bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient inactivation of SARS-CoV-2 by WHO-recommended hand rub formulations and alcohols
Authors: Kratzel Annika , Todt Daniel , V’kovski Philip , Steiner Silvio , Gultom Mitra L. , Thao Tran Thi Nhu , Ebert Nadine , Holwerda Melle , Steinmann Jörg , Niemeyer Daniela , Dijkman Ronald , Kampf Günter , Drosten Christian , Steinmann Eike , Thiel Volker , Pfaender Stephanie 
Published: March 2020

AbstractThe recent emergence of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing COVID-19 is a major burden for health care systems worldwide. It is important to address if the current infection control instructions based on active ingredients are sufficient. We therefore determined the virucidal activity of two alcohol-based hand rub solutions for hand disinfection recommended by the World Health Organization (WHO), as well as commercially available alcohols. Efficient SARS-CoV-2 inactivation was demonstrated for all tested alcohol-based disinfectants. These findings show the successful inactivation of SARS-CoV-2 for the first time and provide confidence in its use for the control of COVID-19.ImportanceThe current COVID-19 outbreak puts a huge burden on the world’s health care systems. Without effective therapeutics or vaccines being available, effective hygiene measure are of utmost importance to prevent viral spreading. It is therefore crucial to evaluate current infection control strategies against SARS-CoV-2. We show the inactivation of the novel coronavirus for the first time and endorse the importance of disinfectant-based hand hygiene to reduce SARS-CoV-2 transmission.
Nephrotic Syndrome Disease Activity Predicts Severity of the Associated Hypercoagulopathy
Authors: Waller Amanda P. , Troost Jonathan P. , Parikh Samir V. , Wolfgang Katelyn J. , Rovin Brad H. , Nieman Marvin T. , Smoyer William E. , Kretzler Matthias , Kerlin Bryce A. ,   for The NEPTUNE Investigators
Published: March 2020

AbstractNephrotic syndrome (NS) is associated with an acquired hypercoagulopathy and strong predilection for life-threatening thrombotic complications. Current anticoagulant prophylaxis guidelines are based upon controversial hypoalbuminemia thresholds. Anticoagulant prophylaxis is thus inconsistently implemented due to a lack of high-grade safety and efficacy data. Development of evidence-based clinical parameters that define thrombosis risk may thus refine safe and effective anticoagulant use. Endogenous thrombin potential (ETP) is a recognized measure of hypercoagulopathy and established predictor of both incident and recurrent thrombosis. This study utilized biorepository samples from a prospective longitudinal cohort study to demonstrate that ETP is proportional to NS disease activity, resulting in multivariable models that are significantly correlated with ETP. The relationship with disease activity was confirmed in a separate cohort. These models revealed that ETP is related to disease activity in a manner dependent on remission status and that proteinuria and hypercholesterolemia exert the strongest influence on ETP. In contrast to prior epidemiology studies, which did not include hypercoagulopathy measures, we found that hypoalbuminemia was less predictive of ETP. These findings are consistent with our previously reported animal model observations and are expected to inform the design of clinical trials that will generate high-grade evidence to guide more effective and safer anticoagulant use and thus reduce life-threatening thrombotic events in patients with NS.
Tracking the Covid-19 pandemic : Simple visualization of the epidemic states and trajectories of select European countries & assessing the effects of delays in official response
Authors: Kévorkian A. , Grenet T. , Gallée H. 
Published: March 2020

AbstractWe present a self-synchronizing and robust method for comparing the progression of the Covid-19 epidemics among multiple countries. In their growth phase the epidemics show power law rather than exponential law time dependences. They are similar enough for the earlier China outbreak to guide other countries projections. The delayed reaction of European countries is shown to produce a significantly worse outcome compared to China.
Morphognostic honey bees communicating nectar location through dance movements
Authors: Portegys Thomas E. 
Published: March 2020

AbstractHoney bees are social insects that forage for flower nectar cooperatively. When an individual forager discovers a flower patch rich in nectar, it returns to the hive and performs a “waggle dance” in the vicinity of other bees that consists of movements communicating the direction and distance to the nectar source. The dance recruits “witnessing” bees to fly to the location of the nectar to retrieve it, thus cooperatively exploiting the environment. Replicating such complex animal behavior is a step forward on the path to artificial intelligence. This project simulates the bee foraging behavior in a cellular automaton using the Morphognosis machine learning model. The model features hierarchical spatial and temporal contexts that output motor responses from sensory inputs. Given a set of bee foraging and dancing exemplars, and exposing only the external input-output of these behaviors to the Morphognosis learning algorithm, a hive of artificial bees can be generated that forage as their biological counterparts do. A comparison of Morphognosis foraging performance with that of an artificial recurrent neural network is also presented.
A high efficient hospital emergency responsive mode is the key of successful treatment of 100 COVID-19 patients in Zhuhai
Authors: Huang Jin , Li Zhonghe , Qu Xiujuan , Zheng Xiaobin , Tu Changli , Chen Meizhu , Tan Cuiyan , Liu Jing , Shan Hong 
Published: March 2020

AbstractBackgroundSince December 2019, Coronavirus Disease 2019 (COVID-19) emerged in Wuhan city and rapidly spread throughout China. The mortality of novel coronavirus pneumonia (NCP) in severe and critical cases is very high. Facing this kind of public health emergency, high efficient administrative emergency responsive mode in designated hospital is needed.MethodAs an affiliated hospital of Sun Yat-sen University, our hospital is the only designated one for diagnosis and treatment of COVID-19 in Zhuhai, a medium-sized city. Novel coronavirus pneumonia department, which is administrative led by the president of hospital directly, has been established at early stage of epidemic crisis in my hospital. In NCP department, there are core members of Pulmonary and Critical Care Medicine (PCCM) specialist and multidisciplinary team. Don’t stick to national guidelines of NCP, based on professional opinion by respiratory professor and expert group, we focused on individualized treatment and timely adjustment of treatment and management strategies in working about COVID-19 patients.Results1. High working efficiency: By Mar 02, 2020, we have completed 2974 citywide consultations and treatment of 366 inpatients, including 101 patients diagnosed with COVID-19. 2. Excellent therapeutic effect: Among 101 hospitalized patients with confirmed COVID-19, all were cured and discharged, except for one death. No secondary hospital infection, no pipeline infection and no pressure sore were found in all patients. 3. Finding and confirming person-to-person transmission characteristic of COVID-19 prior to official release conference: Strengthened protection is key point to zero infection in healthcare group and medical faculty and lower rate of second generation infectious patients. 4. Timely adjustment management and treatment strategy prior to guideline update: The first evidence of digestive tract involvement in COVID-19 has been found, and the earliest clinical trial of chloroquine in the treatment of COVID-19 has been carried out in our hospital.ConclusionsIn our hospital, establishment of NCP department, which is administratively led by the president of hospital directly and specialized conduct by respiratory professor, is the key to success in management and treatment of COVID-19 patients. This hospital emergency responsive mode could provide reference for other hospitals and cities in epidemic situation.
Routes for COVID-19 importation in Brazil
Authors: Candido Darlan Da S , Watts Alexander , Abade Leandro , Kraemer Moritz UG , Pybus Oliver G , Croda Julio , Oliveira Wanderson de , Khan Kamran , Sabino Ester C , Faria Nuno R 
Published: March 2020

HighlightThe global outbreak caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been declared a pandemic by the WHO. As the number of imported SARS-CoV-2 cases is on the rise in Brazil, we use incidence and historical air travel data to estimate the most important routes of importation into the country.
Understanding Epidemic Data and Statistics: A Case Study of COVID-19
Authors: Dehkordi Amirhoshang Hoseinpour , Alizadeh Majid , Derakhshan Pegah , Babazadeh Peyman , Jahandideh Arash 
Published: March 2020

AbstractThe 2019-Novel-Coronavirus (COVID-19) has affected 181 countries and out of about 1197405 confirmed cases (By April 5). Understanding the transmission dynamics of the infection in each country which affected on a daily basis and evaluating the effectiveness of control policies is critical for our further actions. To date, the statistics of COVID-19 reported cases show more than 80 percent of infected had a mild case of disease, while around 14 percent of infected experienced a severe one and about 5 percent are categorized as critical disease victims. Today’s report (2020-04-05; daily updates in the prepared website) shows the confirmed cases of COVID-19 in US, Spain, Italy, and Germany are 308850, 126168, 124632 and 96092; respectively. Calculating the total Case Fatality Rate (CFR) of Italy (2020-04-04), about 13.3% of confirmed cases passed away. Compared to South Korea’s rate of 1.8% (7 times lower than Italy) and China’s 4% (69% lower than Italy), the CFR of Italy is too high. There are some effective policies that yield significant changes in the trend of cases. The lockdown policy in China, Italy and Spain (the effect observed after some days), Shutdown of all non-essential companies in Hubei (the effect observed after 5 days), combined policy in South Korea and reducing working hours in Iran.
US Mortality Due To Congenital Heart Disease Across the Lifespan from 1999-2017 Exposes Persistent Racial/Ethnic Disparities
Authors: Lopez Keila N. , Morris Shaine A. , Tejtel Kristen Sexson , Espaillat Andre , Salemi Jason L. 
Published: March 2020

ABSTRACTBackgroundCongenital heart disease (CHD) accounts for approximately 40% percent of deaths in United States (US) children with birth defects. Previous US data from 1999-2006 demonstrated an overall decrease in CHD mortality. The objective of our study was to assess current trends in US mortality related to CHD from infancy to adulthood over the last 19 years and determine differences by sex and race/ethnicity.MethodsWe conducted an analysis of death certificates from 1999-2017 to calculate annual CHD mortality by age at death, race/ethnicity, and sex. Population estimates used as denominators in mortality rate calculation for infants were based on National Center for Health Statistics live birth data. Mortality rates in individuals>1 year of age utilized US Census Bureau bridged-race estimates as denominators for population estimates. We characterized temporal trends in all-cause mortality, mortality resulting directly due to and related to CHD by age, race/ethnicity, and sex using joinpoint regression.ResultsThere were 47.7 million deaths with 1 in 814 deaths due to CHD (n=58,599). While all-cause mortality decreased 16.4% across all ages, mortality resulting from CHD declined 39.4% overall. The mean annual decrease in CHD mortality was 2.6%, with the largest decrease for those age >65years. The age-adjusted mortality rate decreased from 1.37 to 0.83 per 100,000. Males had higher mortality due to CHD than females throughout the study, although both sexes declined at a similar rate (∼40% overall), with a 3-4% annual decrease between 1999 and 2009, followed by a slower annual decrease of 1.4% through 2017. Mortality resulting from CHD significantly declined among all race/ethnicities studied, although disparities in mortality persisted for non-Hispanic Blacks versus non-Hispanic Whites (mean annual decrease 2.3% versus 2.6%, respectively; age-adjusted mortality rate 1.67 to 1.05 versus 1.35 to 0.80 per 100,000, respectively).ConclusionsWhile overall US mortality due to CHD has decreased over the last 19 years, disparities in mortality persist for males compared to females and for non-Hispanic Blacks compared to non-Hispanic Whites. Determining factors that contribute to these disparities such as access to quality care, timely diagnosis, and maintenance of insurance will be important moving into the next decade.
The Effect of Visual Uncertainty on Implicit Motor Adaptation
Authors: Tsay Jonathan S. , Avraham Guy , Kim Hyosub E. , Parvin Darius E. , Wang Zixuan , Ivry Richard B. 
Published: March 2020

ABSTRACTSensorimotor adaptation is driven by sensory prediction errors, the difference between the predicted and actual feedback. When the position of the feedback is made uncertain, adaptation is attenuated. This effect, in the context of optimal sensory integration models, has been attributed to a weakening of the error signal driving adaptation. Here we consider an alternative hypothesis, namely that uncertainty alters the perceived location of the feedback. We present two visuomotor adaptation experiments to compare these hypotheses, varying the size and uncertainty of a visual error signal. Uncertainty attenuated learning when the error size was small but had no effect when the error size was large. This pattern of results favors the hypothesis that uncertainty does not impact the strength of the error signal, but rather, leads to mis-localization of the error. We formalize these ideas to offer a novel perspective on the effect of visual uncertainty on implicit sensorimotor adaptation.SIGNIFICANCE STATEMENTCurrent models of sensorimotor adaptation assume that the rate of learning will be related to properties of the error signal (e.g., size, consistency, relevance). Recent evidence has challenged this view, pointing to a rigid, modular system, one that automatically recalibrates the sensorimotor map in response to movement errors, with minimal constraint. In light of these developments, this study revisits the influence of feedback uncertainty on sensorimotor adaptation. Adaptation was attenuated in response to a noisy feedback signal, but the effect was only manifest for small errors and not for large errors. This interaction suggests that uncertainty does not weaken the error signal. Rather, it may influence the perceived location of the feedback and thus the change in the sensorimotor map induced by that error. These ideas are formalized to show how the motor system remains exquisitely calibrated, even if adaptation is largely insensitive to the statistics of error signals.
Computational analysis of microRNA-mediated interactions in SARS-CoV-2 infection
Authors: Saçar Demirci Müşerref Duygu , Adan Aysun 
Published: March 2020

AbstractMicroRNAs (miRNAs) are post-transcriptional regulators of gene expression that have been found in more than 200 diverse organisms. Although it is still not fully established if RNA viruses could generate miRNAs that would target their own genes or alter the host gene expression, there are examples of miRNAs functioning as an antiviral defense mechanism. In the case of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there are several mechanisms that would make miRNAs impact the virus, like interfering with replication, translation and even modulating the host expression. In this study, we performed a machine learning based miRNA prediction analysis for the SARS-CoV-2 genome to identify miRNA-like hairpins and searched for potential miRNA – based interactions between the viral miRNAs and human genes and human miRNAs and viral genes. Our PANTHER gene function analysis results indicate that viral derived miRNA candidates could target various human genes involved in crucial cellular processes including transcription. For instance, a transcriptional regulator, STAT1 and transcription machinery might be targeted by virus-derived miRNAs. In addition, many known human miRNAs appear to be able to target viral genes. Considering the fact that miRNA-based therapies have been successful before, comprehending mode of actions of miRNAs and their possible roles during SARS-CoV-2 infections could create new opportunities for the development and improvement of new therapeutics.
Quantification of lactoyl-CoA by liquid chromatography mass spectrometry in mammalian cells and tissues
Authors: Varner Erika L , Trefely Sophie , Bartee David , von Krusenstiern Eliana , Izzo Luke , Bekeova Carmen , O’Connor Roddy S , Seifert Erin L. , Wellen Kathryn , Meier Jordan L. , Snyder Nathaniel W. 
Published: March 2020

AbstractLysine lactoylation is a recently described protein post-translational modification (PTM). However, the biochemical pathways responsible for this acylation remain unclear. Two metabolite-dependent mechanisms have been proposed: enzymatic histone lysine lactoylation derived from lactoyl-coenzyme A (lactoyl-CoA, also termed lactyl-CoA), and non-enzymatic lysine lactoylation resulting from acyl-transfer via lactoyl-glutathione. While the former has precedent in the form of enzyme-catalyzed lysine acylation, the lactoyl-CoA metabolite has not been previously quantified in mammalian systems. Here we use liquid chromatography-high resolution mass spectrometry (LC-HRMS) together with a synthetic standard to detect and validate the presence of lactoyl-CoA in cell and tissue samples. Conducting a retrospective analysis of data from previously analyzed samples revealed the presence of lactoyl-CoA in diverse cell and tissue contexts. In addition, we describe a biosynthetic route to generate13C315N1-isotopically-labeled lactoyl-CoA, providing a co-eluting internal standard for analysis of this metabolite. We estimate lactoyl-CoA concentrations of 1.14×10−8pmol/cell in cell culture and 0.0172 pmol/mg tissue wet weight in mouse heart. These levels are similar to crotonyl-CoA, but between 20-350 times lower than predominant acyl-CoAs such as acetyl-, propionyl-, and succinyl-CoA. Overall our studies provide the first quantitative measurements of lactoyl-CoA and provide a methodological foundation for the interrogation of this novel metabolite in biology and disease.Highlights- Detection of lactoyl-CoA at picomole concentrations across tissues and cells- Lactoyl-CoA was detected at concentrations similar to crontonyl-CoA within HepG2 cells- Isotopically labeled13C315N1-lactoyl-CoA can be prepared by SILEC
Queryfuse is a sensitive algorithm for detection of gene-specific fusions
Authors: Tan Yuxiang 
Published: March 2020

ABSTRACTRecurrent chromosomal translocations, known as fusions, play important roles in carcinogenesis. They can serve as valuable diagnostic and therapeutic targets. RNA-seq is an ideal platform for detecting transcribed fusions, and computational methods have been developed to identify fusion transcripts from RNA-seq data. However, some transciptome realignment procedures for these methods are unnecessary, making this task computationally expensive and time consuming. Therefore, we have developed QueryFuse, a novel hypothesis-based algorithm that identifies gene-specific fusion from pre-aligned RNA-seq data. It is designed to help biologists quickly find and/or computationally validate fusions of interest, together with visualization and detailed properties of supporting reads. By aligning reads to Query genes at the pre-processing step with a more sensitive, memory intensive local aligner, QueryFuse can reduce alignment time and improve detection sensitivity.QueryFuse performed better or at comparable levels with two popular tools (deFuse and TopHatFusion) on both simulated and well-annotated cell-line datasets. Finally, using QueryFuse, we identified a novel fusion event with a potential therapeutic implication in clinical samples. Taken together, our results showed that QueryFuse is efficient and reliable for detecting gene-specific fusion events.
Acute myelitis after SARS-CoV-2 infection: a case report
Authors: Zhao Kang , Huang Jucun , Dai Dan , Feng Yuwei , Liu Liming , Nie Shuke 
Published: March 2020

AbstractWe report a case of acute myelitis in a patient infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A 66-year-old man with coronavirus disease 2019 was admitted with acute flaccid paralysis of the bilateral lower limbs and urinary and bowel incontinence. All serum microbiological test results were negative, except for SARS-CoV-2 nucleic acid testing. Clinical findings indicated post-infectious acute myelitis. He received treatment containing ganciclovir, lopinavir/ritonavir, moxifloxacin, dexamethasone, human immunoglobulin, and mecobalamin. With a diagnosis of post-infectious acute myelitis and comprehensive treatment, paralysis of the bilateral lower extremities ameliorated. After two negative novel coronavirus RNA nasopharyngeal swab tests, he was discharged and transferred to a designated hospital for isolation and rehabilitation therapy.
Optimization of skeletal protein preparation for LC-MS/MS sequencing yields additional coral skeletal proteins inStylophora pistillata
Authors: Peled Yanai , Drake Jeana , Malik Assaf , Almuly Ricardo , Lalzar Maya , Morgenstern David , Mass Tali 
Published: March 2020

AbstractStony corals generate their calcium carbonate exoskeleton in a highly controlled biomineralization process mediated by a variety of macromolecules including proteins. Fully identifying and classifying these proteins is crucial to understanding their role in exoskeleton formation, yet no optimal method to purify and characterize the full suite of extracted coral skeletal proteins has been established and hence their complete composition remains obscure. Here, we tested four skeletal protein purification protocols using acetone precipitation and ultrafiltration dialysis filters to present a comprehensive scleractinian coral skeletal proteome. We identified a total of 60 proteins in the coral skeleton, 44 of which were not present in previously published stony coral skeletal proteomes. Extracted protein purification protocols carried out in this study revealed that no one method captures all proteins and each protocol revealed a unique set of method-exclusive proteins. To better understand the general mechanism of skeletal protein transportation, we further examined the proteins’ gene ontology, transmembrane domains, and signal peptides. We found that transmembrane domain proteins and signal peptide secretion pathways, by themselves, could not explain the transportation of proteins to the skeleton. We therefore propose that some proteins are transported to the skeleton via non-traditional secretion pathways.