bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of electronic health records reveals medication-related interference on point-of-care urine drug screening assays
Authors: Ayala-Lopez Nadia , Colby Jennifer M. , Hughey Jacob J. 
Published: April 2020

AbstractBackgroundPoint-of-care (POC) urine drug screening (UDS) assays provide immediate information for patient management. However, POC UDS assays can produce false positive results, which may not be recognized until confirmatory testing is completed several days later. To minimize the potential for patient harm, it is critical to identify sources of interference. Here we applied an approach based on statistical analysis of electronic health record (EHR) data to identify medications that may cause false positives on POC UDS assays.MethodsFrom our institution’s EHR data, we extracted 120,670 POC UDS and confirmation results, covering 12 classes of target drugs, along with each individual’s prior medication exposures. For a given assay and medication ingredient, we quantified potential interference as an odds ratio from logistic regression. We evaluated interference experimentally by spiking compounds into drug-free urine and testing the spiked samples on the POC device (Integrated E-Z Split Key Cup II, Alere).ResultsOur dataset included 446 false positive UDS results (presumptive positive screen followed by negative confirmation). We quantified potential interference for 528 assay-ingredient pairs. Of the six assay-ingredient pairs we evaluated experimentally, two showed interference capable of producing a presumptive positive: labetalol on the MDMA assay (at 200 μg/mL) and ranitidine on the methamphetamine assay (at 50 μg/mL). Ranitidine also produced a presumptive positive for opiates at 1600 μg/mL and for propoxyphene at 800 μg/mL.ConclusionsThese findings support the generalizability of our approach to use EHR data to identify medications that interfere with clinical immunoassays.
Search for trends of Covid-19 infection in India, China, Denmark, Brazil, France. Germany and the USA on the basis of power law scaling
Authors: Bhattacharya Srijit , De Alokkumar , Islam Md Moinul 
Published: April 2020

AbstractThe corona virus (SARS-CoV-2) or Covid-19 pandemic is growing alarmingly throughout the whole world. Using the power law scaling we analyze the data of different countries and three states of India up to 1st April, 2020 and explain in terms of power law exponent. We find significant reduction in growth of infections in China and Denmark (γ reduced from approximately 2.18 to 0.05 and 11.41 to 6.95, respectively). Very slow reduction is also seen in Brazil and Germany (γ reduced from approximately 6 to 4 and 11 to 7, respectively). Infection in India is growing (γ=9.23) though lesser in number than that in the USA (highest γ of 16 approximately, studied so far), Italy and a few other countries. Among three Indian states the growth in West Bengal (γ=0.64) is much slower than other states like Maharashtra and Kerala (γ=3.23 and 3.32, respectively). Some future predictions, though not rigid, has also been incorporated in our analysis. The earlier lock-down and stricter measures from the Governments concerned are being thought to be the only possible solutions, in the present situation, to fight against this virus.
Fast spread of COVID-19 in Europe and the US suggests the necessity of early, strong and comprehensive interventions
Authors: Ke Ruian , Sanche Steven , Romero-Severson Ethan , Hengartner Nick 
Published: April 2020

AbstratThe COVID-19 pandemic caused more than 800,000 infections and 40,000 deaths by the end of March 2020. However, some of the basic epidemiological parameters, such as the exponential epidemic growth rate andR0are debated. We developed an inference approach to control for confounding factors in data collection, such as underreporting and changes in surveillance intensities, and fitted a mathematical model to infection and death count data collected from eight European countries and the US. In all countries, the early epidemic grew exponentially at rates between 0.19-0.29/day (epidemic doubling times between 2.4-3.7 days). This suggests a highly infectious virus with anR0likely between 4.0 and 7.1. We show that similar levels of intervention efforts are needed, no matter the goal is mitigation or containment. Early, strong and comprehensive intervention efforts to achieve greater than 74-86% reduction in transmission are necessary.One-sentence SummaryWe estimated that COVID-19 spreads rapidly in 8 European countries and the US, suggesting that early, strong and comprehensive interventions are necessary.
EARLY DETECTION OF COVID-19
Authors: Sattar Hashmi Hafiz Abdul , Asif Hafiz Muhammad 
Published: April 2020

AbstractSince SARS-Cov-2 epidemic appeared in Wuhan China, it became challenge for health authorities to counter Covid-19 epidemic. Early evaluation of suspects, screening for Covid-19 and management posed challenge to health authorities especially in developing countries which were not ready to cope with it. Early mild symptoms appeared during course of disease provide a chance to early detect Covid-19. We use retrospective methodology to collect available data on early sign and symptoms of Covid-19 through accessing World Health Organization (WHO) webpages, New England Journal of Medicine (NEJM), Nature Journal, Journal of American Medical Association (JAMA) network, British Medical Journal (BJM), Lancet and other world renowned journal publications to establish a relationship of early symptoms for detection of Covid-19. Data of 2707 Covid-19 laboratory confirmed cases was collected and analyzed for early signs. Available data was categorized into physical and blood biomarkers. This categorized data was assessed for scoring early detection of Covid-19 by scoring Hashmi-Asif Covid-19 formula. Each characteristic was given a score in Hashmi-Asif Covid-19 chart with maximum score of 28. Scoring 16 on chart means Covid-19 will fully develop in near future. Correlation of each sign and symptoms with development of Covid-19 in formula showed significant correlation assessed by Pearson correlation and Spearman Correlation coefficient (rho) showed significant correlation of development of Covid-19 with fever 64.11% (P=0.001), cough 65% and dry mucus 19.67% equally sensitive (P=0.000), leukopenia 19.06% (P=0.006), lymphopenia 52.93% (P=0.005), thrombopenia 19.1% (P=0.013), elevated Aspartate aminotransferase 12.79% (P=0.007) and elevated Alanine aminotransferase 11.34% (P=0.006). Chart can sense Covid-19 progression 72-96 hours earlier compared to usual course of disease and detection by standard method. Chart for early detection provides early quarantine decision to reduce disease spread and give ample time for intervening disease progression to reduce morbidity time due to Covid-19.
Association of COVID-19 Infections in San Francisco in Early March 2020 with Travel to New York and Europe
Authors: Gu Wei , Reyes Kevin , Hsu Elaine , Miller Steve , Chiu Charles 
Published: April 2020

AbstractReal-time dissemination of epidemiological survey data from positive COVID-19 cases is critical to support efforts to contain or reduce spread of viral infection in the community. Here we detected a significant association between domestic travel or travel to Europe and the identification of new cases in San Francisco, California, USA. These findings suggest that domestic and European travelers may need to be prioritized for evaluation of acute infection from COVID-19 in the setting of limited testing capacity.
Development of the reproduction number from coronavirus SARS-CoV-2 case data in Germany and implications for political measures
Authors: Khailaie Sahamoddin , Mitra Tanmay , Bandyophadhyay Arnab , Schips Marta , Mascheroni Pietro , Vanella Patrizio , Lange Berit , Binder Sebastian C. , Meyer-Hermann Michael 
Published: April 2020

AbstractThe novel Coronavirus SARS-CoV-2 (COVID-19) has induced a world-wide pandemic and subsequent non-pharmaceutical interventions (NPI) in order to control the spreading of the virus. NPIs are considered to be critical in order to at least delay the peak number of infected individuals and to prevent the health care system becoming overwhelmed by the number of patients to treat in hospitals or in intensive care units (ICUs). However, there is also increasing concern that the NPIs in place would increase mortality because of other diseases, increase the frequency of suicide and increase the risk of an economic recession with unforeseeable implications. It is therefore instrumental to evaluate the necessity of NPIs and to monitor the progress of containment of virus spreading.We used a data-driven estimation of the evolution of the reproduction number for viral spreading in Germany as well as in all its federal states. Based on an extended infection-epidemic model, parameterized with data from the Robert Koch Institute and, alternatively, with parameters stemming from a fit to the initial phase of COVID-19 spreading in different regions of Italy, we found that the reproduction number was decreased to a range below 1 in all federal states. The development in Germany suggests that NPIs can be partially released based on an established new culture of social distancing, face masks and mutual care within the population. However, any release of measures delays reaching low incidence numbers. The strategy to reduce daily new cases to a sufficiently low level to be controlled by contact tracing and testing turned out to work in Germany. This requires a responsible behaviour of the population, optimised contact tracing techniques and extended testing capacities in contact clusters.Author summaryAs of mid-June Germany was able to control the pandemic to an extent that the health care system was not overwhelmed and the daily new reported infections appear under control. We analysed the evolution of the reproduction number during the epidemic in Germany and the efficiency of non-pharmaceutical interventions (NPIs) in containing viral spread. The results suggest that the cultural change induced by NPIs in interpersonal interactions and distancing allows for a partial release of political measures. However, this requires a functional case isolation and contact tracing of new cases by local health departments, early identification of contact clusters and consequent isolation of those clusters.
Little Risk of the COVID-19 Resurgence on Students in China (outside Hubei) Caused by School Reopening
Authors: Long Cheng , Zeng Tieyong , Fu Xinmiao 
Published: April 2020

AbstractObjectiveSchool reopening has not yet started in China where the COVID-19 outbreak has reached ending stage, largely due to a great concern about COVID-19 infections on students. We attempted to quantitatively evaluate the risk of COVID-19 infections on students caused by school reopening.Study designWe collected the data of the numbers of teachers, population size and newly confirmed COVID-19 cases in the past 14 days in typical provinces/cities of China, and then analyzed the risk of COVID-19 infections in schools with respect to each province/city.MethodsA step-by-step procedure was explored to calculate the probability of COVID-19 infections on students as transmitted from infected teachers. Two critical assumptions for analysis were proposed: (i) only locally generated cases were counted while imported cases were omitted; (ii) the secondary attack rate of the COVID-19 virus in schools is similar to that in households in China, ranging from 3-10%.ResultsThe probability of COVID-19 resurgence within one week on students of primary, middle and high schools in China (outside Hubei) is extremely low (<0.2%) in each province/city, and such probability can be updated daily and weekly based on the newly confirmed cases in the past 14 days. In some areas without newly confirmed cases in the past 14 days, the risk is zero.ConclusionsOur work provides guidance for local governments to make risk level-based policies for school reopening. Currently, the risk of COVID-19 infections on students is extremely low in China (outside Hubei) and therefore school reopening can be initiated without the endanger of infections on students.
A protocol for adding knowledge to Wikidata, a case report
Authors: Waagmeester Andra , Willighagen Egon L. , Su Andrew I , Kutmon Martina , Labra Gayo Jose Emilio , Fernández-Álvarez Daniel , Groom Quentin , Schaap Peter J. , Verhagen Lisa M. , Koehorst Jasper J. 
Published: April 2020

AbstractPandemics, even more than other medical problems, require swift integration of knowledge. When caused by a new virus, understanding the underlying biology may help finding solutions. In a setting where there are a large number of loosely related projects and initiatives, we need common ground, also known as a “commons”. Wikidata, a public knowledge graph aligned with Wikipedia, is such a commons and uses unique identifiers to link knowledge in other knowledge bases However, Wikidata may not always have the right schema for the urgent questions. In this paper, we address this problem by showing how a data schema required for the integration can be modelled with entity schemas represented by Shape Expressions. As a telling example, we describe the process of aligning resources on the genomes and proteomes of the SARS-CoV-2 virus and related viruses as well as how Shape Expressions can be defined for Wikidata to model the knowledge, helping others studying the SARS-CoV-2 pandemic. How this model can be used to make data between various resources interoperable, is demonstrated by integrating data from NCBI Taxonomy, NCBI Genes, UniProt, and WikiPathways. Based on that model, a set of automated applications or bots were written for regular updates of these sources in Wikidata and added to a platform for automatically running these updates. Although this workflow is developed and applied in the context of the COVID-19 pandemic, to demonstrate its broader applicability it was also applied to other human coronaviruses (MERS, SARS, Human Coronavirus NL63, Human coronavirus 229E, Human coronavirus HKU1, Human coronavirus OC4).
The phenotypic changes of γδ T cells in COVID-19 patients
Authors: Lei Lei , Qian Hongbo , Yang Xiaofang , Zhou Xiaobo , Zhang Xingzhe , Zhang Dan , Dai Tongxin , Guo Rui , Shi Lin , Cheng Yanbin , Zhang Baojun , Hu Jinsong , Guo Yaling 
Published: April 2020

AbstractA novel pneumonia-associated respiratory syndrome named coronavirus disease-2019 (COVID-19), which caused by SARS-CoV-2 and broken in Wuhan, China in the end of 2019. Unfortunately, there is no specific antiviral agent or vaccine available to treat SARS-CoV-2 infections. Also, information regarding the immunological characteristics in COVID-19 patients remains limited. Here we collected the blood samples from 18 healthy donors (HD) and 38 COVID-19 patients to analyze changes in γδ T cells. In comparison to HD, the γδ T cells percentage was decreased. γδ T cells are able to immediately respond to SARS-CoV-2 infection and upregulate the activation marker CD25. In addition, the increased expression of CD4 in γδ T cells may serve as a biomarker for the assessment of SARS-CoV-2 infection.
Estimating false-negative detection rate of SARS-CoV-2 by RT-PCR
Authors: Wikramaratna Paul , Paton Robert S , Ghafari Mahan , Lourenço José 
Published: April 2020

AbstractReverse transcription-polymerase chain reaction (RT-PCR) assays are used to test patients and key workers for infection with the causative SARS-CoV-2 virus. RT-PCR tests are highly specific and the probability of false positives is low, but false negatives can occur if the sample contains insufficient quantities of the virus to be successfully amplified and detected. The amount of virus in a swab is likely to vary between patients, sample location (nasal, throat or sputum) and through time as infection progresses. Here, we analyse publicly available data from patients who received multiple RT-PCR tests and were identified as SARS-CoV-2 positive at least once. We identify that the probability of a positive test decreases with time after symptom onset, with throat samples less likely to yield a positive result relative to nasal samples. Empirically derived distributions of the time between symptom onset and hospitalisation allowed us to comment on the likely false negative rates in cohorts of patients who present for testing at different clinical stages. We further estimate the expected numbers of false negative tests in a group of tested individuals and show how this is affected by the timing of the tests. Finally, we assessed the robustness of these estimates of false negative rates to the probability of false positive tests. This work has implications both for the identification of infected patients and for the discharge of convalescing patients who are potentially still infectious.
Mandated Bacillus Calmette-Guérin (BCG) vaccination predicts flattened curves for the spread of COVID-19
Authors: Berg Martha K. , Yu Qinggang , Salvador Cristina E. , Melani Irene , Kitayama Shinobu 
Published: April 2020

AbstractBCG vaccination may reduce the risk of a range of infectious diseases, and, if so, could serve as a protective factor against COVID-19. Here, we compared countries that mandated BCG vaccination at least until 2000 with to countries that did not (140 countries in total). To minimize any systematic effects of reporting biases, we analyzed the rate of the day-by-day increase in both confirmed cases and deaths in the first 30-day period of country-wise outbreaks. The 30-day window was adjusted to begin at the country-wise onset of the pandemic. Linear mixed models revealed a significant effect of mandated BCG policies on the growth rate of both cases and deaths after controlling for median age, gross domestic product per capita, population density, population size, net migration rate, and various cultural dimensions (e.g., individualism and the tightness vs. looseness of social norms). Our analysis suggests that mandated BCG vaccination can be effective in the fight against COVID-19.TeaserNational policies for universal BCG vaccination are associated with flattened growth of country-wise COVID-19 cases and deaths.
Using single-plant -omics in the field to link maize genes to functions and phenotypes
Authors: Felipe Cruz Daniel , De Meyer Sam , Ampe Joke , Sprenger Heike , Herman Dorota , Van Hautegem Tom , De Block Jolien , Inzé Dirk , Nelissen Hilde , Maere Steven 
Published: April 2020

ABSTRACTMost of our current knowledge on plant molecular biology is based on experiments in controlled lab environments. Over the years, lab experiments have generated substantial insights in the molecular wiring of plant developmental processes, stress responses and phenotypes. However, translating these insights from the lab to the field is often not straightforward, in part because field growth conditions are very different from lab conditions. Here, we test a new experimental design to unravel the molecular wiring of plants and study gene-phenotype relationships directly in the field. We molecularly profiled a set of individual maize plants of the same inbred background grown in the same field, and used the resulting data to predict the phenotypes of individual plants and the function of maize genes. We show that the field transcriptomes of individual plants contain as much information on maize gene function as traditional lab-generated transcriptomes of pooled plant samples subject to controlled perturbations. Moreover, we show that field-generated transcriptome and metabolome data can be used to quantitatively predict at least some individual plant phenotypes. Our results show that profiling individual plants in the field is a promising experimental design that could help narrow the lab-field gap.
Neural signatures of performance feedback in the paced auditory serial addition task (PASAT): an ERP study
Authors: Sommer Anja , Ziegler Lukas , Plewnia Christian 
Published: April 2020

AbstractDue to its importance for successful human behavior, research into cognitive control functioning has gained increasing interest. The paced auditory serial addition task (PASAT) has been used to test and train this fundamental function. It is a challenging task, requiring a high cognitive load in a stressful and frustrating environment. Its underlying neural mechanisms, however, are still unclear. To explore the neural signatures of the PASAT and their link to ongoing cognitive processing, feedback locked event-related potentials were derived from healthy participants during an adaptive 2-back version of the PASAT. Larger neural activation after negative feedback was found for feedback related negativity (FRN), P300 and late positive potential (LPP). In early stages of feedback processing (FRN), a larger difference between positive and negative feedback responses was associated with poorer overall performance, whereas this association was inverted for the later stages (P300 and LPP). This indicates stage-dependent associations of neural activation after negative information and cognitive functioning. Conceivably, increased early responses to negative feedback signify distraction whereas higher activity at later stages reflect cognitive control processes to preserve ongoing performance.
Bleaching correction for DNA-measurements in highly diluted solutions using confocal microscopy
Authors: Sparrenberg Lorenz T. , Greiner Benjamin , Mathis Harald P. 
Published: April 2020

AbstractPrecise and reliable determination of the nucleic acid concentration in biological samples still remains a challenge. This is particularly since the established fluorescene-based methods provide insufficient results, when only minute sample quantitites are available for analysis. Among other effects, photobleaching is the main reason for this. Since large molecules diffuse more slowly than small molecules, they are exposed to more excitation cycles and therefore have a higher probability of permanently losing their fluorescence. Solutions with large molecules hence show a reduced fluorescence. In this paper we present a method to correct this effect and thus allow high-precision sample concentration determination in minute sample quantities (< 2 µl drops with concentrations < 20 pg/µl). For this purpose, we used confocal microscopy with single molecule sensitivity. In the first step, we derived calibration curves from DNA solutions with defined fragment length. We analyzed dilution series over a wide concentration range (1 pg/µl – 1000 pg/µl) and measured their specific diffusion coefficients by employing fluorescence correlation spectroscopy. Using this information, we correct the measured fluorescence intensity of the calibration solutions for photobleaching effects. Subsequently, we evaluated our method by analyzing a series of DNA mixtures of varying composition.