bluuebunny/crossref_metadata_2025_split huggingface dataset:
International authorship and collaboration across bioRxiv preprints
Authors: Abdill Richard J. , Adamowicz Elizabeth M. , Blekhman Ran 
Published: April 2020

AbstractAs preprints become integrated into conventional avenues of scientific communication, it’s critical to understand who is included and who is not. However, little is known about which countries are participating or how they collaborate with each other. Here, we present an analysis of all 67,885 preprints posted on bioRxiv (through 2019) using the first comprehensive dataset of country-level preprint author affiliations. We find the plurality of preprints (39%) come from the United States, and that countries such as the U.S. and U.K. are overrepresented on bioRxiv relative to their overall scientific output, while countries including China, Russia, and Turkey show lower bioRxiv adoption. We describe a set of “contributor countries” including Uganda, Croatia and Thailand that appear almost exclusively as non-senior authors on international collaborations. Lastly, we find multiple journals that publish a disproportionate number of preprints from some countries, a dynamic that almost always benefits manuscripts from the U.S.
MINERVA: A facile strategy for SARS-CoV-2 whole genome deep sequencing of clinical samples
Authors: Chen Chen , Li Jizhou , Di Lin , Jing Qiuyu , Du Pengcheng , Song Chuan , Li Jiarui , Li Qiong , Cao Yunlong , Xie X. Sunney , Wu Angela R. , Zeng Hui , Huang Yanyi , Wang Jianbin 
Published: April 2020

AbstractThe novel coronavirus disease 2019 (COVID-19) pandemic poses a serious public health risk. Analyzing the genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from clinical samples is crucial for the understanding of viral spread and viral evolution, as well as for vaccine development. Existing sample preparation methods for viral genome sequencing are demanding on user technique and time, and thus not ideal for time-sensitive clinical samples; these methods are also not optimized for high performance on viral genomes. We have developedMetagenomIc RNAEnRichmentVirAl sequencing (MINERVA), a facile, practical, and robust approach for metagenomic and deep viral sequencing from clinical samples. This approach uses direct tagmentation of RNA/DNA hybrids using Tn5 transposase to greatly simplify the sequencing library construction process, while subsequent targeted enrichment can generate viral genomes with high sensitivity, coverage, and depth. We demonstrate the utility of MINERVA on pharyngeal, sputum and stool samples collected from COVID-19 patients, successfully obtaining both whole metatranscriptomes and complete high-depth high-coverage SARS-CoV-2 genomes from these clinical samples, with high yield and robustness. MINERVA is compatible with clinical nucleic extracts containing carrier RNA. With a shortened hands-on time from sample to virus-enriched sequencing-ready library, this rapid, versatile, and clinic-friendly approach will facilitate monitoring of viral genetic variations during outbreaks, both current and future.
Post-fire changes in plant growth form composition in Andean páramo grassland
Authors: Zomer Maya A. , Ramsay Paul M. 
Published: April 2020

AbstractQuestionsFire suppression policies have been widely adopted in the páramo grasslands of the northern Andes to protect their biodiversity and ecosystem services. Páramos have been regularly burned for many years, and it is not clear how páramo vegetation will respond to significant changes in their fire regimes. This study investigates differences in plant growth form composition, light levels and soil temperatures in páramo plots representing a range of recovery times since the last fire.LocationReserva Ecológica El Ángel and La Bretaña Nature Reserve, Carchi, Northern Ecuador.MethodsWe assessed the frequency of ten páramo growth forms, vegetation height, soil temperature, and light intensity in fifteen fire sites with historical records of fire (<1 – 15 years since fire), and one recently unburned site (at least 40 years since fire). A chronosquence of sites was used to assess potential changes in plant community composition in post-fire succession of páramo.ResultsThe recovery of páramo vegetation after fire comprised three phases: initial recruitment with high growth form diversity, followed by reduced diversity, light and soil temperatures in dense tussock vegetation, and ultimately canopy height stratification with a return of diversity. All but one plant growth forms were represented in each of the three phases, and the changes reflected differences in relative abundance.ConclusionsPost-fire páramo succession is characterized by clear shifts in the relative abundance of plant growth forms, ending with (co-)dominance of upright shrubs. The long-term consequences of such shifts for biodiversity and ecosystem function, given the widespread adoption of fire suppression policies in the páramo need careful, evidence-based consideration.
Flexible machine learning prediction of antigen presentation for rare and common HLA-I alleles
Authors: Bravi Barbara , Tubiana Jérôme , Cocco Simona , Monasson Rémi , Mora Thierry , Walczak Aleksandra M. 
Published: April 2020

SummaryThe recent increase of immunopeptidomic data, obtained by mass spectrometry or binding assays, opens unprecedented possibilities for investigating endogenous antigen presentation by the highly polymorphic human leukocyte antigen class I (HLA-I) protein. We introduce a flexible and easily interpretable peptide presentation prediction method, RBM-MHC. We validate its performance as a predictor of cancer neoantigens and viral epitopes and we use it to reconstruct peptide motifs presented on specific HLA-I molecules. By benchmarking RBM-MHC performance on a wide range of HLA-I alleles, we show its importance to improve prediction accuracy for rarer alleles.
Stationary distributions and metastable behaviour for self-regulating proteins with general lifetime distributions
Authors: Çelik Candan , Bokes Pavol , Singh Abhyudai 
Published: April 2020

AbstractRegulatory molecules such as transcription factors are often present at relatively small copy numbers in living cells. The copy number of a particular molecule fluctuates in time due to the random occurrence of production and degradation reactions. Here we consider a stochastic model for a self-regulating transcription factor whose lifespan (or time till degradation) follows a general distribution modelled as per a multidimensional phase-type process. We show that at steady state the protein copy-number distribution is the same as in a one-dimensional model with exponentially distributed lifetimes. This invariance result holds only if molecules are produced one at a time: we provide explicit counterexamples in the bursty production regime. Additionally, we consider the case of a bistable genetic switch constituted by a positively autoregulating transcription factor. The switch alternately resides in states of up- and downregulation and generates bimodal protein distributions. In the context of our invariance result, we investigate how the choice of lifetime distribution affects the rates of metastable transitions between the two modes of the distribution. The phase-type model, being non-linear and multi-dimensional whilst possessing an explicit stationary distribution, provides a valuable test example for exploring dynamics in complex biological systems.
Pooled CRISPR screening at high sensitivity with an empirically designed sgRNA library
Authors: Henkel Luisa , Rauscher Benedikt , Schmitt Barbara , Winter Jan , Boutros Michael 
Published: April 2020

ABSTRACTGiven their broad utility in functionally annotating genomes, the experimental design of genome-scale CRISPR screens can vary greatly and criteria for optimal experimental implementation and library composition are still emerging. In this study, we report advantages of conducting viability screens in selected Cas9 single cell clones in contrast to Cas9 bulk populations. We further systematically analyzed published CRISPR screens in human cells to identify single-guide (sg)RNAs with consistent high on-target and low off-target activity. Selected guides were collected in a new genome-scale sgRNA library, which efficiently identifies core and context-dependent essential genes. In summary, we show how empirically designed libraries in combination with an optimised experimental design increase the dynamic range in gene essentiality screens at reduced library coverage.
Enhancing KCC2 activity decreases hyperreflexia and spasticity after chronic SCI
Authors: Bilchak Jadwiga N. , Yeakle Kyle , Caron Guillaume , Malloy Dillon C. , Côté Marie-Pascale 
Published: April 2020

AbstractAfter spinal cord injury (SCI), the majority of individuals develop spasticity, a debilitating condition involving involuntary movements, co-contraction of antagonistic muscles, and hyperreflexia. By acting on GABAergic and Ca2+-dependent signaling, current anti-spastic medications lead to serious side effects, including a drastic decrease in motoneuronal excitability which impairs motor function and rehabilitation efforts. Exercise, in contrast, decreases spastic symptoms without decreasing motoneuron excitability. These functional improvements coincide with an increase in expression of the chloride co-transporter KCC2 in lumbar motoneurons. Thus, we hypothesized that spastic symptoms can be alleviated directly through restoration of chloride homeostasis and endogenous inhibition by increasing KCC2 activity. Here, we used the recently developed KCC2 enhancer, CLP257, to evaluate the effects of acutely increasing KCC2 extrusion capability on spastic symptoms after chronic SCI. Sprague Dawley rats received a spinal cord transection at T12 and were either bike-trained or remained sedentary for 5 weeks. Increasing KCC2 activity in the lumbar enlargement improved the rate-dependent depression of the H-reflex and reduced both phasic and tonic EMG responses to muscle stretch in sedentary animals after chronic SCI. Furthermore, the improvements due to this pharmacological treatment mirror those of exercise. Together, our results suggest that pharmacologically increasing KCC2 activity is a promising approach to decrease spastic symptoms in individuals with SCI. By acting to directly to restore endogenous inhibition, this strategy has potential to avoid severe side effects and improve the quality of life of affected individuals.Significance StatementSpasticity is a condition that develops after spinal cord injury (SCI) and causes major complications for individuals. We have previously reported that exercise attenuates spastic symptoms after SCI through an increase in expression of the chloride co-transporter KCC2, suggesting that restoring chloride homeostasis contributes to alleviating spasticity. However, the early implementation of rehabilitation programs in the clinic is often problematic due to co-morbidities. Here, we demonstrate that pharmacologically enhancing KCC2 activity after chronic SCI reduces multiple signs of spasticity, without the need for rehabilitation.
Elevated expression ofACE2in tumor-adjacent normal tissues of cancer patients
Authors: Winkler Tom , Ben-David Uri 
Published: April 2020

AbstractThe rapidly developing COVID-19 pandemic has raised a concern that cancer patients may have increased susceptibility to SARS-CoV-2 infection. This discussion has mostly focused on therapy-induced immune suppression. Here, we examined the expression patterns ofACE2, the receptor through which SARX-CoV2 enters human cells, and found thatACE2mRNA levels are elevated in tumor-adjacent normal tissues of cancer patients, including in normal-adjacent lung tissues of lung cancer patients. These observations raise the possibility that the elevated COVID-19 risk of cancer patients may not be limited to those undergoing immune-suppressing treatment.
Puromycin selection of cells with a high expression of the cytochrome P450 CYP3A4 gene activity from a patient with drug-induced liver injury (DILI) and their lifespan prolongation using a combination of CDK4R24C, cyclin D1 and TERT
Authors: Miyata Shoko , Saku Noriaki , Javaregowda Palaksha Kanive , Ite Kenta , Toyoda Masashi , Kimura Toru , Nishina Hiroshi , Nakazawa Atsuko , Kasahara Mureo , Nonaka Hidenori , Kiyono Tohru , Umezawa Akihiro 
Published: April 2020

ABSTRACTMany drugs have the potential to induce the expression of drug-metabolizing enzymes, particularly cytochrome P450 3A4 (CYP3A4), in hepatocytes. Hepatocytes can accurately evaluate drug-mediated CYP3A4 induction as the gold standard for in vitro hepatic toxicology test, but their lot variation is an issue to be solved. Only a limited number of immortalized hepatocyte cells have been reported. In this study, we generated an immortalized cell expressing CYP3A4 from a patient with drug-induced liver injury (DILI). To generate DILI-derived cells with a high expression of CYP3A4, we employed a three-step approach: 1. Differentiation of DILI-induced pluripotent stem cells (DILI-iPSCs); 2. Immortalization of the differentiated cells; 3. Selection of the cells with puromycin. We hypothesize that cells with a high expression of cytochrome P450 genes can survive even after exposure to cytotoxic antibiotics because of high drug-metabolism activity. Puromycin, one of the cytotoxic antibiotics, was used in this study because of its rapid cytocidal effect at a low concentration. Phenotypic studiesin vitrorevealed that the puromycin-selected cells (HepaSM or SI cells) constitutively expressed the CYP3A4 gene at an extremely high level, and continued to proliferate at least up to 34 population doublings for more than 250 days. The expression profiles were independent of population doublings. Drug-mediated induction test revealed that the cells significantly increased CYP3A4 after exposure to rifampicin, suggesting that the immortalized cells would serve as another useful source for in vitro examination of drug metabolism and CYP3A4 induction.
CD13 is a Critical Regulator of Cell-cell Fusion in Osteoclastogenesis
Authors: Ghosh Mallika , Kalajzic Ivo , Aguila Hector Leonardo , Shapiro Linda H 
Published: April 2020

AbstractIn vertebrates, bone formation is dynamically controlled by the activity of two specialized cell types: the bone-generating osteoblasts and bone-degrading osteoclasts. Osteoblasts produce the soluble receptor activator of NFκB ligand (RANKL) that binds to its receptor RANK on the surface of osteoclast precursor cells to promote osteoclastogenesis, a process that involves cell-cell fusion and assembly of molecular machinery to ultimately degrade the bone. CD13 is a transmembrane aminopeptidase that is highly expressed in cells of myeloid lineage has been shown to regulate dynamin-dependent receptor endocytosis and recycling and is a necessary component of actin cytoskeletal organization. In the present study, we show that CD13-deficient mice display a normal distribution of osteoclast progenitor populations in the bone marrow, but present a low bone density phenotype. Further, the endosteal bone formation rate is similar between genotypes, indicating a defect in osteoclast-specific function in vivo. Loss of CD13 led to exaggerated in vitro osteoclastogenesis as indicated by significantly enhanced fusion of bone marrow-derived multinucleated osteoclasts in the presence of M-CSF and RANKL, resulting in abnormally large cells with remarkably high numbers of nuclei with a concomitant increase in bone resorption activity. Similarly, we also observed increased formation of multinucleated giant cells (MGC) in CD13KObone marrow progenitor cells stimulated with IL-4 and IL-13, suggesting that CD13 may regulate cell-cell fusion events via a common pathway, independent of RANKL signaling. Mechanistically, while expression levels of the fusion-regulatory proteins dynamin and DC-STAMP are normally downregulated as fusion progresses in fusion-competent mononucleated progenitor cells, in the absence of CD13 they are uniformly sustained at high levels, even in mature multi-nucleated osteoclasts. Taken together, we conclude that CD13 may regulate cell-cell fusion by controlling expression and localization of key fusion proteins that are critical for both osteoclast and MGC fusion.
Neural circuit analysis using a novel intersectional split intein-mediated split-Cre recombinase system
Authors: Khoo Audrey Tze Ting , Kim Paul Jong , Kim Ho Min , Je H. Shawn 
Published: April 2020

AbstractThe defining features of a neuron are its functional and anatomical connections with thousands of other neurons in the brain. Together, these neurons form functional networks that direct animal behaviour. Current approaches that allow the interrogation of specific populations of neurons and neural circuits rely heavily on targeting their gene expression profiles or connectivity. However, these approaches are often unable to delineate specific neuronal populations. Here, we developed a novel intersectional split intein-mediated split-Cre recombinase system that can selectively label specific types of neurons based on their gene expression profiles and structural connectivity. We developed this system by splitting Cre recombinase into two fragments with evolved split inteins and subsequently expressed one fragment under the influence of a cell type-specific promoter in a transgenic animal, and delivered the other fragment via retrograde viral gene transfer. This approach results in the reconstitution of Cre recombinase in only specific population of neurons projecting from a specific brain region or in those of a specific neuronal type. Taken together, our split intein-based split-Cre system will be useful for sophisticated characterization of mammalian brain circuits.
Live-cell single particle tracking of PRC1 reveals a highly dynamic system with low target site occupancy
Authors: Huseyin Miles K. , Klose Robert J. 
Published: April 2020

AbstractPolycomb repressive complex 1 (PRC1) is an essential chromatin-based repressor of gene transcription. However, how PRC1 engages with chromatin to identify its target genes and achieve gene repression remains poorly defined, representing a major hurdle to our understanding of Polycomb system function. Here we use genome engineering and single particle tracking to dissect how PRC1 binds to chromatin in live mouse embryonic stem cells. We reveal that PRC1 is highly dynamic, with only a small fraction stably interacting with chromatin. By integrating subunit-specific dynamics, chromatin binding, and abundance measurements, we discover that PRC1 exhibits surprisingly low occupancy at target sites. Furthermore, we employ perturbation approaches to uncover how specific components of PRC1 define its kinetics and chromatin binding. Together, these discoveries provide a quantitative understanding of chromatin binding by PRC1 in live cells, and suggests that chromatin modification, as opposed to PRC1 complex occupancy, is central to gene repression.
The Evolution Of Colouration And Opsins In Tarantulas
Authors: Foley Saoirse , Saranathan Vinodkumar , Piel William H. 
Published: April 2020

ABSTRACTTarantulas paradoxically exhibit a diverse palette of vivid colouration despite their crepuscular to nocturnal habits. The evolutionary origin and maintenance of these colours remains a mystery. In this study, we reconstructed the ancestral states of both blue and green colouration in tarantula setae, and tested how these colours correlate with the presence of stridulation, urtication, and arboreality. Green colouration has likely evolved at least eight times, and blue colouration is likely an ancestral condition that appears to be lost more frequently than gained. While our results indicate that neither colour correlates with the presence of stridulation or urtication, the evolution of green colouration appears to depend upon the presence of arboreality, suggesting that it likely originated for, and functions in, crypsis through substrate matching among leaves. We also constructed a network of opsin homologs across tarantula transcriptomes. Despite their crepuscular tendencies, tarantulas express a full suite of opsin genes – a finding that contradicts current consensus that tarantulas have poor colour vision on the basis of low opsin diversity. Overall, our results support the intriguing hypotheses that blue colouration may have ultimately evolved via sexual selection and perhaps proximately be used in mate choice or predation avoidance due to possible sex differences in mate-searching.
A rapid, low-cost, and highly sensitive SARS-CoV-2 diagnostic based on whole-genome sequencing
Authors: Adastra Per A. , Durand Neva C. , Mitra Namita , Pulido Saul Godinez , Mahajan Ragini , Blackburn Alyssa , Colaric Zane L. , Theisen Joshua W. M. , Weisz David , Dudchenko Olga , Gnirke Andreas , Rao Suhas S.P. , Kaur Parwinder , Aiden Erez Lieberman , Aiden Aviva Presser 
Published: April 2020

AbstractEarly detection of infection with SARS-CoV-2 is key to managing the current global pandemic, as evidence shows the virus is most contagious on or before symptom onset. Here, we introduce a low-cost, high-throughput method for diagnosing and studying SARS-CoV-2 infection. Dubbed Pathogen-Oriented Low-Cost Assembly & Re-Sequencing (POLAR), this method amplifies the entirety of the SARS-CoV-2 genome. This contrasts with typical RT-PCR-based diagnostic tests, which amplify only a few loci. To achieve this goal, we combine a SARS-CoV-2 enrichment method developed by the ARTIC Network (https://artic.network/) with short-read DNA sequencing andde novogenome assembly. Using this method, we can reliably (>95% accuracy) detect SARS-CoV-2 at a concentration of 84 genome equivalents per milliliter (GE/mL). Almost all diagnostic methods currently authorized for use by the United States Food and Drug Administration with the Coronavirus Disease 2019 (COVID-19) Emergency Use Authorization require larger concentrations of the virus to achieve this degree of accuracy. In addition, we can reliably assemble the SARS-CoV-2 genome in the sample, often with no gaps and perfect accuracy. The genotypic data contained in these genome assemblies enable the more effective analysis of disease spread than is possible with an ordinary binary diagnostic. These data can also help identify vaccine and drug targets. Finally, we show that the diagnoses obtained using POLAR of both positive and negative clinical nasopharyngeal swab samples 100% match the diagnoses obtained in a clinical diagnostic lab using the Center for Disease Control’s 2019-Novel Coronavirus test. Using POLAR, a single person can manually process 192 samples over an 8- hour experiment at the cost of ∼$36 per patient (as of December 7th, 2022), enabling a 24-hour turnaround with sequencing and data analysis time. We anticipate that further testing and refinement will allow greater sensitivity in this approach.