bluuebunny/crossref_metadata_2025_split huggingface dataset:
OCD symptom severity and comorbid psychiatric diagnoses in a Swedish genetic epidemiological obsessive-compulsive disorder cohort
Authors: Mahjani Behrang , Mahjani Christina Gustavsson , Reichenberg Abraham , Sandin Sven , Hultman Christina M. , Buxbaum Joseph D. , Grice Dorothy E. 
Published: July 2021

AbstractBackgroundWe have established an epidemiological obsessive-compulsive disorder (OCD) cohort in Sweden. Individuals contributed DNA for genotyping and sequencing and also completed a Swedish translation of the Obsessive-Compulsive Inventory-Revised (OCI-R), a self-report questionnaire for assessing the severity and type of symptoms of OCD. This study made use of the OCI-R data to examine the severity and symptom dimensions of OCD as well as comorbidity with other psychiatric disorders.MethodsOCI-R data for 1,134 individuals were available for this study, 1,010 diagnosed with OCD, and 124 diagnosed with chronic tic disorders without OCD used as a comparison group. We first evaluated the psychometric properties of the Swedish translation of the OCI-R. Then, we linked data from the Swedish national registries to access and analyze psychiatric comorbidities of OCD.ResultsThe Swedish translation of OCI-R demonstrated internal consistency (Cronbach’s α = 0.9) and clear agreement with the OCI-R six-factor model. The mean total OCI-R score for females was significantly higher than for males. The most comorbid psychiatric condition to OCD were anxiety disorders (13.6%) and major depression (12%). We observed that individuals with OCD frequently had additional comorbid psychiatric disorders and that the severity of OCD was significantly higher in individuals with at least one additional psychiatric comorbidity compared to individuals with no psychiatric comorbidity.ConclusionWe showed that the Swedish translation of the OCI-R has appropriate psychometric properties. Using an epidemiological framework, we were able to assess the severity and symptom dimensions of OCD and comorbidity with other psychiatric disorders.
The consequences of differential origin licensing dynamics in distinct chromatin environments
Authors: Mei Liu , Kedziora Katarzyna M. , Song Eun-Ah , Purvis Jeremy E. , Cook Jeanette Gowen 
Published: July 2021

ABSTRACTMCM complexes are loaded onto chromosomes to license DNA replication origins in G1 phase of the cell cycle, but it is not yet known how mammalian MCM complexes are adequately distributed to both euchromatin and heterochromatin. To address this question, we combined time-lapse live-cell imaging with fixed cell immunofluorescence imaging of single human cells to quantify the relative rates of MCM loading in heterochromatin and euchromatin at different times within G1. We report here that MCM loading in euchromatin is faster than in heterochromatin in very early G1, but surprisingly, heterochromatin loading accelerates relative to euchromatin loading in middle and late G1. These different loading dynamics require ORCA-dependent differences in ORC distribution during G1. A consequence of heterochromatin origin licensing dynamics is that cells experiencing a truncated G1 phase from premature cyclin E expression enter S phase with under-licensed heterochromatin, and DNA damage accumulates preferentially in heterochromatin in the subsequent S/G2 phase. Thus G1 length is critical for sufficient MCM loading, particularly in heterochromatin, to ensure complete genome duplication and to maintain genome stability.
Prediction of antigen-responding VHH antibodies by tracking evolution of antibody along time course of immunization
Authors: Matsuda Tomonari , Akazawa-Ogawa Yoko , Komaba Lilian-Kaede , Kiyose Norihiko , Miyazaki Nobuo , Mizuguchi Yusaku , Fukuta Tetsuo , Ito Yuji , Hagihara Yoshihisa 
Published: July 2021

AbstractAntibody maturation is the central function of the adaptive immune response. This process is driven by the repetitive selection of mutations that increase the affinity toward antigens. We hypothesized that precise observation of this process by high-throughput sequencing along time course of immunization will enable us to predict the antibodies reacting to the immunized antigen without any additionalin vitroscreening. An alpaca was immunized by IgG fragments using multiple antigen injections and antibody repertoire development was traced via high-throughput sequencing periodically for months. The sequences were processed into clusters and the antibodies in the 16 most abundant clusters were generated to determine whether the clusters included antigen-binding antibodies. The sequences of most antigen-responsive clusters resembled those of germline cells in the early stages. These sequences were observed to accumulate significant mutations and also showed continuous sequence turnover throughout the experimental period. The foregoing characteristics gave us 75% successful prediction of clusters composed of antigen-responding VHHs against IgG fragment. In addition, the prediction method was applied to the data from other alpaca immunized by epidermal growth factor receptor and 77% successful prediction confirmed the generality of the prediction method. Superior to previous studies, we identified the immune responsive but very rare clusters or sequences from the immunized alpaca without any empirical screening data.Significance StatementWe have developed a method for selecting VHH antibody sequences that react to antigens withoutin vitroscreening by performing a large-scale sequence analysis of VHH along the immunization time course, clustering the sequences, and tracking the evolution of the sequences in the clusters. This method enables the identification of antibodies with low frequencies of occurrence, which has been difficult with existingin silicoantibody identification methods.
Meta-analysis shows both congruence and complementarity of DNA metabarcoding to traditional methods for biological community assessment
Authors: Keck François , Blackman Rosetta C. , Bossart Raphael , Brantschen Jeanine , Couton Marjorie , Hürlemann Samuel , Kirschner Dominik , Locher Nadine , Zhang Heng , Altermatt Florian 
Published: July 2021

AbstractAssessment of the diversity and composition of biological communities is central to studies in ecology as well as for ecological monitoring. Historically, individual taxonomic groups have been assessed separately, while for an understanding of the state and change of biodiversity under ongoing global change an integrated assessment would be necessary. DNA metabarcoding has been proposed to be a highly promising approach especially for the assessment of aquatic communities, and numerous studies have investigated the consistency of this new technique with traditional morpho-taxonomic approaches. These individual studies have used DNA metabarcoding to assess diversity and community structure of aquatic organisms both in marine and freshwater systems globally over the last decade. However, a systematic analysis of the comparability and effectiveness of DNA-based community assessment across all of these studies has hitherto been lacking. Here we performed the first meta-analysis of all available studies comparing traditional methods and DNA metabarcoding to measure and assess biological diversity of key aquatic groups, including microorganisms, macroinvertebrates, and fish. Across 215 datasets, we found that DNA metabarcoding provides diversity estimates (richness) that are globally consistent to those obtained using traditional methods. DNA metabarcoding also generates species inventories that are highly congruent with traditional methods for fish. Contrastingly, however, species inventories of microorganisms and macroinvertebrates obtained by DNA metabarcoding showed pronounced differences to traditional methods, missing some taxa but at the same time detecting otherwise overseen diversity. Our results indicate that DNA metabarcoding is efficient to estimate local and regional richness. The method is generally sufficiently advanced to study the composition of fish communities and replace more invasive traditional methods. For smaller organisms, like macroinvertebrates and microorganisms, DNA metabarcoding may continue to give complementary rather than identical estimates compared to traditional approaches. Systematic and comparable data collection will increase the understanding of different aspects of this complementarity, and increase the effectiveness of the method and adequate interpretation of the results.
PhenoExam: an R package and Web application for the examination of phenotypes linked to genes and gene sets
Authors: Cisterna Alejandro , González-Vidal Aurora , Ruiz Daniel , Ortiz Jordi , Gómez-Pascual Alicia , Chen Zhongbo , Nalls Mike , Faghri Faraz , Hardy John , Díez Irene , Maietta Paolo , Álvarez Sara , Ryten Mina , Botía Juan A. 
Published: July 2021

AbstractGene set based phenotype enrichment analysis (detecting phenotypic terms that emerge as significant in a set of genes) can improve the rate of genetic diagnoses amongst other research purposes. To facilitate diverse phenotype analysis, we developed PhenoExam, a freely available R package for tool developers and a web interface for users, which performs: (1) phenotype and disease enrichment analysis on a gene set; (2) measures statistically significant phenotype similarities between gene sets and (3) detects significant differential phenotypes or disease terms across different databases. PhenoExam achieves these tasks by integrating databases or resources such as the HPO, MGD, CRISPRbrain, CTD, ClinGen, CGI, OrphaNET, UniProt, PsyGeNET, and Genomics England Panel App. PhenoExam accepts both human and mouse genes as input. We developed PhenoExam to assist a variety of users, including clinicians, computational biologists and geneticists. It can be used to support the validation of new gene-to-disease discoveries, and in the detection of differential phenotypes between two gene sets (a phenotype linked to one of the gene set but no to the other) that are useful for differential diagnosis and to improve genetic panels. We validated PhenoExam performance through simulations and its application to real cases. We demonstrate that PhenoExam is effective in distinguishing gene sets or Mendelian diseases with very similar phenotypes through projecting the disease-causing genes into their annotation-based phenotypic spaces. We also tested the tool with early onset Parkinson’s disease and dystonia genes, to show phenotype-level similarities but also potentially interesting differences. More specifically, we used PhenoExam to validate computationally predicted new genes potentially associated with epilepsy. Therefore, PhenoExam effectively discovers links between phenotypic terms across annotation databases through effective integration. The R package is available at https://github.com/alexcis95/PhenoExam and the Web tool is accessible at https://snca.atica.um.es/PhenoExamWeb/.
IL-17+ mast cell/T helper cell axis in the early stages of acne
Authors: Eliasse Yoan , Leveque Edouard , Garidou Lucile , Battut Louise , McKenzie Brienne , Nocera Thérèse , Redoules Daniel , Espinosa Eric 
Published: July 2021

ABSTRACTAcne is a multifactorial disease driven by physiological changes occurring during puberty in the pilosebaceous unit (PSU) that leads to sebum overproduction and a dysbiosis involving notably Cutibacterium acnes. These changes in the PSU microenvironment lead to a shift from a homeostatic to an inflammatory state. Indeed, immunohistochemical analyses have revealed that inflammation and lymphocyte infiltration can be detected even in the infraclinical acneic stages, highlighting the importance of the early stages of the disease. In this study, we utilized a robust multi-pronged approach that included flow cytometry, confocal microscopy, and bioinformatics to comprehensively characterize the evolution of the infiltrating and resident immune cell populations in acneic lesions, beginning in the early stages of their development. Using a discovery cohort of 15 patients, we demonstrated that the composition of immune cell infiltrate is highly dynamic in nature, with the relative abundance of different cell types changing significantly as a function of clinical lesion stage. Within the stages examined, we identified a large population of CD69+ CD4+ T cells, several populations of activated antigen presenting cells, and activated mast cells producing IL-17. IL-17+ mast cells were preferentially located in CD4+ T cell rich areas and we showed that activated CD4+ T cells license mast cells to produce IL-17. Our study reveals that mast cells are the main IL-17 producers in the early stage of acne, underlying the importance of targeting the IL-17+ mast cell/T helper cell axis in therapeutic approaches.
Cherry-picking information: humans actively sample evidence to support prior beliefs
Authors: Kaanders Paula , Sepulveda Pradyumna , Folke Tomas , Ortoleva Pietro , De Martino Benedetto 
Published: July 2021

AbstractNo one likes to be wrong. Previous research has shown that participants may underweight information incompatible with previous choices, a phenomenon called confirmation bias. In this paper we argue that a similar bias exists in the way information is actively sought. We investigate how choice influences information gathering using a perceptual choice task and find that participants sample more information from a previously chosen alternative. Furthermore, the higher the confidence in the initial choice, the more biased information sampling becomes. As a consequence, when faced with the possibility of revising an earlier decision, participants are more likely to stick with their original choice, even when incorrect. Critically, we show that agency controls this phenomenon. The effect disappears in a fixed sampling condition where presentation of evidence is controlled by the experimenter, suggesting that the way in which confirmatory evidence is acquired critically impacts the decision process. These results suggest active information acquisition plays a critical role in the propagation of strongly held beliefs over time.
Stable coexistence in plant-pollinator-herbivore communities requires balanced mutualistic vs antagonistic interactions
Authors: Yacine Youssef , Loeuille Nicolas 
Published: July 2021

AbstractEcological communities consist of multiple species interacting in diverse ways. Understanding the mechanisms supporting coexistence requires accounting for such a diversity. Because most works focus either on mutualism or predation, how pollination and herbivory interactively determine the stable coexistence in plant-pollinator-herbivore communities is still poorly understood. Studying the typical three-species module of such communities, we determine the conditions allowing stable coexistence then investigate how its maintenance constrains the relative interaction strengths. Our results show that coexistence is possible if pollination is sufficiently strong relative to herbivory, while its stability is possible if herbivory is sufficiently strong relative to pollination. A balance between pollination and herbivory is therefore required. Interestingly, shared preferences for plant phenotypes, that would favor such balance, have been frequently reported in the empirical literature. The identified ecological trade-off between attracting pollinators and deterring herbivores therefore also appears as an emergent property of stable plant-pollinator-herbivore communities.
Alevin-fry unlocks rapid, accurate, and memory-frugal quantification of single-cell RNA-seq data
Authors: He Dongze , Zakeri Mohsen , Sarkar Hirak , Soneson Charlotte , Srivastava Avi , Patro Rob 
Published: July 2021

The rapid growth of high-throughput single-cell and single-nucleus RNA sequencing technologies has produced a wealth of data over the past few years. The available technologies continue to evolve and experiments continue to increase in both number and scale. The size, volume, and distinctive characteristics of these data necessitate the development of new software and associated computational methods to accurately and efficiently quantify single-cell and single-nucleus RNA-seq data into count matrices that constitute the input to downstream analyses.We introduce the alevin-fry framework for quantifying single-cell and single-nucleus RNA-seq data. Despite being faster and more memory frugal than other accurate and scalable quantification approaches, alevin-fry does not suffer from the false positive expression or memory scalability issues that are exhibited by other lightweight tools. We demonstrate how alevin-fry can be effectively used to quantify single-cell and single-nucleus RNA-seq data, and also how the spliced and unspliced molecule quantification required as input for RNA velocity analyses can be seamlessly extracted from the same pre-processed data used to generate regular gene expression count matrices.
Fin Shape, Asymmetry, and Evolutionary Ecomorphology in Triggerfishes and Filefishes (Superfamily: Balistoidea)
Authors: George Andrew B. , Westneat Mark W. 
Published: July 2021

ABSTRACTTriggerfishes and filefishes exhibit a wide range of fin and body morphologies, inhabit many marine habitats, and feed on a variety of benthic and pelagic organisms. Particular morphologies are predicted to provide functional advantages for swimming behaviors that facilitate life in diverse habitats and feeding guilds. Ecomorphological relationships can, in turn, inform evolutionary patterns of morphological convergence. We quantified morphological diversity of 80 balistoid species using geometric morphometrics and assigned each species a primary habitat and feeding mode. Results revealed strong evidence for evolutionary integration among body and fin shapes as well as widespread convergence of both high and low aspect ratio (AR) dorsal and anal fins, the fins that power steady locomotion in these fishes. Dorsal and anal fins were determined to be moderately to highly asymmetrical in most species. Families exhibited considerable overlap in fin and body shapes, but triggerfishes generally exhibited higher AR and more asymmetrical fins than filefishes. Fin asymmetry was not strongly associated with ecology. Planktivorous and offshore-pelagic species exhibited high AR dorsal and anal fins suitable for high endurance swimming performance, while benthic grazing and structured reef species exhibited convergence on low AR median fins more suitable for facilitating maneuverability.
Global distribution and richness of Armillaria and related species inferred from public databases and amplicon sequencing datasets
Authors: Koch Rachel A. , Herr Joshua R. 
Published: July 2021

ABSTRACTArmillaria is a globally distributed fungal genus most notably recognized as economically important plant pathogens that are found predominantly in forest and agronomic systems. The genus sensu lato has more recently received attention for its role in woody plant decomposition and in mycorrhizal symbiosis with specific plants. Previous phylogenetic analyses suggest that around 50 species are recognized globally. Despite this previous work, no studies have analyzed the global species richness and distribution of the genus using data derived from fungal community sequencing datasets or barcoding initiatives. To assess the global diversity and species richness of Armillaria, we mined publicly available sequencing datasets derived from numerous primer regions for the ribosomal operon, as well ITS sequences deposited on Genbank, and clustered them akin to metabarcoding studies. Our estimates reveal that species richness ranges from 50 to 60 species, depending on whether the ITS1 or ITS2 marker is used. Eastern Asia represents the biogeographic region with the highest species richness. We also assess the overlap of species across geographic regions and propose some hypotheses regarding the drivers of variability in species diversity and richness between different biogeographic regions.
A simplified method for CRISPR-Cas9 engineering of Bacillus subtilis
Authors: Sachla Ankita J. , Alfonso Alexander J. , Helmann John D. 
Published: July 2021

AbstractThe clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 system from Streptococcus pyogenes has been widely deployed as a tool for bacterial strain construction. Conventional CRISPR-Cas9 editing strategies require design and molecular cloning of an appropriate guide RNA (gRNA) to target genome cleavage and a repair template for introduction of the desired site-specific genome modification. Here, we present a streamlined method that leverages the existing collection of nearly 4000 Bacillus subtilis strains (the BKE collection) with individual genes replaced by an integrated erythromycin (erm) resistance cassette. A single plasmid (pAJS23) with a gRNA targeted to erm allows cleavage of the genome at any non-essential gene, and at sites nearby to many essential genes. This plasmid can be engineered to include a repair template, or the repair template can be co-transformed with the plasmid as either a PCR product or genomic DNA. We demonstrate the utility of this system for generating gene replacements, site-specific mutations, modification of intergenic regions, and introduction of gene-reporter fusions. In sum, this strategy bypasses the need for gRNA design and allows the facile transfer of mutations and genetic constructions with no requirement for intermediate cloning steps.ImportanceBacillus subtilis is a well-characterized Gram-positive model organism and a popular platform for biotechnology. Although many different CRISPR-based genome editing strategies have been developed for B. subtilis, they generally involve the design and cloning of a specific gRNA and repair template for each application. By targeting the erm resistance cassette with an anti-erm gRNA, genome-editing can be directed to any of nearly 4000 gene disruptants within the existing BKE collection of strains. Repair templates can be engineered as PCR products, or specific alleles and constructions can be transformed as chromosomal DNA, thereby bypassing the need for plasmid construction. The described method is rapid, free of off-target effects, and facilitates a wide-range of genome manipulations.“Healing is a matter of time, but it is sometimes also a matter of opportunity.” – Hippocrates
Life history mediates the trade-offs among different components of demographic resilience
Authors: Capdevila Pol , Stott Iain , Cant James , Beger Maria , Rowlands Gwilym , Grace Molly , Salguero-Gómez Roberto 
Published: July 2021

Summary paragraphAccelerating rates of biodiversity loss underscore the need to understand how species achieve resilience –their ability to resist and recover from a/biotic disturbances. Yet, the factors determining the resilience of species remain poorly understood, due to disagreements on its definition and the lack of large-scale analyses. Here, we investigate how the life history of 785 natural populations of animals and plants predict their intrinsic ability to be resilient. We show that demographic resilience can be achieved through different combinations of compensation, resistance, and recovery after a disturbance. We demonstrate that these resilience components are highly correlated with life history traits related to the species’ pace of life and reproductive strategy. Species with longer generation times require longer recovery times post-disturbance, while those with greater reproductive capacity have greater resistance and compensation. Our findings highlight the key role of life history traits to understand species resilience, improving our ability to predict how natural populations cope with disturbance regimes.