bluuebunny/crossref_metadata_2025_split huggingface dataset:
Facets of phylodiversity: evolutionary diversification, divergence and survival as conservation targets
Authors: Kling Matthew M. , Mishler Brent D. , Thornhill Andrew H. , Baldwin Bruce G. , Ackerly David D. 
Published: November 2018

Biodiversity is often described as having multiple facets, including species richness, functional diversity and phylogenetic diversity. In this paper, we argue that phylogenetic diversity itself has three distinct facets—lineage diversification, character divergence and survival time—that can be quantified using distinct branch length metrics on an evolutionary tree. Each dimension is related to different processes of macroevolution, has different spatial patterns and is tied to distinct goals for conserving biodiversity and protecting its future resilience and evolutionary potential. We compared the landscapes identified as top conservation priorities by each of these three metrics in a conservation gap analysis for California, a world biodiversity hotspot, using herbarium data on the biogeography and evolutionary relationships of more than 5000 native plant species. Our analysis incorporated a novel continuous metric of current land protection status, fine-scale data on landscape intactness and an optimization algorithm used to identify complementary priority sites containing concentrations of taxa that are evolutionarily unique, vulnerable due to small range size and/or poorly protected across their ranges. Top conservation priorities included pockets of coastal and northern California that ranked highly for all three phylodiversity dimensions and for species richness, as well as sites uniquely identified by each metric whose value may depend on whether properties such as genetic divergence, high net diversification or independent survival experience are most desirable in an Anthropocene flora.This article is part of the theme issue ‘Biological collections for understanding biodiversity in the Anthropocene’.
Using museum specimens to track morphological shifts through climate change
Authors: MacLean Heidi J. , Nielsen Matthew E. , Kingsolver Joel G. , Buckley Lauren B. 
Published: November 2018

Museum specimens offer a largely untapped resource for detecting morphological shifts in response to climate change. However, morphological shifts can be obscured by shifts in phenology or distribution or sampling biases. Additionally, interpreting phenotypic shifts requires distinguishing whether they result from plastic or genetic changes. Previous studies using collections have documented consistent historical size changes, but the limited studies of other morphological traits have often failed to support, or even test, hypotheses. We explore the potential of collections by investigating shifts in the functionally significant coloration of a montane butterfly,Colias meadii,over the past 60 years within three North American geographical regions. We find declines in ventral wing melanism, which correspond to reduced absorption of solar radiation and thus reduced risk of overheating, in two regions. However, contrary to expected responses to climate warming, we find melanism increases in the most thoroughly sampled region. Relationships among temperature, phenology and morphology vary across years and complicate the distinction between plastic and genetic responses. Differences in these relationships may account for the differing morphological shifts among regions. Our findings highlight the promise of using museum specimens to test mechanistic hypotheses for shifts in functional traits, which is essential for deciphering interacting responses to climate change.This article is part of the theme issue ‘Biological collections for understanding biodiversity in the Anthropocene’.
Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking
Authors: Wagner Jeffrey R. , Churas Christopher P. , Liu Shuai , Swift Robert V. , Chiu Michael , Shao Chenghua , Feher Victoria A. , Burley Stephen K. , Gilson Michael K. , Amaro Rommie E. 
Published: November 2018

1SummaryDocking calculations can be used to accelerate drug discovery by providing predictions of the poses of candidate ligands bound to a targeted protein. However, studies in the literature use varied docking methods, and it is not clear which work best, either in general or for specific protein targets. In addition, a complete docking calculation requires components beyond the docking algorithm itself, such as preparation of the protein and ligand for calculations, and it is difficult to isolate which aspects of a method are most in need of improvement. To address such issues, we have developed the Continuous Evaluation of Ligand Protein Predictions (CELPP), a weekly blinded challenge for automated docking workflows. Participants in CELPP create a workflow to predict protein-ligand binding poses, which is then tasked with predicting 10-100 new (never before released) protein-ligand crystal structures each week. CELPP evaluates the accuracy of each workflow’s predictions and posts the scores online. CELPP is a new cyberinfrastructure resource to identify the strengths and weaknesses of current approaches, help map docking problems to the algorithms most likely to overcome them, and illuminate areas of unmet need in structure-guided drug design.
Chronic corticosterone enhancement aggravates alpha-synuclein brain spreading pathology and substantia nigra neurodegeneration in mice
Authors: Burtscher Johannes , Copin Jean-Christophe , Rodrigues João , Thangaraj Senthil K. , Chiki Anass , de Suduiraut Marie-Isabelle Guillot , Sandi Carmen , Lashuel Hilal A. 
Published: November 2018

AbstractChronic stress and associated heightened glucocorticoid levels are risk factors for depression, a common non-motor symptom in Parkinson’s disease (PD). However, how heightened glucocorticoids influence PD neuropathology [alpha-synuclein (α-Syn) containing Lewy pathology and neurodegeneration] and disease progression is unclear. To address this knowledge gap, we investigated the impact of chronic corticosterone administration on α-Syn pathology, neurodegeneration, behavior and mitochondrial function in a mouse model of α-Syn pathology spreading after intracerebral injection of α-Syn preformed fibrils (PFFs). Our results demonstrate that heightened corticosterone aggravates neurodegeneration and α-Syn pathology spreading, intriguingly to specific brain regions, such as the entorhinal cortex. Corticosterone-treatment abolished distinct physiological adaptations after PFF-injection and induced differential physiological and behavioral consequences. Taken together, our work points to elevated glucocorticoids as a risk factor for the development of the neuropathological hallmarks of PD. Strategies aimed at reducing glucocorticoid levels might slow down pathology spreading and disease progression in synucleinopathy.
A Combined Behavioral and Neuroimaging Battery to Test Positive Appraisal Style Theory of Resilience in Longitudinal Studies
Authors: Kampa Miriam , Schick Anita , Yuen Kenneth , Sebastian Alexandra , Chmitorz Andrea , Saase Victor , Wessa Michèle , Tüscher Oliver , Kalisch Raffael 
Published: November 2018

AbstractResilience is the maintenance or rapid recovery of mental health during and after stressor exposure. It is becoming increasingly clear that resilience results from a complex and dynamic process of adaptation to stressors involving the biological, psychological and social levels. Positive appraisal style theory of resilience (PASTOR) claims that the common final pathway to maintained mental health lies in the non-negative (non-catastrophizing, non-pessimistic) appraisal of potential stressors, permitting the organism to fine-tune stress responses to optimal levels, thus avoiding unnecessary stress, inefficient deployment of resources and concomitant deleterious allostatic load effects. Successful adaptation consists in developing or strengthening a positive appraisal style. Another key element of PASTOR is that a positive appraisal style is strongly determined by the efficacy and efficiency of the neural and cognitive processes that underlie positive stressor appraisal. We here present a combined behavioral and functional magnetic resonance imaging (fMRI) battery designed to assess such processes repeatedly in longitudinal settings. The battery includes tests of stress reactivity and recovery, reward sensitivity, safety learning and memory in the context of fear conditioning and extinction, volitional situation-focused reappraisal, volitional self-focused reappraisal, and emotional interference inhibition, along with structural MRI and resting-state MRI scans. A detailed description of the battery methods is provided. The feasibility of the battery was successfully tested in N=55 healthy subjects; group results of the individual tasks largely replicate existing literature.
Acquired interbacterial defense systems protect against interspecies antagonism in the human gut microbiome
Authors: Ross Benjamin D. , Verster Adrian J. , Radey Matthew C. , Schmidtke Danica T. , Pope Christopher E. , Hoffman Lucas R. , Hajjar Adeline M. , Peterson S. Brook , Borenstein Elhanan , Mougous Joseph D. 
Published: November 2018

AbstractThe impact of direct interactions between co-resident microbes on microbiome composition is not well understood. Here we report the occurrence of acquired interbacterial defense (AID) gene clusters in bacterial residents of the human gut microbiome. These clusters encode arrays of immunity genes that protect against type VI secretion toxin-mediated intra- and inter-species bacterial antagonism. Moreover, the clusters reside on mobile elements and we demonstrate that their transfer is sufficient to confer toxin resistance in vitro and in gnotobiotic mice. Finally, we identify and validate the protective capacity of a recombinase-associated AID subtype (rAID-1) present broadly in Bacteroidales genomes. These rAID-1 gene clusters have a structure suggestive of active gene acquisition and include predicted immunity factors of toxins deriving from diverse organisms. Our data suggest that neutralization of contact-dependent interbacterial antagonism via AID systems shapes human gut microbiome ecology.
DNA methylation modules associate with incident cardiovascular disease and cumulative risk factor exposure
Authors: Westerman Kenneth , Sebastiani Paola , Jacques Paul , Liu Simin , DeMeo Dawn , Ordovás José M. 
Published: November 2018

1AbstractBackgroundEpigenome-wide association studies using DNA methylation have the potential to uncover novel biomarkers and mechanisms of cardiovascular disease (CVD) risk. However, the direction of causation for these associations is not always clear, and investigations to-date have generally failed to replicate at the level of individual loci. Here, we undertook module- and region-based DNA methylation analyses of incident CVD in the Women’s Health Initiative (WHI) and Framingham Heart Study Offspring Cohort (FHS) in order to find more robust epigenetic biomarkers for cardiovascular risk.Methods and FindingsWe applied weighted gene correlation network analysis (WGCNA) and the Comb-p algorithm to find methylation modules and regions associated with incident CVD in the WHI dataset. We discovered two modules whose activation correlated with CVD risk and replicated across cohorts. One of these modules was enriched for development-related processes and overlaps strongly with epigenetic aging sites. For the other, we showed preliminary evidence for monocyte-specific effects and statistical links to cumulative exposure to traditional cardiovascular risk factors. Additionally, we found three regions (associated with the genes SLC9A1, SLC1A5, and TNRC6C) whose methylation associates with CVD risk.ConclusionsIn sum, we present several epigenetic associations with incident CVD that reveal disease mechanisms related to development and monocyte biology. Furthermore, we show that epigenetic modules may act as a molecular readout of cumulative cardiovascular risk factor exposure, with implications for the improvement of clinical risk prediction.
Imputed gene associations identify replicable trans-acting genes enriched in transcription pathways and complex traits
Authors: Wheeler Heather E. , Ploch Sally , Barbeira Alvaro N. , Bonazzola Rodrigo , Andaleon Angela , Sishpirani Alireza Fotuhi , Saha Ashis , Battle Alexis , Roy Sushmita , Im Hae Kyung 
Published: November 2018

AbstractRegulation of gene expression is an important mechanism through which genetic variation can affect complex traits. A substantial portion of gene expression variation can be explained by both local (cis) and distal (trans) genetic variation. Much progress has been made in uncovering cis-acting expression quantitative trait loci (cis-eQTL), but trans-eQTL have been more difficult to identify and replicate. Here we take advantage of our ability to predict the cis component of gene expression coupled with gene mapping methods such as PrediXcan to identify high confidence candidate trans-acting genes and their targets. That is, we correlate the cis component of gene expression with observed expression of genes in different chromosomes. Leveraging the shared cis-acting regulation across tissues, we combine the evidence of association across all available GTEx tissues and find 2356 trans-acting/target gene pairs with high mappability scores. Reassuringly, trans-acting genes are enriched in transcription and nucleic acid binding pathways and target genes are enriched in known transcription factor binding sites. Interestingly, trans-acting genes are more significantly associated with selected complex traits and diseases than target or background genes, consistent with percolating trans effects. Our scripts and summary statistics are publicly available for future studies of trans-acting gene regulation.
NDV-3A vaccination protects mice fromCandida albicansbiofilm infection
Authors: Alqarihi Abdullah , Singh Shakti , Edwards John E. , Ibrahim Ashraf S. , Uppuluri Priya 
Published: November 2018

AbstractNDV-3A, a novel fungal vaccine undergoing clinical trials, contains a recombinant version of theCandida albicansrAls3 N-terminus protein (rAls3p-N) in aluminum hydroxide. In a Phase 1b/2a clinical trial, NDV-3A protected women from recurrent vulvovaginal candidiasis. Here, we reveal that active immunization in mice with NDV-3A induces high titers of anti-rAls3p-N antibodies that interfere withC. albicansability to adhere to and invade endothelial cells, and form biofilmin vitro. The anti-rAls3p-N antibodies also protect againstC. albicansbiofilm formation in a central venous catheter mouse model. Finally, anti-rAls3p-N antibodies significantly inhibit yeast dispersal from the hyphal layers of biofilms. Overall these preclinical studies suggest that NDV-3A may serve as an immunotherapeutic strategy for prevention of infections on indwelling medical devices.
Truncated, uncapped mRNA 5’ ends targeted by cytoplasmic recapping cluster at CAGE tags and some transcripts are alternatively spliced
Authors: Berger Mikaela R. , Alvarado Rolando , Kiss Daniel L. 
Published: November 2018

AbstractUntil cytoplasmic recapping was discovered, decapping was thought to irreversibly destine an mRNA to degradation. Contradicting this idea, we readily observe mRNAs targeted by cytoplasmic capping in uncapped, yet stable forms. 5’ RACE shows that nearly all uncapped ends correspond to CAGE tags and that the recapping of ZNF207 mRNA may be restricted to a single splice isoform. A modified RACE approach detected uncapped 5’ RNA ends mapping to 46 mRNAs in dominant negative cytoplasmic capping enzyme expressing and normal cells. 11 of 46 cloned mRNAs also contained splice isoform-limiting sequences. Collectively, these data reinforce earlier work and suggest that alternative splicing may play a role in targeting transcripts for– and/or determining the position of– cytoplasmic capping.
Reduced mitochondrial lipid oxidation leads to fat accumulation in myosteatosis
Authors: Gumucio Jonathan P , Qasawa Austin H , Ferrara Patrick J , Malik Afshan N , Funai Katsuhiko , McDonagh Brian , Mendias Christopher L 
Published: November 2018

AbstractMyosteatosis is the pathological accumulation of lipid that can occur in conjunction with atrophy and fibrosis following skeletal muscle injury. Little is known about the mechanisms by which lipid accumulates in myosteatosis, but many clinical studies have demonstrated the degree of lipid infiltration negatively correlates with muscle function and regeneration. Our objective was to determine the pathological changes that result in lipid accumulation in injured muscle fibers. We used a rat model of rotator cuff injury in this study, as the rotator cuff muscle group is particularly prone to the development of myosteatosis after injury. Muscles were collected from uninjured controls, or 10, 30, or 60 days after injury, and analyzed using a combination of muscle fiber contractility assessments, RNA sequencing, and undirected metabolomics, lipidomics and proteomics, along with bioinformatics techniques, to identify potential pathways and cellular processes that are dysregulated after rotator cuff tear. Bioinformatics analyses indicated that mitochondrial function was likely disrupted after injury. Based on these findings, and given the role that mitochondria play in lipid metabolism, we then performed targeted biochemical and imaging studies and determined that mitochondrial dysfunction and reduced fatty acid oxidation likely leads to the accumulation of lipid in myosteatosis.
The effects of the angiotensin II receptor antagonist losartan on appetitive versus aversive learning
Authors: Pulcu Erdem , Shkreli Lorika , Holst Carolina Guzman , Woud Marcella L. , Craske Michelle G. , Browning Michael , Reinecke Andrea 
Published: November 2018

AbstractExposure therapy is a first-line treatment for anxiety disorders but remains ineffective in a large proportion of patients. A proposed mechanism of exposure involves a form of inhibitory learning where the association between a stimulus and an aversive outcome is suppressed by a new association with an appetitive or neutral outcome. The blood pressure medication losartan augments fear extinction in rodents and might have similar synergistic effects on human exposure therapy, but the exact cognitive mechanisms underlying these effects remain unknown. In this study, we used a reinforcement learning paradigm with compound rewards and punishments to test the prediction that losartan augments learning from appetitive relative to aversive outcomes. Healthy volunteers (N=53) were randomly assigned to single-dose losartan (50mg) versus placebo. Participants then performed a reinforcement learning task which simultaneously probes appetitive and aversive learning. Participant choice behaviour was analysed using both a standard reinforcement learning model and by analysis of choice switching behaviour. Losartan significantly reduced learning rates from aversive events (losses) when participants were first exposed to the novel task environment, while preserving learning from positive outcomes. The same effect was seen in choice switching behaviour. Losartan enhances learning from positive relative to negative events. This effect may represent a computationally defined neurocognitive mechanism by which the drug could enhance the effect of exposure in clinical populations.
MolMeDB: Molecules on Membranes Database
Authors: Juračka Jakub , Šrejber Martin , Melíková Michaela , Bazgier Václav , Berka Karel 
Published: November 2018

AbstractBiological membranes act as barriers or reservoirs for many compounds within the human body. As such, they play an important role in pharmacokinetics and pharmacodynamics of drugs and other molecular species. Until now, most membrane/drug interactions have been inferred from simple partitioning between octanol and water phases. However, the observed variability in membrane composition and among compounds themselves stretches beyond such simplification as there are multiple drug-membrane interactions. Numerous experimental and theoretical approaches are used to determine the molecule-membrane interactions with variable accuracy, but there is no open resource for their critical comparison. For this reason, we have built Molecules on Membranes Database (MolMeDB), which gathers data about over 3600 compound-membrane interactions including partitioning, penetration, and positioning. The data have been collected from scientific articles published in peer-reviewed journals and complemented by inhouse calculations from high-throughput COSMOmic approach to set up a baseline for further comparison. The data in MolMeDB are fully searchable and browsable by means of name, SMILES, membrane, method, or dataset and we offer the collected data openly for further reuse and we are open to further additions. MolMeDB can be a powerful tool that could help researchers better understand the role of membranes and to compare individual approaches used for the study of molecule/membrane interactions.Database URL:http://molmedb.upol.cz.
Prefix-Free Parsing for Building Big BWTs
Authors: Boucher Christina , Gagie Travis , Kuhnle Alan , Langmead Ben , Manzini Giovanni , Mun Taher 
Published: November 2018

AbstractHigh-throughput sequencing technologies have led to explosive growth of genomic databases; one of which will soon reach hundreds of terabytes. For many applications we want to build and store indexes of these databases but constructing such indexes is a challenge. Fortunately, many of these genomic databases are highly-repetitive—a characteristic that can be exploited to ease the computation of the Burrows-Wheeler Transform (BWT), which underlies many popular indexes. In this paper, we introduce a preprocessing algorithm, referred to as prefix-free parsing, that takes a text T as input, and in one-pass generates a dictionary D and a parse P of T with the property that the BWT of T can be constructed from D and P using workspace proportional to their total size and O(|T|)-time. Our experiments show that D and P are significantly smaller than T in practice, and thus, can fit in a reasonable internal memory even when T is very large. In particular, we show that with prefix-free parsing we can build an 131-megabyte run-length compressed FM-index (restricted to support only counting and not locating) for 1000 copies of human chromosome 19 in 2 hours using 21 gigabytes of memory suggesting that we can build a 6.73 gigabyte index for 1000 complete human-genome haplotypes in approximately 102 hours using about 1 terabyte of memory
The Barcode, UMI, Set format and BUStools
Authors: Melsted Páll , Ntranos Vasilis , Pachter Lior 
Published: November 2018

AbstractWe introduce the Barcode-UMI-Set format (BUS) for representing pseudoalignments of reads from single-cell RNA-seq experiments. The format can be used with all single-cell RNA-seq technologies, and we show that BUS files can be efficiently generated. BUStools is a suite of tools for working with BUS files and facilitates rapid quantification and analysis of single-cell RNA-seq data. The BUS format therefore makes possible the development of modular, technology-specific, and robust workflows for single-cell RNA-seq analysis.