bluuebunny/crossref_metadata_2025_split huggingface dataset:
SHORT COMMUNICATION: Validation of a novel milk progesterone based tool to monitor luteolysis in dairy cows. Performance on cost-effective, on-farm measured data
Authors: Adriaens Ines , Saeys Wouter , Geerinckx Katleen , De Ketelaere Bart , Aernouts Ben 
Published: January 2019

INTERPRETATIVE SUMMARYValidation of luteolysis monitoring tool Adriaens.Recently, a novel progesterone-based monitoring algorithm using synergistic control, PMASC, was developed. This algorithm employs the known luteal dynamics of the progesterone profile to estimate the moment of luteolysis with minimal dependence on the absolute measurement values. As its value and implementability strongly dependends on the number of samples it requires to obtain the desired accuracy, its performance on cost-effective, ‘smart’ sampled and on-farm measured data is demonstrated.SHORT COMMUNICATIONValidation of a novel milk progesterone based tool to monitor luteolysis in dairy cows. Performance on cost-effective, on-farm measured data
Balancing sensitivity and specificity in distinguishing TCR groups by CDR sequence similarity
Authors: Thakkar Neerja , Bailey-Kellogg Chris 
Published: January 2019

AbstractRepertoire sequencing is enabling deep explorations into the cellular immune response, including the characterization of commonalities and differences among T cell receptor (TCR) repertoires from different individuals, pathologies, and antigen specificities. In seeking to understand the generality of patterns observed in different groups of TCRs, it is necessary to balance how well each pattern represents the diversity among TCRs from one group (sensitivity) vs. how many TCRs from other groups it also represents (specificity). The variable complementarity determining regions (CDRs), particularly the third CDRs (CDR3s) interact with MHC-presented epitopes from putative antigens, and thus encode the determinants of recognition. We here systematically characterize the predictive power that can be obtained from CDR3 sequences, using representative, readily interpretable methods for evaluating CDR sequence similarity and then clustering and classifying sequences based on similarity. An initial analysis of CDR3s of known structure, clustered by structural similarity, helps calibrate the limits of sequence diversity among CDRs that might have a common mode of interaction with presented epitopes. Subsequent analyses demonstrate that this same range of sequence similarity strikes an appropriate specificity/sensitivity balance in distinguishing twins from non-twins based on overall CDR3 repertoires, classifying CDR3 repertoires by antigen specificity, and distinguishing general pathologies. We conclude that within this fairly broad range of sequence similarity, matching CDR3 sequences are likely to share specificities.
Large-scale proteomic analysis of human prefrontal cortex identifies proteins associated with cognitive trajectory in advanced age
Authors: Wingo Aliza P. , Dammer Eric B. , Breen Michael S. , Logsdon Benjamin A. , Duong Duc M. , Troncosco Juan C. , Thambisetty Madhav , Beach Thomas G. , Serrano Geidy E. , Reiman Eric M. , Caselli Richard J. , Lah James J. , Seyfried Nicholas T. , Levey Allan I. , Wingo Thomas S. 
Published: January 2019

AbstractIn advanced age, some individuals maintain a stable cognitive trajectory while others experience a rapid decline. Such variation in cognitive trajectory is only partially explained by traditional neurodegenerative pathologies. Hence, to identify new processes underlying variation in cognitive trajectory, we perform an unbiased proteome-wide association study of cognitive trajectory in a discovery (n=104) and replication cohort (n=39) of initially cognitively unimpaired, longitudinally assessed older-adult brain donors. We find 579 proteins associated with cognitive trajectory after meta-analysis. Notably, we present novel evidence for increased neuronal mitochondrial activities in cognitive stability regardless of the burden of traditional neuropathologies. Furthermore, we provide additional evidence for increased synaptic activities and decreased inflammation and apoptosis in cognitive stability. Importantly, we nominate proteins associated with cognitive trajectory, particularly the 38 proteins that act independently of neuropathologies and are also hub proteins of protein co-expression networks, as promising targets for future mechanistic studies of cognitive trajectory.
Comparing rates of introgression in parasitic feather lice with differing dispersal capabilities
Authors: Doña Jorge , Sweet Andrew D. , Johnson Kevin P. 
Published: January 2019

AbstractOrganisms vary in their dispersal abilities, and these differences can have important biological consequences, such as impacting the likelihood of hybridization events. However, there is still much to learn about the factors influencing hybridization, and specifically how dispersal ability affects the opportunities for hybridization. Here, using the ecological replicate system of dove wing and body lice (Insecta: Phthiraptera), we show that species with higher dispersal abilities exhibited increased genomic signatures of introgression. Specifically, we found a higher proportion of introgressed genomic reads and more reticulated phylogenetic networks in wing lice, the louse group with higher dispersal abilities. Our results are consistent with the hypothesis that differences in dispersal ability might drive the extent of introgression through hybridization.
Continent-wide structure of bacterial microbiomes of European Drosophila melanogaster suggests host-control
Authors: Wang Yun , Kapun Martin , Waidele Lena , Kuenzel Sven , Bergland Alan , Staubach Fabian 
Published: January 2019

AbstractThe relative importance of host-control, environmental effects, and stochasticity in the assemblage of host-associated microbiomes has been much debated. With recent sampling efforts, the underpinnings of D. melanogaster’s microbiome structure have become tractable on larger spatial scales. We analyzed the microbiome among fly populations that were sampled across Europe by the European Drosophila Population Genomics Consortium (DrosEU). We combined environmental data on climate and food-substrate, dense genomic data on host population structure, and microbiome profiling. Food-substrate, temperature, and host population-structure correlated with microbiome-structure. The microbes, whose abundance was co-structured with host populations, also differed in abundance between flies and their substrate in an independent survey, suggesting host-control. Patterns of enrichment and depletion of microbes between host and substrate were consistent with a model of host-control, where the host manipulates its microbiome for its benefit. Putative host-control was bacterial strain specific, supporting recent evidence for high specificity of D. melanogaster-microbe interaction.
Imaging the spontaneous flow of thought: Distinct periods of cognition contribute to dynamic functional connectivity during rest
Authors: Gonzalez-Castillo Javier , Caballero-Gaudes César , Topolski Natasha , Handwerker Daniel A. , Pereira Francisco , Bandettini Peter A. 
Published: January 2019

AbstractBrain functional connectivity (FC) changes have been measured across seconds using fMRI. This is true for both rest and task scenarios. Moreover, it is well accepted that task engagement alters FC, and that dynamic estimates of FC during and before task events can help predict their nature and performance. Yet, when it comes to dynamic FC (dFC) during rest, there is no consensus about its origin or significance. Some argue that rest dFC reflects fluctuations in on-going cognition, or is a manifestation of intrinsic brain maintenance mechanisms, which could have predictive clinical value. Conversely, others have concluded that rest dFC is mostly the result of sampling variability, head motion or fluctuating sleep states. Here, we present novel analyses suggesting that rest dFC is influenced by short periods of distinct mental processing, and that the cognitive nature of such mental processes can be inferred blindly from the data. As such, several different behaviorally relevant whole-brain FC configurations may occur during a single rest scan even when subjects were continuously awake and displayed minimal motion. In addition, using low dimensional embeddings as visualization aids, we show how FC states—commonly used to summarize and interpret resting dFC—can accurately and robustly reveal periods of externally imposed tasks; however, they may be less effective in capturing periods of distinct cognition during rest.
Role of Disulfide Bonds and Topological Frustration in the Kinetic Partitioning of Lysozyme Folding Pathways
Authors: Muttathukattil Aswathy N. , Singh Prashant Chandra , Reddy Govardhan 
Published: January 2019

AbstractDisulfide bonds in proteins can strongly influence the folding pathways by constraining the conformational space. Hen egg white lysozyme has four disulfide bonds and is widely studied for its antibacterial properties. Experiments on lysozyme infer that the protein folds through a fast and a slow pathway. However, the reasons for the kinetic partitioning in the folding pathways are not completely clear. Using a coarse-grained protein model and simulations, we show that two out of the four disulfide bonds, which are present in theα-domain of lysozyme, are responsible for the slow folding pathway. In this pathway, a kinetically trapped intermediate state, which is close to the native state is populated. In this state, the orientation ofα-helices present in theα-domain are misaligned relative to each other. The protein in this state has to partially unfold by breaking down the inter-helical contacts between the misaligned helices to fold to the native state. However, the topological constraints due to the two disulfide bonds present in theα-domain make the protein less flexible, and it is trapped in this conformation for hundreds of milliseconds. On disabling these disulfide bonds, we find that the kinetically trapped intermediate state and slow folding pathway disappear. Simulations mimicking the folding of protein without disulfide bonds in oxidative conditions show that the native disulfide bonds are formed as the protein folds indicating that folding guides the formation of disulfide bonds. The sequence of formation of the disulfide bonds is Cys64-Cys80 → Cys76-Cys94 → Cys30-Cys115 → Cys6-Cys127. Any disul-fide bond, which forms before its precursor in the sequence has to break and follow the sequence for the protein to fold. These results show that lysozyme also serves as a very good model system to probe the role of disulfide bonds and topological frustration in protein folding. The predictions from the simulations can be verified by single molecule fluorescence resonance energy transfer (FRET) or single molecule pulling experiments, which can probe heterogeneity in the folding pathways.
Computational Analysis Revealed Five Novel Mutations in HumanIL2RGgene Related to X-SCID
Authors: Mohammed Tamadur Babiker Abbas , Ali Asma Ali Hassan , Elemam Areeg ElsirAbdelgadir , Altayb Wala Omer Mohammed , Abbas Tebyan Ameer Abdelhameed , Hassan Mohamed Ahmed Salih 
Published: January 2019

ABSTRACTBackgroundX linked severe combined immunodeficiency (X-SCID) is a life-threatening disorder. It is due to mutation of the interleukin two receptor gamma-chain (IL2RG) gene. Nonsynonymous SNPs (nsSNPs) are the most common polymorphism, known to be deleterious or disease-causing variations because they alter protein sequence, structure, and function. Objective: is to reveal the effect of harmful SNPs in the function and structure of IL2RG protein.MethodData on IL2RG was investigated from dbSNP/NCBI database. Prediction of damaging effect was done using sift, polyphen, provean and SNAP2.more software were used for more analysis: phd-snp, and and go, Pmut, Imutant.modeling was done using chimera and project hope. Gene interaction was done by gene mania.3UTR prediction was done using polymiRTS software.ResultThe in-silico prediction identified 1479 SNPs within IL2RG gene out of which 253 were coding SNPs, 50 took place in the miRNA 3 UTR, 21 occurred in 5 UTR region and 921 occurred in intronic regions. a total of 12 missense nsSNPs were found to be damaging by both a sequence homology-based tool (SIFT) and a structural homology-based method (PolyPhen), Five of them were novel; rs1322436793(G305R), rs1064794027(C182Y), rs111033620(G114D), rs193922347 (Y105C) and rs1293196743(Y91C), Two SNPs(Rs144075871andrs191726889) out of 50 in the 3UTR region were predicted to disrupt miRNAs binding sites and affect the gene expression.ConclusionsComputational analysis of SNPs has become a very valuable tool in order to discriminate neutral SNPs from damaging SNPs. This study revealed 5 novel nsSNPs in the IL2RG gene by using different software and 21 SNPs in 3UTR. These SNPs could be considered as important candidates in causing diseases related to IL2RG mutation and could be used as diagnostic markers.
Distinguishing the signatures of local environmental filtering and regional trait range limits in the study of trait-environment relationships
Authors: Denelle Pierre , Violle Cyrille , Munoz François 
Published: January 2019

AbstractUnderstanding the imprint of environmental filtering on community assembly along environmental gradients is a key objective of trait-gradient analyses. Depending on local constraints, this filtering generally entails that species departing from an optimum trait value have lower abundances in the community. The Community-Weighted Mean (CWM) and Variance (CWV) of trait values are then expected to depict the optimum and intensity of filtering, respectively. However, the trait distribution within the regional species pool and its limits can also affect local CWM and CWV values apart from the effect of environmental filtering. The regional trait range limits are more likely to be reached in communities at the extremes of environmental gradients. Analogous to the mid-domain effect in biogeography, decreasing CWV values in extreme environments can then represent the influence of regional trait range limits rather than stronger filtering in the local environment. We name this effect the “Trait-Gradient Boundary Effect” (TGBE). First, we use a community assembly framework to build simulated communities along a gradient from a species pool and environmental filtering with either constant or varying intensity while accounting for immigration processes. We demonstrate the significant influence of TGBE, in parallel to environmental filtering, on CWM and CWV at the extremes of the environmental gradient. We provide a statistical tool based on Approximate Bayesian Computation to decipher the respective influence of local environmental filtering and regional trait range limits. Second, as a case study, we reanalyze the functional composition of alpine plant communities distributed along a gradient of snow cover duration. We show that leaf trait convergence found in communities at the extremes of the gradient reflect an influence of trait range limits rather than stronger environmental filtering. These findings challenge correlative trait-environment relationships and call for more explicitly identifying the mechanisms responsible of trait convergence/divergence along environmental gradients.
Preformed Chromatin Topology Assists Transcriptional Robustness ofShhduring Limb Development
Authors: Paliou Christina , Guckelberger Philine , Schöpflin Robert , Heinrich Verena , Esposito Andrea , Chiariello Andrea M. , Bianco Simona , Annunziatella Carlo , Helmuth Johannes , Haas Stefan , Jerković Ivana , Brieske Norbert , Wittler Lars , Timmermann Bernd , Nicodemi Mario , Vingron Martin , Mundlos Stefan , Andrey Guillaume 
Published: January 2019

AbstractLong-range gene regulation involves physical proximity between enhancers and promoters to generate precise patterns of gene expression in space and time. However, in some cases proximity coincides with gene activation, whereas in others preformed topologies already exist before activation. In this study, we investigate the preformed configuration underlying the regulation of theShhgene by its unique limb enhancer, theZRS, in vivoduring mouse development. Abrogating the constitutive transcription covering theZRSregion led to a shift within theShh-ZRScontacts and a moderate reduction inShhtranscription. Deletion of the CTCF binding sites around theZRSresulted in a loss of theShh-ZRSpreformed interaction and a 50% decrease inShhexpression but no phenotype, suggesting an additional, CTCF-independent mechanism of promoter-enhancer communication. This residual activity, however, was diminished by combining the loss of CTCF binding with a hypomorphic ZRS allele resulting in severeShhloss-of-function and digit agenesis. Our results indicate that the preformed chromatin structure of theShhlocus is sustained by multiple components and acts to reinforce enhancer-promoter communication for robust transcription.
Temporal changes in species composition affect a ubiquitous species’ views of patch quality
Authors: Bledsoe Ellen K. , Ernest S. K. Morgan 
Published: January 2019

AbstractMetacommunity theory, particularly the patch dynamics archetype, suggests that an organism’s perspective of patch quality can depend solely on the local competitive environment. Across landscapes, however, shifts in species composition often co-occur with shifts in habitat, making it difficult to disentangle the role of competitors and environment on assessments of patch quality. Using 26 years of rodent community time-series data, we show that perception of patch quality by a small, ubiquitous granivore (Chaetodipus penicillatus) shifted with both spatial and temporal changes in species composition. In the mid-1990s,C. baileyi, a novel competitor, colonized and the study site.C. penicillatuspatch preference shifted with increasing abundance ofC. baileyi, including corresponding changes in estimated survival, probability of movement between patches, and the arrival of new individuals in patches. Changes in energy use on patches due to the establishment ofC. baileyipoint to a potential mechanism for the differences in patch quality perceived byC. penicillatus. These results demonstrate that experimental time-series data can be used to examine how changes in species composition and, specifically, changes in the competitive landscape, can affect perception of patch quality and patch preference.
Semi-blind sparse affine spectral unmixing of autofluorescence-contaminated micrographs
Authors: Rossetti Blair J. , Wilbert Steven A. , Welch Jessica L. Mark , Borisy Gary G. , Nagy James G. 
Published: January 2019

AbstractSpectral unmixing methods attempt to determine the concentrations of different fluorophores present at each pixel location in an image by analyzing a set of measured emission spectra. Unmixing algorithms have shown great promise for applications where samples contain many fluorescent labels; however, existing methods perform poorly when confronted with autofluorescence-contaminated images. We propose an unmixing algorithm designed to separate fluorophores with overlapping emission spectra from contamination by autofluorescence and background fluorescence. First, we formally define a generalization of the linear mixing model, called the affine mixture model (AMM), that specifically accounts for background fluorescence. Second, we use the AMM to derive an affine nonnegative matrix factorization method for estimating endmember spectra from reference images. Lastly, we propose a semi-blind sparse affine spectral unmixing (SSASU) algorithm that uses knowledge of the estimated endmembers to learn the autofluorescence and background fluorescence spectra on a per-image basis. When unmixing real-world spectral images contaminated by autofluorescence, SSASU was shown to have a similar reconstruction error but greatly improved proportion indeterminacy as compared to existing methods. The source code used for this paper was written in Julia and is available with the test data at https://github.com/brossetti/ssasu.
Identification of sample mix-ups and mixtures in microbiome data in Diversity Outbred mice
Authors: Lobo Alexandra K. , Traeger Lindsay L. , Keller Mark P. , Attie Alan D. , Rey Federico E. , Broman Karl W. 
Published: January 2019

AbstractIn a Diversity Outbred mouse project with genotype data on 500 mice, including 297 with microbiome data, we identified three sets of sample mix-ups (two pairs and one trio) as well as at least 15 microbiome samples that appear to be mixtures of pairs of mice. The microbiome data consisted of shotgun sequencing reads from fecal DNA, used to characterize the gut microbial communities present in these mice. These sequence reads included sufficient reads derived from the host mouse to identify the individual. A number of microbiome samples appeared to contain a mixture of DNA from two mice. We describe a method for identifying sample mix-ups in such microbiome data, as well as a method for evaluating sample mixtures in this context.
Mycobacterium abscessus virulence traits unraveled by transcriptomic profiling in amoeba and macrophages
Authors: Dubois Violaine , Pawlik Alexandre , Bories Anouchka , Moigne Vincent Le , Sismeiro Odile , Legendre Rachel , Varet Hugo , Rodriguez Pilar , Gaillard Jean-Louis , Coppée Jean-Yves , Brosch Roland , Herrmann Jean-Louis , Girard-Misguich Fabienne 
Published: January 2019

AbstractFree-living amoebae might represent an evolutionary niche. In order to get more insights into the potential amoebal training ground forMycobacterium abscessus, we characterized its full transcriptome in amoeba (Ac) and macrophages (Mφ), as well as theMycobacterium chelonaeintra-Ac transcriptome for comparison. Up-regulated genes in Ac allowedM. abscessusto resist environmental stress and induce defense mechanisms, as well as showing switch from carbohydrate carbon sources to fatty acid metabolism. Eleven genes implicated in the adaptation to intracellular stress, were mutated, with all but one confirmed to be involved inM. abscessusintra-Mφ survival. Cloning two of these genes inM. chelonaeincreased its intra-Mφ survival. One mutant was particularly attenuated in Mφ that corresponded to the deletion of an Eis N-acetyl transferase protein (MAB_4532c). Taken together,M. abscessustranscriptomes revealed the intracellular lifestyle of the mycobacteria, with Ac largely contributing to the enhancement ofM. abscessusintra-Mφ survival.