bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heterologous SARS-CoV-2 Booster Vaccinations – Preliminary Report
Authors: Atmar Robert L. , Lyke Kirsten E. , Deming Meagan E. , Jackson Lisa A. , Branche Angela R. , El Sahly Hana M. , Rostad Christina A. , Martin Judith M. , Johnston Christine , Rupp Richard E. , Mulligan Mark J. , Brady Rebecca C. , Frenck Robert W. , Bäcker Martín , Kottkamp Angelica C. , Babu Tara M. , Rajakumar Kumaravel , Edupuganti Srilatha , Dobryzynski David , Posavad Christine M. , Archer Janet I. , Crandon Sonja , Nayak Seema U. , Szydlo Daniel , Zemanek Jillian , Islas Clara P. Dominguez , Brown Elizabeth R. , Suthar Mehul S. , McElrath M. Juliana , McDermott Adrian B. , O’Connell Sarah E. , Montefiori David C. , Eaton Amanda , Neuzil Kathleen M. , Stephens David S. , Roberts Paul C. , Beigel John H. ,   the DMID 21-0012 Study Group
Published: October 2021

ABSTRACTBackgroundWhile Coronavirus disease 2019 (Covid-19) vaccines are highly effective, breakthrough infections are occurring. Booster vaccinations have recently received emergency use authorization (EUA) for certain populations but are restricted to homologous mRNA vaccines. We evaluated homologous and heterologous booster vaccination in persons who had received an EUA Covid-19 vaccine regimen.MethodsIn this phase 1/2 open-label clinical trial conducted at ten U.S. sites, adults who received one of three EUA Covid-19 vaccines at least 12 weeks prior to enrollment and had no reported history of SARS-CoV-2 infection received a booster injection with one of three vaccines (Moderna mRNA-1273 100-μg, Janssen Ad26.COV2.S 5×1010 virus particles, or Pfizer-BioNTech BNT162b2 30-μg; nine combinations). The primary outcomes were safety, reactogenicity, and humoral immunogenicity on study days 15 and 29.Results458 individuals were enrolled: 154 received mRNA-1273, 150 received Ad26.CoV2.S, and 153 received BNT162b2 booster vaccines. Reactogenicity was similar to that reported for the primary series. Injection site pain, malaise, headache, and myalgia occurred in more than half the participants. Booster vaccines increased the neutralizing activity against a D614G pseudovirus (4.2-76-fold) and binding antibody titers (4.6-56-fold) for all combinations; homologous boost increased neutralizing antibody titers 4.2-20-fold whereas heterologous boost increased titers 6.2-76-fold. Day 15 neutralizing and binding antibody titers varied by 28.7-fold and 20.9-fold, respectively, across the nine prime-boost combinations.ConclusionHomologous and heterologous booster vaccinations were well-tolerated and immunogenic in adults who completed a primary Covid-19 vaccine regimen at least 12 weeks earlier.(Funded by National Institute of Allergy and Infectious Diseases; Clinical Trials.gov number, NCT04889209)
Chromosome-level assembly of the common vetch reference genome (Vicia sativa)
Authors: Xi Hangwei , Nguyen Vy , Ward Christopher , Liu Zhipeng , Searle Iain R. 
Published: October 2021

AbstractBackgroundVicia sativa L. (Common Vetch, n = 6) is an annual, herbaceous, climbing legume that is distributed in tropical, sub-tropical and temperate climates. Originating in the Fertile Crescent of the Middle East, V. sativa is now widespread and grows in the Mediterranean basin, West, Central and Eastern Asia, North and South America. V. sativa is of economic importance as a forage legume in countries such as Australia, China, and the USA and contributes valuable nitrogen to agricultural rotation cropping systems. To accelerate precision genome breeding and genomics-based selection of this legume, we here present a chromosome-level reference genome sequence for V. sativa.ResultsWe applied a combination of long-read Oxford Nanopore sequencing, short-read Illumina sequencing, and high-throughput chromosome conformation data (CHiCAGO and Hi-C) analysis to construct a chromosome-level genome of V. sativa. The chromosome-level assembly of six pseudo-chromosomes has a total genome length of 1.9 gigabases (Gb) with a median contig length of 684 kb. Benchmarking Universal Single-Copy Orthologs (BUSCO) of the assembly demonstrated a very high completeness of 98 % of the dicotyledonous orthologs. RNA-seq analysis and gene modelling enabled the annotation of 58,415 protein-coding genes.ConclusionsThe high-quality chromosome-level genome assembly of V. sativa will provide novel insights into vetch genome evolution and be a valuable resource for genomic breeding, genetic diversity and for understanding adaption to diverse arid environments.
A dual endosymbiosis drives nutritional adaptation to hematophagy in the invasive tick Hyalomma marginatum
Authors: Buysse Marie , Floriano Anna Maria , Gottlieb Yuval , Nardi Tiago , Comandatore Francesco , Olivieri Emanuela , Giannetto Alessia , Palomar Ana , Makepeace Ben , Bazzocchi Chiara , Cafiso Alessandra , Sassera Davide , Duron Olivier 
Published: October 2021

AbstractMany animals are dependent on microbial partners that provide essential nutrients lacking from their diet. Ticks, whose diet consists exclusively on vertebrate blood, rely on maternally inherited bacterial symbionts to supply B vitamins. While previously studied tick species consistently harbor a single lineage of those nutritional symbionts, we evidence here that the invasive tick Hyalomma marginatum harbors a unique dual-partner nutritional system between an ancestral symbiont, Francisella, and a more recently acquired symbiont, Midichloria. Using metagenomics, we show that Francisella exhibits extensive genome erosion that endangers the nutritional symbiotic interactions: Its genome includes folate and riboflavin biosynthesis pathways but deprived functional biotin biosynthesis on account of massive pseudogenization. Co-symbiosis compensates this deficiency since the Midichloria genome encompasses an intact biotin operon, which was primarily acquired via lateral gene transfer from unrelated intracellular bacteria commonly infecting arthropods. Thus, in H. marginatum, a mosaic of co-evolved symbionts incorporating gene combinations of distant phylogenetic origins emerged to prevent the collapse of an ancestral nutritional symbiosis. Such dual endosymbiosis was never reported in other blood feeders but was recently documented in agricultural pests feeding on plant sap, suggesting that it may be a key mechanism for advanced adaptation of arthropods to specialized diets.
New cycle, same old mistakes? Overlapping vs. discrete generations in long-term recurrent selection
Authors: Labroo Marlee R. , Rutkoski Jessica E. 
Published: October 2021

AbstractBackgroundRecurrent selection is a foundational breeding method for quantitative trait improvement. It typically features rapid breeding cycles that can lead to high rates of genetic gain. In recurrent phenotypic selection, generations do not overlap, which means that breeding candidates are evaluated and considered for selection for only one cycle. With recurrent genomic selection, candidates can be evaluated based on genomic estimated breeding values indefinitely, therefore facilitating overlapping generations. Candidates with true high breeding values that were discarded in one cycle due to underestimation of breeding value could be identified and selected in subsequent cycles. The consequences of allowing generations to overlap in recurrent selection are unknown. We assessed whether maintaining overlapping and discrete generations led to differences in genetic gain for phenotypic, genomic truncation, and genomic optimum contribution recurrent selection by simulation of traits with various heritabilities and genetic architectures across fifty breeding cycles. We also assessed differences of overlapping and discrete generations in a conventional breeding scheme with multiple stages and cohorts.ResultsWith phenotypic selection, overlapping generations led to decreased genetic gain compared to discrete generations due to increased selection error bias. Selected individuals, which were in the upper tail of the distribution of phenotypic values, tended to also have high absolute error relative to their true breeding value compared to the overall population. Without repeated phenotyping, these individuals erroneously believed to have high value were repeatedly selected across cycles, leading to decreased genetic gain. With genomic truncation selection, overlapping and discrete generations performed similarly as updating breeding values precluded repeatedly selecting individuals with inaccurately high estimates of breeding values in subsequent cycles. Overlapping generations did not outperform discrete generations in the presence of a positive genetic trend with genomic truncation selection, as past generations had lower mean genetic values than the current generation of selection candidates. With genomic optimum contribution selection, overlapping and discrete generations performed similarly, but overlapping generations slightly outperformed discrete generations in the long term if the targeted inbreeding rate was extremely low.ConclusionsMaintaining discrete generations in recurrent phenotypic selection leads to increased genetic gain, especially at low heritabilities, by preventing selection error bias. With genomic truncation selection and genomic optimum contribution selection, genetic gain does not differ between discrete and overlapping generations assuming non-genetic effects are not present. Overlapping generations may increase genetic gain in the long term with very low targeted rates of inbreeding in genomic optimum contribution selection.
A multi-dataset evaluation of frame censoring for motion correction in task-based fMRI
Authors: Jones Michael S. , Zhu Zhenchen , Bajracharya Aahana , Luor Austin , Peelle Jonathan E. 
Published: October 2021

AbstractSubject motion during fMRI can affect our ability to accurately measure signals of interest. In recent years, frame censoring—that is, statistically excluding motion-contaminated data within the general linear model using nuisance regressors—has appeared in several task-based fMRI studies as a mitigation strategy. However, there have been few systematic investigations quantifying its efficacy. In the present study, we compared the performance of frame censoring to several other common motion correction approaches for task-based fMRI using open data and reproducible workflows. We analyzed eight publicly-available datasets representing eleven distinct tasks in child, adolescent, and adult participants. Performance was quantified using maximum t-values in group analyses, and ROI-based mean activation and split-half reliability in single subjects. We compared frame censoring across several thresholds to the use of 6 and 24 canonical motion regressors, wavelet despiking, robust weighted least squares, and untrained ICA-based denoising, for a total of 240 separate analyses. Thresholds used to identify censored frames were based on both motion estimates (FD) and image intensity changes (DVARS). Relative to standard motion regressors, we found consistent improvements for modest amounts of frame censoring (e.g., 1–2% data loss), although these gains were frequently comparable to what could be achieved using other techniques. Importantly, no single approach consistently outperformed the others across all datasets and tasks. These findings suggest that the choice of a motion mitigation strategy depends on both the dataset and the outcome metric of interest.
Top-down predictions of visual features dynamically reverse their bottom-up processing in the occipito-ventral pathway to facilitate stimulus disambiguation and behavior
Authors: Yan Yuening , Zhan Jiayu , Ince Robin A.A. , Schyns Philippe G. 
Published: October 2021

AbstractThe prevalent conception of vision-for-categorization suggests an interplay of two dynamic flows of information within the occipito-ventral pathway. The bottom-up flow progressively reduces the high-dimensional input into a lower-dimensional representation that is compared with memory to produce categorization behavior. The top-down flow predicts category information (i.e. features) from memory that propagates down the same hierarchy to facilitate input processing and behavior. However, the neural mechanisms that support such dynamic feature propagation up and down the visual hierarchy and how they facilitate behavior remain unclear. Here, we studied them using a prediction experiment that cued participants (N = 11) to the spatial location (left vs. right) and spatial frequency (SF, Low, LSF, vs. High, HSF) contents of an upcoming Gabor patch. Using concurrent MEG recordings of each participant’s neural activity, we compared the top-down flow of representation of the predicted Gabor contents (i.e. left vs. right; LSF vs. HSF) to their bottom-up flow. We show (1) that top-down prediction improves speed of categorization in all participants, (2) the top-down flow of prediction reverses the bottom-up representation of the Gabor stimuli, going from deep right fusiform gyrus sources down to occipital cortex sources contra-lateral to the expected Gabor location and (3) that predicted Gabors are better represented when the stimulus is eventually shown, leading to faster categorizations. Our results therefore trace the dynamic top-down flow of a predicted visual content that chronologically and hierarchically reversed bottom-up processing, further facilitates visual representations in early visual cortex and subsequent categorization behavior.
The Hair Cell Analysis Toolbox: A machine learning-based whole cochlea analysis pipeline
Authors: Buswinka Christopher J. , Osgood Richard T. , Simikyan Rubina G. , Rosenberg David B. , Indzhykulian Artur A. 
Published: October 2021

AbstractOur sense of hearing is mediated by sensory hair cells, precisely arranged and highly specialized cells subdivided into two subtypes: outer hair cells (OHCs) which amplify sound-induced mechanical vibration, and inner hair cells (IHCs) which convert vibrations into electrical signals for interpretation by the brain. One row of IHCs and three rows of OHCs are arranged tonotopically; cells at a particular location respond best to a specific frequency which decreases from base to apex of the cochlea. Loss of hair cells at a specific place affects hearing performance at the corresponding tonotopic frequency. To better understand the underlying cause of hearing loss in patients (or experimental animals) a plot of hair cell survival along the cochlear frequency map, known as a cochleogram, can be generated post-mortem, involving manually counting thousands of cells. Currently, there are no widely applicable tools for fast, unsupervised, unbiased, and comprehensive image analysis of auditory hair cells that work well either with imaging datasets containing an entire cochlea or smaller sampled regions. Current microscopy tools allow for imaging of auditory hair cells along the full length of the cochlea, often yielding more data than feasible to manually analyze. Here, we present a machine learning-based hair cell analysis toolbox for the comprehensive analysis of whole cochleae (or smaller regions of interest). The Hair Cell Analysis Toolbox (HCAT) is a software that automates common image analysis tasks such as counting hair cells, classifying them by subtype (IHCs vs OHCs), determining their best frequency based on their location along the cochlea, and generating cochleograms. These automated tools remove a considerable barrier in cochlear image analysis, allowing for faster, unbiased, and more comprehensive data analysis practices. Furthermore, HCAT can serve as a template for deep-learning-based detection tasks in other types of biological tissue: with some training data, HCAT’s core codebase can be trained to develop a custom deep learning detection model for any object on an image.
Aperiodic EEG activity masks the dynamics of neural oscillations during loss of consciousness from propofol
Authors: Brake Niklas , Duc Flavie , Rokos Alexander , Arseneau Francis , Shahiri Shiva , Khadra Anmar , Plourde Gilles 
Published: October 2021

AbstractEEGs are known to provide biomarkers for consciousness. Although EEG correlates of loss of consciousness (LOC) are often ascribed to changes in neural synchrony, mounting evidence suggests that some changes result from asynchronous neural activity. By combining EEG recordings of humans undergoing propofol administration with biophysical modelling, we present here a principled decomposition of EEG changes during LOC into synchronous and asynchronous sources. Our results reveal that IPSP decay rate and mean spike rate shape aperiodic EEG features, and that propofol’s effects on these parameters largely explain the changes in EEG spectra following propofol infusion. We further show that traditional spectral EEG analysis likely conflates these effects with changes in rhythmic activity, thereby masking the true dynamics of neural synchrony. We conclude that the well-documented propofol-induced alpha rhythm in fact appears before LOC, and that the moment of LOC is uniquely correlated with the sudden appearance of a delta rhythm.
A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy
Authors: Greaney Allison J. , Starr Tyler N. , Eguia Rachel T. , Loes Andrea N. , Khan Khadija , Karim Farina , Cele Sandile , Bowen John E. , Logue Jennifer K. , Corti Davide , Veesler David , Chu Helen Y. , Sigal Alex , Bloom Jesse D. 
Published: October 2021

AbstractMany SARS-CoV-2 variants have mutations at key sites targeted by antibodies. However, it is unknown if antibodies elicited by infection with these variants target the same or different regions of the viral spike as antibodies elicited by earlier viral isolates. Here we compare the specificities of polyclonal antibodies produced by humans infected with early 2020 isolates versus the B.1.351 variant of concern (also known as Beta or 20H/501Y.V2), which contains mutations in multiple key spike epitopes. The serum neutralizing activity of antibodies elicited by infection with both early 2020 viruses and B.1.351 is heavily focused on the spike receptor-binding domain (RBD). However, within the RBD, B.1.351-elicited antibodies are more focused on the “class 3” epitope spanning sites 443 to 452, and neutralization by these antibodies is notably less affected by mutations at residue 484. Our results show that SARS-CoV-2 variants can elicit polyclonal antibodies with different immunodominance hierarchies.
Taxonomic classification methods reveal a new subgenus in the paramyxovirus subfamily Orthoparamyxovirinae
Authors: Wells Heather L. , Loh Elizabeth , Nava Alessandra , Lee Mei Ho , Lee Jimmy , Sukor Jum R. A. , Navarrete-Macias Isamara , Liang Eliza , Firth Cadhla , Epstein Jonathan , Rostal Melinda , Zambrana-Torrelio Carlos , Murray Kris , Daszak Peter , Goldstein Tracey , Mazet Jonna A.K. , Lee Benhur , Hughes Tom , Durigon Edison , Anthony Simon J. 
Published: October 2021

AbstractAs part of a broad One Health surveillance effort to detect novel viruses in wildlife and people, we report several paramyxoviruses sequenced primarily from bats during 2013 and 2014 in Brazil and Malaysia, including seven from which we recovered full-length genomes. Of these, six represent the first full-length paramyxovirus genomes sequenced from the Americas, including two sequences which are the first full-length bat morbillivirus genomes published to date. Our findings add to the vast number of viral sequences in public repositories that have been increasing considerably in recent years due to the rising accessibility of metagenomics. Taxonomic classification of these sequences in the absence of phenotypic data has been a significant challenge, particularly in the paramyxovirus subfamily Orthoparamyxovirinae, where the rate of discovery of novel sequences has been substantial. Using pairwise amino acid sequence classification (PASC), we describe a novel genus within this subfamily tentatively named Jeishaanvirus, which we propose should include as subgenera Jeilongvirus, Shaanvirus, and a novel South American subgenus Cadivirus. We also highlight inconsistencies in the classification of Tupaia virus and Mojiang virus using the same demarcation criteria and show that members of the proposed subgenus Shaanvirus are paraphyletic. Importantly, this study underscores the critical importance of sequence length in PASC analysis as well as the importance of biological characteristics such as genome organization in the taxonomic classification of viral sequences.
PyMVPD: A toolbox for multivariate pattern dependence
Authors: Fang Mengting , Poskanzer Craig , Anzellotti Stefano 
Published: October 2021

AbstractCognitive tasks engage multiple brain regions. Studying how these regions interact is key to understand the neural bases of cognition. Standard approaches to model the interactions between brain regions rely on univariate statistical dependence. However, newly developed methods can capture multivariate dependence. Multivariate Pattern Dependence (MVPD) is a powerful and flexible approach that trains and tests multivariate models of the interactions between brain regions using independent data. In this article, we introduce PyMVPD: an open source toolbox for Multivariate Pattern Dependence. The toolbox includes pre-implemented linear regression models and artificial neural network models of the interactions between regions. It is designed to be easily customizable. We demonstrate example applications of PyMVPD using well-studied seed regions such as the fusiform face area (FFA) and the parahippocampal place area (PPA). Next, we compare the performance of different model architectures. Overall, artificial neural networks outperform linear regression. Importantly, the best performing architecture is region-dependent: MVPD subdivides cortex in distinct, contiguous regions whose interaction with FFA and PPA is best captured by different models.
Development of a metatranscriptomic analysis method for multiple intestinal sites and its application to the common marmoset intestine
Authors: Uehara Mika , Inoue Takashi , Kominato Minori , Hase Sumitaka , Sasaki Erika , Toyoda Atsushi , Sakakibara Yasubumi 
Published: October 2021

AbstractBackgroundThe intestinal microbiome is closely related to host health, and metatranscriptomic analysis can assess the functional activity of microbiomes by quantifying the bacterial gene expression level, which helps to elucidate the interaction between the microbiome and the environment. However, functional changes in the microbiome along the host intestinal tract remain unknown, and previous analytical methods have limitations, such as potentially overlooking unknown genes due to dependence on existing databases and being unable to take full advantage of metatranscriptome to reveal the functional change among multiple environments.ResultTo close these gaps, we develop a novel method that integrates metagenome and metatranscriptome to analyze the functional activity of microbiomes between intestinal sites. This method reconstructs a reference metagenomic sequence across multiple intestinal sites, allowing the gene expression levels of microbiome including unknown bacterial genes to be compared between multiple sites. As a result of applying this method to metatranscriptomic analysis in the intestinal tract of common marmoset, the reconstructed metagenome covered most of the expressed genes and it revealed that the changes in bacterial gene expressions among the caecum, transverse colon, and faeces were more dynamic and sensitive to environmental shifts than its abundance. In typical, the coenzyme synthesis gene and antibacterial resistance gene were more highly expressed in the caecum and transverse colon than in faeces, while there was no significant change in abundance of these genes.ConclusionOur findings demonstrate that an analytical method that integrates metagenome and metatranscriptome in multiple intestinal sites captures functional changes in the microbiomes at the gene resolution level.