bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large-scale silane bead-based SARS-CoV-2 testing of a nursing home in Spain identifies a viral reservoir during lockdown period
Authors: Weber Nicholas D. , Goñi-Salaverri Ainhoa , Rodríguez Jose A. , Unfried Juan Pablo , Alameda Daniel , Fernández-Alonso Mirian , Sáez Elena , Maestro-Galilea Sheila , Alegre Felix , Carmona-Torre Francisco , Marin-Oto Marta , Olagüe Cristina , Odriozola Leticia , Navarro-Alonso Mar , Sanchez-Ostiz Rafael , Argemi Josepmaria , Pozo Jose Luis del , Lara-Astiaso David 
Published: February 2021

AbstractBackgroundSpain is one of the countries most heavily affected by the COVID-19 pandemic. As in other countries such as UK and USA, nursing homes have been an important human reservoir for the virus and the population with the highest mortality worldwide. The presence of asymptomatic carriers within nursing homes is one of the factors that could provoke new outbreaks during the relaxing of lockdown measures.MethodsWe developed a high-throughput protocol for RNA extraction of patient samples based on silane magnetic beads in multi-well plates. The sensitivity, specificity and reproducibility rates were assessed using positive and negative clinical samples from the Clinica Universidad de Navarra, Spain. We utilized the protocol to test a pilot cohort of 138 residents and 87 staff from a nursing home in Northern Navarre, Spain.FindingsOur protocol showed high sensitivity (100%), specificity (96·0%) and linear correlation with PCR cycle threshold values obtained with a standard testing kit (R2 = 0·807, p=3E-05). Testing of 225 individuals from the nursing home revealed 63 residents (46%) and 14 staff (16%) positive for SARS-CoV-2. Only 18 of the positive residents (28·6%) were symptomatic at time of testing. During follow-up, 6 PCR-negative symptomatic residents were retested and resulted positive. One-month mortality among positive residents was higher than in negative residents (15·9% vs 1·3%), regardless of age or comorbidities.InterpretationRapid silane bead-based RNA extraction expanded the testing capabilities and COVID-19 patients were promptly identified. Personal and public health measures were enacted to avoid spreading and tighten clinical surveillance. The ability to easily adapt the technical capabilities of academic research centers to large-scale testing for SARS-CoV-2 could provide an invaluable tool for ensuring a safe lifting of lockdown in countries with high numbers of cases.FundingEuropean Molecular Biology Organization and Genomics Unit, Cima Universidad de Navarra.
Gene expression plasticity, genetic variation and fatty acid remodelling in divergent populations of a tropical bivalve species
Authors: Le Luyer J. , Milhade L. , Reisser C. , Soyez C. , Monaco C. J. , Belliard C. , Le Moullac G. , Ky C.-L. , Pernet F. 
Published: February 2021

AbstractOcean warming is a particularly challenging threat for tropical marine bivalves’ species because many live already near their upper thermal limits. The thermal sensitivity of organisms is a strong contributor to the biogeographic boundaries of populations and species. The potential of thermal plastic response (range of thermal breadth) is typically reduced for marine populations living in stable thermal environments, e.g., in extreme latitudes organisms as traduced in the climatic variability hypothesis. However, regional-scale heterogeneity among tropical environments, such as archipelagos in French Polynesia, might also serve in modulating this plastic potential. The questions remain now, how tropical organisms are able to cope with abnormally elevated temperature on long-term (several weeks) and how environmental-variability might drive the potential of resilience? To answer these questions, we benefit from two ecologically divergent populations of a marine tropical mollusc species,Pinctada margaritifera, that usually experience either large diurnal variations (tide-pools, Marquesas archipelago) or lower temperature with stable to moderate variations (Gambier archipelago). Individuals were maintained in common garden experiment at several controlled temperature conditions (23°C, 28°C, 32°C and 34°C) over a 48 days period. We explored genetic divergence as well as thermal plastic responses by combining lipidomic and transcriptomic approaches. We show thatP. margaritiferahave capacities to adjust to long-term elevated temperatures that was thus far largely underestimated. Furthermore, we identified genetic variation between populations that overlapped with genes expression variations, including genes involved in the respiration machinery, a central process delimiting critical temperatures in marine invertebrates. This study is the first of a series looking at the global adaptation and acclimation mechanisms in response to climate change inPinctadaspecies.
AnLRframework incorporating sensitivity analysis to model multiple direct and secondary transfer events on skin surface
Authors: Gill Peter , Bleka Øyvind , Roseth Arne , Fonneløp Ane Elida 
Published: February 2021

AbstractBayesian logistic regression is used to model the probability of DNA recovery following direct and secondary transfer and persistence over a 24 hour period between deposition and sample collection. Sub-source level likelihood ratios provided the raw data for activity-level analysis. Probabilities of secondary transfer are typically low, and there are challenges with small data-sets with low numbers of positive observations. However, the persistence of DNA over time can be modelled by a single logistic regression for both direct and secondary transfer, except that the time since deposition must be compensated by anoffsetvalue for the latter. This simplifies the analysis. Probabilities are used to inform an activity-level Bayesian Network that takes account of alternative propositions e.g. time of assault and time of social activities. The model is extended in order to take account of multiple contacts between person of interest and ‘ victim’. Variables taken into account include probabilities of direct and secondary transfer, along with background DNA from unknown individuals. The logistic regression analysis is Bayesian -for each analysis, 4000 separate simulations were carried out. Quantile assignments enable calculation of a plausible range of probabilities and sensitivity analysis is used to describe the corresponding variation ofLRs that occur when modelled by the Bayesian network. It is noted that there is need for consistent experimental design, and analysis, to facilitate inter-laboratory comparisons. Appropriate recommendations are made. The open-source program written in R-code ALTRaP (Activity Level, Transfer, Recovery and Persistence) enables analysis of complex multiple transfer propositions that are commonplace in cases-work e.g. between those who cohabit. A number of case examples are provided. ALTRaP can be used to replicate the results and can easily be modified to incorporate different sets of data and variables.
Evolution of lower levels of inter-locus sexual conflict inD. melanogasterpopulations under strong selection for rapid development
Authors: Mital Avani , Sarangi Manaswini , Dey Snigdhadip , Joshi Amitabh 
Published: February 2021

AbstractD. melanogasterlaboratory populations subjected to selection for rapid development and early reproduction have been found to have evolved reduced adult body size and lower levels of inter-locus sexual conflict compared to their ancestral controls. We tested the contribution of a smaller body to the evolution of reduced sexual conflict in these populations, since body size differences are known to affect sexual conflict levels in this species. We cultured larvae from the control populations at high density to obtain flies as small as those from the selected populations. The effect of body size reduction on sexual conflict was asymmetric, with smaller body size resulting in reduced male manipulative ability but not female resistance to mating-induced harm. These results were not due to differences in behavioural patterns of smaller flies, such as differences in overall mating exposure of females to different types of males. We hypothesize that evolution for rapid development and the correlated reduction in body size has resulted in lower male manipulative ability, and sexually antagonistic co-evolution has lowered female resistance to such manipulations. These populations have also evolved incipient reproductive isolation from their controls, likely through sexual conflict (reported earlier), and our results support the view that this is an outcome of strong, directional selection for rapid development.
No evidence for somatosensory attenuation during action observation of self-touch
Authors: Kilteni Konstantina , Engeler Patrick , Boberg Ida , Maurex Linnea , Ehrsson H. Henrik 
Published: February 2021

AbstractThe discovery of mirror neurons in the macaque brain in the 1990s triggered investigations on putative human mirror neurons and their potential functionality. The leading proposed function has been action understanding: accordingly, we understand the actions of others by ‘simulating’ them in our own motor system through a direct matching of the visual information to our own motor programs. Furthermore, it has been proposed that this simulation involves the prediction of the sensory consequences of the observed action, similar to the prediction of the sensory consequences of our executed actions. Here, we tested this proposal by quantifying somatosensory attenuation behaviorally during action observation. Somatosensory attenuation manifests during voluntary action and refers to the perception of self-generated touches as less intense than identical externally generated touches because the self-generated touches are predicted from the motor command. Therefore, we reasoned that if an observer simulates the observed action and, thus, he/she predicts its somatosensory consequences, then he/she should attenuate tactile stimuli simultaneously delivered to his/her corresponding body part. In three separate experiments, we found a systematic attenuation of touches during executed self-touch actions, but we found no evidence for attenuation when such actions were observed. Failure to observe somatosensory attenuation during observation of self-touch is not compatible with the hypothesis that the putative human mirror neuron system automatically simulates the observed action. In contrast, our findings emphasize a sharp distinction between the motor representations of self and others.
Evolution of gene-rich germline restricted chromosomes in black-winged fungus gnats through introgression (Diptera: Sciaridae)
Authors: Hodson Christina N. , Jaron Kamil S. , Gerbi Susan , Ross Laura 
Published: February 2021

AbstractGermline restricted DNA has evolved in diverse animal taxa, and is found in several vertebrate clades, nematodes, and flies. In these lineages, either portions of chromosomes or entire chromosomes are eliminated from somatic cells early in development, restricting portions of the genome to the germline. Little is known about why germline restricted DNA has evolved, especially in flies, in which three diverse families, Chironomidae, Cecidomyiidae, and Sciaridae exhibit germline restricted chromosomes (GRCs). We conducted a genomic analysis of germline restricted chromosomes in the fungus gnatBradysia(Sciara)coprophila(Diptera: Sciaridae), which carries two large germline restricted “L” chromosomes. We sequenced and assembled the genome ofB. coprophila, and used differences in sequence coverage and k-mer frequency between somatic and germ tissues to identify GRC sequence and compare it to the other chromosomes in the genome. We found that the GRCs inB. coprophilaare large, gene-rich, and have many genes with paralogs on other chromosomes in the genome. We also found that the GRC genes are extraordinarily divergent from their paralogs, and have sequence similarity to another Dipteran family (Cecidomyiidae) in phylogenetic analyses, suggesting that these chromosomes have arisen in Sciaridae through introgression from a related lineage. These results suggest that the GRCs may have evolved through an ancient hybridization event, raising questions about how this may have occurred, how these chromosomes became restricted to the germline after introgression, and why they were retained over time.
Resting-state brain activity can predict target-independent aptitude in fMRI-neurofeedback training
Authors: Nakano Takashi , Takamura Masahiro , Nishimura Haruki , Machizawa Maro , Ichikawa Naho , Yoshino Atsuo , Okada Go , Okamoto Yasumasa , Yamawaki Shigeto , Yamada Makiko , Suhara Tetsuya , Yoshimoto Junichiro 
Published: February 2021

AbstractNeurofeedback (NF) aptitude, which refers to an individual’s ability to change its brain activity through NF training, has been reported to vary significantly from person to person. The prediction of individual NF aptitudes is critical in clinical NF applications. In the present study, we extracted the resting-state functional brain connectivity (FC) markers of NF aptitude independent of NF-targeting brain regions. We combined the data in fMRI-NF studies targeting four different brain regions at two independent sites (obtained from 59 healthy adults and six patients with major depressive disorder) to collect the resting-state fMRI data associated with aptitude scores in subsequent fMRI-NF training. We then trained the regression models to predict the individual NF aptitude scores from the resting-state fMRI data using a discovery dataset from one site and identified six resting-state FCs that predicted NF aptitude. Next we validated the prediction model using independent test data from another site. The result showed that the posterior cingulate cortex was the functional hub among the brain regions and formed predictive resting-state FCs, suggesting NF aptitude may be involved in the attentional mode-orientation modulation system’s characteristics in task-free resting-state brain activity.
homeRNA: A self-sampling kit for the collection of peripheral blood and stabilization of RNA
Authors: Haack Amanda J. , Lim Fang Yun , Kennedy Dakota S. , Day John H. , Adams Karen N. , Lee Jing J. , Berthier Erwin , Theberge Ashleigh B. 
Published: February 2021

ABSTRACTGene expression analysis (e.g., targeted gene panels, transcriptomics) from whole blood can elucidate mechanisms of immune function and aid in the discovery of biomarkers. Conventional venipuncture offers only a small snapshot of our broad immune landscape as immune responses may occur outside of the time and location parameters available for conventional venipuncture. A self-operated method that enables flexible sampling of liquid whole blood coupled with immediate stabilization of cellular RNA is instrumental in facilitating capture and preservation of acute or transient immune fluxes. To this end, we developedhomeRNA: a kit for self-collection of peripheral blood (∼0.5 mL) and immediate stabilization of cellular RNA, using the Tasso- SST™ blood collection device with a specially designed stabilizer tube containing RNAlater™. To assess the feasibility ofhomeRNA for self-collection and stabilization of whole blood RNA, we conducted a pilot study (n = 47 participants) where we senthomeRNA to participants aged 21-69, located across 10 US states (94% successful blood collections, n = 61/65). Among participants who successfully collected blood, 93% reported no or minimal pain/discomfort using the kit (n = 39/42), and 79% reported very easy/somewhat easy stabilization protocol (n = 33/42). Total RNA yield from the stabilized samples ranged between 0.20 µg and 5.99 µg (mean = 1.51 µg), and all but one RNA Integrity Number (RIN) values were above 7.0 (mean = 8.1), indicating limited RNA degradation. Results from this study demonstrate the self-collection and RNA stabilization of whole blood withhomeRNA by participants themselves, in their own home.
Intermolecular interactions drive protein adaptive and co-adaptive evolution at both species and population levels
Authors: Peng Junhui , Svetec Nicolas , Zhao Li 
Published: February 2021

AbstractProteins are the building blocks for almost all the functions in cells. Understanding the molecular evolution of proteins and the forces that shape protein evolution is essential in understanding the basis of function and evolution. Previous studies have shown that adaptation frequently occurs at the protein surface, such as in genes involved in host-pathogen interactions. However, it remains unclear whether adaptive sites are distributed randomly or at regions associated with particular structural or functional characteristics across the genome, since many proteins lack structural or functional annotations. Here, we seek to tackle this question by combining large-scale bioinformatic prediction, structural analysis, phylogenetic inference, and population genomic analysis ofDrosophilaprotein-coding genes. We found that protein sequence adaptation is more relevant to function-related rather than structure-related properties. Interestingly, intermolecular interactions contribute significantly to protein adaptation. We further showed that intermolecular interactions, such as physical interactions may play a role in the co-adaptation of fast-adaptive proteins. We found that strongly differentiated amino acids across geographic regions in protein-coding genes are mostly adaptive, which may contribute to the long-term adaptive evolution. This strongly indicates that a number of adaptive sites tend to be repeatedly mutated and selected in evolution, in the past, present, and maybe future. Our results highlight the important roles of intermolecular interactions and co-adaptation in the adaptive evolution of proteins both at the species and population levels.
Effects of treatment with three antibiotics, vancomycin, neomycin, and AVNM on gut microbiome in C57BL/6 mice
Authors: Ray Pratikshya , Chakraborty Subhayan , Ghosh Arindam , Aich Palok 
Published: February 2021

AbstractHigher organisms, especially mammals, harbor diverse microbiota in the gut that plays a major role in maintaining health and physiological homeostasis. Perturbation of gut flora helps identifying their roles. Antibiotics are potent perturbing agents of microbiome. Select antibiotics like vancomycin, neomycin, and AVNM (an antibiotic cocktail containing ampicillin, vancomycin, neomycin, and metronidazole) were used to perturb the gut microbiota of C57BL/6 male mice to understand their roles in host immunity and metabolism. The current study revealed that the resulting gut microbial composition was different, and diversity (at the phylum and genus level) was reduced differentially following each antibiotic treatment. Vancomycin treatment caused a significant increase in Verrucomicrobia and Proteobacteria phyla. The treatment with neomycin yielded an increase in the Bacteroidetes phylum, while the treatment with AVNM led to an increase in Proteobacteria phylum with lowest diversity of microbiome in the gut. The current results also revealed that the different antibiotics treatment caused variation in the cecal index, expression of immune genes (TNF-α, IL-10, IFN-γ) in the colon, and short-chain fatty acids (SCFA) level in the blood of mice. A strong correlation was observed for antibiotic-induced differential dysbiosis patterns of gut microbiota and the altered immune and SCFA profile of the host. The outcome of the present study could be clinically important.
Assessing evolutionary and developmental transcriptome dynamics in homologous cell types
Authors: Feregrino Christian , Tschopp Patrick 
Published: February 2021

ABSTRACTBackgroundDuring development, complex organ patterns emerge through the precise temporal and spatial specification of different cell types. On an evolutionary timescale, these patterns can change, resulting in morphological diversification. It is generally believed that homologous anatomical structures are built – largely – by homologous cell types. However, whether a common evolutionary origin of such cell types is always reflected in the conservation of their intrinsic transcriptional specification programs is less clear.ResultsHere, using a paradigm of morphological diversification, the tetrapod limb, and singlecell RNA-sequencing data from two distantly related species, chicken and mouse, we assessed the transcriptional dynamics of homologous cell types during embryonic patterning. We developed a user-friendly bioinformatics workflow to detect gene co-expression modules and test for their conservation across developmental stages and species boundaries. Using mouse limb data as reference, we identified 19 gene co-expression modules with varying tissue or cell type-restricted activities. Testing for co-expression conservation revealed modules with high evolutionary turnover, while others seemed maintained – to different degrees, in module make-up, density or connectivity – over developmental and evolutionary timescales.ConclusionsWe present an approach to identify evolutionary and developmental dynamics in gene co-expression modules during patterning-relevant stages of homologous cell type specification.
A systematic analysis of Trypanosoma brucei chromatin factors identifies novel protein interaction networks associated with sites of transcription initiation and termination
Authors: Staneva Desislava P. , Carloni Roberta , Auchynnikava Tatsiana , Tong Pin , Rappsilber Juri , Jeyaprakash A. Arockia , Matthews Keith R. , Allshire Robin C. 
Published: February 2021

AbstractNucleosomes composed of histones are the fundamental units around which DNA is wrapped to form chromatin. Transcriptionally active euchromatin or repressive heterochromatin is regulated in part by the addition or removal of histone post-translational modifications (PTMs) by ‘writer’ and ‘eraser’ enzymes, respectively. Nucleosomal PTMs are recognised by a variety of ‘reader’ proteins which alter gene expression accordingly. The histone tails of the evolutionarily divergent eukaryotic parasite Trypanosoma brucei have atypical sequences and PTMs distinct from those often considered universally conserved. Here we identify 68 predicted readers, writers and erasers of histone acetylation and methylation encoded in the T. brucei genome and, by epitope tagging, systemically localize 63 of them in the parasite’s bloodstream form. ChIP-seq demonstrated that fifteen candidate proteins associate with regions of RNAPII transcription initiation. Eight other proteins exhibit a distinct distribution with specific peaks at a subset of RNAPII transcription termination regions marked by RNAPIII-transcribed tRNA and snRNA genes. Proteomic analyses identified distinct protein interaction networks comprising known chromatin regulators and novel trypanosome-specific components. Notably, several SET-domain and Bromo-domain protein networks suggest parallels to RNAPII promoter-associated complexes in conventional eukaryotes. Further, we identify likely components of TbSWR1 and TbNuA4 complexes whose enrichment coincides with the SWR1-C exchange substrate H2A.Z at RNAPII transcriptional start regions. The systematic approach employed provides detail of the composition and organization of the chromatin regulatory machinery in Trypanosoma brucei and establishes a route to explore divergence from eukaryotic norms in an evolutionarily ancient but experimentally accessible eukaryote.