bluuebunny/crossref_metadata_2025_split huggingface dataset:
Weather Conditions and COVID-19 Transmission: Estimates and Projections
Authors: Xu Ran , Rahmandad Hazhir , Gupta Marichi , DiGennaro Catherine , Ghaffarzadegan Navid , Jalali Mohammad S. 
Published: May 2020

AbstractBackgroundUnderstanding and projecting the spread of COVID-19 requires reliable estimates of how weather components are associated with the transmission of the virus. Prior research on this topic has been inconclusive. Identifying key challenges to reliable estimation of weather impact on transmission we study this question using one of the largest assembled databases of COVID-19 infections and weather.MethodsWe assemble a dataset that includes virus transmission and weather data across 3,739 locations from December 12, 2019 to April 22, 2020. Using simulation, we identify key challenges to reliable estimation of weather impacts on transmission, design a statistical method to overcome these challenges, and validate it in a blinded simulation study. Using this method and controlling for location-specific response trends we estimate how different weather variables are associated with the reproduction number for COVID-19. We then use the estimates to project the relative weather-related risk of COVID-19 transmission across the world and in large cities.ResultsWe show that the delay between exposure and detection of infection complicates the estimation of weather impact on COVID-19 transmission, potentially explaining significant variability in results to-date. Correcting for that distributed delay and offering conservative estimates, we find a negative relationship between temperatures above 25 degrees Celsius and estimated reproduction number (Ȓ), with each degree Celsius associated with a 3.1% (95% CI, 1.5% to 4.8%) reduction inȒ. Higher levels of relative humidity strengthen the negative effect of temperature above 25 degrees. Moreover, one millibar of additional pressure increasesȒby approximately 0.8 percent (95% CI, 0.6% to 1%) at the median pressure (1016 millibars) in our sample. We also find significant positive effects for wind speed, precipitation, and diurnal temperature onȒ. Sensitivity analysis and simulations show that results are robust to multiple assumptions. Despite conservative estimates, weather effects are associated with a 43% change inȒbetween the 5thand 95thpercentile of weather conditions in our sample.ConclusionsThese results provide evidence for the relationship between several weather variables and the spread of COVID-19. However, the (conservatively) estimated relationships are not strong enough to seasonally control the epidemic in most locations.
Multiple early introductions of SARS-CoV-2 into a global travel hub in the Middle East
Authors: Tayoun Ahmad Abou , Loney Tom , Khansaheb Hamda , Ramaswamy Sathishkumar , Harilal Divinlal , Deesi Zulfa Omar , Varghese Rupa Murthy , Al Suwaidi Hanan , Alkhajeh Abdulmajeed , AlDabal Laila Mohamed , Uddin Mohammed , Hamoudi Rifat , Halwani Rabih , Senok Abiola , Hamid Qutayba , Nowotny Norbert , Alsheikh-Ali Alawi 
Published: May 2020

AbstractInternational travel played a significant role in the early global spread of SARS-CoV-2. Understanding transmission patterns from different regions of the world will further inform global dynamics of the pandemic. Using data from Dubai in the United Arab Emirates (UAE), a major international travel hub in the Middle East, we establish SARS-CoV-2 full genome sequences from the index and early COVID-19 patients in the UAE. The genome sequences are analysed in the context of virus introductions, chain of transmissions, and possible links to earlier strains from other regions of the world. Phylogenetic analysis showed multiple spatiotemporal introductions of SARS-CoV-2 into the UAE from Asia, Europe, and the Middle East during the early phase of the pandemic. We also provide evidence for early community-based transmission and catalogue new mutations in SARS-CoV-2 strains in the UAE. Our findings contribute to the understanding of the global transmission network of SARS-CoV-2.
Ethnicity, comorbidity, socioeconomic status, and their associations with COVID-19 infection in England: a cohort analysis of UK Biobank data
Authors: Prats-Uribe Albert , Paredes Roger , Prieto-Alhambra Daniel 
Published: May 2020

AbstractObjectivesRecent data suggest higher COVID-19 rates and severity in Black, Asian, and minority ethnic (BAME) communities. The mechanisms underlying such associations remain unclear. We aimed to study the association between ethnicity and risk of COVID-19 infection and disentangle any correlation with socioeconomic deprivation or previous comorbidity.DesignProspective cohort.SettingUK Biobank linked to Hospital Episode Statistics (HES) and COVID-19 tests until 14 April 2020.ParticipantsUK Biobank participants from England, excluding drop-outs and deaths.Main measuresCOVID-19 infection based on a positive PCR test. Ethnicity was self-reported and classified using Office of National Statistics groups. Socioeconomic status was based on index of multiple deprivation quintiles. Comorbidities were self-reported and completed from HES.AnalysesMultivariable Poisson analysis to estimate incidence rate ratios of COVID-19 infection according to ethnicity, adjusted for socioeconomic status, alcohol drinking, smoking, body mass index, age, sex, and comorbidity.Results415,582 participants were included, with 1,416 tested and 651 positive for COVID-19. The incidence of COVID-19 was 0.61% (95% CI: 0.46%-0.82%) in Black/Black British participants, 0.32% (0.19%-0.56%) in ‘other’ ethnicities, 0.32% (0.23%-0.47%) in Asian/Asian British, 0.30% (0.11%-0.80%) in Chinese, 0.16% (0.06%-0.41%) in mixed, and 0.14% (0.13%-0.15%) in White. Compared with White participants, Black/Black British participants had an adjusted relative risk (RR) of 3.30 (2.39-4.55), Chinese participants 3.00 (1.11-8.06), Asian/Asian British participants 2.04 (1.36-3.07), ‘other’ ethnicities 1.93 (1.08-3.45), and mixed ethnicities 1.07 (0.40-2.86). Socioeconomic status (adjusted RR 1.93 (1.51-2.46) for the most deprived), obesity (adjusted RR 1.04 (1.02-1.05) per kg/m2) and comorbid hypertension, chronic obstructive pulmonary disease, asthma, and specific renal diseases were also associated with increased risk of COVID-19.ConclusionsCOVID-19 rates in the UK are higher in BAME communities, those living in deprived areas, obese patients, and patients with previous comorbidity. Public health strategies are needed to reduce COVID-19 infections among the most susceptible groups.
ProgNet: Covid-19 prognosis using recurrent and convolutional neural networks
Authors: Fakhfakh Mohamed , Bouaziz Bassem , Gargouri Faiez , Chaari Lotfi 
Published: May 2020

Abstract—Humanity is facing nowadays a dramatic pandemic episode with the Coronavirus propagation over all continents. The Covid-19 disease is still not well characterized, and many research teams all over the world are working on either therapeutic or vaccination issues. Massive testing is one of the main recommendations. In addition to laboratory tests, imagery-based tools are being widely investigated. Artificial intelligence is therefore contributing to the efforts made to face this pandemic phase.Regarding patients in hospitals, it is important to monitor the evolution of lung pathologies due to the virus. A prognosis is therefore of great interest for doctors to adapt their care strategy. In this paper, we propose a method for Covid-19 prognosis based on deep learning architectures. The proposed method is based on the combination of a convolutional and recurrent neural networks to classify multi-temporal chest X-ray images and predict the evolution of the observed lung pathology. When applied to radiological time-series, promising results are obtained with an accuracy rates higher than 92%.
Mitochondrial cytochromecliberates the nucleophosmin-sequestered ARF tumor suppressor in the nucleolus
Authors: González-Arzola Katiuska , Díaz-Quintana Antonio , Bernardo-García Noelia , Á. Casado-Combreras Miguel , Elena-Real Carlos A. , Velázquez-Cruz Alejandro , Gil-Caballero Sergio , Velázquez-Campoy Adrián , Szulc Elzbieta , Ayala Isabel , Arranz Rocío , Salvatella Xavier , Valpuesta José M. , Hermoso Juan A. , De la Rosa Miguel A. , Díaz-Moreno Irene 
Published: May 2020

AbstractThe alternative reading frame (ARF) protein is crucial in the cellular response to oncogenic stress, being likewise the second most frequently inactivated gene in a wide spectrum of human cancers. ARF is usually sequestered in the nucleolus by the well-known oncogenic nucleophosmin (NPM) protein and is liberated in response to cell damage to exhibit its tumor-suppressor ability. However, the mechanism underlying ARF activation is unknown. Here we show that mitochondria-to-nucleus translocation of cytochromecupon DNA damage leads to the break-off of the NPM-ARF ensemble and subsequent release of ARF from the nucleoli. Our structural and subcellular data support a molecular model in which the hemeprotein triggers the extended-to-compact conformation of NPM and competes with ARF for binding to NPM.
Genetic architecture of a body color cline inDrosophila americana
Authors: Sramkoski Lisa L. , McLaughlin Wesley N. , Cooley Arielle M. , Yuan David C. , John Alisha , Wittkopp Patricia J. 
Published: May 2020

AbstractPhenotypic variation within a species is often structured geographically in clines. InDrosophila americana, a longitudinal cline for body color exists within North America that appears to be due to local adaptation. Thetanandebonygenes have been hypothesized to contribute to this cline, with alleles of both genes that lighten body color found inD. americana. These alleles are similar in sequence and function to the allele fixed inD. americana’smore lightly pigmented sister species,Drosophila novamexicana. To test this hypothesis, we examined the frequency and geographic distribution ofD. novamexicana-like alleles oftanandebonyinD. americana. Among alleles from over 100 strains ofD. americanaisolated from 21 geographic locations, we failed to identify additional alleles oftanorebonywith as much sequence similarity toD. novamexicanaas the alleles previously described. However, using genetic analysis of 51D. americanastrains derived from 20 geographic locations, we identified one new allele ofebonyand one new allele oftansegregating inD. americanathat are functionally equivalent to theD. novamexicanaallele. An additional 5 alleles oftanalso showed marginal evidence of functional similarity. Given the rarity of these alleles, however, we conclude that they are unlikely to be driving the pigmentation cline. Indeed, phenotypic distributions of the 51 backcross populations analyzed indicate a more complex genetic architecture, with diversity in the number and effects of loci altering pigmentation observed both within and among populations ofD. americana. This genetic heterogeneity poses a challenge to association studies and genomic scans for clinal variation, but might be common in natural populations.
CD8 T cells induce destruction of bone marrow stromal niches and hematopoietic stem cell dysfunction in chronic viral infections
Authors: Isringhausen Stephan , Kovtonyuk Larisa , Suessbier Ute , Kraeutler Nike J. , Gomariz Alvaro , Helbling Patrick M. , Wong Hui Chyn , Nagasawa Takashi , Manz Markus G. , Oxenius Anette , Nombela-Arrieta César 
Published: May 2020

AbstractChronic viral infections are associated with hematopoietic suppression and bone marrow (BM) failure, which have been linked to hematopoietic stem cell (HSC) exhaustion. However, how persistent viral infectious challenge and ensuing inflammatory responses target BM tissues and perturb hematopoietic homeostasis remains poorly understood. Here, we combine extensive functional analyses with advanced 3D microscopy to demonstrate that chronic infection with lymphocytic choriomeningitis virus clone 13 results in the long-term impairment of HSC function, concomitant with a persistent destruction of the HSC-supportive stromal networks of mesenchymal CXCL12-abundant reticular cells. During infections, long lasting injuries and aberrant transcriptional programs of the stromal infrastructure diminish the capacity of the BM microenvironment to adequately support HSC maintenance. Mechanistically, BM immunopathology is elicited by virus-specific, activated CD8 T cells, which accumulate in the BM via interferon-dependent mechanisms. Combined inhibition of type I and II IFN pathways completely preempts viral-mediated degeneration of CARc networks and protects HSCs from persistent dysfunction. Hence, viral infections and ensuing immune reactions chronically interfere with BM function by disrupting essential stromal-derived, hematopoietic-supporting cues.
Conservative route to genome compaction in a miniature annelid
Authors: Martín-Durán José M. , Vellutini Bruno C. , Marlétaz Ferdinand , Cetrangolo Viviana , Cvetesic Nevena , Thiel Daniel , Henriet Simon , Grau-Bové Xavier , Carrillo-Baltodano Allan M. , Gu Wenjia , Kerbl Alexandra , Marquez Yamile , Bekkouche Nicolas , Chourrout Daniel , Gómez-Skarmeta Jose Luis , Irimia Manuel , Lenhard Boris , Worsaae Katrine , Hejnol Andreas 
Published: May 2020

SummaryThe causes and consequences of genome reduction in animals are unclear, because our understanding of this process mostly relies on lineages with often exceptionally high rates of evolution. Here, we decode the compact 73.8 Mb genome of Dimorphilus gyrociliatus, a meiobenthic segmented worm. The D. gyrociliatus genome retains traits classically associated with larger and slower-evolving genomes, such as an ordered, intact Hox cluster, a generally conserved developmental toolkit, and traces of ancestral bilaterian linkage. Unlike some other animals with small genomes, the analysis of the D. gyrociliatus epigenome revealed canonical features of genome regulation, excluding the presence of operons and trans-splicing. Instead, the gene dense D. gyrociliatus genome presents a divergent Myc pathway, a key physiological regulator of growth, proliferation, and genome stability in animals. Altogether, our results uncover a conservative route to genome compaction in annelids, reminiscent of that observed in the vertebrate Takifugu rubripes.
Efficient Estimation of Large-Scale Spatial Capture-Recapture Models
Authors: Turek Daniel , Milleret Cyril , Ergon Torbjørn , Brøseth Henrik , de Valpine Perry 
Published: May 2020

AbstractCapture-recapture methods are a common tool in ecological statistics, which have been extended to spatial capture-recapture models for data accompanied by location information. However, standard formulations of these models can be unwieldy and computationally intractable for large spatial scales, many individuals, and/or activity center movement. We provide a cumulative series of methods that yield dramatic improvements in Markov chain Monte Carlo (MCMC) estimation for two examples. These include removing unnecessary computations, integrating out latent states, vectorizing declarations, and restricting calculations to the locality of individuals. Our approaches leverage the flexibility provided by thenimbleR package. In our first example, we demonstrate an improvement in MCMC efficiency (the rate of generating effectively independent posterior samples) by a factor of 100. In our second example, we reduce the computing time required to generate 10,000 posterior samples from 4.5 hours down to five minutes, and realize an increase in MCMC efficiency by a factor of 25. We also explain how these approaches can be applied generally to other spatially-indexed hierarchical models. R code is provided for all examples, as well as an executable web-appendix.
A metabolic CRISPR-Cas9 screen in Chinese hamster ovary cells identifies glutamine-sensitive genes
Authors: la Cour Karottki Karen Julie , Hefzi Hooman , Li Songyuan , Pedersen Lasse Ebdrup , Spahn Philipp , Joshi Chintan , Ruckerbauer David , Bort Juan Hernandez , Thomas Alex , Lee Jae Seong , Borth Nicole , Lee Gyun Min , Kildegaard Helene Faustrup , Lewis Nathan E. 
Published: May 2020

AbstractOver the past decades, optimization of media formulation and feeding strategies have fueled a many-fold improvement in CHO-based biopharmaceutical production. While Design of Experiments (DOE) and media screens have led to many advances, genome editing offers another avenue for enhancing cell metabolism and bioproduction. However the complexity of metabolism, involving thousands of genes, makes it unclear which engineering strategies will result in desired traits. Here we developed a comprehensive pooled CRISPR screen for CHO cell metabolism, including ∼16,000 gRNAs against ∼2500 metabolic enzymes and regulators. We demonstrated the value of this screen by identifying a glutamine response network in CHO cells. Glutamine is particularly important since it is often substantially over-fed to drive increased TCA cycle flux but can lead to accumulation of toxic ammonia. Within the glutamine-response network, the deletion of a novel and poorly characterized lipase,Abhd11, was found to substantially increase growth in glutamine-free media by altering the regulation of the TCA cycle. Thus, the screen provides an invaluable targeted platform to comprehensively study genes involved in any metabolic trait.
Stable kinetochore–microtubule attachments restrict MTOC position and spindle elongation in acentrosomal oocytes
Authors: Courtois Aurélien , Yoshida Shuhei , Kitajima Tomoya S. 
Published: May 2020

SummaryIn mouse oocytes, acentriolar MTOCs functionally replace centrosomes and act as microtubule nucleation sites. Microtubules nucleated from MTOCs initially assemble into an unorganized ball-like structure, which then transforms into a bipolar spindle carrying MTOCs at its poles, a process called spindle bipolarization. In mouse oocytes, spindle bipolarization is promoted by kinetochores but the mechanism by which kinetochore–microtubule attachments contribute to spindle bipolarity remains unclear. This study demonstrates that the stability of kinetochore–microtubule attachment is essential for confining MTOC positions at the spindle poles and for limiting spindle elongation. MTOC sorting is gradual and continues even in the metaphase spindle. When stable kinetochore–microtubule attachments are disrupted, the spindle is unable to restrict MTOCs at its poles and fails to terminate its elongation. Stable kinetochore fibers are directly connected to MTOCs and to the spindle poles, and thus may serve as a measure that defines proper spindle length. These findings reinforce the hypothesis that kinetochores act as scaffolds for acentrosomal spindle bipolarity.
Single-cell atlas of human developing and azoospermia patients’ testicles reveals the roadmap and defects in somatic microenvironment
Authors: Zhao LiangYu , Yao ChenCheng , Xing XiaoYu , Jing Tao , Li Peng , Zhu ZiJue , Yang Chao , Zhai Jing , Tian RuHui , Chen HuiXing , Luo JiaQiang , Liu NaChuan , Deng ZhiWen , Lin XiaoHan , Li Na , Fang Jing , Sun Jie , Wang ChenChen , Zhou Zhi , Li Zheng 
Published: May 2020

ABSTRACTNon-obstructive azoospermia (NOA) affects 1% of men. However, the unknowns of NOA pathogenesis and even normal spermatogenic microenvironment establishment severely limit the clinical efficacy of NOA treatment. We profiled > 80,000 human testicular single-cell transcriptomes from 10 healthy donors spanning the range from infant to adult and 7 NOA patients. Sertoli cells, which form the scaffold in the testicular microenvironment, exhibited the most obvious damages in NOA patients. We identified the roadmap of Sertoli cell maturation. Notably, Sertoli cells of patients with congenital causes (Klinefelter syndrome and Y chromosome microdeletions) are mature but with abnormal immune response, while the cells in idiopathic NOA (iNOA) are basically physiologically immature. Furthermore, inhibition of Wnt signaling promotes the maturation of Sertoli cells from iNOA patients, allowing these cells to regain their ability to support germ cell survival. We provide a novel perspective on the development of diagnostic methods and therapeutic targets for NOA.
Thermogenic genes are blunted whereas brown adipose tissue identity is preserved in human obesity
Authors: Jespersen Naja Z. , Andersen Maja W. , Jensen Verena H. , Stærkær Thit W , Severinsen Mai C.K. , Peijs Lone , Soares Ricardo , Forss Isabel , Andersen Eline S. , Hahn Christoffer H. , Homøe Preben , Mandrup Susanne , Pedersen Bente K. , Nielsen Søren , Scheele Camilla 
Published: May 2020

AbstractObesity associates with a reduction in cold-induced glucose tracer uptake in brown adipose tissue in humans, suggesting loss of thermogenic capacity. We therefore hypothesized that a whitening of BAT occurs in obesity and assessed the molecular characteristics of deep neck BAT in a cohort of 24 normal weight, 24 overweight and 22 obese individuals in comparison with subcutaneous abdominal white adipose tissue (WAT). We found that the major marker of BAT thermogenesis,UCP1, was associated with central but not general obesity. We performed transcriptomic analysis of BAT in a cohort of 27 individuals classified as normal weight, over-weight or obese, and additionally four subjects with type 2 diabetes (T2DM), dispersed among the 3 BMI groups. We identified 3204 differentially expressed genes between BAT and WAT in samples from normal weight individuals, including genes involved in thermogenesis, but also revealing differences in developmental and immune system related genes. In BAT from individuals with overweight or obesity, 202 genes were downregulated and 66 of these were involved in cellular respiratory pathways, likely reflecting previously observed reduction in thermogenic function with obesity. Importantly, most BAT selective genes werenotaffected, and isolated adipose progenitors differentiated into thermogenic adipocytes with equal frequency regardless of BMI group. In conclusion, our data suggest a retained BAT identity, with a selective reduction of thermogenic genes, in human obesity.
Novel NGS Pipeline for Virus Discovery from a Wide Spectrum of Hosts and Sample Types
Authors: Plyusnin Ilya , Kant Ravi , Jääskeläinen Anne J. , Sironen Tarja , Holm Liisa , Vapalahti Olli , Smura Teemu 
Published: May 2020

ABSTRACTThe study of the microbiome data holds great potential for elucidating the biological and metabolic functioning of living organisms and their role in the environment. Metagenomic analyses have shown that humans, along with e.g. domestic animals, wildlife and arthropods, are colonized by an immense community of viruses. The current Coronavirus pandemic (COVID-19) heightens the need to rapidly detect previously unknown viruses in an unbiased way. The increasing availability of metagenomic data in this era of next-generation sequencing (NGS), along with increasingly affordable sequencing technologies, highlight the need for reliable and comprehensive methods to manage such data. In this article, we present a novel stand-alone pipeline called LAZYPIPE for identifying both previously known and novel viruses in host-associated or environmental samples and give examples of virus discovery based on it. LAZYPIPE is a Unix-based pipeline for automated assembling and taxonomic profiling of NGS libraries implemented as a collection of C++, Perl, and R scripts.