β strands, especially the residue pairing pattern, can greatly facilitate the tertiary structure prediction of mainly β proteins. In this work, we developed a novel algorithm to identify the residue pairing in β strands from a predicted residue contact map. This method adopts the ridge detection technique to capture the characteristic pattern of β-β interactions from the map and then utilizes a multi-stage random forest framework to predict β-β contacts at the residue level. According to our tests, our method could effectively improve the prediction of β-β contacts even from a highly noisy contact map. Moreover, the refined β-β contact information could effectively improve the structural modeling of mainly β proteins.
A common allele in FGF21 associated with preference for sugar consumption lowers body fat in the lower body and increases blood pressure
Authors: Frayling Timothy M. , Beaumont Robin N. , Jones Samuel E. , Yaghootkar Hanieh , Tuke Marcus A. , Ruth Katherine S. , Casanova Francesco , West Ben , Locke Jonathan , Sharp Seth , Ji Yingjie , Thompson William , Harrison Jamie , Lindgren Cecilia M. , Grarup Niels , Murray Anna , Freathy Rachel M. , Weedon Michael N. , Tyrrell Jessica , Wood Andrew R. 
Published: November 2017

SummaryFibroblast Growth Factor 21 (FGF21) is a hormone that induces weight loss in model organisms. These findings have led to trials in humans of FGF21 analogues with some showing weight loss and lipid lowering effects. Recent genetic studies have shown that a common allele in the FGF21 gene alters the balance of macronutrients consumed but there was little evidence of an effect on metabolic traits. We studied a common FGF21 allele (A:rs838133) in 451,099 people from the UK Biobank study. We replicated the association between the A allele and higher percentage carbohydrate intake. We then showed that this allele is more strongly associated with body fat distribution, with less fat in the lower body, and higher blood pressure, than it is with BMI, where there is only nominal evidence of an effect. These human phenotypes of naturally occurring variation in the FGF21 gene will inform decisions about FGF21’s therapeutic potential.
Wnt/β-Catenin Signaling Controls Spatio-Temporal Elasticity Patterns in Extracellular Matrix duringHydraMorphogenesis
Authors: Veschgini Mariam , Petersen Hendrik O. , Kaufmann Stefan , Abuillan Wasim , Suzuki Ryo , Burghammer Manfred , Özbek Suat , Holstein Thomas W. , Tanaka Motomu 
Published: November 2017

AbstractAlbeit ample evidence has suggested the remodeling of extracellular matrix (ECM) in animals plays crucial roles in development and diseases, little is understood how ECM mechanics correlates with tissue morphogenesis. In this study, we quantitatively determined how spatio-temporal elasticity patterns in ECM change during the asexual reproduction of freshwater polypHydra. We first determined the mesoscopic protein arrangement inHydraECM (mesoglea) by grazing-incidence small-angle X-ray scattering with nano-beam (nano-GISAXS). Our data unraveled fibrillar type I collagen inHydramesoglea (Hcol-I) takes an anisotropic, more strongly distorted hexagonal lattice compared to those in vertebrates that could be attributed to the lower proline content and lack of lysin-crosslinks in Hcol-1 fibers. Then, we “mapped” the spatio-temporal changes in ECM stiffnessex vivowith aid of nano-indentation. We identified three representative elasticity patterns during tissue growth along the oral-aboral body axis of the animals. Our complementary proteome analysis demonstrated that the elasticity patterns of the ECM correlate with a gradient like distribution of proteases. Perturbations of the oral Wnt/β-catenin signaling center further indicated that ECM elasticity patterns are governed by Wnt/β-catenin signaling. Theex vivobiomechanical phenotyping ofHydramesoglea established in this study will help us gain comprehensive insights into the spatio-temporal coordination of biochemical and biomechanical cues in tissue morphogenesisin vivo.
QUETZAL - an open source C++ template library for coalescence-based environmental demogenetic models inference
Authors: Becheler Arnaud , Coron Camille , Dupas Stéphane 
Published: November 2017

1AbstractThe purpose of this article is to introduce an implementation framework enabling us, using available genetic samples, to understand and foresee the behavior of species living in a fragmented and temporally changing environment. To this aim, we first present a model of coalescence which is conditioned to environment, through an explicit modeling of population growth and migration. The parameters of this model can be infered using Approximate Bayesian Computation techniques, which supposes that the considered model can be efficiently simulated. We next present Quetzal, a C++ library composed of reusable generic components and designed to efficiently implement a wide range of coalescence-based environmental demogenetic models.
Multivariate pattern analysis of fMRI data for imaginary and real colours in grapheme-colour synaesthesia
Authors: Ruiz Mathieu J. , Dojat Michel , Hupé Jean-Michel 
Published: November 2017

AbstractGrapheme-colour synaesthesia is a subjective phenomenon related to perception and imagination, in which some people involuntarily but systematically associate specific, idiosyncratic colours to achromatic letters or digits. Its investigation is relevant to unravel the neural correlates of colour perception in isolation from low-level neural processing of spectral components, as well as the neural correlates of imagination by being able to reliably trigger imaginary colour experiences. However, functional MRI studies using univariate analyses failed to provide univocal evidence of the activation of the ‘colour network’ by synaesthesia. Applying Multivariate (multivoxel) Pattern Analysis (MVPA) on 20 synaesthetes and 20 control participants, we tested whether the neural processing of real colours (concentric rings) and synaesthetic colours (black graphemes) shared patterns of activations. Region of interest analyses in retinotopically and anatomically defined visual regions revealed neither evidence of shared circuits for real and synaesthetic colour processing, nor processing difference between synaesthetes and controls. We also found no correlation with individual experiences, characterised by measuring the strength of synaesthetic associations. The whole brain, searchlight, analysis led to similar results. We conclude that identifying the neural correlates of the synaesthetic experience of colours may still be beyond the reach of present technology and data analysis techniques.
Integrated molecular, clinical, and ontological analysis identifies overlooked disease relationships
Authors: Haynes Winston A. , Vashisht Rohit , Vallania Francesco , Liu Charles , Gaskin Gregory L. , Bongen Erika , Lofgren Shane , Sweeney Timothy E. , Utz Paul J. , Shah Nigam H. , Khatri Purvesh 
Published: November 2017

AbstractExisting knowledge of human disease relationships is incomplete. To establish a comprehensive understanding of disease, we integrated transcriptome profiles of 41,000 human samples with clinical profiles of 2 million patients, across 89 diseases. Based on transcriptome data, autoimmune diseases clustered with their specific infectious triggers, and brain disorders clustered by disease class. Clinical profiles clustered diseases according to the similarity of their initial manifestation and later complications, identifying disease relationships absent in prior co-occurrence analyses. Our integrated analysis of transcriptome and clinical profiles identified overlooked, therapeutically actionable disease relationships, such as between myositis and interstitial cystitis. Our improved understanding of disease relationships will identify disease mechanisms, offer novel therapeutic targets, and create synergistic research opportunities.
Meiosis leads to pervasive segregation distortion and copy-number variation in accessory chromosomes of the wheat pathogenZymoseptoria tritici
Authors: Fouché Simone , Plissonneau Clémence , McDonald Bruce A. , Croll Daniel 
Published: November 2017

AbstractMeiosis is one of the most conserved molecular processes in eukaryotes. The fidelity of pairing and segregation of homologous chromosomes has a major impact on the proper transmission of genetic information. Aberrant chromosomal transmission can have major phenotypic consequences, yet the mechanisms are poorly understood. Fungi are excellent models to investigate processes of chromosomal transmission, because many species have highly polymorphic genomes that include accessory chromosomes. Inheritance of accessory chromosomes is often unstable and chromosomal losses have little impact on fitness. We analyzed chromosomal inheritance in 477 progeny coming from two crosses of the fungal wheat pathogenZymoseptoria tritici. For this, we developed a high-throughput screening method based on restriction site associated DNA sequencing (RAD-seq) that generated dense coverage of genetic markers along each chromosome. We identified rare instances of chromosomal duplications (disomy) in core chromosomes. Accessory chromosomes showed high overall frequencies of disomy. Chromosomal rearrangements were found exclusively on accessory chromosomes and were more frequent than disomy. Accessory chromosomes present in only one of the parents in an analyzed cross were inherited at significantly higher rates than the expected 1:1 segregation ratio. Both the chromosome and the parental background had significant impacts on the rates of disomy, losses, rearrangements and segregation distortion. We found that chromosomes with higher sequence similarity and lower repeat content were inherited more faithfully. The large number of rearranged progeny chromosomes identified in this species will enable detailed analyses of the mechanisms underlying chromosomal rearrangement.
Streptococcus pyogenesinfection and the human proteome with a special focus on the IgG-cleaving enzyme IdeS
Authors: Karlsson Christofer A. Q. , Järnum Sofia , Winstedt Lena , Kjellman Christian , Björck Lars , Linder Adam , Malmström Johan A. 
Published: November 2017

AbstractInfectious diseases are characterized by a complex interplay between host and pathogen, but how these interactions impact the host proteome is unclear. Here we applied a novel mass spectrometry based proteomics strategy to investigate how the human proteome is transiently modified by the pathogenStreptococcus pyogenes, with a particular focus on bacterial cleavage of IgGin vivo. In invasive diseases,S. pyogenesevokes a massive host response in blood, whereas superficial diseases are characterized by a local leakage of several blood plasma proteins at the site of infection including IgG.S. pyogenesproduces IdeS, a protease cleaving IgG in the lower hinge region and we find highly effective IdeS-cleavage of IgG in samples from local IgG poor microenvironments. The results show that IdeS contributes to the adaptation ofS. pyogenesto its normal ecological niches. Additionally, the work identifies novel clinical opportunities forin vivopathogen detection.
ReprDB and panDB: minimalist databases with maximal microbial representation
Authors: Zhou Wei , Gay Nicole , Oh Julia 
Published: November 2017

AbstractBackgroundProfiling of shotgun metagenomic samples is hindered by a lack of unified microbial reference genome databases that i) assemble genomic information from all open access microbial genomes, ii) have relatively small sizes, and iii) are compatible to various metagenomic read mapping tools. Moreover, computational tools to rapidly compile and update such databases to accommodate the rapid increase in new reference genomes do not exist. As a result, database-guided analyses often fail to profile a substantial fraction of metagenomic shotgun sequencing reads from complex microbiomes.ResultsWe report pipelines that efficiently traverse all open access microbial genomes and assemble non-redundant genomic information. The pipelines result in two species-resolution microbial reference databases of relatively small sizes: reprDB, which assembles microbial representative or reference genomes, and panDB, for which we developed a novel iterative alignment algorithm to identify and assemble non-redundant genomic regions in multiple sequenced strains. With the databases, we managed to assign taxonomic labels and genome positions to the majority of metagenomic reads from human skin and gut microbiomes, demonstrating a significant improvement over a previous database-guided analysis on the same datasets.ConclusionsreprDB and panDB leverage the rapid increases in the number of open access microbial genomes to more fully profile metagenomic samples. Additionally, the databases exclude redundant sequence information to avoid inflated storage or memory space and indexing or analyses time. Finally, the novel iterative alignment algorithm significantly increases efficiency in pan-genome identification and can be useful in comparative genomic analyses.
Urbanization-driven changes in web-building are decoupled from body size in an orb-web spider
Authors: Dahirel Maxime , De Cock Maarten , Vantieghem Pieter , Bonte Dries 
Published: November 2017

AbstractIn animals, behavioural responses may play an important role in determining population persistence in the face of environmental changes. Body size is a key trait central to many life history traits and behaviours. While behaviours are typically assumed to be highly plastic, size correlations may impose constraints on their adaptive value when size itself is subject to environmental changes.Urbanization is an important human-induced rapid environmental change that imposes multiple selection pressures on both body size and (size-constrained) behaviour. How these combine to shape behavioural responses of urban-dwelling species is unclear.Using web-building, an easily quantifiable behaviour linked to body size, and the garden spider Araneus diadematus as a model, we disentangle direct behavioural responses to urbanization and body size constraints across a network of 63 selected populations differing in urbanization intensity at two spatial scales.Spiders were smaller in highly urbanized sites (local scale only), in line with expectations based on reduced prey biomass availability and the Urban Heat Island effect. The use of multivariate mixed modelling reveals that although web traits and body size are correlated within populations, behavioural responses to urbanization do not appear to be constrained by size: there is no evidence of size-web correlations among populations or among landscapes. Spiders thus altered different components of their web-building behaviours independently in response to urbanization: mesh width and web surface decreased independently with urbanization at the local scale, while web surface also increased with urbanization at the landscape scale. These responses are expected to compensate, at least in part, for reduced prey biomass availability.Our results demonstrate that responses in typically size-dependent behaviours may be decoupled from size changes, thereby allowing fitness maximisation in novel environments. The spatial scale of the behavioural responses to urbanization suggest contributions of both genetic adaptation and plasticity. Although fecundity decreased with local-scale urbanization, Araneus diadematus abundances were remarkably similar across urbanization gradients; behavioural responses thus appear overall successful at the population level.
Minimum requirements for reprogramming and maintaining cell fate in theArabidopsisroot
Authors: Drapek Colleen , Sparks Erin E. , Marhavy Peter , Andersen Tonni G. , Hennacy Jessica H. , Geldner Niko , Benfey Philip N. 
Published: November 2017

AbstractChanges in gene regulation during differentiation are governed by networks of transcription factors. To identify the minimal network for endodermal differentiation in theArabidopsisroot, we asked what transcription factors are sufficient to program a non-native cell-type into endodermis. Our results show the transcription factors SHORTROOT and MYB36 have limited ability to reprogram a non-native cell-type (the epidermis) and that this reprogramming is reversible in the absence of additional cues. The stele-derived signaling peptide CIF2 stabilizes SHORTROOT-induced reprogramming. The outcome is a partially impermeable barrier deposited in the sub-epidermal cell layer that has a transcriptional signature similar to endodermis. The trans-differentiation mechanism depends on the expression of genes downstream in the gene regulatory network but is independent of SHORTROOT movement. These results highlight a non cell-autonomous induction mechanism for endodermis that resembles differentiation in many animal systems.One Sentence SummarySHORTROOT and CIF2 combined can induce and stabilize an endodermis in sub-epidermal cells and do so in a non cell-autonomous manner.
Anterior temporal lobe morphometry predicts categorization ability
Authors: Garcin B. , Urbanski M. , Schotten M. Thiebaut De , Levy R. , Volle E. 
Published: November 2017

AbstractCategorization is the mental operation by which the brain classifies objects and events. It is classically assessed using semantic and non-semantic matching or sorting tasks. These tasks show a high variability in performance across healthy controls and the cerebral bases supporting this variability remain unknown. In this study we performed a voxel-based morphometry study to explore the relationships between semantic and shape categorization tasks and brain morphometric differences in 50 controls. We found significant correlation between categorization performance and the volume of the grey matter in the right anterior middle and inferior temporal gyri. Semantic categorization tasks were associated with more rostral temporal regions than shape categorization tasks. A significant relationship was also shown between white matter volume in the right temporal lobe and performance in the semantic tasks. Tractography revealed that this white matter region involved several projection and association fibers, including the arcuate fasciculus, inferior fronto-occipital fasciculus, uncinate fasciculus, and inferior longitudinal fasciculus. These results suggest that categorization abilities are supported by the anterior portion of the right temporal lobe and its interaction with other areas.HighlightsAnterior temporal lobe morphometry correlates with categorization performancesSemantic is associated with a more rostral temporal region than shape categorizationSemantic categorization performances are associated with right temporal connections
“A mosquito bites and a butterfly flies": a specific response type of frontal patients in a similarity task
Authors: Garcin Béatrice , Volle Emmanuelle , Funkiewiez Aurélie , Miller Bruce L , Dubois Bruno , Levy Richard 
Published: November 2017

AbstractBackgroundPatients with neurodegenerative diseases affecting the frontal lobes have difficulties in categorization tasks, such as the similarity tasks. They give two types of unusual response to the question: “In what way are an orange and a banana alike?”, either a differentiation (“one is yellow, the other is orange”) or a concrete similarity (“they are sweet”).ObjectiveTo characterize the categorization deficit of frontal patients and develop a short diagnostic tool to assess the nature of these difficulties.MethodWe analyzed the responses provided by frontal and non-frontal neurodegenerative patients in a novel verbal similarity task (SimiCat). We included 40 frontal patients with behavioral variant fronto-temporal dementia (bvFTD) and progressive supranuclear palsy (PSP), 23 patients with Alzheimer’s disease (AD) and 41 healthy matched controls. Responses that did not correspond to the expected taxonomic category (e.g.: fruits) were considered as errors.ResultsAll patients groups were impaired at the SimiCat test compared to controls. Differentiation errors were specific of frontal patients. Receiver operating characteristic analyses showed that a cut-off of two differentiation errors or more achieved 85% sensitivity of 100% specificity to discriminate bvFTD from AD. A short version of the test (<5 min) showed similar discriminative validity as the full version.ConclusionDifferentiation responses were specific of frontal patients. The SimiCat demonstrates good discriminative validity to differentiate bvFTD and AD. The short version of the test is a promising diagnostic tool that will need validation in future studies.