bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modelling the impact of health-related variables, age, migration, and socio-economic factors in the geographical distribution of early tested case-fatality risks associated with COVID-19 in Mexico
Authors: Ramírez-Aldana Ricardo , Gomez-Verjan Juan Carlos , Bello-Chavolla Omar Yaxmehen , García-Peña Carmen 
Published: November 2020

ABSTRACTCOVID-19 is a respiratory disease caused by SARS-CoV-2, which has significantly impacted economic and public healthcare systems world-wide. SARS-CoV-2 is highly lethal in older adults (>65 years old) and in cases with underlying medical conditions including chronic respiratory diseases, immunosuppression, and cardio-metabolic diseases including severe obesity, diabetes, and hypertension. The course of the COVID-19 pandemic in Mexico has led to many fatal cases in younger patients attributable to cardio-metabolic conditions. Here, we aimed to perform an early spatial epidemiological analysis for the COVID-19 outbreak in Mexico to evaluate how tested case-fatality risks (t-CFRs) are geographically distributed and to explore spatial predictors of early t-CFRs considering the variation of their impact on COVID-19 fatality across different states in Mexico, controlling for the severity of the disease. As results, considering health related variables; diabetes and obesity were highly associated with COVID-19 fatality. We identified that both external and internal migration had an important impact over early COVID-19 risks in Mexico, with external migration having the second highest impact when analyzing Mexico as a whole. Physicians-to-population ratio, as a representation of urbanity, population density, and overcrowding households, has the highest impact on t-CFRs, whereas the age group of 10 to 39 years was associated with lower risks. Geographically, the states of Quintana Roo, Baja California, Chihuahua, and Tabasco had higher t-CFRs and relative risks comparing with a national standard, suggesting that risks in these states were above of what was nationally expected; additionally, the strength of the association between some spatial predictors and the COVID-19 fatality risks variates by zone depending on the predictor.
A randomized trial on the regular use of potent mouthwash in COVID-19 treatment
Authors: Mukhtar Khalid , Qassim Suelen , Al Qahtani Shaikha Ali , Danjuma Mohamed Ibn-Masud , Mohamedali Mohamed , Farhan Housamaddeen Al , Khudair Mohammed F. , El Tayeh Abdel Rehim , Al-Dosari Mohammed , Babiker Mohamed Elhassan , Hassib Ahmed , Elmustafa Rumaisa Mohamed , Elhadary Wesal , Abdulkarim Morwan , Singh Rajvir , Al.Maslamani Muna 
Published: November 2020

1.AbstractIn this work we tried to study the effect of the regular use of potent mouthwash in COVID19 cases, on the premise that it may speedup the recovery, through the repeated reduction of microbial load, of both, the 2019-nCOV and oral microbiota; thus slowing the disease progression and lowering the incidence of superinfections.Through a randomized controlled trial, a mixed solution of Hydrogen peroxide 2% and chlorhexidine gluconate, to be used for oral rinsing and gargling three times daily, was tested in cases admitted to COVID treatment facility, versus the standard (only) COVID19-treatment protocol, starting with 46 cases in each group, matched in terms of disease severity, of symptoms, and average cycle threshold value (CT-value) for the COVID PCR test on diagnosis.Our findings showed statistically significant improvement in terms of a higher conversion rate to “COVID19-negative PCR” by five days of treatment (6/46 Vs 0/46), improvement in “symptoms severity” after two days of treatment, and less intubation and mortality (0/46 Vs 3/46) with all P-value < 0.05. There was also a trend of improvement in other outcome variables, though with no statistically significant difference; namely “shorter hospital stays,” “less progression in Oxygen requirements”, “less rate of plasma transfusion”, and better “gross extent of improvement”.Our findings support a beneficial role in treating active cases (Disease) and anticipates better outcome should implemented earlier in course of the disease; thus, suggest a role in limiting the spread (Pandemic), as an additional preventive method. Additionally, we think the repeated reduction in the microbial load might have been sufficient to induce a strain in a possible viral-microbial interaction, resulting in slowing down of the disease progress.
Delay-robust Estimation of the Reproduction Number and Comparative Evaluation on Generated Synthetic Data
Authors: Heidrich Benedikt , Mühlpfordt Tillmann , Hagenmeyer Veit , Mikut Ralf 
Published: November 2020

AbstractThe reproduction number is an indicator of the evolution of an epidemic. Consequently, accurate estimators for this number are essential for decision making in politics. Many estimators use filtered data as input to compensate for fluctuations of reported cases. However, for daily-based estimations, this filtering leads to delays. Some approaches use small window sizes for filtering to overcome this issue. This, in turn, leads to an increased periodic behavior of estimators. To overcome these issues, in the present paper, we introduce an estimator for the reproduction number that uses an acausally filtered number of cases as input, hence avoiding both the periodic behavior and the delay. For the filter size, we suggest using a multiple of one week since reported cases often exhibit a weekly pattern. We show that this approach is more robust against periodicities, and that it does not exhibit any delays in the estimation compared to estimators with smaller filter sizes.Moreover, often it is hard to examine estimators in detail because a ground truth is missing. For analyzing different properties of the estimators, we propose a method to generate synthetic datasets that can be taken as ground truths. Importantly, the synthetic data contains all relevant real-world behavior.Finally, we apply the proposed estimator to the publicly available coronavirus disease 2019 (COVID-19) data for Germany. We compare the proposed estimator to two estimators used by the federal German Robert Koch Institut (RKI). We observe that our estimator is more stable than the benchmarks especially if the reproduction number is close to 1. Based on the observation that the proposed estimator appears more robust, it may be a useful asset when considering governmental interventions.The accompanying source code is published under the Apache-2.0 license (https://github.com/timueh/C0VID-19).
Rapid disappearance of influenza following the implementation of COVID-19 mitigation measures in Hamilton, Ontario
Authors: Zhang Kevin , Misra Avika , Kim Patrick J. , Moghadas Seyed M. , Langley Joanne M. , Smieja Marek 
Published: November 2020

AbstractBackgroundPublic health measures, such as social distancing and closure of schools and non-essential services, were rapidly implemented in Canada to interrupt the spread of the novel coronavirus disease 2019 (COVID-19).ObjectiveWe sought to investigate the impact of mitigation measures during the spring wave of COVID-19 on the incidence of other laboratory-confirmed respiratory viruses in Hamilton, Ontario.MethodsAll nasopharyngeal swab specimens (n = 57,503) submitted for routine respiratory virus testing at a regional laboratory serving all acute-care hospitals in Hamilton, Ontario between January 2010 and June 2020 were reviewed. Testing for influenza A/B, respiratory syncytial virus, human metapneumovirus, parainfluenza I–III, adenovirus and rhinovirus/enterovirus was done routinely using a laboratory-developed polymerase chain reaction multiplex respiratory viral panel. A Bayesian linear regression model was used to determine the trend of positivity rates of all influenza samples for the first 26 weeks of each year from 2010 to 2019. The mean positivity rate of Bayesian inference was compared with the weekly reported positivity rate of influenza samples in 2020.ResultsThe positivity rate of influenza in 2020 diminished sharply following the population-wide implementation of COVID-19 interventions. Weeks 12-26 reported 0% positivity for influenza, with the exception of 0.1% reported in week 13.ConclusionsPublic health measures implemented during the COVID-19 pandemic were associated with a reduced incidence of other respiratory viruses and should be considered to mitigate severe seasonal influenza and other respiratory virus pandemics.
Building a pathway for diversity in plant sciences in Argentina: highlighting the work of women scientists through virtual activities
Authors: Auge Gabriela Alejandra , de Leone María José , Deanna Rocío , Oliferuk Sonia , Ribone Pamela Anahí , Welchen Elina 
Published: November 2020

AbstractEncouraging the participation of a diverse workforce in academia increases plurality as it broadens the range of skills, ways of thinking and experiences. Institutions and professional societies have been putting efforts on building plans that help make workplaces, conferences, education and extension programs more relatable to a highly diverse population. Argentina has an overall gender-balanced workforce in the sciences (~53% women/total), with an even higher representation in disciplines related to plant sciences. However, media outlets and national conferences related to genetics, botany, plant physiology, ecology and molecular biology, fail to reflect those numbers as the proportion of women invited for interviews, plenary lectures, and symposia falls below ~30%. As a way to increase the visibility of the wealth of plant science topics and experimental approaches in which Argentinian women work, and to facilitate connections among them across the country and abroad, we created the Argentinian Women in Plant Science network (https://argplantwomen.weebly.com/). This group has grown to over 200 members, representing a wide range of career stages and research topics. Since April, and taking advantage of the confinement situation, our weekly webinar series highlighting women plant scientists has reached an average audience of 60-70 participants, with a record of 100. Recently, we have begun a series of open professional development webinars to reach a wider public. Our first webinar, focused on Scientific poster design, had ~250 participants, most of them undergrad and graduate students from all over the country covering a diverse range of disciplines, including the social sciences. Even though we have immersed ourselves in the plant science community with our weekly seminars, we have expanded our goals with activities aimed to reach out to a much wider audience with webinars and teacher training workshops, hopefully making plant science more attainable to all.
A multisite genomic epidemiology study of Clostridioides difficile infections in the U.S. supports differential roles of healthcare versus community spread for two common strains
Authors: Miles-Jay Arianna , Young Vincent B. , Pamer Eric G. , Savidge Tor C. , Kamboj Mini , Garey Kevin W. , Snitkin Evan S. 
Published: November 2020

ABSTRACTClostridioides difficile is the leading cause of healthcare-associated infectious diarrhea. However, it is increasingly appreciated that healthcare-associated infections derive from both community and healthcare transmission, and that the primary sites of C. difficile transmission may be strain dependent. We conducted a multisite genomic epidemiology study to assess differential genomic evidence of healthcare vs. community spread for two of the most common C. difficile strains in the U.S.: sequence type (ST) 1 (associated with Ribotype 027) and ST2 (associated with Ribotype 014/020). Isolates recovered from stool specimens collected during standard clinical care at three geographically distinct U.S. medical centers between 2010 and 2018 underwent whole genome sequencing and phylogenetic analyses. ST1 and ST2 isolates both displayed some evidence of phylogenetic clustering by study site, but clustering was stronger and more apparent in ST1, consistent with our healthcare-based study more comprehensively sampling local transmission of ST1 compared to ST2 strains. Analyses of pairwise single nucleotide variant (SNV) distance distributions were also consistent with more evidence of healthcare transmission of ST1 compared to ST2, with 44% of ST1 isolates being within 2 SNVs of another isolate from the same geographic collection site compared to 5.5% of ST2 isolates (p-value = <0.001). Conversely, ST2 isolates were more likely to have close genetic neighbors across disparate geographic sites compared to ST1 isolates, further supporting non-healthcare routes of spread for ST2 and highlighting the potential for misattributing genomic similarity among ST2 isolates to recent healthcare transmission. Finally, we estimated a lower evolutionary rate for the ST2 lineage compared to the ST1 lineage using Bayesian timed phylogenomic analyses, and hypothesize that this may contribute to observed differences in geographic concordance among closely related isolates. Together, these findings suggest that ST1 and ST2, while both common causes of C. difficile infection in hospitals, show differential reliance on community and hospital spread. This conclusion supports the need for strain-specific criteria for interpreting genomic linkages and emphasizes the importance of considering differences in the epidemiology of circulating strains when devising interventions to reduce the burden of C. difficile infections.DATA SUMMARYAll whole genome sequence data was uploaded to the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under Bioproject accessions PRJNA595724, PRJNA561087, and PRJNA594943. Metadata that comply with patient privacy rules are included in the Supplementary Materials.
An altered balance of integrated and segregated brain activity is a marker of cognitive deficits following sleep deprivation
Authors: Cross Nathan E. , Pomares Florence B. , Nguyen Alex , Perrault Aurore A. , Jegou Aude , Uji Makoto , Lee Kangjoo , Razavipour Fatemeh , Bin Ka’b Ali Obaï , Aydin Umit , Benali Habib , Grova Christophe , Dang-Vu Thien Thanh 
Published: November 2020

AbstractSleep deprivation (SD) leads to impairments in cognitive function. Here, we tested the hypothesis that cognitive changes in the sleep-deprived brain can be explained by information processing within and between large-scale cortical networks. We acquired functional magnetic resonance imaging (fMRI) scans of 20 healthy volunteers during attention and executive tasks following a regular night of sleep, a night of sleep deprivation, and a recovery nap containing non-rapid eye movement (NREM) sleep. Overall, sleep deprivation was associated with increased cortex-wide functional integration, driven by a rise of integration within cortical networks. The ratio of within vs between network integration in the cortex increased further in the recovery nap, suggesting that prolonged wakefulness drives the cortex toward a state resembling sleep. This balance of integration and segregation in the sleep-deprived state was tightly associated with deficits in cognitive performance. This was a distinct and better marker of cognitive impairment than conventional indicators of homeostatic sleep pressure, as well as the pronounced thalamo-cortical connectivity changes that occurs towards falling asleep. Importantly, restoration of the balance between segregation and integration of cortical activity was also related to performance recovery after the nap, demonstrating a bi-directional effect. These results demonstrate that intra- and inter-individual differences in cortical network integration and segregation during task performance may play a critical role in vulnerability to cognitive impairment in the sleep deprived state.Significance StatementSleep deprivation has significant negative consequences for cognitive function. Understanding how changes in brain activity underpin changes in cognition is important not only to discover why performance declines following extended periods of wakefulness, but also for answering the fundamental question of why we require regular and recurrent sleep for optimal performance. Finding neural correlates that predict performance following sleep deprivation also has the potential to understand which individuals are particularly vulnerable to sleep deprivation, and what aspects of brain function may protect them from these negative consequences on performance. Finally, understanding how perturbations to regular (well-rested) brain functioning affect cognitive performance, will provide important insight into how underlying principles of information processing in the brain may support cognition generally.
Prevalence of low back pain among working Ethiopian population: A systematic review and meta-analysis
Authors: Arero Amanuel Godana , Arero Godana , Mohammed Shimels Hussien , Eftekhari Sahar 
Published: November 2020

AbstractBackground and objectiveLow back pain (LBP) as musculoskeletal disorder remains a common health problem and is one of the most prevalent occupational injuries affecting adults living in both developed and developing countries. To increase the power and improve the estimates of the prevalence of LBP among the working Ethiopian population, a comprehensive meta-analysis was carried out.MethodsA comprehensive systematic literature search was conducted in multiple international electronic bibliographic databases such as Web of Science, Pub Med, EMBASE, Scopus, and Google Scholar. Population-based Studies into the Prevalence of LBP among the working population living in Ethiopia were included. Methodological quality for included studies was appraised using an adapted tool. Meta-analyses, Meta-regression, and sensitivity analysis were conducted. Funnel plot symmetry visualization followed by Begg’s rank correlation and Egger’s regression asymmetry test methods were performed to detect the existence of publication bias. Heterogeneity between studies was assessed by using the Cochrane Q and I2-statistics.ResultsIn all 719 articles were identified and 13 articles with 6513 participants met the inclusion criteria for meta-analyses after filtering. The pooled point and twelve-month prevalence of LBP among working Ethiopian population was 49% (95% CI 40; 58) and 56% (95% CI 49; 62) respectively.ConclusionThe results showed a high prevalence of LBP among working Ethiopian population, especially among Teachers. We believe that Prevention strategies addressing the early onset of LBP among the working population would most likely be the answer to the burden of LBP on future economies in Ethiopia.
SARS-CoV-2 infection hospitalization, severity, criticality, and fatality rates
Authors: Seedat Shaheen , Chemaitelly Hiam , Ayoub Houssein , Makhoul Monia , Mumtaz Ghina R. , Kanaani Zaina Al , Khal Abdullatif Al , Kuwari Einas Al , Butt Adeel A. , Coyle Peter , Jeremijenko Andrew , Kaleeckal Anvar Hassan , Latif Ali Nizar , Shaik Riyazuddin Mohammad , Yassine Hadi M. , Al Kuwari Mohamed G. , Al Romaihi Hamad Eid , Al-Thani Mohamed H. , Bertollini Roberto , Abu-Raddad Laith J. 
Published: November 2020

AbstractBackgroundThis study aimed to estimate the age-stratified and overall morbidity and mortality rates of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection based on an analysis of the pervasive SARS-CoV-2 epidemic in Qatar, a country with <9% of the population being ≥50 years of age.MethodsInfection disease outcomes were investigated using a Bayesian approach applied to an age-structured mathematical model describing SARS-CoV-2 transmission and disease progression in the population. The model was fitted to infection and disease time-series and age-stratified data. Two separate criteria for classifying morbidity were used: one based on actual recorded hospital admission (acute-care or intensive-care-unit hospitalization) and one based on clinical presentation as per World Health Organization classification of disease severity or criticality.ResultsAll outcomes showed very strong age dependence, with low values for those <50 years of age, but rapidly growing rates for those ≥50 years of age. The strong age dependence was particularly pronounced for infection criticality rate and infection fatality rate. Infection acute-care and intensive-care-unit bed hospitalization rates were estimated at 13.10 (95% CI: 12.82-13.24) and 1.60 (95% CI: 1.58-1.61) per 1,000 infections, respectively. Infection severity and criticality rates were estimated at 3.06 (95% CI: 3.01-3.10) and 0.68 (95% CI: 0.67-0.68) per 1,000 infections, respectively. Infection fatality rate was estimated at 1.85 (95% CI: 1.74-1.95) per 10,000 infections.ConclusionsSARS-CoV-2 severity and fatality in Qatar was not high and demonstrated a very strong age dependence with <4 infections in every 1,000 being severe or critical and <2 in every 10,000 being fatal. Epidemic expansion in nations with young populations may lead to lower disease burden than previously thought.
Predicting COVID-19 (Coronavirus Disease) Outbreak Dynamics Using SIR-based Models: Comparative Analysis of SIRD and Weibull-SIRD
Authors: Sedaghat Ahmad , Mosavi Amir 
Published: November 2020

AbstractThe SIR type models are built by a set of ordinary differential equations (ODE), which are strongly initial value dependant. To fit multiple biological data with SIR type equations requires fitting coefficients of these equations by an initial guess and applying optimization methods. These coefficients are also extremely initial value-dependent. In the vast publication of these types, we hardly see, among simple to highly complicated SIR type methods, that these methods presented more than a maximum of two biological data sets. We propose a novel method that integrates an analytical solution of the infectious population using Weibull distribution function into any SIR type models. The Weibull-SIRD method has easily fitted 4 set of COVID-19 biological data simultaneously. It is demonstrated that the Weibull-SIRD method predictions for susceptible, infected, recovered, and deceased populations from COVID-19 in Kuwait and UAE are superior compared with SIRD original ODE model. The proposed method here opens doors for new deeper studying of biological dynamic systems with realistic biological data trends than providing some complicated, cumbersome mathematical methods with little insight into biological data’s real physics.
Brain transcriptomic changes in Japanese quail reveal roles for neurotensin and urocortin 3 in avian parental care
Authors: Lopes Patricia C. , de Bruijn Robert 
Published: November 2020

AbstractFor many species, parental care critically affects offspring survival. But what drives animals to display parental behaviours towards young? In mammals, pregnancy-induced physiological transformations seem key in preparing the neural circuits that lead towards attraction (and reduced-aggression) to young. Beyond mammalian maternal behaviour, knowledge of the neural mechanisms that underlie parental care is severely lacking. We took advantage of a domesticated bird species, the Japanese quail, for which parental behaviour towards chicks can be induced through a sensitization procedure, a process that is not effective in all animals. We used the variation in parental responses to study neural transcriptomic changes associated with the sensitization procedure itself and with the outcome of the procedure (i.e., presence of parental behaviours). Out of the brain regions studied, we found that most differences in gene expression were located in the hypothalamus. Two genes identified are of particular interest, as no role in avian parental care was known for those genes. One is neurotensin, previously only demonstrated to be causally associated with maternal care in mammals. The other one is urocortin 3, causally demonstrated to affect young-directed neglect and aggression in mammals. Our work opens new avenues of research into understanding the neural basis of parental care in non-placental species.