bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimation of stroke outcomes based on time to thrombolysis and thrombectomy
Authors: Allen Michael , Pearn Kerry , Stein Ken , James Martin 
Published: July 2020

AbstractBackground & MotivationStroke outcomes following revascularization therapy (intravenous thrombolysis, IVT, and/or mechanical thrombectomy, MT) depend critically on time from stroke onset to treatment. Different service configurations may prioritise time to IVT or time to MT. In order to evaluate alternative acute stroke care configurations, it is necessary to estimate clinical outcomes given differing times to IVT and MT.MethodModel using an algorithm coded in Python. This is available at https://github.com/MichaelAllen1966/stroke_outcome_algorithmResultsWe demonstrate how the code may be used to estimate clinical outcomes given varying times to IVT and MT.ConclusionPython code has been developed and shared to enable estimation of clinical outcome given times to IVT and MT. Here we share pseudocode and links to full Python code.
The association between Internet Usage and Overweight/Obesity modified by Gender: Evidence from a nationally representative survey in Nepal
Authors: Rana Juwel , Islam Md. Momin , Oldroyd John , Samad Nandeeta , Islam Rakibul M. 
Published: July 2020

AbstractObjectiveUsing a nationally representative data, we examined the associations between internet use and overweight/obesity in people aged 15-49 years in Nepal, and the extent to which these associations vary by gender.Materials and methodsThe study analyzed the nationally representative Nepal Demographic and Health Survey (NDHS) 2016 data, collected between June 2016 and January 2017. The outcome was overweight/obesity. Exposures were internet use (IU) in the last twelve months and internet use frequency (FIU) in the last month. Multivariable ordinal logistic regression models were fitted to estimate the total effects of IU and FIU on overweight/obesity adjusted for minimal sufficient adjustment set of potential confounders. P-difference was extracted using a Wald test for the models with interaction terms.ResultsOf the 10,380 participants, 33.9% used internet in the last 12 months, and 13.1 % used less than/at least once in a week, and 17.5% used internet almost every day. The prevalence of overweight/obesity by IU was 38% (95% CI: 35.9%, 40.1%) for male and 44.1% (95% CI: 41.6%, 46.6) for female. The risk of overweight and obesity was significantly 1.55 times higher (aOR: 1.55; 95% CI: 1.40, 1.73; p < 0.001) among those participants who used the internet compared to the individual who did not use the internet in the last 12 months or earlier of the interview. Similar associations were observed when using the augmented measure of exposure-FIU. We observed modification effect of gender in the associations of IU (p-difference<0.001) and FIU (p-difference<0.002) with overweight and obesity in Nepal.ConclusionsOur findings suggest that it is imperative for future overweight/obesity interventions in LMICs, including Nepal, to discourage unnecessary internet use, particularly among males.
Combined short and long-read sequencing reveals a complex transcriptomic architecture of African swine fever virus
Authors: Torma Gábor , Tombácz Dóra , Csabai Zsolt , Moldován Norbert , Mészáros István , Zádori Zoltán , Boldogkői Zsolt 
Published: July 2020

ABSTRACTAfrican swine fever virus (ASFV) is a large DNA virus belonging to theAsfarviridaefamily. Despite its agricultural importance, little is known about the fundamental molecular mechanisms of this pathogen. Understanding of genetic regulation provides new insights into the virus pathogenicity, which can help prevent epidemics. Short-read sequencing (SRS) is able to produce a huge amount of high-precision sequencing reads for transcriptomic profiling, but it is inefficient for the comprehensive annotation of transcriptomes. Long-read sequencing (LRS) is able to overcome some of the limitations of SRS, but they also have drawbacks, such as low-coverage and high error rate. The limitations of the two approaches can be surmounted by the combined use of these techniques. In this study, we used Illumina SRS and Oxford Nanopore Technologies LRS platforms with multiple library preparation methods (amplified and direct cDNA sequencings and native RNA sequencing) for constructing the transcriptomic atlas of ASFV. This work identified a large number of novel genes, transcripts and RNA isoforms, and annotated the precise termini of previously described RNA molecules. In contrast to the current view that the ASFV transcripts are monocistronic, we detected a significant extent of polycistronism. A multifaceted meshwork of transcriptional overlaps is also discovered.
The landscape of SARS-CoV-2 RNA modifications
Authors: Miladi Milad , Fuchs Jonas , Maier Wolfgang , Weigang Sebastian , Pedrosa Núria Díaz i , Weiss Lisa , Lother Achim , Nekrutenko Anton , Ruzsics Zsolt , Panning Marcus , Kochs Georg , Gilsbach Ralf , Grüning Björn 
Published: July 2020

AbstractIn 2019 the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the first documented cases of severe lung disease COVID-19. Since then, SARS-CoV-2 has been spreading around the globe resulting in a severe pandemic with over 500.000 fatalities and large economical and social disruptions in human societies. Gaining knowledge on how SARS-Cov-2 interacts with its host cells and causes COVID-19 is crucial for the intervention of novel therapeutic strategies. SARS-CoV-2, like other coronaviruses, is a positive-strand RNA virus. The viral RNA is modified by RNA-modifying enzymes provided by the host cell. Direct RNA sequencing (DRS) using nanopores enables unbiased sensing of canonical and modified RNA bases of the viral transcripts. In this work, we used DRS to precisely annotate the open reading frames and the landscape of SARS-CoV-2 RNA modifications. We provide the first DRS data of SARS-CoV-2 in infected human lung epithelial cells. From sequencing three isolates, we derive a robust identification of SARS-CoV-2 modification sites within a physiologically relevant host cell type. A comparison of our data with the DRS data from a previous SARS-CoV-2 isolate, both raised in monkey renal cells, reveals consistent RNA modifications across the viral genome. Conservation of the RNA modification pattern during progression of the current pandemic suggests that this pattern is likely essential for the life cycle of SARS-CoV-2 and represents a possible target for drug interventions.
Haloferax volcanii immersed liquid biofilms develop independently of known biofilm machineries and exhibit rapid honeycomb pattern formation
Authors: Schiller Heather , Schulze Stefan , Mutan Zuha , de Vaulx Charlotte , Runcie Catalina , Schwartz Jessica , Rados Theopi , Bisson Filho Alexandre W. , Pohlschroder Mechthild 
Published: July 2020

AbstractThe ability to form biofilms is shared by many microorganisms, including archaea. Cells in a biofilm are encased in extracellular polymeric substances that typically include polysaccharides, proteins, and extracellular DNA, conferring protection while providing a structure that allows for optimal nutrient flow. In many bacteria, flagella and evolutionarily conserved type IV pili are required for the formation of biofilms on solid surfaces or floating at the air-liquid interface of liquid media. Similarly, in many archaea it has been demonstrated that type IV pili and, in a subset of these species, archaella are required for biofilm formation on solid surfaces. Additionally, in the model archaeon Haloferax volcanii, chemotaxis and AglB-dependent glycosylation play important roles in this process. H. volcanii also forms immersed biofilms in liquid cultures poured into Petri dishes. This study reveals that mutants of this haloarchaeon that interfere with the biosynthesis of type IV pili or archaella, as well as a chemotaxis-targeting transposon and aglB-deletion mutants, lack obvious defects in biofilms formed in liquid cultures. Strikingly, we have observed that these liquid-based biofilms are capable of rearrangement into honeycomb-like patterns that rapidly form upon removal of the Petri dish lid, a phenomenon that is not dependent on changes in light or oxygen concentration but can be induced by controlled reduction of humidity. Taken together, this study demonstrates that H. volcanii requires novel, as-yet-unidentified strategies for immersed liquid biofilm formation and also exhibits rapid structural rearrangements.ImportanceThis first molecular biological study of archaeal immersed liquid biofilms advances our basic-biological understanding of the model archaeon Haloferax volcanii. Data gleaned from this study also provide an invaluable foundation for future studies to uncover components required for immersed liquid biofilms in this haloarchaeon and also potentially for liquid biofilm formation in general, which is poorly understood compared to the formation of biofilms on surfaces. Moreover, this first description of rapid honeycomb pattern formation is likely to yield novel insights into the underlying structural architecture of extracellular polymeric substances and cells within immersed liquid biofilms.
Understanding photothermal interactions will help expand production range and increase genetic diversity of lentil (Lens culinarisMedik.)
Authors: Wright Derek M. , Neupane Sandesh , Heidecker Taryn , Haile Teketel A. , Coyne Clarice J. , McGee Rebecca J. , Udupa Sripada , Henkrar Fatima , Barilli Eleonora , Rubiales Diego , Gioia Tania , Logozzo Giuseppina , Marzario Stefania , Mehra Reena , Sarker Ashutosh , Dhakal Rajeev , Anwar Babul , Sarkar Debashish , Vandenberg Albert , Bett Kirstin E. 
Published: July 2020

SummaryLentil (Lens culinarisMedik.) is cultivated under a wide range of environmental conditions, which led to diverse phenological adaptations and resulted in a decrease in genetic variability within breeding programs due to reluctance in using genotypes from other environments.We phenotyped 324 genotypes across nine locations over three years to assess their phenological response to the environment of major lentil production regions and to predict days from sowing to flowering (DTF) using a photothermal model.DTF was highly influenced by the environment and is sufficient to explain adaptation. We were able to predict DTF reliably in most environments using a simple photothermal model, however, in certain site-years, results suggest there may be additional environmental factors at play. Hierarchical clustering of principal components revealed the presence of eight groups based on the responses of DTF to contrasting environments. These groups are associated with the coefficients of the photothermal model and revealed differences in temperature and photoperiod sensitivity.Expanding genetic diversity is critical to the success of a breeding program; understanding adaptation will facilitate the use of exotic germplasm. Future climate change scenarios will result in increase temperature and/or shifts in production areas, we can use the photothermal model to identify genotypes most likely to succeed in these new environments.
RNAseq analysis of rodent spaceflight experiments is confounded by sample collection techniques
Authors: Polo San-Huei Lai , Saravia-Butler Amanda M. , Boyko Valery , Dinh Marie T. , Chen Yi-Chun , Fogle Homer , Reinsch Sigrid S. , Ray Shayoni , Chakravarty Kaushik , Marcu Oana , Chen Rick B. , Costes Sylvain V. , Galazka Jonathan M. 
Published: July 2020

SummaryTo understand the physiological changes that occur in response to spaceflight, mice are transported to the International Space Station (ISS) and housed for variable periods of time before euthanasia on-orbit or return to Earth. Sample collection under such difficult conditions introduces confounding factors that need to be identified and addressed. We found large changes in the transcriptome of mouse tissues dissected and preserved on-orbit compared to tissues from mice euthanized on-orbit, preserved, and dissected after return to Earth. Changes due to preservation method eclipsed those between flight and ground samples making it difficult to identify spaceflight-specific changes. Follow-on experiments to interrogate the roles of euthanasia methods, tissue and carcass preservation protocols, and library preparation methods suggested that differences due to preservation protocols are exacerbated when coupled with polyA selection. This has important implications for the interpretation of existing datasets and the design of future experiments.
The KDEL Trafficking Receptor Exploits pH to Tune the Strength of an Unusual Short Hydrogen Bond
Authors: Wu Zhiyi , Newstead Simon , Biggin Philip C. 
Published: July 2020

AbstractThe endoplasmic reticulum (ER) is the main site of protein synthesis in eukaryotic cells and requires a high concentration of luminal chaperones to function. During protein synthesis, ER luminal chaperones are swept along the secretory pathway and must be retrieved to maintain cell viability. ER protein retrieval is achieved by the KDEL receptor, which recognises a C-terminal Lys-Asp-Glu-Leu (KDEL) sequence. Recognition of ER proteins by the KDEL receptor is pH dependent, with binding occurring under acidic conditions in the Golgi and release under conditions of higher pH in the ER. Recent crystal structures of the KDEL receptor in the apo and peptide bound state suggested that peptide binding drives the formation of a short-hydrogen bond that locks the KDEL sequence in the receptor and activates the receptor for COPI binding in the cytoplasm. Using quantum mechanical calculations we demonstrate that the strength of this short hydrogen bond is reinforced following protonation of a nearby histidine, linking receptor protonation to high affinity peptide binding. Protonation also controls the wetting of a cavity adjacent to the peptide binding site, leading to a conformational change that ultimately allows the complex to be recognized by the COPI system.
Metformin chlorination byproducts in drinking water exhibit marked toxicity to nematode worms, human cells, and mice
Authors: Zhang Runshuai , He Yuanzhen , Yao Luxia , Chen Jie , Zhu Shihao , Rao Xinxin , Tang Peiyuan , You Jia , Hua Guoqiang , Zhang Lu , Ju Feng , Wu Lianfeng 
Published: July 2020

AbstractMetformin (MET), a worldwide used drug for type 2 diabetes, has been found with the largest amount by weight among all drugs in aquatic environment, including the drinking water sources where chlorination inevitably transforms MET into chlorination byproducts. Although MET has health-promoting properties, whether or how its chlorination byproducts affect health remains largely unknown. Here we reveal that MET chlorination byproducts Y (C4H6ClN5) and C (C4H6ClN3) exhibit marked toxicity, even higher than that of the well-known poisonous arsenic, to live worms and human cells. Moreover, both byproducts are harmful to mice and Y at 250 ng/L destroys the mouse small intestine integrity. Strikingly, we detected MET and byproduct C in worldwide drinking water. Both byproducts are increasingly produced with more MET present during chlorination process. Unprecedentedly, we unveil boiling and activated carbon adsorption as effective solutions that are in urgent demand globally for removing these byproducts from water.
Long-term Reconstruction of Human Airway Epithelium-like Structurein Vivowith hESCs-derived organoid cells
Authors: Chen Yong , Han Le , Zhao Shanshan , Feng Jianqi , Li Lian , Rong Zhili , Lin Ying 
Published: July 2020

AbstractHuman embryonic stem cells (hESCs) derived lung organoids (HLOs) provide a promising model to study human lung development and disease. However, whether HLO cells could reconstitute airway epithelial structurein vivoremains unclear. Here we established an orthotopic xenograft system for hESCs-derived HLOs, enabling stable reconstruction of human airway epitheliumin vivo. Removal of the mouse airway epithelium by naphthalene (NA) treatment enabled xenografted organoid cells survival, differentiation, and reconstruction of airway pseudostratified epithelium in immune-compromised NSG mice. Compared to unsorted pool cells, CD47highcells generated more ciliated cells and possessed thicker pseudostratified epithelium. RNA-seq data revealed that CD47highcells highly expressed epithelial cell, lung progenitor, lung proximal cell and embryonic lung development associated genes. These data reveal that HLOs hold cell therapy potential in regenerative medicine by long-term reconstituting airway epithelium.
Myofibril and mitochondria morphogenesis are coordinated by a mechanical feedback mechanism in muscle
Authors: Avellaneda Jerome , Rodier Clement , Daian Fabrice , Rival Thomas , Luis Nuno Miguel , Schnorrer Frank 
Published: July 2020

AbstractComplex animals build specialised muscle to match specific biomechanical and energetic needs. Hence, composition and architecture of sarcomeres as well as mitochondria are muscle type specific. However, mechanisms coordinating mitochondria with sarcomere morphogenesis are elusive. Here we useDrosophilamuscles to demonstrate that myofibril and mitochondria morphogenesis are intimately linked. In flight muscles, the muscle selectorspaltinstructs mitochondria to intercalate between myofibrils, which in turn mechanically constrain mitochondria into elongated shapes. Conversely in cross-striated muscles, mitochondria networks surround myofibril bundles, contacting myofibrils only with thin extensions. To investigate the mechanism causing these differences, we manipulated mitochondrial dynamics and found that increased mitochondrial fusion during myofibril assembly prevents mitochondrial intercalation in flight muscles. Strikingly, this coincides with the expression of cross-striated muscle specific sarcomeric proteins. Consequently, flight muscle myofibrils convert towards a partially cross-striated architecture. Together, these data suggest a biomechanical feedback mechanism downstream ofspaltsynchronizing mitochondria with myofibril morphogenesis.
A multipass membrane protein interacts with the cGMP-dependent protein kinase to regulate critical calcium signals in malaria parasites
Authors: Balestra Aurélia C. , Koussis Konstantinos , Klages Natacha , Howell Steven A. , Flynn Helen R. , Bantscheff Marcus , Pasquarello Carla , Perrin Abigail J. , Brusini Lorenzo , Arboit Patrizia , Sanz Olalla , Castaño Laura Peces-Barba , Withers-Martinez Chrislaine , Hainard Alexandre , Ghidelli-Disse Sonja , Snijders Ambrosius P. , Baker David A. , Blackman Michael J. , Brochet Mathieu 
Published: July 2020

AbstractIn malaria parasites, all cGMP-dependent signalling is mediated through a single cGMP-dependent protein kinase (PKG), a major function of which is to control essential calcium signals. However, how PKG transmits these signals in the absence of known second messenger-dependent calcium channels or scaffolding proteins is unknown. Here we identify a polytopic membrane protein, ICM1, with homology to transporters and calcium channels that is tightly-associated with PKG in bothPlasmodium falciparumasexual blood stages andP. bergheigametocytes. Phosphoproteomic analyses in bothPlasmodiumspecies reveal multiple ICM1 phosphorylation events dependent upon PKG activity. Stage-specific depletion ofP. bergheiICM1 blocks gametogenesis due to the inability of mutant parasites to mobilise intracellular calcium upon PKG activation, whilst conditional loss ofP. falciparumICM1 results in reduced calcium mobilisation, defective egress and lack of invasion. Our findings provide new insights into atypical calcium homeostasis in malaria parasites essential for pathology and disease transmission.
Inhibition of CRISPR-Cas12a DNA Targeting by Nucleosomes and Chromatin
Authors: Strohkendl Isabel , Saifuddin Fatema A. , Gibson Bryan A. , Rosen Michael K. , Russell Rick , Finkelstein Ilya J. 
Published: July 2020

AbstractGenome engineering nucleases, including CRISPR-Cas12a, must access chromatinized DNA. Here, we investigate howAcidaminococcus sp. Cas12a cleaves DNA within human nucleosomes and phase-condensed nucleosome arrays. Using quantitative kinetics approaches, we show that dynamic nucleosome unwrapping regulates DNA target accessibility to Cas12a. Nucleosome unwrapping determines the extent to which both steps of Cas12a binding–PAM recognition and R-loop formation–are inhibited by the nucleosome. Nucleosomes inhibit Cas12a binding even beyond the canonical core particle. Relaxing DNA wrapping within the nucleosome by reducing DNA bendability, adding histone modifications, or introducing a target-proximal nuclease-inactive Cas9 enhances DNA cleavage rates over 10-fold. Surprisingly, Cas12a readily cleaves DNA linking nucleosomes within chromatin-like phase separated nucleosome arrays—with DNA targeting reduced only ~4-fold. This work provides a mechanism for the observation that on-target cleavage within nucleosomes occurs less often than off-target cleavage within nucleosome-depleted regions of cells. We conclude that nucleosome wrapping restricts accessibility to CRISPR-Cas nucleases and anticipate that increasing nucleosome breathing dynamics will improve DNA binding and cleavage in eukaryotic cells.
Inhibitors of VPS34 and lipid metabolism suppress SARS-CoV-2 replication
Authors: Silvas Jesus A. , Jureka Alexander S. , Nicolini Anthony M. , Chvatal Stacie A. , Basler Christopher F. 
Published: July 2020

ABSTRACTTherapeutics targeting replication of SARS coronavirus 2 (SARS-CoV-2) are urgently needed. Coronaviruses rely on host membranes for entry, establishment of replication centers and egress. Compounds targeting cellular membrane biology and lipid biosynthetic pathways have previously shown promise as antivirals and are actively being pursued as treatments for other conditions. Here, we tested small molecule inhibitors that target membrane dynamics or lipid metabolism. Included were inhibitors of the PI3 kinase VPS34, which functions in autophagy, endocytosis and other processes; Orlistat, an inhibitor of lipases and fatty acid synthetase, is approved by the FDA as a treatment for obesity; and Triacsin C which inhibits long chain fatty acyl-CoA synthetases. VPS34 inhibitors, Orlistat and Triacsin C inhibited virus growth in Vero E6 cells and in the human airway epithelial cell line Calu-3, acting at a post-entry step in the virus replication cycle. Of these the VPS34 inhibitors exhibit the most potent activity.
Membrane voltage-dependent activation of the flagellar protein export engine
Authors: Minamino Tohru , Morimoto Yusuke V. , Kinoshita Miki , Namba Keiichi 
Published: July 2020

AbstractIon motive force (IMF) consists of the electric potential difference (ΔΨ) and the ion concentration difference (ΔpI) across the cytoplasmic membrane. The flagellar protein export machinery is an ion/protein antiporter utilizing IMF to drive ion-coupled protein export, but it remains unknown how. Here, we report a ΔΨ-dependent activation mechanism of the transmembrane export gate complex. Depletions of both H+and Na+gradients nearly diminished flagellar protein export in the absence of the cytoplasmic ATPase complex, but an increase in ΔΨ by an upward shift of external pH from 7.5 to 8.5 dramatically recovered it. An increase in the cytoplasmic level of export substrates and gain-of-function mutations in FlhA enhanced protein export at external pH 7.5 in the absence of Na+in a similar manner to ΔΨ increase. We propose that the export gate complex has a voltage-gated mechanism to activate the ion/protein antiporter of the flagellar protein export engine.