bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gore Cardioform atrial septal occluder: deployment procedure and techniques for closing challenging secundum atrial septal defects
Authors: Aggarwal Varun , Mohan Arjun K. , Bass John , Steinberger Julia , Said Sameh M. , Qureshi Athar M. 
Published: October 2021

AbstractOstium secundum atrial septal defects are mostly closed in the cardiac catheterisation laboratories using either Amplatzer® (Abbott Laboratories, IL) atrial septal occluder, Gore® Cardioform septal occluder and more recently using the recently approved (US FDA approval June 2019) Gore® Cardioform atrial septal defect occluder (W. L. Gore & Associates, AZ). Similar to any new device in the market, there is a learning curve to the deployment of this device. We therefore aim to report the key features about this new Gore Cardioform atrial septal defect occluder device with special emphasis on technical aspects that can be employed during transcatheter closure of challenging ostium secundum atrial septal defects using this device.
TWISTS, CROSSED PRODUCTS AND INVERSE SEMIGROUP COHOMOLOGY
Authors: STEINBERG BENJAMIN 
Published: October 2021

AbstractTwisted étale groupoid algebras have recently been studied in the algebraic setting by several authors in connection with an abstract theory of Cartan pairs of rings. In this paper we show that extensions of ample groupoids correspond in a precise manner to extensions of Boolean inverse semigroups. In particular, discrete twists over ample groupoids correspond to certain abelian extensions of Boolean inverse semigroups, and we show that they are classified by Lausch’s second cohomology group of an inverse semigroup. The cohomology group structure corresponds to the Baer sum operation on twists.We also define a novel notion of inverse semigroup crossed product, generalizing skew inverse semigroup rings, and prove that twisted Steinberg algebras of Hausdorff ample groupoids are instances of inverse semigroup crossed products. The cocycle defining the crossed product is the same cocycle that classifies the twist in Lausch cohomology.
Genome-wide association study of physical and microstructure-related traits in peanut shell
Authors: Cui Kailu , Qi Feiyan , Sun Ziqi , Feng Jingjing , Huang Bingyan , Dong Wenzhao , Zhang Xinyou 
Published: October 2021

AbstractPeanut shell plays key roles in protecting the seed from diseases and pest infestation but also in the processing of peanut and is an important byproduct of peanut production. Most studies on peanut shell have focused on the utilization of its chemical applications, but the genetic basis of shell-related traits is largely unknown. A panel of 320 peanut (Arachis hypogaea) accessions including var.hypogaea, var.vulgaris, var.fastigiataand var.hirsutawas used to study the genetic basis of two physical and five microstructure-related traits in peanut shell. Significant phenotypic differences were revealed among the accessions of var.hypogaea, var.hirsuta, var.vulgarisand var.fastigiatafor mechanical strength, thickness, three sclerenchymatous layer projections and main cell shape of the sclerenchymatous layer. We identified 10 significant single nucleotide polymorphisms (SNPs) through genome-wide association study (P< 5.0 × 10−6) combining the shell-related traits and high-quality SNPs. In total, 192 genes were located in physical proximity to the significantly associated SNPs, and 11 candidate genes were predicted related to their potential contribution to the development and structure of the peanut shell. All SNPs were detected on the B genome demonstrating the biased contribution of the B genome for the phenotypical make-up of peanut. Exploring the newly identified candidate genes will provide insight into the molecular pathways that regulate peanut shell-related traits and provide valuable information for molecular marker-assisted breeding of an improved peanut shell.
Molecular characterization of Vigna marina (Burm.f.) Merr. from the Andaman and Nicobar Islands for salt tolerance using SSR markers
Authors: Prithivi M. , Venkatesan K. , Manimaran D. R. , Gautam R. K. , Singh P. K. , Sakthivel K. , Ahmed S. K. Zamir , Pandey S. K. , Rao Shyam Sunder 
Published: October 2021

AbstractBeachpea (Vigna marina) is a halophytic wild leguminous plant which occurs throughout tropical and subtropical beaches of world. As quantitative trait loci (QTLs) for salt tolerance in V. marina and its crossability with other Vigna species are known, the current study was undertaken to know the presence of these QTLs in the V. marina accessions along with check varieties of pulses. Accordingly, 20 Vigna genotypes (15 accessions of V. marina collected from sea-shore areas of Andaman and Nicobar Islands along with five check varieties of green gram and black gram) were subjected to molecular characterization using seven simple sequence repeat (SSR) markers associated with salt tolerance. Of the markers used, only four SSR markers amplified in the studied germplasm. Number of alleles detected per primer and size of alleles ranged from 1 to 3 and 100 to 325 bp, respectively. Polymorphism information content and heterozygosity values ranged from 0.305 to 0.537 and 0.375 to 0.612, respectively. Three major clusters, cluster I, II and III were obtained at Jaccard's similarity coefficient value of 0.48 through the un-weighted paired group method with arithmetic means method of cluster analysis. It grouped green gram and black gram genotypes in clusters I (04) and II (01), whereas all V. marina genotypes were grouped in cluster III (15). Principal co-ordinate analysis explained 85.9% of genetic variation among genotypes which was further confirmed by cluster analysis. This study indicated the effectiveness of SSR markers in separating cultivated Vigna species from wild V. marina. The findings will be useful for transferring trait of robust salt tolerance of V. marina in cultivated Vigna species using marker-assisted breeding.
Paleosecular Variation and the Time‐Averaged Geomagnetic Field Since 10 Ma
Authors: de Oliveira Wellington P. , Hartmann Gelvam A. , Terra‐Nova Filipe , Brandt Daniele , Biggin Andrew J. , Engbers Yael A. , Bono Richard K. , Savian Jairo F. , Franco Daniel R. , Trindade Ricardo I. F. , Moncinhatto Thiago R. 
Published: October 2021

AbstractInvestigations into long‐term geomagnetic variations provide useful information regarding paleomagnetic field behavior. In this study, we assess the latitudinal structure of paleosecular variation (PSV) and the time‐averaged field (TAF) for the Brunhes normal and Matuyama reverse chrons, and for the 0–10 Ma period, from an updated and reviewed paleodirectional database spanning the past 10 Myr. The new database comprises 2,543 paleomagnetic sites from igneous rocks, providing improvements in the geographic and temporal distributions of high‐quality data relative to previous compilations. In addition, the new data collection differs considerably in application of strict selection criteria. Statistical analysis of the virtual geomagnetic pole (VGP) dispersion curve of Model G reveals a low latitudinal dependence of PSV for the last 10 Myr. For this period, we present a zonal TAF model based on the latitudinal distribution of inclination anomaly data. The best estimates found for axial quadrupole and octupole components were about 3% and 1% relative to axial dipole component, respectively. The new statistical models for the Brunhes and Matuyama chrons have different patterns in both PSV and TAF, in compliance with earlier studies. Our quantitative assessments indicate an apparent hemispheric PSV asymmetry, particularly in the Brunhes chron, with a stronger latitudinal signature in the southern hemisphere compared to the north. These findings suggest that equatorial PSV asymmetry, that has previously been found in modern, historical and millennial scale geomagnetic models, has persisted over the past 0.78 Ma.
A New Open Source Implementation of Lagrangian Filtering: A Method to Identify Internal Waves in High‐Resolution Simulations
Authors: Shakespeare Callum J. , Gibson Angus H. , Hogg Andrew McC. , Bachman Scott D. , Keating Shane R. , Velzeboer Nick 
Published: October 2021

AbstractIdentifying internal waves in complex flow fields is a long‐standing problem in fluid dynamics, oceanography and atmospheric science, owing to the overlap of internal waves temporal and spatial scales with other flow regimes. Lagrangian filtering—that is, temporal filtering in a frame of reference moving with the flow—is one proposed methodology for performing this separation. Here we (a) describe an improved implementation of the Lagrangian filtering methodology and (b) introduce a new freely available, parallelized Python package that applies the method. We show that the package can be used to directly filter output from a variety of common ocean models including MITgcm, Regional Ocean Modeling System and MOM5 for both regional and global domains at high resolution. The Lagrangian filtering is shown to be a useful tool to both identify (and thereby quantify) internal waves, and to remove internal waves to isolate the non‐wave flow field.
Estimating the Geoelectric Field and Electric Power Transmission Line Voltage During a Geomagnetic Storm in Alberta, Canada Using Measured Magnetotelluric Impedance Data: The Influence of Three‐Dimensional Electrical Structures in the Lithosphere
Authors: Cordell Darcy , Unsworth Martyn J. , Lee Benjamin , Hanneson Cedar , Milling David K. , Mann Ian R. 
Published: October 2021

AbstractEstimating the effect of geomagnetic disturbances on power grid infrastructure is an important problem since they can induce damaging currents in electric power transmission lines. In this study, an array of magnetotelluric (MT) impedance measurements in Alberta and southeastern British Columbia are used to estimate the geoelectric field resulting from a magnetic storm on September 8, 2017. The resulting geoelectric field is compared to the geoelectric field modeled using the more common method that uses a piecewise‐continuous 1‐D conductivity model. The 1‐D model assumes horizontal layers, which result in orthogonal induced electric fields while the measured MT impedance data can account for fully 3‐D conductivity structure. The geoelectric field derived from measured MT impedance data is partially polarized in southern Alberta, and the geoelectric field magnitude is largest in northeastern Alberta where the resistive Canadian Shield outcrops. The induced voltage in the Alberta transmission network is estimated to be ∼120 V larger in northeastern Alberta when using the measured MT impedances compared to the piecewise‐continuous 1‐D model. Estimated voltages on transmission lines oriented NW‐SE in southern Alberta are 10%–20% larger when using the MT impedances due to the polarized geoelectric field. As shown with forward modeling tests, the polarization is due to a feature in the lower crust (20–30 km depth) called the Southern Alberta British Columbia conductor that is associated with a Proterozoic tectonic suture zone. This forms an important link between ancient tectonic processes and modern‐day geoelectric hazards that cannot be modeled with a 1‐D analysis.
Calcium-dependent signalling in B-cell lymphomas
Authors: Berditchevski Fedor , Fennell Eanna , Murray Paul G. 
Published: October 2021

AbstractInduced waves of calcium fluxes initiate multiple signalling pathways that play an important role in the differentiation and maturation of B-cells. Finely tuned transient Ca+2fluxes from the endoplasmic reticulum in response to B-cell receptor (BCR) or chemokine receptor activation are followed by more sustained calcium influxes from the extracellular environment and contribute to the mechanisms responsible for the proliferation of B-cells, their migration within lymphoid organs and their differentiation. Dysregulation of these well-balanced mechanisms in B-cell lymphomas results in uncontrolled cell proliferation and resistance to apoptosis. Consequently, several cytotoxic drugs (and anti-proliferative compounds) used in standard chemotherapy regimens for the treatment of people with lymphoma target calcium-dependent pathways. Furthermore, ~10% of lymphoma associated mutations are found in genes with functions in calcium-dependent signalling, including those affecting B-cell receptor signalling pathways. In this review, we provide an overview of the Ca2+-dependent signalling network and outline the contribution of its key components to B cell lymphomagenesis. We also consider how the oncogenic Epstein-Barr virus, which is causally linked to the pathogenesis of a number of B-cell lymphomas, can modify Ca2+-dependent signalling.
Negative feedback of SNRK to circ-SNRK regulates cardiac function post-myocardial infarction
Authors: Wang Zhi-Yan , Liu Xiao-Xiao , Deng Yun-Fei 
Published: October 2021

AbstractA limited delivery of oxygen and metabolic substrate to the heart caused by myocardial infarction (MI) impairs the cardiac function, and often results in heart failure. Here, we identified a circRNA (circ-SNRK) from SNRK (sucrose nonfermenting 1-related kinase, which can increase the cardiac mitochondrial efficiency) in cardiomyocytes (CMs). Circ-SNRK can sponge the miR-33 and in turn improved the ATP synthesis via SNRK, proving the existence of circ-SNRK - miR-33 - SNRK axis. Furthermore, we found that protein NOVA1 (NOVA alternative splicing regulator 1) could accelerate the circ-SNRK formation; a cleaved peptide (~55 kDa) from SNRK enters the nucleus and blocks the cyclization of circ-SNRK via binding to NOVA1. The aforementioned negative feedback of SNRK to circ-SNRK limited the SNRK at a proper level, and inhibited the protective role of circ-SNRK in ischemic heart. In addition, our in vivo experiment indicated that the overexpression of exogenic circ-SNRK could break this loop and improves the cardiac function post-MI in rats. Together, our results demonstrated that the negative loop of circ-SNRK with SNRK regulates the energy metabolism in CMs, thus might be a potential therapeutic target for heart failure.
Inhibition of the ubiquitin-proteasome system by an NQO1-activatable compound
Authors: Giovannucci Tatiana A. , Salomons Florian A. , Haraldsson Martin , Elfman Lotta H. M. , Wickström Malin , Young Patrick , Lundbäck Thomas , Eirich Jürgen , Altun Mikael , Jafari Rozbeh , Gustavsson Anna-Lena , Johnsen John Inge , Dantuma Nico P. 
Published: October 2021

AbstractMalignant cells display an increased sensitivity towards drugs that reduce the function of the ubiquitin-proteasome system (UPS), which is the primary proteolytic system for destruction of aberrant proteins. Here, we report on the discovery of the bioactivatable compound CBK77, which causes an irreversible collapse of the UPS, accompanied by a general accumulation of ubiquitylated proteins and caspase-dependent cell death. CBK77 caused accumulation of ubiquitin-dependent, but not ubiquitin-independent, reporter substrates of the UPS, suggesting a selective effect on ubiquitin-dependent proteolysis. In a genome-wide CRISPR interference screen, we identified the redox enzyme NAD(P)H:quinone oxidoreductase 1 (NQO1) as a critical mediator of CBK77 activity, and further demonstrated its role as the compound bioactivator. Through affinity-based proteomics, we found that CBK77 covalently interacts with ubiquitin. In vitro experiments showed that CBK77-treated ubiquitin conjugates were less susceptible to disassembly by deubiquitylating enzymes. In vivo efficacy of CBK77 was validated by reduced growth of NQO1-proficient human adenocarcinoma cells in nude mice treated with CBK77. This first-in-class NQO1-activatable UPS inhibitor suggests that it may be possible to exploit the intracellular environment in malignant cells for leveraging the impact of compounds that impair the UPS.
A chemical probe based on the PreQ1 metabolite enables transcriptome-wide mapping of binding sites
Authors: Balaratnam Sumirtha , Rhodes Curran , Bume Desta Doro , Connelly Colleen , Lai Christopher C. , Kelley James A. , Yazdani Kamyar , Homan Philip J. , Incarnato Danny , Numata Tomoyuki , Schneekloth Jr John S. 
Published: October 2021

AbstractThe role of metabolite-responsive riboswitches in regulating gene expression in bacteria is well known and makes them useful systems for the study of RNA-small molecule interactions. Here, we study the PreQ1 riboswitch system, assessing sixteen diverse PreQ1-derived probes for their ability to selectively modify the class-I PreQ1 riboswitch aptamer covalently. For the most active probe (11), a diazirine-based photocrosslinking analog of PreQ1, X-ray crystallography and gel-based competition assays demonstrated the mode of binding of the ligand to the aptamer, and functional assays demonstrated that the probe retains activity against the full riboswitch. Transcriptome-wide mapping using Chem-CLIP revealed a highly selective interaction between the bacterial aptamer and the probe. In addition, a small number of RNA targets in endogenous human transcripts were found to bind specifically to 11, providing evidence for candidate PreQ1 aptamers in human RNA. This work demonstrates a stark influence of linker chemistry and structure on the ability of molecules to crosslink RNA, reveals that the PreQ1 aptamer/ligand pair are broadly useful for chemical biology applications, and provides insights into how PreQ1, which is similar in structure to guanine, interacts with human RNAs.
Staphylococcal phages and pathogenicity islands drive plasmid evolution
Authors: Humphrey Suzanne , San Millán Álvaro , Toll-Riera Macarena , Connolly John , Flor-Duro Alejandra , Chen John , Ubeda Carles , MacLean R. Craig , Penadés José R. 
Published: October 2021

AbstractConjugation has classically been considered the main mechanism driving plasmid transfer in nature. Yet bacteria frequently carry so-called non-transmissible plasmids, raising questions about how these plasmids spread. Interestingly, the size of many mobilisable and non-transmissible plasmids coincides with the average size of phages (~40 kb) or that of a family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs, ~11 kb). Here, we show that phages and PICIs from Staphylococcus aureus can mediate intra- and inter-species plasmid transfer via generalised transduction, potentially contributing to non-transmissible plasmid spread in nature. Further, staphylococcal PICIs enhance plasmid packaging efficiency, and phages and PICIs exert selective pressures on plasmids via the physical capacity of their capsids, explaining the bimodal size distribution observed for non-conjugative plasmids. Our results highlight that transducing agents (phages, PICIs) have important roles in bacterial plasmid evolution and, potentially, in antimicrobial resistance transmission.
A proteomics sample metadata representation for multiomics integration and big data analysis
Authors: Dai Chengxin , Füllgrabe Anja , Pfeuffer Julianus , Solovyeva Elizaveta M. , Deng Jingwen , Moreno Pablo , Kamatchinathan Selvakumar , Kundu Deepti Jaiswal , George Nancy , Fexova Silvie , Grüning Björn , Föll Melanie Christine , Griss Johannes , Vaudel Marc , Audain Enrique , Locard-Paulet Marie , Turewicz Michael , Eisenacher Martin , Uszkoreit Julian , Van Den Bossche Tim , Schwämmle Veit , Webel Henry , Schulze Stefan , Bouyssié David , Jayaram Savita , Duggineni Vinay Kumar , Samaras Patroklos , Wilhelm Mathias , Choi Meena , Wang Mingxun , Kohlbacher Oliver , Brazma Alvis , Papatheodorou Irene , Bandeira Nuno , Deutsch Eric W. , Vizcaíno Juan Antonio , Bai Mingze , Sachsenberg Timo , Levitsky Lev I. , Perez-Riverol Yasset 
Published: October 2021

AbstractThe amount of public proteomics data is rapidly increasing but there is no standardized format to describe the sample metadata and their relationship with the dataset files in a way that fully supports their understanding or reanalysis. Here we propose to develop the transcriptomics data format MAGE-TAB into a standard representation for proteomics sample metadata. We implement MAGE-TAB-Proteomics in a crowdsourcing project to manually curate over 200 public datasets. We also describe tools and libraries to validate and submit sample metadata-related information to the PRIDE repository. We expect that these developments will improve the reproducibility and facilitate the reanalysis and integration of public proteomics datasets.
Calibrated rare variant genetic risk scores for complex disease prediction using large exome sequence repositories
Authors: Lali Ricky , Chong Michael , Omidi Arghavan , Mohammadi-Shemirani Pedrum , Le Ann , Cui Edward , Paré Guillaume 
Published: October 2021

AbstractRare variants are collectively numerous and may underlie a considerable proportion of complex disease risk. However, identifying genuine rare variant associations is challenging due to small effect sizes, presence of technical artefacts, and heterogeneity in population structure. We hypothesize that rare variant burden over a large number of genes can be combined into a predictive rare variant genetic risk score (RVGRS). We propose a method (RV-EXCALIBER) that leverages summary-level data from a large public exome sequencing database (gnomAD) as controls and robustly calibrates rare variant burden to account for the aforementioned biases. A calibrated RVGRS strongly associates with coronary artery disease (CAD) in European and South Asian populations by capturing the aggregate effect of rare variants through a polygenic model of inheritance. The RVGRS identifies 1.5% of the population with substantial risk of early CAD and confers risk even when adjusting for known Mendelian CAD genes, clinical risk factors, and a common variant genetic risk score.
NLRP3 phosphorylation in its LRR domain critically regulates inflammasome assembly
Authors: Niu Tingting , De Rosny Charlotte , Chautard Séverine , Rey Amaury , Patoli Danish , Groslambert Marine , Cosson Camille , Lagrange Brice , Zhang Zhirong , Visvikis Orane , Hacot Sabine , Hologne Maggy , Walker Olivier , Wong Jeimin , Wang Ping , Ricci Roméo , Henry Thomas , Boyer Laurent , Petrilli Virginie , Py Bénédicte F. 
Published: October 2021

AbstractNLRP3 controls the secretion of inflammatory cytokines IL-1β/18 and pyroptosis by assembling the inflammasome. Upon coordinated priming and activation stimuli, NLRP3 recruits NEK7 within hetero-oligomers that nucleate ASC and caspase-1 filaments, but the apical molecular mechanisms underlying inflammasome assembly remain elusive. Here we show that NEK7 recruitment to NLRP3 is controlled by the phosphorylation status of NLRP3 S803 located within the interaction surface, in which NLRP3 S803 is phosphorylated upon priming and later dephosphorylated upon activation. Phosphomimetic substitutions of S803 abolish NEK7 recruitment and inflammasome activity in macrophages in vitro and in vivo. In addition, NLRP3-NEK7 binding is also essential for NLRP3 deubiquitination by BRCC3 and subsequently inflammasome assembly, with NLRP3 phosphomimetic mutants showing enhanced ubiquitination and degradation than wildtype NLRP3. Finally, we identify CSNK1A1 as the kinase targeting NLRP3 S803. Our findings thus reveal NLRP3 S803 phosphorylation status as a druggable apical molecular mechanism controlling inflammasome assembly.