bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic variance of Open Reading Frames (ORFs) and Spike protein in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
Authors: Tsai Ping-Hsing , Wang Mong-Lien , Yang De-Ming , Liang Kung-How , Chou Shih-Jie , Chiou Shih-Hwa , Lin Ta-Hsien , Wang Chin-Tien , Chang Tai-Jay 
Published: August 2020

Background:
The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused severe pneumonia at December 2019. Since then, it has been wildly spread from Wuhan, China, to Asia, European, and United States to become the pandemic worldwide. Now coronavirus disease 2019 were globally diagnosed over 3 084 740 cases with mortality of 212 561 toll. Current reports variants are found in SARS-CoV-2, majoring in functional ribonucleic acid (RNA) to transcribe into structural proteins as transmembrane spike (S) glycoprotein and the nucleocapsid (N) protein holds the virus RNA genome; the envelope (E) and membrane (M) alone with spike protein form viral envelope. The nonstructural RNA genome includes ORF1ab, ORF3, ORF6, 7a, 8, and ORF10 with highly conserved information for genome synthesis and replication in ORF1ab.

Methods:
We apply genomic alignment analysis to observe SARS-CoV-2 sequences from GenBank (http://www.ncbi.nim.nih.gov/genebank/): MN 908947 (China, C1); MN985325 (United States: WA, UW); MN996527 (China, C2); MT007544 (Australia: Victoria, A1); MT027064 (United States: CA, UC); MT039890 (South Korea, K1); MT066175 (Taiwan, T1); MT066176 (Taiwan, T2); LC528232 (Japan, J1); and LC528233 (Japan, J2) and Global Initiative on Sharing All Influenza Data database (https://www.gisaid.org). We adopt Multiple Sequence Alignments web from Clustalw (https://www.genome.jp/tools-bin/clustalw) and Geneious web (https://www.geneious.com.

Results:
We analyze database by genome alignment search for nonstructural ORFs and structural E, M, N, and S proteins. Mutations in ORF1ab, ORF3, and ORF6 are observed; specific variants in spike region are detected.

Conclusion:
We perform genomic analysis and comparative multiple sequence of SARS-CoV-2. Large scaling sequence alignments trace to localize and catch different mutant strains in United possibly to transmit severe deadly threat to humans. Studies about the biological symptom of SARS-CoV-2 in clinic animal and humans will be applied and manipulated to find mechanisms and shield the light for understanding the origin of pandemic crisis.
Host metabolic reprogramming in response to SARS-Cov-2 infection
Authors: Moolamalla S T R , Chauhan Ruchi , Deva Priyakumar U , Vinod P K 
Published: August 2020

AbstractUnderstanding the pathogenesis of SARS-CoV-2 is important for developing effective treatment strategies. Viruses hijack the host metabolism to redirect the resources for their replication and survival. How SARS-CoV-2 influences the host metabolism is still unclear. In this study, we analyzed transcriptomic data obtained from different human respiratory cell lines and patient samples (Swab, PBMC, lung biopsy, BALF) to understand the metabolic alterations in response to SARS-CoV-2 infection. For this purpose, the expression pattern of metabolic genes in the human genome-scale metabolic network model Recon3D was explored. We identified metabolic genes and pathways and reporter metabolites under each SARS-CoV-2-infected condition and compared them to identify common and unique changes in the metabolism. Our analysis revealed host-dependent dysregulation of glycolysis, mitochondrial metabolism, amino acid metabolism, glutathione metabolism, polyamine synthesis, and lipid metabolism. We observed different metabolic changes that are pro- and antiviral in nature. We generated hypotheses on how antiviral metabolism can be targeted/enhanced for reducing viral titers. These warrant further exploration with more samples and in vitro studies to test predictions.
Bashing irreproducibility withshournal
Authors: Kirchner Tycho , Riege Konstantin , Hoffmann Steve 
Published: August 2020

1AbstractThe Linux shell is arguably one of the most important computational tools across various scientific disciplines. Its high flexibility makes it the platform of choice for many file operations and smaller scripting tasks. Also, many stand-alone programs are called from the Linux shell - typically followed by multiple command-line parameters. However, in larger analysis projects, keeping track of the work quickly becomes challenging, as a typical shell workflow involves the iterative execution of commands with many parameters, modification of scripts, and editing of configuration files. Too often, researchers find themselves in the uncomfortable position that a computational result generated a few weeks ago can no longer be reproduced, despite having taken great care documenting the work manually. On the other hand, there is a lack of tools able to record the researcher’s shell activity automatically with reasonably low runtime- and storage overhead. To close this critical gap, we developedshournal, a program that tightly integrates with the Linux shell and automatically records every shell command along with the files it reads or writes. Besides logging command- and file metadata, such as working directory, file path, and checksums,shournalcan be configured to archive scripts or configuration files that are not regularly under version control viagitorsvn.
Setting Limits on Neural Network’s Predictive Capacity in T1D Blood Glucose Concentration
Authors: Chuna Thomas 
Published: August 2020

AbstractThe ability to anticipate changes in blood glucose (BG) concentration would have a great impact on Type 1 diabetics (T1D). In order to create T1D treatment plans, patients collect a BG concentration time series. It has been demonstrated that various types of recurrent neural networks, such as Long Short Term Memory (LSTM), have success forecasting T1D BG concentrations. However, limited work has been done to characterize the T1D time series or set limits on neural network’s predictive capacity. In this work, a T1D patient’s 14 day BG concentration time series is studied. First, I test the time series stationarity. Then I use auto-correlation analysis, spectral analysis, and Gaussian process regression to characterize the T1D BG time series. Finally, the LSTM’s prediction quality is quantified and interpreted at different prediction intervals. The success or failure of the LSTM’s predictions are interpreted using the characterization of the time series.
Measurement lessons of a repeated cross-sectional household food insecurity survey during the COVID-19 pandemic in Mexico
Authors: Gaitán-Rossi P. , Vilar-Compte M. , Teruel G. , Pérez-Escamilla R. 
Published: August 2020

ObjectiveTo validate the telephone modality of the Latin American and Caribbean Food Security Scale (ELCSA) included in three waves of a phone survey to estimate the monthly household food insecurity (HFI) prevalence during the COVID-19 pandemic in Mexico.DesignWe examined the reliability and internal validity of the ELCSA scale in three repeated waves of a cross-sectional surveys with Rasch models. We estimated the monthly prevalence of food insecurity in the general population and in households with and without children, and compared them with a national 2018 survey. We tested concurrent validity by testing associations of HFI with socioeconomic status and anxiety.SettingENCOVID-19 is a monthly telephone cross-sectional survey collecting information on the well-being of Mexican households during the pandemic lockdown. Surveys used probabilistic samples and we used data from April (n=833), May (n=850), and June 2020 (n=1,674).ParticipantsMexicans 18 years or older who had a mobile telephone.ResultsELCSA had adequate model fit and HFI was associated, within each wave, with more poverty and anxiety. The COVID-19 lockdown was associated with an important reduction in food security; decreasing stepwise from 38.9% in 2018 to 24.9% in June 2020 in households with children.ConclusionsTelephone surveys are a feasible strategy to monitor food insecurity with ELCSA
Seroprevalence of SARS-CoV-2 in Niger State: A Pilot Cross Sectional Study
Authors: Majiya Hussaini , Aliyu-Paiko Mohammed , Balogu Vincent T , Musa Dickson A , Salihu Ibrahim M , Kawu Abdullahi A , Bashir Yakubu I , Sani Aishat A , John Baba , Muhammad Amina T , Jibril Fatima L , Bala Ezekiel , Obaje Nuhu G , Aliyu Yahaya B. , Muhammad Ramatu G , Mohammed Hadiza , Gimba Usman N , Uthman Abduljelili , Liman Hadiza M , Sule Alfa A , Joseph Kolo J , Makusidi Mohammed M , Isah Mohammed D , Abdullahi Ibrahim , Ndagi Umar , Waziri Bala , Bisallah Chindo I , Dadi-Mamud Naomi J , Ibrahim Kolo , Adamu Abu Kasim 
Published: August 2020

AbstractBackgroundCoronavirus Disease 2019 (COVID-19) Pandemic caused by SARS-CoV-2 is ongoing causing human and socioeconomic losses.ObjectiveTo know how far the virus has spread in Niger State, Nigeria, a pilot study was carried out to determine the SARS-CoV-2 seroprevalence, patterns, dynamics, and risk factors in the state.MethodsA cross sectional study design and Clustered-Stratified-Random sampling strategy were used to select 185 test participants across the state. SARS-CoV-2 IgG and IgM Rapid Test Kits (Colloidal gold immunochromatography lateral flow system) were used to determine the presence or absence of the antibodies to the virus in the blood of sampled participants across Niger State as from 26th June 2020 to 30th June 2020. The test kits were validated using the blood samples of some of the Nigeria Center for Disease Control (NCDC) confirmed positive and negative COVID-19 cases in the State. SARS-CoV-2 IgG and IgM Test results were entered into the EPIINFO questionnaire administered simultaneously with each test. EPIINFO was then used for to calculate arithmetic mean and percentage, odd ratio, chi-square, and regression at 95% Confidence Interval of the data generated.ResultsThe seroprevalence of SARS-CoV-2 in Niger State was found to be 25.41% and 2.16% for the positive IgG and IgM respectively. Seroprevalence among age groups, gender and by occupation varied widely. COVID-19 asymptomatic rate in the state was found to be 46.81%. The risk analyses showed that the chances of infection are almost the same for both urban and rural dwellers in the state. However, health care workers, those that experienced flu-like symptoms and those that have had contact with person (s) that travelled out of Nigeria in the last six (6) months (February -June 2020) are twice (2 times) at risk of being infected with the virus. More than half (54.59%) of the participants in this study did not practice social distancing at any time since the pandemic started. Discussions about knowledge, practice and attitude of the participants are included.ConclusionThe observed Niger State SARS-CoV-2 seroprevalence and infection patterns means that the virus is widely spread, far more SARS CoV-2 infections occurred than the reported cases and high asymptomatic COVID-19 across the state.
A comparative analysis between a SIRD compartmental model and the Richards growth model
Authors: Macêdo Antônio M. S. , Brum Arthur A. , Duarte-Filho Gerson C. , Almeida Francisco A. G. , Ospina Raydonal , Vasconcelos Giovani L. 
Published: August 2020

AbstractWe propose a compartmental SIRD model with time-dependent parameters that can be used to give epidemiological interpretations to the phenomenological parameters of the Richards growth model. We illustrate the use of the map between these two models by fitting the fatality curves of the COVID-19 epidemic data in Italy, Germany, Sweden, Netherlands, Cuba, and Japan.
Descriptive analysis of the Autism Spectrum Quotient (AQ) in a sample of Brazilian adults
Authors: Alves Ana Luíza Costa , de Paula Jonas Jardim , de Miranda Débora Marques , Romano-Silva Marco Aurélio 
Published: August 2020

ABSTRACTBackgroundThe Autism Spectrum Disorder is characterized by the presence of difficulties in social interaction, inflexible, repetitive and/or stereotyped behaviors and interests. The Autism Spectrum Quotient (AQ) is a self-report instrument with 50 items created to quantify autistic traits in individuals older than 18 years with average or above-average intelligence.ObjectivesThe principal aim was to present a brief descriptive analysis of the AQ in a heterogeneous sample of Brazilian adults, also, to measure the clinical validity of the scale.MethodWe recruited all the participants in Brazil (N=1024). Then we described the distribution in the general population (N=385) and investigated the AQ accuracy in a sample of autistic adults (N=32).ResultsOur results suggested that autism traits were normally distributed in the population, but Brazilian adults have shown a different profile from the original study. Further, we found that 24 adults from the sample had a clinical score on the AQ, compatible with their previous autism diagnosis.DiscussionOur population probably reports more symptoms compared to other because the original clinical score represents a lower percentile in our sample. Also, future work will be required to adequate the use of the AQ in the Brazilian population.
Mathematical Analysis, Model and Prediction of COVID-19 Data
Authors: Tong Yit C. 
Published: August 2020

AbstractA simple and effective mathematical procedure for the description of observed COVID-19 data and calculation of future projections is presented. An exponential function E(t) with a time-varying Growth Constant k(t) is used. E(t) closely approximates observed COVID-19 Daily Confirmed Cases with NRMSD’s of 1 to 2%. An example of prediction of future cases is presented. The Effective Growth Rates of a discrete SIR model were estimated on the basis of k(t) for COVID-19 data for Germany, and were found to be consistent with those reported in a previous study (1). The proposed procedure, which involves less than ten basic algebraic, logarithm and exponentiation operations for each data point, is suitable for use in promoting interdisciplinary research, exchange and sharing of information.
Sleep Abnormalities in the Synaptopathies – SYNGAP1-related Intellectual Disability and Phelan-McDermid syndrome
Authors: Smith-Hicks Constance , Stowe Robert C. , McCormack Maria , Holder J. Lloyd 
Published: August 2020

ABSTRACTNeurodevelopmental disorders are frequently associated with sleep disturbances. One class of neurodevelopmental disorders, the genetic synaptopathies, is caused by mutations in genes encoding proteins found at the synapse. Mutations in these genes cause derangement of synapse development and function. We utilized a validated sleep instrument, Children’s Sleep Habits Questionnaire (CSHQ) to discover what sleep abnormalities occur in individuals with two synaptopathies – Phelan-McDermid syndrome (PMD) and SYNGAP1-related Intellectual Disability (SYNGAP1-ID) when compared with healthy controls. We found both PMD and SYNGAP1-ID have significant sleep abnormalities with SYNGAP1-ID having greater severity of sleep disturbance than PMD. We found that sleep disturbances were more severe for both disorders in individuals 10 years and older compared with those less than 10 years old. Individuals with either disorder were more likely to use sleep aids than healthy controls.Furthermore, review of polysomnography studies for individuals with SYNGAP1-ID revealed significant reduction in rapid eye movement (REM) sleep content and delayed REM latency demonstrating abnormalities in sleep architecture. In conclusion, sleep disturbances are a significant phenotype in the synaptopathies PMD and SYNGAP1-ID. Improved sleep is a viable clinical endpoint for future clinical trials for these neurodevelopmental disorders.
Performing Qualitative Mask Fit Testing without a Commercial Kit: Fit Testing Which can be Performed at Home and at Work
Authors: O’Kelly Eugenia , Arora Anmol , Pearson Charlotte , Ward James , Clarkson P. John 
Published: August 2020

AbstractIntroductionQualitative fit testing is a popular method of ensuring the fit of sealing face masks such as N95 and FFP3 masks. Increased demand due to the COVID-19 pandemic has led to shortages in testing equipment and has forced many institutions to abandon fit testing. Three key materials are required for qualitative fit testing: the test solution, nebulizer, and testing hood. Accessible alternatives to the testing solution have been studied. This exploratory qualitative study evaluates alternatives to the nebulizer and hoods for performing qualitative fit testing.MethodsFour devices were trialed to replace the test kit nebulizer. Two enclosures were tested for their ability to replace the test hood. Three researchers evaluated promising replacements under multiple mask fit conditions to assess functionality and accuracy.ResultsThe aroma diffuser and smaller enclosures allowed participants to perform qualitative fit tests quickly and with high accuracy.Discussion & ConclusionAroma diffusers show significant promise in their ability to allow individuals to quickly, easily, and inexpensively perform qualitative fit testing. Our findings indicate that aroma diffusers and homemade testing hoods may allow for qualitative fit testing when conventional apparatus is unavailable. Additional research is needed to evaluate the safety and reliability of these devices.
Social Behaviors Associated with a Positive COVID-19 Test Result
Authors: Speaker Sidra , Doherty Christine , Pfoh Elizabeth R. , Dunn Aaron , Hair Bryan , Shaker Victoria , Daboul Lynn , Rothberg Michael B. 
Published: August 2020

AbstractObjectiveTo compare behaviors of individuals who tested positive for COVID-19 relative to non-infected individuals.MethodsWe sent COVID positive cases and age/gender matched controls a survey regarding their social behaviors via MyChart (online patient portal). We called cases if they did not complete the electronic survey within two days. Data was collected from May-June 2020. Survey responses for cases without a close contact and controls were compared using Pearson chi-square or Fisher’s Exact tests as appropriate.ResultsA total of 339 participants completed the survey (113 cases, 226 controls); 45 (40%) cases had known contact with COVID-19. Cases were more likely to have recently traveled (4% vs. 0%, p=0.01) or to work outside the home (40% vs. 25%, p=0.02). There was no difference in the rates of attending private or public gatherings, mask/glove use, hand-washing, cleaning surfaces and cleaning mail/groceries between cases and controls.ConclusionsSixty percent of cases had no known contact with COVID-19, indicating ongoing community transmission and underlining the importance of contact tracing. The greater percentage of cases who work outside the home provides further evidence for social distancing.
Extended lifetime of respiratory droplets in a turbulent vapour puff and its implications on airborne disease transmission
Authors: Chong Kai Leong , Ng Chong Shen , Hori Naoki , Yang Rui , Verzicco Roberto , Lohse Detlef 
Published: August 2020

AbstractTo mitigate the COVID-19 pandemic, it is key to slow down the spreading of the life-threatening coronavirus (SARS-CoV-2). This spreading mainly occurs through virus-laden droplets expelled at speaking, screaming, shouting, singing, coughing, sneezing, or even breathing [1–7]. To reduce infections through such respiratory droplets, authorities all over the world have introduced the so-called “2-meter distance rule” or “6-foot rule”. However, there is increasing empirical evidence, e.g. through the analysis of super-spreading events [6, 8–11], that airborne transmission of the coronavirus over much larger distances plays a major role [1–3, 7, 12–15], with tremendous implications for the risk assessment of coronavirus transmission. It is key to better and fundamentally understand the environmental ambient conditions under which airborne transmission of the coronavirus is likely to occur, in order to be able to control and adapt them. Here we employ direct numerical simulations of a typical respiratory aerosol in a turbulent jet of the respiratory event within a Lagrangian-Eulerian approach [16–18] with 5000 droplets, coupled to the ambient velocity, temperature, and humidity fields to allow for exchange of mass and heat [19] and to realistically account for the droplet evaporation under different ambient conditions. We found that for an ambient relative humidity of 50% the lifetime of the smallest droplets of our study with initial diameter of 10 µm gets extended by a factor of more than 30 as compared to what is suggested by the classical picture of Wells [20, 21], due to collective effects during droplet evaporation and the role of the respiratory humidity [22], while the larger droplets basically behave ballistically. With increasing ambient relative humidity the extension of the lifetimes of the small droplets further increases and goes up to 150 times for 90% relative humidity, implying more than two meters advection range of the respiratory droplets within one second. Smaller droplets live even longer and travel further. Our results may explain why COVID-19 superspreading events can occur for large ambient relative humidity such as in cooled-down meat-processing plants [10] or in pubs with poor ventilation. We anticipate our tool and approach to be starting points for larger parameter studies and for optimizing ventilation and indoor humidity controlling concepts, which in the upcoming autumn and winter both will be key in mitigating the COVID-19 pandemic.
Total testosterone is not associated with lean mass or handgrip strength in pre-menopausal females: findings from the NHANES
Authors: Alexander Sarah E. , Abbott Gavin , Aisbett Brad , Wadley Glenn D. , Hnatiuk Jill A. , Lamon Séverine 
Published: August 2020

AbstractTestosterone is a naturally occurring hormone that has been positively associated with lean mass and strength in males. Whether endogenous testosterone is related to lean mass and strength in females is unknown.ObjectiveTo examine the relationship between endogenous testosterone concentration and lean mass and handgrip strength in healthy, pre-menopausal females.MethodsSecondary data from the 2013-2014 National Health and Nutrition Examination Survey (NHANES)were used. Females were aged 18-40 (n=753, age 30 ± 6 yr, mean ± SD) and pre-menopausal. Multivariate linear regression models were used to examine associations between total testosterone, height-adjusted lean mass and handgrip strength.ResultsMean ± SD testosterone concentration was 1.0 ± 0.6 nmol·L-1 and mean free androgen index (FAI) was 0.02 ± 0.02. Mean fat-free mass index (FFMI) was 16.4 ± 3.0 kg·m-2 and mean handgrip strength was 61.7 ± 10.5 kg. In females, testosterone was not associated with FFMI (β=0.08; 95%CI: −0.02, 0.18; p=0.11) or handgrip strength (β=0.03; 95%CI: −0.11, 0.17; p=0.67) in a statistically significant manner. Conversely, FAI was positively associated with FFMI (β=0.17; 95%CI: 0.01, 0.33; p=0.04) but not handgrip strength (β=0.19; 95%CI: −0.02, 0.21; p=0.10).ConclusionsThese findings indicate that FAI, but not total testosterone, is associated with FFMI in females. The small coefficients however suggest that FAI only accounts for a minor proportion of the variance in FFMI, highlighting the complexity of the regulation of lean mass in female physiology. FAI nor total testosterone are associated with handgrip strength in females when testosterone concentrations are not altered pharmacologically.