bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid and accurate identification of COVID-19 infection through machine learning based on clinical available blood test results
Authors: Wu Jiangpeng , Zhang Pengyi , Zhang Liting , Meng Wenbo , Li Junfeng , Tong Chongxiang , Li Yonghong , Cai Jing , Yang Zengwei , Zhu Jinhong , Zhao Meie , Huang Huirong , Xie Xiaodong , Li Shuyan 
Published: April 2020

AbstractSince the sudden outbreak of coronavirus disease 2019 (COVID-19), it has rapidly evolved into a momentous global health concern. Due to the lack of constructive information on the pathogenesis of COVID-19 and specific treatment, it highlights the importance of early diagnosis and timely treatment. In this study, 11 key blood indices were extracted through random forest algorithm to build the final assistant discrimination tool from 49 clinical available blood test data which were derived by commercial blood test equipments. The method presented robust outcome to accurately identify COVID-19 from a variety of suspected patients with similar CT information or similar symptoms, with accuracy of 0.9795 and 0.9697 for the cross-validation set and test set, respectively. The tool also demonstrated its outstanding performance on an external validation set that was completely independent of the modeling process, with sensitivity, specificity, and overall accuracy of 0.9512, 0.9697, and 0.9595, respectively. Besides, 24 samples from overseas infected patients with COVID-19 were used to make an in-depth clinical assessment with accuracy of 0.9167. After multiple verification, the reliability and repeatability of the tool has been fully evaluated, and it has the potential to develop into an emerging technology to identify COVID-19 and lower the burden of global public health. The proposed tool is well-suited to carry out preliminary assessment of suspected patients and help them to get timely treatment and quarantine suggestion. The assistant tool is now available online at http://lishuyan.lzu.edu.cn/COVID2019_2/.FundingThis work was supported by the Fundamental Research Funds for the Central Universities (lzujbky-2020-sp11) and the Gansu Provincial COVID-19 Science and Technology Major Project, China.
Building an International Consortium for Tracking Coronavirus Health Status
Authors: Segal Eran , Zhang Feng , Lin Xihong , King Gary , Shalem Ophir , Shilo Smadar , Allen William E. , Grad Yonatan H. , Greene Casey S. , Alquaddoomi Faisal , Anders Simon , Balicer Ran , Bauman Tal , Bonilla Ximena , Booman Gisel , Chan Andrew T. , Cohen Ori , Coletti Silvano , Davidson Natalie , Dor Yuval , Drew David A. , Elemento Olivier , Evans Georgina , Ewels Phil , Gale Joshua , Gavrieli Amir , Geiger Benjamin , Hajirasouliha Iman , Jerala Roman , Kahles Andre , Kallioniemi Olli , Keshet Ayya , Landua Gregory , Meir Tomer , Muller Aline , Nguyen Long H. , Oresic Matej , Ovchinnikova Svetlana , Peterson Hedi , Rajagopal Jay , Rätsch Gunnar , Rossman Hagai , Rung Johan , Sboner Andrea , Sigaras Alexandros , Spector Tim , Steinherz Ron , Stevens Irene , Vilo Jaak , Wilmes Paul ,   CCC (Coronavirus Census Collective)
Published: April 2020

Information is the most potent protective weapon we have to combat a pandemic, at both the individual and global level. For individuals, information can help us make personal decisions and provide a sense of security. For the global community, information can inform policy decisions and offer critical insights into the epidemic of COVID-19 disease. Fully leveraging the power of information, however, requires large amounts of data and access to it. To achieve this, we are making steps to form an international consortium, Coronavirus Census Collective (CCC, coronaviruscensuscollective.org), that will serve as a hub for integrating information from multiple data sources that can be utilized to understand, monitor, predict, and combat global pandemics. These sources may include self-reported health status through surveys (including mobile apps), results of diagnostic laboratory tests, and other static and real-time geospatial data. This collective effort to track and share information will be invaluable in predicting hotspots of disease outbreak, identifying which factors control the rate of spreading, informing immediate policy decisions, evaluating the effectiveness of measures taken by health organizations on pandemic control, and providing critical insight on the etiology of COVID-19. It will also help individuals stay informed on this rapidly evolving situation and contribute to other global efforts to slow the spread of disease.In the past few weeks, several initiatives across the globe have surfaced to use daily self-reported symptoms as a means to track disease spread, predict outbreak locations, guide population measures and help in the allocation of healthcare resources. The aim of this paper is to put out a call to standardize these efforts and spark a collaborative effort to maximize the global gain while protecting participant privacy.
Rapid implementation of mobile technology for real-time epidemiology of COVID-19
Authors: Drew David A. , Nguyen Long H. , Steves Claire J. , Wolf Jonathan , Spector Tim D. , Chan Andrew T. 
Published: April 2020

AbstractThe rapid pace of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic (COVID-19) presents challenges to the robust collection of population-scale data to address this global health crisis. We established the COronavirus Pandemic Epidemiology (COPE) consortium to bring together scientists with expertise in big data research and epidemiology to develop a COVID-19 Symptom Tracker mobile application that we launched in the UK on March 24, 2020 and the US on March 29, 2020 garnering more than 2.25 million users to date. This mobile application offers data on risk factors, herald symptoms, clinical outcomes, and geographical hot spots. This initiative offers critical proof-of-concept for the repurposing of existing approaches to enable rapidly scalable epidemiologic data collection and analysis which is critical for a data-driven response to this public health challenge.One Sentence SummaryCOVID-19 symptom tracker for smartphones
Rapid evidence summary on SARS-CoV-2 survivorship and disinfection, and a reusable PPE protocol using a double-hit process
Authors: Derraik José G B , Anderson William A , Connelly Elisabeth A , Anderson Yvonne C 
Published: April 2020

ABSTRACTIn the COVID-19 pandemic caused by SARS-CoV-2, hospitals are stretched beyond capacity. There are widespread reports of dwindling supplies of personal protective equipment (PPE), which are paramount to protect frontline medical/nursing staff and to minimize further spread of the virus. We carried out a rapid review to summarize the existing evidence on SARS-CoV-2 survivorship and methods to disinfect PPE gear, particularly N95 filtering facepiece respirators (FFR). In the absence of data on SARS-CoV-2, we focused on the sister virus SARS-CoV-1. We propose a two-step disinfection process, which is conservative in the absence of robust evidence on SARS-CoV-2. This disinfection protocol is based on an initial storage of PPE for ≥4 days, followed by ultraviolet light (UVC), dry heat treatment, or chemical disinfection. Importantly, each of the two steps is based on independent disinfection mechanisms, so that our proposed protocol is a multiplicative system, maximising the efficacy of our disinfection process. This method could be rapidly implemented in other healthcare settings, while testing of each method is undertaken, increasing the frontline supply of PPE, and avoiding many of the upstream issues of supply chain disruption currently being faced.
Chaos theory applied to the outbreak of Covid-19: an ancillary approach to decision-making in pandemic context
Authors: Mangiarotti S. , Peyre M. , Zhang Y. , Huc M. , Roger F. , Kerr Y. 
Published: April 2020

AbstractPredicting the course of an epidemic is difficult, predicting the course of a pandemic from an emerging virus even more so. The validity of most predictive models relies on numerous parameters, involving biological and social characteristics often unknown or highly uncertain. Data of the COVID-19 epidemics in China, Japan, South Korea and Italy were used to build up deterministic models without strong hypothesis. These models were then applied to other countries to identify the closest scenarios in order to foresee their coming behaviour. The models enabled to predict situations that were confirmed little by little, proving that these tools can be efficient and useful for decision-making in a quickly evolving operational context.
COVID-19 Excess Deaths in the United States, New York City, and Michigan During April 2020
Authors: Wetzler Harry , Wetzler Erica 
Published: April 2020

AbstractBackgroundIt has been suggested that many of those who died from COVID-19 were older, had more comorbidities, and would have died within a short period anyway. We estimated the number and percent of excess deaths due to COVID-19 In April 2020 in the United States, New York City, and Michigan.MethodsFor each locale we calculated attributable fractions in the exposed comparing observed COVID-19 deaths and expected deaths. In addition, we estimated the number of months it would take for the excess deaths to occur without the virus and the proportions of the populations that were infected leading to the April deaths. We compared the excess deaths from the attributable fraction method to those obtained by comparing weekly deaths in 2019 and 2020.ResultsUsing an assumed infection fatality rate of 1%, the percentages of excess deaths were 95%, 97%, and 95% in the US, NYC, and MI equivalent to 54,560; 14,951; and 3,338 deaths, respectively. Absent the virus these deaths would have occurred over 21.0, 29.2, and 18.4 months in the respective locations. An estimated 1.7% of the US population was infected between March 13 and April 10, 2020. Nearly 19% were infected in NYC.ConclusionsOver 75% of COVID-19 deaths in April 2020 were excess deaths meaning they would not have occurred in April without SARS-CoV-2 but would have been spread out over the ensuing 18 to 29 months. Confirmed cases in the US under-report the actual number of infections by at least an order of magnitude. Excess death numbers calculated using the attributable fraction in the exposed are similar to those obtained from weekly mortality reports.
Molecular development of muscle spindle and Golgi tendon organ sensory afferents revealed by single proprioceptor transcriptome analysis
Authors: Oliver Katherine M. , Florez-Paz Danny M. , Badea Tudor C. , Mentis George Z. , Menon Vilas , de Nooij Joriene C. 
Published: April 2020

AbstractAnatomical and physiological analyses have long revealed differences between proprioceptive groups Ia, II, and Ib sensory neurons, yet the molecular correlates of these three muscle afferent subtypes remain unknown. We performed single cell RNA sequencing of genetically identified adult proprioceptors and, using unbiased bioinformatics approaches, detected five molecularly distinct neuronal clusters. Validation of cluster-specific transcripts in dorsal root ganglia (DRG) and skeletal muscle provides evidence these clusters correspond to functionally distinct muscle spindle (MS) or Golgi tendon organ (GTO) afferent proprioceptors. Remarkably, while we uncovered just one type of GTO afferents, four of the five clusters represent MS afferents, thus demonstrating a previously unappreciated diversity among these muscle proprioceptors.In vitroelectrophysiological recordings reveal just two broadly distinct proprioceptor types, and suggest that the refinement of functional subtype diversity may occur along multiple axes of maturation. Lineage analysis between proprioceptor transcriptomes at different developmental stages show little or no correlation for transcripts that define adult MS or GTO afferents, supporting the idea that proprioceptor subtype identity emerges late in development. Together, our data provide the first comprehensive molecular signature for groups Ia and II MS afferents and group Ib GTO afferents, and offer new strategies for genetic interrogation of the role of these individual proprioceptor subtypes in regulating voluntary motor behavior.
Neuronal kinase SGK1.1 protects against brain damage after status epilepticus
Authors: Martin-Batista Elva , Maglio Laura E. , Armas-Capote Natalia , Hernandez Guadalberto , de la Rosa Diego Alvarez , Giraldez Teresa 
Published: April 2020

ABSTRACTEpilepsy is a neurological condition associated to significant brain damage produced bystatus epilepticus(SE) including neurodegeneration, gliosis and ectopic neurogenesis. Reduction of these processes constitutes a useful strategy to improve recovery and ameliorate negative outcomes after an initial insult. SGK1.1, the neuronal isoform of the serum and glucocorticoids-regulated kinase 1 (SGK1), has been shown to increase M-current density in neurons, leading to reduced excitability and protection against seizures. We now show that SGK1.1 activation potently reduces levels of neuronal death and gliosis after SE induced by kainate, even in the context of high seizure activity. This neuroprotective effect is not exclusively a secondary effect of M-current activation but is also directly linked to decreased apoptosis levels through regulation of Bim and Bcl-xLcellular levels. Our results demonstrate that this newly described antiapoptotic role of SGK1.1 activation acts synergistically with the regulation of cellular excitability, resulting in a significant reduction of SE-induced brain damage. The protective role of SGK1.1 occurs without altering basal neurogenesis in brain areas relevant to epileptogenesis.SIGNIFICANCE STATEMENTApproaches to control neuronal death and inflammation are of increasing interest in managing epilepsy, one of the most important idiopathic brain diseases. We have previously shown that activation of SGK1.1 reduces neuronal excitability by increasing M-current levels, significantly reducing seizure severity. We now describe a potent neuroprotective role of SGK1.1, which dramatically reduces neuronal death and gliosis after status epilepticus. This effect is partially dependent on M-current activation and includes an additional anti-apoptotic role of SGK1.1. Our data strongly support the relevance of this kinase as a potential target for epilepsy treatment.
Characterization Of Yellow Root Cassava And Food Products: Investigation Of Cyanogenic Glycosides And Pro-Vitamin A
Authors: Odoemelam Chiemela S. , Percival Benita , Ahmad Zeeshan , Chang Ming-Wei , Scholey Dawn , Burton Emily , Okafor Polycarp N. , Wilson Philippe B. 
Published: April 2020

AbstractObjectiveCyanide is a highly toxic compound, and the consumption of products containing cyanide is of singificant public health concern. In contrast,β-carotene possesses essential nutritional attributes related to human health, therefore the characterisation and quanfication of both compounds in food products is both fundamental and necessary. This investigation sought to identify the cyanide and β-carotene levels in two flours produced from the roots of two varieties of cassava (Manihot esculenta crantz), namely UMUCASS-38 (TMS 01/1371) and NR 8082, and their associated food products.ResultsThe fresh tuber, raw flour and food products were analysed for levels of residual cyanide andβ-carotene using standard analytical methods. The cyanide content of NR 8082 (18.01±0.01 ppm) and UMUCASS 38 (17.02±0.02 ppm) flours were significantly higher (p< 0.05) than the residual cyanide levels determined in the cookies (10.00±0.00 ppm) and cake (7.10±0.14 ppm). The levels of β-carotene determined in the sample varied significantly (p< 0.05). The highest levels of β-carotene (6.53±0.02 µg/g) were determined in raw roots of UMUCASS 38 while NR 8082 levels of β-carotene were 1.12±0.02 µg/g. Processing the roots into flour reduced the β-carotene content to 4.78±0.01 µg/g and 0.76±0.02 µg/g in UMUCASS 38 and NR8082 flours, respectively. Cookies and cake produced from flour derived from the UMUCASS 38 variety had 2.15±0.01 µg/g and 2.84±0.04 µg/g of β-carotene, respectively.
SARS-CoV-2 and SARS-CoV differ in their cell tropism and drug sensitivity profiles
Authors: Bojkova Denisa , McGreig Jake E. , McLaughlin Katie-May , Masterson Stuart G. , Widera Marek , Krähling Verena , Ciesek Sandra , Wass Mark N. , Michaelis Martin , Cinatl Jindrich 
Published: April 2020

AbstractSARS-CoV-2 is a novel coronavirus currently causing a pandemic. We show that the majority of amino acid positions, which differ between SARS-CoV-2 and the closely related SARS-CoV, are differentially conserved suggesting differences in biological behaviour. In agreement, novel cell culture models revealed differences between the tropism of SARS-CoV-2 and SARS-CoV. Moreover, cellular ACE2 (SARS-CoV-2 receptor) and TMPRSS2 (enables virus entry via S protein cleavage) levels did not reliably indicate cell susceptibility to SARS-CoV-2. SARS-CoV-2 and SARS-CoV further differed in their drug sensitivity profiles. Thus, only drug testing using SARS-CoV-2 reliably identifies therapy candidates. Therapeutic concentrations of the approved protease inhibitor aprotinin displayed anti-SARS-CoV-2 activity. The efficacy of aprotinin and of remdesivir (currently under clinical investigation against SARS-CoV-2) were further enhanced by therapeutic concentrations of the proton pump inhibitor omeprazole (aprotinin 2.7-fold, remdesivir 10-fold). Hence, our study has also identified anti-SARS-CoV-2 therapy candidates that can be readily tested in patients.
Achieving high-quality ddRAD-like reference catalogs for non-model species: the power of overlapping paired-end reads
Authors: Driller Maximilian , Arantes Larissa Souza , Vilaça Sibelle Torres , Carrasco-Valenzuela Tomás , Heeger Felix , Mbedi Susan , Chevallier Damien , De Thoisy Benoit , Mazzoni Camila J 
Published: April 2020

AbstractReduced representation libraries (RRS) allow large scale studies on non-model species to be performed without the need for a reference genome, by building a pseudo-reference locus catalog directly from the data. However, using closely-related high-quality genomes can help maximize nucleotide variation identified from RRS libraries. While chromosome-level genomes remain unavailable for most species, researchers can still invest in building high-quality and project-specificde novolocus catalogs. Among methods that use restriction enzymes (RADSeq), those including fragment size selection to help obtain the desired number of loci - such as double-digest RAD (ddRAD) - are highly flexible but can present important technical issues. Inconsistent size selection reproducibility across libraries and variable coverage across fragment lengths can affect genotyping confidence, number of identified single nucleotide polymorphisms (SNPs), and quality and completeness of thede novoreference catalog. We have developed a strategy to optimize locus catalog building from ddRAD-like data by sequencing overlapping reads that recreate original fragments and add information about coverage per fragment size. Furtherin silicosize selection and digestion steps limit the filtered dataset to well-covered sets of loci and identity thresholds are estimated based on sequence pairwise comparisons. We have developed a full workflow that identifies a set of reduced-representation single-copy orthologs (R2SCOs) for any given species and that includes estimating and evaluating allelic variation in comparison with SNP calling results. We also show how to use our concept in an established RADSeq pipeline - Stacks - and confirm that our approach increases average coverage and number of SNPs called per locus in the final catalog. We have demonstrated our full workflow using newly generated data from five sea turtle species and provided further proof-of-principle using published hybrid sea turtle and primate datasets. Finally, we showed that a project-specific set of R2SCOs perform better than a draft genome as a reference.
Dopaminergic modulation of reward discounting in healthy rats: a systematic review and meta-analysis
Authors: Castrellon Jaime J. , Meade James , Greenwald Lucy , Hurst Katlyn , Samanez-Larkin Gregory R. 
Published: April 2020

AbstractAlthough numerous studies have suggested that pharmacological alteration of the dopamine (DA) system modulates reward discounting, these studies have produced inconsistent findings. Here, we conducted a systematic review and pre-registered meta-analysis to evaluate DA drug-mediated effects on reward discounting of time, probability, and effort costs in studies of healthy rats. This produced a total of 1,343 articles to screen for inclusion/exclusion. From the literature, we identified 117 effects from approximately 1,549 individual rats. Using random-effects with maximum-likelihood estimation, we meta-analyzed placebo-controlled drug effects for (1) DA D1-like receptor agonists and (2) antagonists, (3) D2-like agonists and (4) antagonists, and (5) DA transporter-modulating drugs. Meta-analytic effects showed that DAT-modulating drugs decreased reward discounting. While D1-like and D2-like antagonists both increased discounting, agonist drugs for those receptors had no significant effect on discounting behavior. A number of these effects appear contingent on study design features like cost type, rat strain, and microinfusion location. These findings suggest a nuanced relationship between DA and discounting behavior and urge caution when drawing generalizations about the effects of pharmacologically manipulating dopamine on reward-based decision making.
Activation of SnRK2 by the Raf-like kinase ARK represents a common mechanism of ABA response in embryophytes
Authors: Islam Mousona , Inoue Takumi , Hiraide Mayuka , Khatun Nobiza , Jahan Akida , Kuwata Keiko , Umezawa Taishi , Yotsui Izumi , Sakata Yoichi , Takezawa Daisuke 
Published: April 2020

ABSTRACTThe Raf-like protein kinase ARK previously identified in the mossPhyscomitrella patensacts as an upstream regulator of subgroup III SnRK2, the key regulator of abscisic acid (ABA) and abiotic stress responses. However, the mechanisms underlying activation of ARK by ABA and abiotic stress for the regulation of SnRK2 including the role of ABA receptor-associated group A PP2C (PP2C-A) are not understood. We identified Ser1029 as the phosphorylation site in the activation loop of ARK, which provided a possible mechanism for regulation of its activity. Analysis of transgenicarklines expressing ARK-GFP with Ser1029-to-Ala mutation indicated that this replacement causes reductions in ABA-induced gene expression, stress tolerance and SnRK2 activity. Immunoblot analysis using an anti-phosphopeptide antibody indicated that ABA treatments rapidly stimulate Ser1029 phosphorylation in wild type. The phosphorylation profile of Ser1029 in ABA-hypersensitiveppabi1lacking PP2C-A was similar to that in wild type, whereas little Ser1029 phosphorylation was observed in ABA-insensitivearkmissense lines. Furthermore, newly isolatedppabi1 arklines showed ABA-insensitive phenotypes similar to those ofarklines. These results indicate that ARK is a primary activator of SnRK2, preceding negative regulation by PP2C-A in bryophytes, which provides a prototypal mechanism for ABA and abiotic stress-responses in embryophytes.One sentence summaryPhysiological characterization of various moss mutants revealed a common mechanism for phytohormone responses under water deficit in all land plants.