bluuebunny/crossref_metadata_2025_split huggingface dataset:
A geospatial mapping pipeline for ecologists
Authors: van den Hoogen Johan , Robmann Niamh , Routh Devin , Lauber Thomas , van Tiel Nina , Danylo Olga , Crowther Thomas W. 
Published: July 2021

AbstractGeospatial modelling can give fundamental insights in the biogeography of life, providing key information about the living world in current and future climate scenarios. Emerging statistical and machine learning approaches can help us to generate new levels of predictive accuracy in exploring the spatial patterns in ecological and biophysical processes. Although these statistical models cannot necessarily represent the essential mechanistic insights that are needed to understand global biogeochemical processes under ever-changing environmental conditions, they can provide unparalleled predictive insights that can be useful for exploring the variation in biophysical processes across space. As such, these emerging tools can be a valuable approach to complement existing mechanistic approaches as we aim to understand the biogeography of Earth’s ecosystems. Here, we present a comprehensive methodology that efficiently handles large datasets to produce global predictions. This mapping pipeline can be used to generate quantitative, spatially explicit predictions, with a particular emphasis on spatially-explicit insights into the evaluation of model uncertainties and inaccuracies.
DnoisE: Distance denoising by Entropy. An open-source parallelizable alternative for denoising sequence datasets
Authors: Antich Adrià , Palacín Creu , Turon Xavier , Wangensteen Owen S. 
Published: July 2021

AbstractDNA metabarcoding is broadly used in biodiversity studies encompassing a wide range of organisms. Erroneous amplicons are generated during amplification and sequencing procedures and constitute one of the major sources of concern for the interpretation of metabarcoding results. Several denoising programs have been implemented to detect and eliminate these errors. However, almost all denoising software currently available has been designed to process non-coding ribosomal sequences, most notably prokaryotic 16S rDNA. The growing number of metabarcoding studies using coding markers such as COI or RuBisCO demands a re-assessment and calibration of denoising algorithms. Here we present DnoisE, the first denoising program designed to detect erroneous reads and merge them with the correct ones using information from the natural variability (entropy) associated to each codon position in coding barcodes. We have developed an open-source software using a modified version of the UNOISE3 algorithm. DnoisE implements different merging procedures as options, and can incorporate codon entropy information either retrieved from the data or supplied by the user. In addition, the algorithm of DnoisE is parallelizable, greatly reducing run times on computer clusters. Our program also allows different input file formats, so it can be readily incorporated into existing metabarcoding pipelines.
Mutualism-enhancing mutations dominate early adaptation in a microbial community
Authors: Venkataram Sandeep , Kuo Huan-Yu , Hom Erik F. Y. , Kryazhimskiy Sergey 
Published: July 2021

AbstractSpecies interactions drive evolution while evolution shapes these interactions. The resulting eco-evolutionary dynamics, their outcomes and their repeatability depend on how adaptive mutations available to community members affect fitness and ecologically relevant traits. However, the diversity of adaptive mutations is not well characterized, and we do not know how this diversity is affected by the ecological milieu. Here we use barcode lineage tracking to address this gap in a competitive mutualism between the yeastSaccharomyces cerevisiaeand the algaChlamydomonas reinhardtii. We find that yeast has access to many adaptive mutations with diverse ecological consequences, in particular, those that increase and reduce the yields of both species. The presence of the alga does not change which mutations are adaptive in yeast (i.e., there is no fitness trade-off for yeast between growing alone or with alga), but rather shifts selection to favor yeast mutants that increase the yields of both species and make the mutualism stronger. Thus, in the presence of the alga, adaptations contending for fixation in yeast are more likely to enhance the mutualism, even though cooperativity is not directly favored by natural selection in our system. Our results demonstrate that ecological interactions not only alter the trajectory of evolution but also dictate its repeatability; in particular, weak mutualisms can repeatably evolve to become stronger.
SPE-51, a sperm secreted protein with an Immunoglobulin-like domain, is required for sperm-egg fusion inC. elegans
Authors: Mei Xue , Druzhinina Marina , Dharia Sunny , Krauchunas Amber R. , Ni Julie , Singaravelu Gunasekaran , Gu Sam Guoping , Shakes Diane C. , Grant Barth D. , Singson Andrew W. 
Published: July 2021

AbstractDespite the importance of fertilization, the molecular basis of sperm-egg interaction is not well understood. In a forward genetics screen for fertility mutants inCaenorhabditis eleganswe identifiedspe-51. Mutant worms make sperm that are unable to fertilize the oocyte but otherwise normal by all available measurements. Thespe-51gene encodes a secreted protein that includes an immunoglobulin (Ig)-like domain and a hydrophobic sequence of amino acids. The SPE-51 protein acts cell-autonomously and localizes to the surface of the spermatozoa. This is the first example of a secreted protein required for the interactions between the sperm and egg with genetic validation for a specific function in fertilization. Our analyses of these genes begin to build a paradigm for sperm-secreted or reproductive tract-secreted proteins that coat the sperm surface and influence their survival, motility, and/or the ability to fertilize the egg.
Effectiveness of SARS-CoV-2 mRNA Vaccines for Preventing Covid-19 Hospitalizations in the United States
Authors: Tenforde Mark W. , Patel Manish M. , Ginde Adit A. , Douin David J. , Talbot H. Keipp , Casey Jonathan D. , Mohr Nicholas M. , Zepeski Anne , Gaglani Manjusha , McNeal Tresa , Ghamande Shekhar , Shapiro Nathan I. , Gibbs Kevin W. , Files D. Clark , Hager David N. , Shehu Arber , Prekker Matthew E. , Erickson Heidi L. , Exline Matthew C. , Gong Michelle N. , Mohamed Amira , Henning Daniel J. , Steingrub Jay S. , Peltan Ithan D. , Brown Samuel M. , Martin Emily T. , Monto Arnold S. , Khan Akram , Hough C. Terri , Busse Laurence , ten Lohuis Caitlin C. , Duggal Abhijit , Wilson Jennifer G. , Gordon Alexandra June , Qadir Nida , Chang Steven Y. , Mallow Christopher , Gershengorn Hayley B. , Babcock Hilary M. , Kwon Jennie H. , Halasa Natasha , Chappell James D. , Lauring Adam S. , Grijalva Carlos G. , Rice Todd W. , Jones Ian D. , Stubblefield William B. , Baughman Adrienne , Womack Kelsey N. , Lindsell Christopher J. , Hart Kimberly W. , Zhu Yuwei , Olson Samantha M. , Stephenson Meagan , Schrag Stephanie J. , Kobayashi Miwako , Verani Jennifer R. , Self Wesley H. ,   For the Influenza and Other Viruses in the Acutely Ill (IVY) Network
Published: July 2021

ABSTRACTBackgroundAs SARS-CoV-2 vaccination coverage increases in the United States (US), there is a need to understand the real-world effectiveness against severe Covid-19 and among people at increased risk for poor outcomes.MethodsIn a multicenter case-control analysis of US adults hospitalized March 11 - May 5, 2021, we evaluated vaccine effectiveness to prevent Covid-19 hospitalizations by comparing odds of prior vaccination with an mRNA vaccine (Pfizer-BioNTech or Moderna) between cases hospitalized with Covid-19 and hospital-based controls who tested negative for SARS-CoV-2.ResultsAmong 1210 participants, median age was 58 years, 22.8% were Black, 13.8% were Hispanic, and 20.6% had immunosuppression. SARS-CoV-2 lineage B.1.1.7 was most common variant (59.7% of sequenced viruses). Full vaccination (receipt of two vaccine doses ≥14 days before illness onset) had been received by 45/590 (7.6%) cases and 215/620 (34.7%) controls. Overall vaccine effectiveness was 86.9% (95% CI: 80.4 to 91.2%). Vaccine effectiveness was similar for Pfizer-BioNTech and Moderna vaccines, and highest in adults aged 18-49 years (97.3%; 95% CI: 78.9 to 99.7%). Among 45 patients with vaccine-breakthrough Covid hospitalizations, 44 (97.8%) were ≥50 years old and 20 (44.4%) had immunosuppression. Vaccine effectiveness was lower among patients with immunosuppression (59.2%; 95% CI: 11.9 to 81.1%) than without immunosuppression (91.3%; 95% CI: 85.5 to 94.7%).ConclusionDuring March–May 2021, SARS-CoV-2 mRNA vaccines were highly effective for preventing Covid-19 hospitalizations among US adults. SARS-CoV-2 vaccination was beneficial for patients with immunosuppression, but effectiveness was lower in the immunosuppressed population.
Impact of the national test strategy on the development of the Covid-19 pandemic in Denmark
Authors: Busk Peter K. , Kristiansen Thomas Birk , Engsig-Karup Allan 
Published: July 2021

AbstractDuring the Covid-19 pandemic, Denmark has pursued a unique mass testing strategy culminating in testing of more than 8,000 citizens per 100,000 inhabitants per day in the Spring 2021. The strategy includes free access to Covid-19 testing and since 2021, compulsory documentation for negative test or vaccination for access to workplace, educational institutions, restaurants, and many other places.In the present study we analysed the effect of the Danish mass testing strategy throughout relevant stages of the pandemic. Mass testing was found not to have impact on the number of hospitalizations during the pandemic. Furthermore, during the highest level of testing in the spring 2021 the fraction of positive tests increased slightly on comparable days indicating that mass testing at best, did not reduce the prevalence of Covid-19.The relationship between positives in antigen testing and in PCR testing indicated that many patients are not tested early in their infection where the risk of transmission is highest.A likely explanation for the lack of impact of mass testing on hospitalizations and infections is that the testing increases risk-behaviour of the tested persons and that a high fraction of false negatives at low Covid-19 prevalence combined with increased risk-behaviour outweighs beneficial effects of mass testing.
Define and visualize pathological architectures of human tissues from spatially resolved transcriptomics using deep learning
Authors: Chang Yuzhou , He Fei , Wang Juexin , Chen Shuo , Li Jingyi , Liu Jixin , Yu Yang , Su Li , Ma Anjun , Allen Carter , Lin Yu , Sun Shaoli , Liu Bingqiang , Otero Jose , Chung Dongjun , Fu Hongjun , Li Zihai , Xu Dong , Ma Qin 
Published: July 2021

AbstractSpatially resolved transcriptomics provides a new way to define spatial contexts and understand biological functions in complex diseases. Although some computational frameworks can characterize spatial context via various clustering methods, the detailed spatial architectures and functional zonation often cannot be revealed and localized due to the limited capacities of associating spatial information. We present RESEPT, a deep-learning framework for characterizing and visualizing tissue architecture from spatially resolved transcriptomics. Given inputs as gene expression or RNA velocity, RESEPT learns a three-dimensional embedding with a spatial retained graph neural network from the spatial transcriptomics. The embedding is then visualized by mapping as color channels in an RGB image and segmented with a supervised convolutional neural network model. Based on a benchmark of sixteen 10x Genomics Visium spatial transcriptomics datasets on the human cortex, RESEPT infers and visualizes the tissue architecture accurately. It is noteworthy that, for the in-house AD samples, RESEPT can localize cortex layers and cell types based on a pre-defined region-or cell-type-specific genes and furthermore provide critical insights into the identification of amyloid-beta plaques in Alzheimer’s disease. Interestingly, in a glioblastoma sample analysis, RESEPT distinguishes tumor-enriched, non-tumor, and regions of neuropil with infiltrating tumor cells in support of clinical and prognostic cancer applications.
LptB2FG is an ABC transporter with Adenylate Kinase activity regulated by LptC/A recruitment
Authors: Baeta Tiago , Giandoreggio-Barranco Karine , Ayala Isabel , Moura Elisabete C. C. M. , Sperandeo Paola , Polissi Alessandra , Simorre Jean-Pierre , Laguri Cedric 
Published: July 2021

ABSTRACTLipopolysaccharide (LPS) is an essential glycolipid covering the surface of gram-negative bacteria. Its transport involves a dedicated 7 protein transporter system, the Lpt machinery, that physically spans the entire cell envelope. LptB2FG complex is an ABC transporter that hydrolyses Adenosine Triphosphate (ATP) to extract LPS from the inner membrane (IM). LptB2FG was extracted directly from IM with its original lipid environment by Styrene-Maleic acids polymers(SMA). SMA-LptB2FG in nanodiscs displays ATPase activity and a previously uncharacterized Adenylate Kinase (AK) activity. It catalyzes phosphotransfer between two ADP molecules to generate ATP and AMP. ATPase and AK activities of LptB2FG are both stimulated by the interaction on the periplasmic side with LptC and LptA partners and inhibited by the presence of LptC transmembrane helix. Isolated ATPase module (LptB) has weak AK activity in absence of LptF and LptG, and one mutation, that weakens affinity for ADP, has AK activity similar to that of fully assembled complex. LptB2FG is thus capable of producing ATP from ADP depending on the assembly of the Lpt bridge and the AK activity might be important to ensure efficient LPS transport in fully assembled Lpt system.
Sequence Determines the Switch in the Fibril Forming Regions in the Low Complexity FUS Protein and Its Variants
Authors: Kumar Abhinaw , Chakraborty Debayan , Mugnai Mauro Lorenzo , Straub John E. , Thirumalai D. 
Published: July 2021

AbstractResidues spanning distinct regions of the low-complexity domain of the RNA-binding protein, Fused in Sarcoma (FUS-LC), form fibril structures with different core morphologies. NMR experiments show that the 214 residue FUS-LC forms a fibril with an S-bend (core-1, residues 39-95), while the rest of the protein is disordered. In contrast, the fibrils of the C-terminal variant (FUS-LC-C; residues 111-214) has a U-bend topology (core-2, residues 112-150). Absence of the U-bend in FUS-LC implies that the two fibril cores do not coexist. Computer simulations show that these perplexing findings could be understood in terms of the population of sparsely-populated fibril-like excited states in the monomer. The propensity to form core-1 is higher compared to core-2. We predict that core-2 forms only in truncated variants that do not contain the core-1 sequence. At the monomer level, sequence-dependent enthalpic effects determine the relative stabilities of the core-1 and core-2 topologies.TOC graphic
Large-scale deregulation of gene expression by artificial light at night in tadpoles of common toads
Authors: Touzot Morgane , Lefebure Tristan , Lengagne Thierry , Secondi Jean , Dumet Adeline , Konecny-Dupre Lara , Veber Philippe , Navratil Vincent , Duchamp Claude , Mondy Nathalie 
Published: July 2021

AbstractArtificial light at night (ALAN) affects numerous physiological and behavioural mechanisms in various species by potentially disturbing circadian timekeeping systems. Although gene-specific approaches have already shown the deleterious effect of ALAN on the circadian clock, immunity and reproduction, large-scale transcriptomic approaches with ecologically relevant light levels are still lacking to assess the global impact of ALAN on biological processes. Moreover, studies have focused mainly on variations in gene expression during the night in the presence of ALAN but never during the day. In a controlled laboratory experiment, transcriptome sequencing of Bufo bufo tadpoles revealed that ALAN affected gene expression at both night and daytime with a dose-dependent effect and globally induced a downregulation of genes. ALAN effects were detected at very low levels of illuminance (0.1 lux) and affected mainly genes related to the innate immune system and, to a lesser extend to lipid metabolism. These results indicate that a broad range of physiological pathways is impacted at the molecular level by very low levels of ALAN potentially resulting in reduced survival under environmental immune challenges.
Cellular toxicity of iHAP1 and DT-061 does not occur through PP2A-B56 targeting
Authors: Vit Gianmatteo , Duro Joana , Rajendraprasad Girish , Hertz Emil P.T. , Kauffeldt Holland Lya Katrine , Weisser Melanie Bianca , McEwan Brennan C. , Lopez-Mendez Blanca , Montoya Guillermo , Mailand Niels , Maeda Kenji , Kettenbach Arminja , Barisic Marin , Nilsson Jakob 
Published: July 2021

AbstractPP2A is an abundant phosphoprotein phosphatase that acts as a tumor suppressor. For this reason, compounds able to activate PP2A are attractive anticancer agents. The small molecule compounds iHAP1 and DT-061 have recently been reported by Leonard et al. (2020) and Morita et al. (2020) inCellto selectively stabilize specific PP2A-B56 complexes which mediate cell killing. Here, we show that this is not the case and question key findings in these papers. Through genome wide CRISPR-Cas9 screens, we uncover the biological pathways targeted by these compounds. We find that iHAP1 directly blocks microtubule assembly bothin vitroandin vivoand thus acts as a microtubule poison. In contrast, DT-061 disrupts both the Golgi apparatus and the endoplasmic reticulum and we directly visualize DT-061 in cytoplasmic granules that co-localize with Golgi markers. Our work demonstrates that iHAP1 and DT-061 cannot be used for dissecting PP2A-B56 biology.
Synthetic metabolic pathways for conversion of CO2 into secreted short-to medium-chain hydrocarbons using cyanobacteria
Authors: Yunus Ian S. , Anfelt Josefine , Hudson Elton P. , Jones Patrik R. 
Published: July 2021

AbstractThe objective of this study was to implement direct sunlight-driven conversion of CO2 into a naturally excreted ready-to-use fuel. We engineered four different synthetic metabolic modules for biosynthesis of short-to medium-chain length hydrocarbons in the model cyanobacterium Synechocystis sp. PCC 6803. In module 1, the combination of a truncated clostridial n-butanol pathway with over-expression of the native cyanobacterial aldehyde deformylating oxygenase resulted in small quantities of propane when cultured under closed conditions. Direct conversion of CO2 into propane was only observed in strains with CRISPRi-mediated repression of three native putative aldehyde reductases. In module 2, three different pathways towards pentane were evaluated based on the polyunsaturated fatty acid linoleic acid as an intermediate. Through combinatorial evaluation of bioreaction ingredients it was concluded that linoleic acid undergoes a spontaneous non-enzymatic reaction to yield pentane and hexanal. When Synechocystis was added to the bioreaction, hexanal was converted into 1-hexanol, but there was no further stimulation of pentane biosynthesis. For modules 3 and 4, several different acyl-ACP thioesterases were evaluated in combination with two different decarboxylases. Small quantities of 1-heptene and 1-nonene were observed in strains expressing the desaturase-like enzyme UndB from Pseudomonas mendocina in combination with C8-C10 preferring thioestersaes. When UndB instead was combined with a C12-specific ‘UcFatB1 thioesterase, this resulted in ten-fold increase of alkene biosynthesis. When UndB was replaced with the light-dependent FAP decarboxylase, both undecane and tridecane accumulated, albeit with a 10-fold drop in productivity. Optimization of the RBS, promoter and gene order in these synthetic operons resulted in 1-alkene bioproductivity of 230 mg/L after 10 d with 15% carbon partitioning. In conclusion, the direct bioconversion of CO2 into secreted and ready-to-use hydrocarbon fuel was accomplished and optimal results were obtained with UndB and a C12 chain-length specific thioesterase.HighlightsMultiple repression of endogenous aldehyde reductases/dehydrogenases by CRISPRi enabled propane biosynthesisBiosynthesis of short-medium chain hydrocarbons (C7-C11) in a cyanobacterium was demonstrated for the first timeThe final enzymes of the hydrocarbon pathways influenced both productivity and product profileAll volatile products were naturally secreted and accumulated outside of the cell
PlotXpress, a webtool for normalization and visualization of reporter expression data
Authors: Brandorff Elias , Galland Marc , Goedhart Joachim 
Published: July 2021

AbstractIn molecular cell biology, reporter assays are frequently used to investigate gene expression levels. Reporter assays employ a gene that encodes a light-emitting protein, of which the luminescence is quantified as a proxy of gene expression. Commercial parties provide reporter assay kits that include protocols and specialized detection machinery. However, downstream analysis of the output data and their presentation are not standardized. We have developed plotXpress to fill this gap, providing a free, open-source platform for the semi-automated analysis and standardized visualisation of experimental gene reporter data. Users can upload raw luminescence data acquired from a reporter gene assay with an internal control. In plotXpress, the data is corrected for sample variation with the internal control and the average for each condition is calculated. When a reference condition is selected the fold change is calculated for all other conditions, based on the selected reference. The results are shown as dot plots with a statistical summary, which can be adjusted to create publication-grade plots without requiring coding skills. Altogether, plotXpress is an open-source, low-threshold, web-based tool, that promotes a standardized and reproducible analysis while providing an appealing visualization of reporter data. The webtool can be accessed at: https://huygens.science.uva.nl/PlotXpress/Abstract Figure
Identifying cellular-to-phenotype associations by elucidating hierarchical relationships in high-dimensional cytometry data
Authors: Chan Adam , Jiang Wei , Blyth Emily , Yang Jean , Patrick Ellis 
Published: July 2021

AbstractHigh-throughput single cell technologies hold the promise of discovering novel cellular relationships with disease. However, analytical workflows constructed for these technologies to associate cell proportions with disease often employ unsupervised clustering techniques that overlook the valuable hierarchical structures that have been used to define cell types. We present treekoR, a framework that empirically recapitulates these structures, facilitating multiple quantifications and comparisons of cell type proportions. Our results from twelve case studies reinforce the importance of quantifying proportions relative to parent populations in the analyses of cytometry data — as failing to do so can lead to missing important biological insights.