bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional randomness despite high taxonomic turnover across an elevational gradient in a global biodiversity hotspot: A case study of hawkmoths and birds
Authors: Mungee Mansi , Athreya Ramana 
Published: December 2019

AbstractAimWe examined the patterns and processes of taxonomic and functional dissimilarities for two disparate organismal groups (ectothermic hawkmoths and endothermic birds) across a broad tropical elevational gradient.LocationEaglenest Wildlife Sanctuary (northeast India), eastern Himalayan global biodiversity hotspot.Taxon4,731 hawkmoths; 15,387 birdsMethodsTurnover and nestedness components for taxonomic and functional dissimilarities were obtained using the methods developed by Baselga (2013) and Leprieur et al., 2012. We used Generalized Dissimilarity Modeling (GDM) with geographic distance, contemporary and historic climatic variables to assess the relative importance of dispersal and environmental processes in determining the beta diversity. Functional redundancy (FRed) was calculated for both organismal groups using the Simpson’s diversity indices. Null modeling was used to determine randomness in species and trait distributions.ResultsTurnover dominated taxonomic and functional dissimilarities, however the contribution of nestedness was considerably higher to the latter. Overall, the rate of dissimilarity with distance, for both facets of diversity, was significantly higher for birds, with stronger contributions of geographic distance and historic climate; whereas the hawkmoth dissimilarities were strongly correlated with only contemporary climate. Taxonomic dissimilarities deviated significantly from null, whereas functional dissimilarities exhibited high redundancy and randomness.Main ConclusionsOverall, our results suggest that while the drivers of beta-diversity exhibit idiosyncrasy and taxon-specificity; for a given taxa, they are consistent across the two facets of dissimilarity. More importantly, regardless of the principal predictor, the net result was that of high taxonomic turnover, which is de-coupled to a high degree from functional turnover in these tropical ecosystems. The large redundancy in trait values, despite high species turnover, indicates functional resilience of these tropical communities. The consistency of this pattern, across two disparate organismal groups, is suggestive of a key mechanism in which tropical communities may retain functionality of ecosystems in a changing environment.
Disentangling the contribution of each descriptive characteristic of every single mutation to its functional effects
Authors: Sruthi C. K. , Prakash Meher K. 
Published: December 2019

AbstractMutational effects predictions continue to improve in accuracy as advanced artificial intelligence (AI) algorithms are trained on exhaustive experimental data. The next natural questions to ask are if it is now possible to gain insights into which attribute of the mutation contributes how much to the mutational effects, and if one can develop universal rules for mapping the descriptors to mutational effects. In this work, we mainly address the former aspect using a framework of interpretable AI. Relations between the physico-chemical descriptors and their contributions to the mutational effects are extracted by analyzing the data on 29,832 variants from 8 systematic deep-mutational scan studies. It is found that the intuitive dependences of fitness and solubility on the distance of the amino acid from active site could be extracted and quantified. The dependence of the mutational effect contributions on the number of contacts an amino acid has or the BLOSUM score descriptor of the change showed universal trends. Our attempts in the present work to explain the quantitative differences in the dependence on conservation and SASA across proteins were not successful. The work nevertheless brings transparency into the predictions, development of rules, and will hopefully lead to uncovering the universalities among these rules.
Transposable element landscape inDrosophilapopulations selected for longevity
Authors: Fabian Daniel K. , Dönertaş Handan Melike , Fuentealba Matías , Partridge Linda , Thornton Janet M. 
Published: December 2019

ABSTRACTTransposable elements (TEs) inflict numerous negative effects on health and fitness as they replicate by integrating into new regions of the host genome. Even though organisms employ powerful mechanisms to demobilize TEs, transposons gradually lose repression during aging. The rising TE activity causes genomic instability and was implicated in age-dependent neurodegenerative diseases, inflammation and the determination of lifespan. It is therefore conceivable that long-lived individuals have improved TE silencing mechanisms resulting in reduced TE expression relative to their shorter-lived counterparts and fewer genomic insertions. Here, we test this hypothesis by performing the first genome-wide analysis of TE insertions and expression in populations ofDrosophila melanogasterselected for longevity through late-life reproduction for 50-170 generations from four independent studies. Contrary to our expectation, TE families were generally more abundant in long-lived populations compared to non-selected controls. Although simulations showed that this was not expected under neutrality, we found little evidence for selection driving TE abundance differences. Additional RNA-seq analysis revealed a tendency for reducing TE expression in selected populations, which might be more important for lifespan than regulating genomic insertions. We further find limited evidence of parallel selection on genes related to TE regulation and transposition. However, telomeric TEs were genomically and transcriptionally more abundant in long-lived flies, suggesting improved telomere maintenance as a promising TE-mediated mechanism for prolonging lifespan. Our results provide a novel viewpoint indicating that reproduction at old age increases the opportunity of TEs to be passed on to the next generation with little impact on longevity.
RADAR: Differential analysis of MeRIP-seq data with a random effect model
Authors: Zhang Zijie , Zhan Qi , Eckert Mark , Zhu Allen , Chryplewicz Agnieszka , De Jesus Dario F , Ren Decheng , Kulkarni Rohit N , Lengyel Ernst , He Chuan , Chen Mengjie 
Published: December 2019

AbstractEpitranscriptome profiling using MeRIP-seq is a powerful technique for in vivo functional studies of reversible RNA modifications. We develop RADAR, a comprehensive analytical tool for detecting differentially methylated loci in MeRIP-seq data. RADAR enables accurate identification of altered methylation sites by accommodating variability of pre-immunoprecipitation expression level and post-immunoprecipitation count using different strategies. In addition, it is compatible with complex study design when covariates need to be incorporated in the analysis. Through simulation and real datasets analyses, we show that RADAR leads to more accurate and reproducible differential methylation analysis results than alternatives, which is available at https://github.com/scottzijiezhang/RADAR.
Evolutionarily ancient BAH-PHD protein mediates Polycomb silencing
Authors: Wiles Elizabeth T. , McNaught Kevin J. , De Silva Saumya M. , Kaur Gurmeet , Selker Jeanne M. , Ormsby Tereza , Aravind L. , Musselman Catherine A. , Selker Eric U. 
Published: December 2019

AbstractMethylation of histone H3 lysine 27 (H3K27) is widely recognized as a transcriptionally repressive chromatin modification but the mechanism of repression remains unclear. We devised and implemented a forward genetic scheme to identify factors required for H3K27 methylation-mediated silencing in the filamentous fungus Neurospora crassa and identified a bromo-adjacent homology (BAH)-plant homeodomain (PHD)-containing protein, EPR-1 (Effector of Polycomb Repression 1; NCU07505). EPR-1 associates with H3K27 methylation in vivo and in vitro, and loss of EPR-1 de-represses H3K27-methylated genes without loss of H3K27 methylation. EPR-1 is not fungal-specific; orthologs of EPR-1 are present in a diverse array of eukaryotic lineages, suggesting an ancestral EPR-1 was a component of a primitive Polycomb repression pathway.SignificancePolycomb group (PcG) proteins are employed by a wide variety of eukaryotes for the maintenance of gene repression. Polycomb repressive complex 2 (PRC2), a multimeric complex of PcG proteins, catalyzes the methylation of histone H3 lysine 27 (H3K27). In the filamentous fungus, Neurospora crassa, H3K27 methylation represses scores of genes, despite the absence of canonical H3K27 methylation effectors that are present in plants and animals. We report the identification and characterization of an H3K27 methylation effector, EPR-1, in N. crassa and demonstrate its widespread presence and early eukaryotic origins with phylogenetic analyses. These findings indicate that an ancient EPR-1 may have been part of a nascent Polycomb repression system in eukaryotes.
Climate change and local host availability drive the northern range boundary in the rapid northward expansion of the eastern giant swallowtail butterfly
Authors: Wilson J. Keaton , Casajus Nicolas , Hutchinson Rebecca A. , McFarland Kent P. , Kerr Jeremy T. , Berteaux Dominique , Larrivée Maxim , Prudic Kathleen L. 
Published: December 2019

ABSTRACTAimsSpecies distributions result from both biotic and abiotic interactions across large spatial scales. The interplay of these interactions as climate changes quickly has been understudied, particularly in herbivorous insects. Here, we investigate the relative impacts these influences on the putative northern range expansion of the giant swallowtail butterfly in North America.LocationNorth America.Time period1959-2018.Major taxa studiedEastern Giant swallowtail,Papilio cresphontes(Lepidoptera: Papilionidae); common hop tree,Ptelea trifoliata; common prickly ash,Zanthoxylum americanum; southern prickly ash,Zanthoxylum clava-herculis(Saphidales: Rutaceae).MethodsWe used data from museum collections and citizen science repositories to generate species distribution models. Distribution models were built for each species over two time periods (T1 = 1959-1999; T2 = 2000-2018).ResultsModels forP. cresphontesand associated host plants had high predictive accuracy on spatially-explicit test data (AUC 0.810-0.996). Occurrence data align with model outputs, providing strong evidence for a northward range expansion in the last 19 years (T2) byP. cresphontes. Host plants have shifted in more complex ways, and result in a change in suitable habitat forP. cresphontesin its historic range.P. cresphonteshas a northern range which now closely aligns with its most northern host plant - continued expansion northward is unlikely, and historic northern range limits were likely determined by abiotic, not biotic, factors.Main conclusionsBiotic and abiotic factors have driven the rapid northern range expansion in the giant swallowtail butterfly across North America in the last 20 years. A number of bioclimatic variables are correlated with this expansion, notably an increase in mean annual temperature and minimum winter temperature. We predict a slowing of northward range expansion in the next 20-50 years as butterflies are now limited by the range of host plants, rather than abiotic factors.
Deviant cortical sulcation related to schizophrenia, but not cognitive deficits, likely predate brain development in the second trimester
Authors: MacKinley ML. , Sabesan P. , Palaniyappan L. 
Published: December 2019

ObjectivesAberrant cortical development, inferred from cortical folding measures, is linked to the risk of schizophrenia. Cortical folds develop in a time-locked fashion during fetal growth. We leveraged this temporal specificity of sulcation to investigate the approximate timing of the prenatal insult linked to schizophrenia as well as the cognitive impairment seen in this illness.MethodsAnatomical T1 MRI scans from a publicly available dataset of 68 patients with schizophrenia and 72 controls were used to evaluate the sulcal depth. 5 major primary sulci that are invariable, representing lobar development (calcarine sulcus, superior temporal sulcus, superior frontal sulcus, intraparietal sulcus and inferior frontal sulcus) with formation representing distinct developmental periods were chosen. Sulcal depth was measured using BrainVISA software.ResultsA repeated measure Analysis of Variance with 5 sulci and 2 hemispheres as within-subject factors and gender, age and intracranial volume as covariates revealed a significant effect of diagnosis (F[1,134]=14.8, p=0.0002). Control subjects had had deeper superior temporal (left t=3.2, p=0.002; right t=2.8, p=0.006), right inferior frontal (t=2.7, p=0.007) and left calcarine (t=2.2, p=0.03) sulci. A deeper superior frontal sulcus predicted better overall cognitive scores (F[1,54]=8.7, p=0.005) among patients.ConclusionOur results suggest that the gestational cortical disruption underlying schizophrenia is likely to predate, if not, coincide with the appearance of calcarine sulcus (early 2nd trimester) and affects frontal, temporal and occipital lobes. Nevertheless, the burden of cognitive deficits may relate specifically to aberrant superior frontal development occurring in late 2nd trimester.
Perinatal selective serotonin reuptake inhibitor exposure and behavioral outcomes: a systematic review and meta-analyses of animal studies
Authors: Ramsteijn A.S. , Van de Wijer L. , Rando J. , van Luijk J. , Homberg J.R. , Olivier J.D.A. 
Published: December 2019

AbstractIn the Western world, 2-5% of pregnant women use selective serotonin reuptake inhibitor (SSRI) antidepressants. There is no consensus on the potential long-term neurodevelopmental outcomes of early SSRI exposure. Our aim was to determine whether there is an overall effect of perinatal SSRI exposure in animals on a spectrum of behavioral domains. After a comprehensive database search in PubMed, PsycINFO, and Web of Science, we included 99 publications. We performed nine meta-analyses and two qualitative syntheses corresponding to different behavioral categories, aggregating data from thousands of animals. We found evidence for reduced activity and exploration behavior (standardized mean difference (SMD) −0.28 [-0.38, −0.18]), more passive stress coping (SMD −0.37 [-0.52, −0.23]), and less efficient sensory processing (SMD −0.37 [-0.69, −0.06]) in SSRI-versus vehicle-exposed animals. No differences were found for anxiety (p=0.06), social behavior, learning and memory, ingestive- and reward behavior, motoric behavior, or reflex and pain sensitivity. Exposure in the period equivalent to the human third trimester was associated with the strongest effects.HighlightsPerinatal SSRI exposure in rodents alters outcomes in three behavioral domains.It leads to reduced activity, passive stress coping, and weaker sensory processing.Females are understudied but seem to be less vulnerable than males.Early postnatal exposure in rodents leads to the largest effects on behavior.This is equivalent to the third trimester of pregnancy in humans.
Metrics for conservation success: using the ‘Bird-Friendliness Index’ to evaluate grassland and aridland bird community resilience across the Northern Great Plains ecosystem
Authors: Michel Nicole L. , Burkhalter Curtis , Wilsey Chad B. , Holloran Matt , Holloran Alison , Langham Gary M. 
Published: December 2019

AbstractAimEvaluating conservation effectiveness is essential to protect at-risk species and to maximize the limited resources available to land managers. Over 60% of North American grassland and aridlands have been lost since the 1800s. Birds in these habitats are among the most imperiled in North America, yet most remaining habitats are unprotected. Despite the need to measure impact, conservation efforts on private and working lands are rarely evaluated, due in part to limited availability of suitable methods.LocationNorthern Great PlainsMethodsWe developed a novel metric to evaluate grassland and aridland bird community response to habitat management practices, the Bird-Friendliness Index (BFI), consisting of density estimates of grassland and aridland birds weighted by conservation need and a functional diversity metric to incorporate resiliency. We used the BFI to inform three assessments: 1) a spatial prioritization to identify ecologically significant areas for grassland and aridland birds, 2) estimation of temporal trends in grassland and aridland bird community resilience, and 3) evaluation of the effects of land management practices on grassland and aridland bird communities.ResultsThe most resilient bird communities were found in the Prairie Potholes region of Alberta, Saskatchewan, northern Montana, and North Dakota, and the lowest BFI values in the southern and western regions of the Northern Great Plains. BFI values varied little over time on average, but trends varied regionally, largely in response to interannual relative variability in grassland and aridland bird densities.Main conclusionsBFI values increased in response to simulated habitat management, suggesting that practices recommended for use in bird-friendly grassland habitat management plans will increase the abundance and resilience of the grassland and aridland bird community, and will be detected using the BFI. The BFI is a tool by which conservationists and managers can carry out accountable conservation now and into the future.
Phagocytic glia are obligatory intermediates in transmission of mutant huntingtin aggregates across neuronal synapses
Authors: Donnelly Kirby M. , DeLorenzo Olivia R. , Zaya Aprem D.A. , Pisano Gabrielle E. , Thu Wint M. , Luo Liqun , Kopito Ron R. , Panning Pearce Margaret M. 
Published: December 2019

ABSTRACTEmerging evidence supports the hypothesis that pathogenic protein aggregates associated with neurodegenerative diseases spread from cell to cell through the brain in a manner akin to infectious prions. Here, we show that mutant huntingtin (mHtt) aggregates associated with Huntington disease transfer anterogradely from presynaptic to postsynaptic neurons in the adult Drosophila olfactory system. Trans-synaptic transmission of mHtt aggregates is inversely correlated with neuronal activity and blocked by inhibiting caspases in presynaptic neurons, implicating synaptic dysfunction and cell death in aggregate spreading. Remarkably, mHtt aggregate transmission across synapses requires the glial scavenger receptor Draper and involves a transient visit to the glial cytoplasm, indicating that phagocytic glia act as obligatory intermediates in aggregate spreading between synaptically-connected neurons. These findings expand our understanding of phagocytic glia as double-edged players in neurodegeneration—by clearing neurotoxic protein aggregates, but also providing an opportunity for prion-like seeds to evade phagolysosomal degradation and propagate further in the brain.
Baseline characteristics and long‐term outcomes of eosinophilic fasciitis in 89 patients seen at a single center over 20 years
Authors: Mango Robert L. , Bugdayli Kubra , Crowson Cynthia S. , Drage Lisa A. , Wetter David A. , Lehman Julia S. , Peters Margot S. , Davis Mark D. , Chowdhary Vaidehi R. 
Published: December 2019

AbstractAimEosinophilic fasciitis (EF) is a rare, fibrosing disorder of skin and subcutaneous tissue. This study was undertaken to describe its clinical and laboratory features and identify prognostic factors associated with outcome.MethodsWe conducted a retrospective review of all EF patients evaluated at our institution from 1 January1997 to 30 December 2016. Kaplan‐Meier methods were used to determine treatment response rates over time. Potential associations between baseline characteristics and complete response were examined using Cox models adjusted for age and sex. Time‐dependent covariates were used to examine treatment effects.ResultsWe identified 89 EF patients, with a female‐to‐male ratio of 1:1. Clinical features included groove sign in 26 (29%), peau d'orange/dimpling in 22 (25%), inflammatory arthritis in 9 (10%) and muscle weakness in 9 (10%). Aldolase was elevated in 11/36 (31%). Complete response rate was 60% (95% confidence interval [CI]: 35‐75) at 3 years. Diagnostic delay was inversely associated with treatment response (hazards ratio: 0.84 per 1 month increase; 95% CI: 0.73‐0.98). No baseline characteristics correlated with treatment response, but a trend toward positive association of elevated aldolase, hypergammaglobulinemia and presence of hematologic disorders was noted. Methotrexate was the most commonly used immunosuppressant in 79%, hydroxychloroquine in 45%, mycophenolate mofetil in 18% and azathioprine in 8%. No single immunosuppressant agent was associated with a superior response during treatment.ConclusionsEF is characterized by relatively high response rates. Consensus diagnostic criteria, standardized management algorithms, and large prospective multi‐center cohorts are needed to develop an evidence‐directed approach to this challenging condition.
Blunt Traumatic Aortic Injury in the Pan‐scan Era
Authors: Yu Louis , Baumann Brigitte M. , Raja Ali S. , Mower William R. , Langdorf Mark I. , Medak Anthony J. , Anglin Deirdre R. , Hendey Gregory W. , Nishijima Daniel , Rodriguez Robert M. 
Published: December 2019

AbstractBackgroundIn the era of frequent head‐to‐pelvis computed tomography (CT) for adult blunt trauma evaluation, we sought to update teachings regarding aortic injury by determining 1) the incidence of aortic injury; 2) the proportion of patients with isolated aortic injury (without other concomitant thoracic injury); 3) the clinical implications of aortic injury (hospital mortality, length of stay [LOS], and rate of surgical interventions); and 4) the screening value of traditional risk factors/markers (such as high‐energy mechanism and widened mediastinum on chest x‐ray [CXR]) for aortic injury, compared to newer criteria from the recently developed NEXUS Chest CT decision instrument (DI).MethodsWe conducted a preplanned analysis of patients prospectively enrolled in the NEXUS Chest studies at 10 Level I trauma centers with the following inclusion criteria: age > 14 years, blunt trauma within 6 hours of ED presentation, and receiving chest imaging during ED trauma evaluation.ResultsOf 24,010 enrolled subjects, 42 (0.17%, 95% confidence interval [CI] = 0.13% to 0.24%) had aortic injury. Most patients (79%, 95% CI = 64% to 88%) had an associated thoracic injury, with rib fractures, pneumothorax/hemothorax, and pulmonary contusion occurring most frequently. Compared to patients without aortic injury this cohort had similar mortality (9.5%, 95% CI = 3.8% to 22.1% vs. 5.8%, 95% CI = 5.4% to 6.3%), longer median hospital LOS (11 days vs. 3 days, p < 0.01), and higher median Injury Severity Score (29 vs. 5, p < 0.001). High‐energy mechanism and widened mediastinum on CXR had low sensitivity for aortic injury (76% [95% CI = 62% to 87%] and 33% [95% CI = 21% to 49%], respectively), compared to the NEXUS Chest CT DI (sensitivity 100% [95% CI = 92% to 100%]).ConclusionsAortic injury is rare in adult ED blunt trauma patients who survive to receive imaging. Most ED aortic injury patients have associated thoracic injuries and survive to hospital discharge. Widened mediastinum on CXR and high‐energy mechanism have relatively low screening sensitivity for aortic injury, but the NEXUS Chest DI detected all cases.