bluuebunny/crossref_metadata_2025_split huggingface dataset:
Entry screening and multi-layer mitigation of COVID-19 cases for a safe university reopening
Authors: Elbanna Ahmed , Wong George N. , Weiner Zach J. , Wang Tong , Zhang Hantao , Liu Zhiru , Tkachenko Alexei , Maslov Sergei , Goldenfeld Nigel 
Published: September 2020

SummaryWe have performed detailed modeling of the COVID-19 epidemic within the State of Illinois at the population level, and within the University of Illinois at Urbana-Champaign at a more detailed level of description that follows individual students as they go about their educational and social activities.We ask the following questions:How many COVID-19 cases are expected to be detected by entry screening?Will this initial “bump” in cases be containable using the mitigation steps being undertaken at UIUC?Our answers are:Assuming that there are approximately 45,000 students returning to campus in the week beginning August 15, 2020, our most conservative estimate predicts that a median of 270 ± 90 (minimum-maximum range) COVID-19 positive cases will be detected by entry screening. The earliest estimate for entry screening that we report was made on July 24th and predicted 198 ± 90 (68% CI) positive cases.If the number of returning students is less, then our estimate just needs to be scaled proportionately.This initial bump will be contained by entry screening initiated isolation and contact tracing, and once the semester is underway, by universal masking, a hybrid teaching model, twice-weekly testing, isolation, contact tracing, quarantining and the use of the Safer Illinois exposure notification app.
Analyzing inherent biases in SARS-CoV-2 PCR and serological epidemiologic metrics
Authors: Makhoul Monia , Abou-Hijleh Farah , Seedat Shaheen , Mumtaz Ghina R , Chemaitelly Hiam , Ayoub Houssein , Abu-Raddad Laith J. 
Published: September 2020

AbstractBackgroundProspective observational data show that infected persons with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remain polymerase chain reaction (PCR) positive for a prolonged duration, and that detectable antibodies develop slowly with time. We aimed to analyze how these effects can bias key epidemiological metrics used to track and monitor SARS-CoV-2 epidemics.MethodsAn age-structured mathematical model was constructed to simulate progression of SARS-CoV-2 epidemics in populations. PCR testing to diagnose infection and cross-sectional surveys to measure seroprevalence were also simulated. Analyses were conducted on simulated outcomes assuming a natural epidemic time course and an epidemic in presence of interventions.ResultsThe prolonged PCR positivity biased the epidemiological measures. There was a lag of 10 days between the true epidemic peak and the actually-observed peak. Prior to epidemic peak, PCR positivity rate was 2-fold higher than that based only on current active infection, and half of those tested positive by PCR were in the prolonged PCR positivity stage after infection clearance. Post epidemic peak, PCR positivity rate poorly predicted true trend in active infection. Meanwhile, the prolonged PCR positivity did not appreciably bias estimation of the basic reproduction number R0. The time delay in development of detectable antibodies biased measured seroprevalence. The actually-observed seroprevalence substantially underestimated true prevalence of ever infection, with the underestimation being most pronounced around epidemic peak.ConclusionsCaution is warranted in interpreting PCR and serological testing data, and any drawn inferences need to factor the effects of the investigated biases for an accurate assessment of epidemic dynamics.
A Low-cost, Low-energy Wearable ECG System with Cloud-Based Arrhythmia Detection
Authors: Huda Nurul , Khan Sadia , Abid Ragib , Shuvo Samiul Based , Labib Mir Maheen , Hasan Taufiq 
Published: September 2020

AbstractContinuously monitoring the Electrocardiogram (ECG) is an essential tool for Cardiovascular Disease (CVD) patients. In low-resource countries, the hospitals and health centers do not have adequate ECG systems, and this unavailability exacerbates the patients’ health condition. Lack of skilled physicians, limited availability of continuous ECG monitoring devices, and their high prices, all lead to a higher CVD burden in the developing countries. To address these challenges, we present a low-cost, low-power, and wireless ECG monitoring system with deep learning-based automatic arrhythmia detection. Flexible fabric-based design and the wearable nature of the device enhances the patient’s comfort while facilitating continuous monitoring. An AD8232 chip is used for the ECG Analog Front-End (AFE) with two 450 mi-Ah Li-ion batteries for powering the device. The acquired ECG signal can be transmitted to a smart-device over Bluetooth and subsequently sent to a cloud server for analysis. A 1-D Convolutional Neural Network (CNN) based deep learning model is developed that provides an accuracy of 94.03% in classifying abnormal cardiac rhythm on the MIT-BIH Arrhythmia Database.Index TermsWearable ECG, deep learning, arrhythmia detection.
Selecting COVID-19 Convalescent Plasma for Neutralizing Antibody Potency Using a High-capacity SARS-CoV-2 Antibody Assay
Authors: Goodhue Meyer E , Simmons G , Grebe E , Gannett M , Franz S , Darst O , Di Germanio C , Stone M , Contestable P , Prichard A , Reik R , Vassallo R , Young P , Busch MP , Williamson P , Dumont LJ 
Published: September 2020

AbstractBACKGROUNDEfficacy of COVID-19 convalescent plasma (CCP) to treat COVID-19 is hypothesized to be associated with the concentration of neutralizing antibodies (nAb) to SARS-CoV-2. High capacity serologic assays detecting binding antibodies (bAb) have been developed, nAb assays are not adaptable to high-throughput testing. We sought to determine the effectiveness of using surrogate bAb signal-to-cutoff ratios (S/CO) in predicting nAb titers using a pseudovirus reporter viral particle neutralization (RVPN) assay.METHODSCCP donor serum collected by 3 US blood collectors was tested with a bAb assay (Ortho Clinical Diagnostics VITROS Anti-SARS-CoV-2 Total, CoV2T) and a nAb RVPN assay. CoV2T prediction effectiveness at S/CO thresholds was evaluated for RVPN nAb NT50 titers using receiver operating characteristic analysis.RESULTS753 CCPs were tested with median CoV2T S/CO of 71.2 and median NT50 of 527.5. Proportions of CCP donors with NT50 over various target nAb titers were 86% ≥1:80, 76% ≥1:160, and 62%≥1:320. Increasing CoV2Ts reduced the sensitivity to predict NT50 titers, while specificity to identify those below thresholds increased. As the targeted NT50 increased, the positive predictive value fell with reciprocal increase in negative predictive value. S/CO thresholds were thus less able to predict target NT50 titers.CONCLUSIONSelection of a clinically effective nAb titer will impact availability of CCP. Product release with CoV2T assay S/CO thresholds must balance the risk of releasing products below target nAb titers with the cost of false negatives. A two-step testing scheme may be optimal, with nAb testing on CoV2T samples with S/COs below thresholds.
Estimation of a state of Corona 19 epidemic in August 2020 by multistage logistic model: a case of EU, USA, and World
Authors: Batista Milan 
Published: September 2020

AbstractThe article provides an estimate of the size and duration of the Covid-19 epidemic in August 2020 for the European Union (EU), the United States (US), and the World using a multistage logistical epidemiological model.
Modeling an epidemic in an imaginary small town
Authors: Bell Graham 
Published: September 2020

ABSTRACTThe course of an epidemic in an imaginary small town has been simulated with an agent-based model. The reproduction number R of the virus could be counted directly, and was roughly, but not precisely, exponentially distributed. The number of secondary infections was greater for an infection which was itself one of many secondary infections because of environmental heterogeneity, which created variance of R among sites and could drive the spread of infection, even when global R < 1. Different kinds of intervention were deployed to curtail the spread of infection. Measures applied to the general population, such as closing down sites and services or regulating individual behaviour, did not reduce the total number of individuals infected during the epidemic unless they were maintained until the virus became extinct. This was primarily because measures taken to reduce indirect transmission tended to increase direct transmission, and vice versa. Consequently, the overall effect of any combination of interventions was much less than the sum of their separate effects. On the other hand, the quarantine of infected or exposed individuals was effective in driving the virus to extinction and caused a permanent and substantial reduction in the number of cases.
Engineering high-yield biopolymer secretion creates an extracellular protein matrix for living materials
Authors: Charrier Marimikel , Orozco-Hidalgo Maria Teresa , Tjahjono Nicholas , Li Dong , Molinari Sara , Ryan Kathleen R. , Ashby Paul D. , Rad Behzad , Ajo-Franklin Caroline M. 
Published: September 2020

ABSTRACTThe bacterial extracellular matrix forms autonomously, giving rise to complex material properties and multicellular behaviors. Synthetic matrix analogues can replicate these functions, but require exogenously added material or have limited programmability. Here we design a two-strain bacterial system that self-synthesizes and structures a synthetic extracellular matrix of proteins. We engineeredCaulobacter crescentusto secrete an extracellular matrix protein composed of elastin-like polypeptide (ELP) hydrogel fused to Supercharged SpyCatcher (SC(-)). This biopolymer was secreted at levels of 60 mg/L, an unprecedented level of biopolymer secretion by a gram-negative bacterium. The ELP domain was swapped with either a crosslinkable variant of ELP or resilin-like polypeptide, demonstrating this system is flexible. The SC(-)-ELP matrix protein bound specifically and covalently to the cell surface of aC. crescentusstrain that displays a high-density array of SpyTag peptides via its engineered Surface-layer. Our work develops protein design rules for Type I secretion inC. crescentus, and demonstrates the autonomous secretion and assembly of programmable extracellular protein matrices, offering a path forward towards the formation of cohesive engineered living materials.IMPORTANCEEngineered living materials (ELM) aim to mimic characteristics of natural occurring systems, bringing the benefits of self-healing, synthesis, autonomous assembly, and responsiveness to traditional materials. Previous research has shown the potential of replicating the bacterial extracellular matrix (ECM) to mimic biofilms. However, these efforts require energy intensive processing or have limited tunability. We propose a bacterially-synthesized system that manipulates the protein content of the ECM, allowing for programmable interactions and autonomous material formation. To achieve this, we engineered a two-strain system to secrete a synthetic extracellular protein matrix (sEPM). This work is a step towards understanding the necessary parameters to engineering living cells to autonomously construct ELMs.
Analysis of Biological Noise in an Organelle Size Control System
Authors: Bauer David , Ishikawa Hiroaki , Wemmer Kimberly A. , Kondev Jane , Marshall Wallace F. 
Published: September 2020

AbstractAnalysis of fluctuation in organelle size provides a new way to probe the mechanisms of organelle size control systems. By analyzing cell-to-cell variation and within-cell fluctuations of flagellar length inChlamydomonas, we show that the flagellar length control system exhibits both types of variation. Cell to cell variation is dominated by cell size, while within-cell variation results from dynamic fluctuations that are subject to a constraint, providing evidence for a homeostatic size control system. We analyzed a series of candidate genes affecting flagella and found that flagellar length variation is increased in mutations which increase the average flagellar length, an effect that we show is consistent with a theoretical model for flagellar length regulation based on length-dependent intraflagellar transport balanced by length-independent disassembly. Comparing the magnitude and time-scale of length fluctuations with simple models suggests that tubulin assembly is not directly coupled with IFT-mediated arrival and that observed fluctuations involve tubulin assembly and disassembly events involving large numbers of tubulin dimers. Cells with greater differences in their flagellar lengths show impaired swimming but improved gliding motility, raising the possibility that cells have evolved mechanisms to tune intrinsic noise in length. Taken together our results show that biological noise exists at the level of subcellular structures, with a corresponding effect on cell function, and can provide new insights into the mechanisms of organelle size control.
Integrative proteomic and phosphoproteomic analysis of granulosa cells during follicular atresia in porcine
Authors: Yang Feng , Liu Qiang , Chen Yanhong , Ye Huizhen , Wang Han , Zeng Shenming 
Published: September 2020

AbstractOvarian follicular atresia is a natural physiological process; however, the mechanism is not fully understood. In this study, quantitative proteomic and phosphoproteomic analyses of granulosa cells (GC) in healthy (H), slightly atretic (SA), and atretic follicles (A) of porcine were performed by TMT labeling, enrichment of phosphopeptides and LC-MS/MS analysis. In total, 6,201 proteins were quantified and 4,723 phosphorylation sites of 1,760 proteins were quantified. In total, 24 (11 up, 13 down) and 50 (29 up, 21 down) proteins with a fold change (FC) > 5 were identified in H/SA and H/A, respectively. In addition, there were 20 (H/SA, up) and 39 (H/A, up) phosphosites with an FC > 7, that could serve as potential biomarkers for distinguishing different quality categories of follicles. Western blotting and immunofluorescence confirmed the reliability of the proteomic analysis. Some key proteins (e.g., MIF, beta catenin, integrin β2), phosphosites (e.g., S76 of caspase6, S22 and S636 of lamin A/C), pathways (e.g., apoptosis, regulation of actin cytoskeleton pathway), transcription factors (e.g., STAT5A, FOXO1, and BCLAF1), and kinases (e.g., PBK, CDK5, CDK12, AKT3) involved in atresia process were revealed via further analysis of the differentially expressed proteins (DEPs) and phosphorylated proteins (DEPPs). Collectively, the proteomic and phosphoproteomic profiling and functional research in the current study comprehensively analyzed the dynamic changes in protein expression and phosphorylation during follicular atresia and provided some new explanations regarding the regulation of this process.
Prophylactic Application of Tailocins Prevents Infection byPseudomonas syringae
Authors: Baltrus David A. , Clark Meara , Hockett Kevin L. , Mollico Madison , Smith Caitlin , Weaver Savannah 
Published: September 2020

AbstractTailocins are phage-derived bacteriocins that demonstrate great potential as agricultural antimicrobials given their high killing efficiency and their precise strain-specific targeting ability. Our group has recently categorized and characterized tailocins produced by and tailocin sensitivities of the phytopathogenPseudomonas syringae, and here we extend these experiments to test whether prophylactic tailocin application can prevent infection ofNicotiana benthamianabyP. syringae pv. syringaeB728a. Specifically, we demonstrate that multiple strains can produce tailocins that prevent infection by strain B728a and engineer a deletion mutant to prove that tailocin targeting is responsible for this protective effect. Lastly, we provide evidence that heritable resistance mutations do not explain the minority of cases where tailocins fail to prevent infection. Our results extend previous reports of prophylactic use of tailocins against phytopathogens, and establish a model system with which to test and optimize tailocin application for prophylactic treatment to prevent phytopathogen infection.
Impact of COVID-19 pandemic on cancer care delivery : A Real World Experience
Authors: Pandey A , Mala R , Neelam C , Mridula P , Ravindra S , Kanchan M , Umesh Y , Shivkant S 
Published: September 2020

BackgroundThere is lack of information on impact of Corona Virus Disease (COVID-19) pandemic on routine cancer care delivery.Aims and ObjectivesTo evaluate the change in Day Care Chemotherapy (DCC) and Out Patient Department (OPD) patient numbers before and after COVID-19 national lockdown.Material and MethodsDemographic data, diagnosis, type and frequency of chemotherapy delivered in Day Care between 1st February 2020 to 31st July 2020 were retrieved. Out Patient Department daily patient numbers were collected. Descriptive statistics, Odds ratio, Chi-square and Student T test were used to measure change in pattern of DDC and OPD patient numbers before and after 24th March 2020 (day of Lockdown). Pearson correlation coefficient was used to measure the strength of correlation between rise in COVID-19 cases and patient numbers.Results3192 DCC and 8209 OPD visits were recorded in 126 working days. Median age was 47 years(SD + 19.06). Breast (17%) and Gall bladder(15%) were the most common cancers receiving chemotherapy. There was a significant decrease in number of DCC delivered in post COVID lockdown [mean 21.97 (+ 9.7)] compared to pre COVID lockdown [mean 33.30 (+11.4)], t=4.11, p = 0.001.There was a significant decrease in number of OPD visits in post COVID lockdown [mean 47.13 (+ 18.8)] compared to pre COVID lockdown [mean 89.91 (+30.0)], t=7.09, p = 0.001. The odds of receiving weekly chemotherapy over non weekly regimes significantly decreased post COVID lockdown with Odds ratio of 0.52 (95% CI, 0.36-0.75) with Chi square of 12.57, p =0.001. Daily COVID cases in State and OPD patient number were found to be moderately positively correlated on Pearson correlation coefficient, r = 0.35,p =0.001.ConclusionThere was a significant fall in patient visit and chemotherapy cycles immediately after lockdown. The numbers increased later despite rise in COVID-19 cases.
Genetic ancestry contributes to somatic mutations in lung cancers from admixed Latin American populations
Authors: Carrot-Zhang Jian , Soca-Chafre Giovanny , Patterson Nick , Thorner Aaron R. , Nag Anwesha , Watson Jacqueline , Genovese Giulio , Rodriguez July , Gelbard Maya K. , Corrales-Rodriguez Luis , Mitsuishi Yoichiro , Ha Gavin , Campbell Joshua D. , Oxnard Geoffrey R. , Arrieta Oscar , Cardona Andres F. , Gusev Alexander , Meyerson Matthew 
Published: September 2020

AbstractInherited lung cancer risk, particularly in non-smokers, is poorly understood. Genomic and ancestry analysis of 1,153 lung cancers from Latin America revealed striking associations between Native American ancestry and their somatic landscape, including tumor mutational burden (TMB), and specific driver mutations in EGFR, KRAS, and STK11. A local Native American ancestry risk score predicted EGFR and KRAS mutation frequency more strongly than global ancestry, suggesting that germline genetics (rather than environmental exposure) underlie these disparities.SignificanceThe frequency of somatic EGFR and KRAS mutations in lung cancer varies by ethnicity but we do not understand why. Our study suggests that the variation in EGFR and KRAS is directly associated with genetic ancestry and suggests further studies to identify germline alleles that underpin this association.
MT5-MMP controls APP and β-CTF/C99 metabolism through proteolytic-dependent and -independent mechanisms relevant for Alzheimer’s disease
Authors: García-González Laura , Paumier Jean-Michel , Louis Laurence , Pilat Dominika , Bernard Anne , Stephan Delphine , Jullien Nicolas , Checler Frédéric , Nivet Emmanuel , Khrestchatisky Michel , Baranger Kévin , Rivera Santiago 
Published: September 2020

ABSTRACTWe previously discovered the implication of membrane-type 5-matrix metalloproteinase (MT5-MMP) in Alzheimer’s disease AD pathogenesis. Here we shed new light on pathogenic mechanisms by which MT5-MMP controls APP processing and the fate of amyloid beta peptide (Aβ), its precursor C99 and C83. We found in HEK carrying theAPPSwedish familial mutation (HEKswe) that MT5-MMP-mediated processing of APP that releases the soluble 95 kDa form (sAPP95), was hampered by the removal of the C-terminal non-catalytic domains of MT5-MMP. Catalytically inactive MT5-MMP variants increased the levels of Aβ and promoted APP/C99 sorting in the endo-lysosomal system. We found interaction of C99 with the C-terminal portion of MT5-MMP, the deletion of which caused a strong degradation of C99 by the proteasome, preventing Aβ accumulation. These findings reveal novel mechanisms for MT5-MMP control of APP metabolism and C99 fate involving proteolytic and non-proteolytic actions mainly mediated by the C-terminal part of the proteinase.
Towards establishing no observed adverse effect levels (NOAEL) for different sources of dietary phosphorus in feline adult diets: results from a 7 month feeding study
Authors: Coltherd Jennifer C. , Alexander Janet , Pink Claire , Rawlings John , Elliott Jonathan , Haydock Richard , Carvell-Miller Laura J. , Biourge Vincent , Molina Luis , Butterwick Richard , Logan Darren W. , Watson Phillip , Bakke Anne Marie 
Published: September 2020

AbstractHigh dietary phosphorus (P), particularly soluble salts, may contribute to chronic kidney disease development in cats. The aim of this study was to assess the safety of P supplied at 1g/1000kcal from a highly soluble P salt in P-rich dry format feline diets. Seventy-five healthy adult cats (n=25/group) were fed either a low P control (1.4g/1000 kcal; calcium:phosphorus ratio, Ca:P 0.97) or one of two test diets with 4g/1000 kcal (4184kJ); Ca:P 1.04 or 5g/1000kcal; Ca:P 1.27, both incorporating 1g/1000kcal (4184kJ) sodium tripolyphosphate (STPP) – for a period of 30 weeks in a randomised parallel-group study. Health markers in blood and urine, glomerular filtration rate, renal ultrasound and bone density were assessed at baseline and at regular time points. At the end of the test period, responses following transition to a commercial diet (total P – 2.34g/1000kcal, Ca:P 1.3) for a 4-week washout period were also assessed. No adverse effects on general, kidney or bone (skeletal) function and health were observed. P and Ca balance, some serum biochemistry parameters and regulatory hormones were increased in cats fed test diets from week 2 onwards (p≤0.05). Data from the washout period suggest that increased serum creatinine and urea values observed in the two test diet groups were influenced by dietary differences during the test period, and not indicative of changes in renal function. The present data suggest NOAELs for feline diets containing 1g P/1000kcal (4184kJ) from STPP and total phosphorus level of up to 5g/1000kcal (4184kJ) when fed for 30 weeks.