bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variation in SARS-CoV-2 free-living survival and environmental transmission can modulate the intensity of emerging outbreaks
Authors: Ogbunugafor C. Brandon , Miller-Dickson Miles D. , Meszaros Victor A. , Gomez Lourdes M. , Murillo Anarina L. , Scarpino Samuel V. 
Published: May 2020

AbstractVariation in free-living, microparasite survival can have a meaningful impact on the ecological dynamics of established and emerging infectious diseases. Nevertheless, resolving the importance of environmental transmission in the ecology of epidemics remains a persistent challenge, requires accurate measuring the free-living survival of pathogens across reservoirs of various kinds, and quantifying the extent to which interaction between hosts and reservoirs generates new infections. These questions are especially salient for emerging pathogens, where sparse and noisy data can obfuscate the relative contribution of different infection routes. In this study, we develop a mechanistic, mathematical model that permits both direct (host-to-host) and indirect (environmental) transmission and then fit this model to empirical data from 17 countries affected by an emerging virus (SARS-CoV-2). From an ecological perspective, our model highlights the potential for environmental transmission to drive complex, non-linear dynamics during infectious disease outbreaks. Summarizing, we propose that fitting such models with environmental transmission to real outbreak data from SARS-CoV-2 transmission highlights that variation in environmental transmission is an underappreciated aspect of the ecology of infectious disease, and an incomplete understanding of its role has consequences for public health interventions.
Detection of Cytomegalovirus infection in infants with biliary atresia: A meta-analysis
Authors: Mohamed Sagad Omer Obeid , Ali Almigdad H. M. , Elbathani Mohamed Elata Hassan , Abdallah Osman Omer Ali , Ahmed Assad Ahmed Mohammed , Ibrahim Abazr A. H. , Elhassan Almutasim B. E. , Salman Mohammed Suliman Tawer , Elnil Mahmoud , Elkhidir Ibrahim H. E. , Elhassan Mazin A.M. , Abuzied Abdulhamid Ibrahim Hassan 
Published: May 2020

AbstractBackgroundBiliary atresia (BA) is a leading cause of end-stage liver disease and the most common indication of liver transplantation in children. Several reports attributed BA to both prenatal and perinatal aetiologies, including a viral infection-induced auto-immune response that targets the bile ducts. Cytomegalovirus (CMV) remains the most common virus being linked to BA. This meta-analysis estimates to what extent CMV infection is detected in patients with BA.MethodsThis study was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The databases of MEDLINE/PubMed, WHO-Virtual Health Library (VHL), ScienceDirect, and Google Scholar were used for the systematic search. Random effects model was used to estimate the pooled prevalence estimate with the corresponding 95% confidence interval (CI) using StatsDirect statistical software. Heterogeneity among the included studies was estimated using the I2 statistics. Publication bias was determined based on Begg’s test, Egger’s test, and examination of the funnel plot. Subgroup analyses and meta-regression were used to explore the moderators of heterogeneity between studies.ResultsA total of 13 studies that fulfilled the eligibility criteria were included in the meta-analysis. The pooled overall prevalence of CMV infection in patients with BA was 24.5% (95% CI 11.9 %– 33.9%). In subgroup and meta-regression analyses, the prevalence of CMV infection in patients with BA was correlated with the geographical areas (p = .001) but not with the study year (p = .153).ConclusionsThe available data demonstrate that the detection of CMV infection is common in infants with BA. There is still a need for large studies with appropriate controls to examine various aspects of the association between CMV infection and BA.AbbreviationsBA = biliary atresia, CMV = cytomegalovirus.
Estimation of the Potential Impact of COVID-19 Responses on the HIV Epidemic: Analysis using the Goals Model
Authors: Stover John , Chagoma Newton , Taramusi Isaac , Teng Yu , Glaubius Rob , Mahiane Guy 
Published: May 2020

SummaryWe applied a simulation model of HIV to analyze the effects of 3 and 6-month disruptions in health services as a result of COVID-19. We found that disruptions to primary prevention programs (male circumcision, behavior change programs, condom distribution) would have small but transitory effects on new infections that might be more than offset by reductions in commercial and multi-partner sex due to lock downs. However, if COVID-19 leads to disruptions in ART services the impacts on mortality could be severe, doubling or tripling the estimated number of HIV deaths in 2020.
Effects of home confinement on mental health and lifestyle behaviours during the COVID-19 outbreak: Insight from the “ECLB-COVID19” multi countries survey
Authors: Ammar Achraf , Trabelsi Khaled , Brach Michael , Chtourou Hamdi , Boukhris Omar , Masmoudi Liwa , Bouaziz Bassem , Bentlage Ellen , How Daniella , Ahmed Mona , Mueller Patrick , Mueller Notger , Aloui Asma , Hammouda Omar , Paineiras-Domingos Laisa Liane , Braakman-jansen Annemarie , Wrede Christian , Bastoni Sophia , Pernambuco Carlos Soares , Mataruna Leonardo , Taheri Morteza , Irandoust Khadijeh , Khacharem Aïmen , Bragazzi Nicola L , Chamari Karim , Glenn Jordan M , Bott Nicholas T , Gargouri Faiez , Chaari Lotfi , Batatia Hadj , Ali Gamal Mohamed , Abdelkarim Osama , Jarraya Mohamed , Abed Kais El , Souissi Nizar , Van Gemert-Pijnen Lisette , Riemann Bryan L , Riemann Laurel , Moalla Wassim , Gómez-Raja Jonathan , Epstein Monique , Sanderman Robbert , Schulz Sebastian , Jerg Achim , Al-Horani Ramzi , Mansi Taysir , Jmail Mohamed , Barbosa Fernando , Santos Fernando , Šimunič Boštjan , Pišot Rado , Cowan Donald , Gaggioli Andrea , Bailey Stephen J , Steinacker Jürgen , Driss Tarak , Hoekelmann Anita 
Published: May 2020

AbstractBackgroundAlthough recognised as effective measures to curb the spread of the COVID-19 outbreak, social distancing and self-isolation, have been suggested to generate burden throughout the population. To provide scientific data to help identify risk-factors for the psychosocial strain during the COVID-19 outbreak, an international cross-disciplinary online survey was circulated in April 2020. This report outlines the mental, emotional and behavioural consequences of COVID-19 home confinement.MethodThirty-five research organisations from four continents promoted the survey through their networks to the general society, in Ten different languages. Questions were presented in a differential format with questions related to responses “before” and “during” confinement period.Results1047 replies (54% women) from Western-Asia (36%), North-Africa (40%), Europe (21%) and other countries (3%) were analysed. The COVID-19 home confinement evoked a negative effect on mental wellbeing and emotional status (P < 0.001; 0.43 ≤ d ≤ 0.65) with a greater proportion of individuals experiencing psychosocial and emotional disorders (10% to 16.5%). These psychosocial tolls were associated with unhealthy lifestyle behaviours with a greater proportion of individuals experiencing (i) physical (+15.2%) and social (71.2%) inactivity, (ii) poor sleep quality (12.8%), (iii) unhealthy diet behaviours (10%), and (iv) unemployment (6%). Conversely, participants demonstrated a greater use (15%) of technology solutions during the confinement period.ConclusionThese findings elucidate the risk of psychosocial strain during the current home confinement period and provide a clear remit for the urgent implementation of technology-based intervention to foster an Active and Healthy Confinement Lifestyle (AHCL).
Long-term individual and population functional outcomes in older adults with atrial fibrillation
Authors: Parks Anna L. , Jeon Sun Y. , Boscardin W. John , Steinman Michael A. , Smith Alexander K. , Fang Margaret C. , Shah Sachin J. 
Published: May 2020

AbstractBackgroundOlder adults with atrial fibrillation (AF) have multiple risk factors for disablement. Long-term function and the contribution of strokes to disability has not been previously characterized.MethodsWe performed a longitudinal, observational study in the nationally representative Health and Retirement Study (1992-2014). We included participants ≥65 years with Medicare claims who met incident AF diagnosis claims criteria. We examined the association of incident stroke with three functional outcomes: independence with activities of daily living (ADL) and instrumental activities of daily living (IADL) and community-dwelling. We fit separate logistic regression models with repeated measures adjusting for comorbidities and demographics to estimate the effect of stroke on function. We estimate the contribution of strokes to the overall population burden of functional impairment using the method of recycled predictions.ResultsAmong 3530 participants (median age 79 years, 53% women, median CHA2DS2-VASc 5), 262 had a stroke over 17,396 person-years. Independent of stroke and accounting for population comorbidities, annually, ADL dependence increased by 4.4%, IADL dependence increased by 3.9%, and nursing home residence increased by 1.2% (p<0.05 for all). Accounting for comorbidities, of those who experienced a stroke, 31.9% developed new ADL dependence, 26.5% developed new IADL dependence, and 8.6% newly moved to a nursing home (p<0.05 for all). Considering all causes of function loss, 1.7% of ADL disability-years, 1.2% of IADL disability-years, and 7.3% of nursing home years could be attributed to stroke over 7.4years.ConclusionOlder adults lose substantial function over time following AF diagnosis, independent of stroke. Stroke was associated with a significant decline in function and an increase in the likelihood of nursing home move, but stroke did not accelerate subsequent disability accrual. Because of the high background rate of functional loss, stroke was not the dominant determinant of population-level disability in older adults with AF.Impact statementWe certify that this work is novel. Little is known about long-term function (ADL, IADL, community-dwelling) among older adults with AF and the association with stroke. This nationally representative study finds a high rate of function loss independent of stroke, and among those who suffer a stroke, a dramatic and immediate decline in function. Because of the high rate of function loss independent of stroke and the relatively low rate of stroke, on a population level, stroke is not the dominant determinant of disability in older adults with AF.
Phenomenological Modelling of COVID-19 epidemics in Sri Lanka, Italy and Hebei Province of China
Authors: Attanayake A.M.C.H. , Perera S.S.N. , Jayasinghe S. 
Published: May 2020

AbstractThe COVID-19 pandemic has resulted in increasing number of infections and deaths on a daily basis. There is no specific treatment or vaccine identified and the focus has been preventive measures based on statistical and mathematical models. These have relied on analyzing the behavior of populations and characteristics of the infection and applying modelling techniques. The analysis of epidemiological curve fitting on number of daily infections across affected countries could give useful insights on the characteristics of the epidemic. A variety of phenomenological models are available to capture dynamics of disease spread and growth. Data for this study used the number of daily new infections and cumulative number of infections in COVID-19 in three selected countries, Sri Lanka, Italy and Hebei province of China, from the first day of appearance of cases to 20th April 2020. In this study Gompertz, Logistic and Exponential growth curves were fitted on cumulative number of infections across countries. Akaike’s information criteria (AIC) was used in determining the best fitting curve for each country. Results revealed that the most appropriate growth curves for Sri Lanka, Italy and China-Hebei are Exponential, Gompertz and Logistic curves respectively. The overall growth rate and final epidemic size evaluated from best models for the three countries and short-term forecasts were also generated. Log incidences over time in each country were regressed before and after the identified peak time of the respective outbreaks of countries. Hence, doubling time/halving time together with daily growth rates and predictions were estimated. Findings altogether demonstrate that outbreak seems extinct in Hebei-China whereas further transmissions are possible in Sri Lanka. In Italy, current outbreak transmits in a decreasing rate.
Prediction of 7-year’s Conversion from Subjective Cognitive Decline to Mild Cognitive Impairment
Authors: Yue Ling , Hu Dan , Zhang Han , Wen Junhao , Wu Ye , Li Wei , Sun Lin , Li Xia , Wang Jinghua , Li Guanjun , Wang Tao , Shen Dinggang , Xiao Shifu 
Published: May 2020

AbstractSubjective cognitive decline (SCD) is a high-risk yet less understood status years before Alzheimer’s disease (AD). This work included 76 SCD individuals with two (baseline and seven years later) neuropsychological evaluations and a baseline T1-MRI. A machine learning-based model was trained based on 198 baseline neuroimage features and a battery of 25 clinical measurements to discriminate 24 progressive SCDs from 52 stable SCDs. The SCD progression was satisfactorily predicted with combined features. A history of stroke, a low education level, a low baseline MoCA score, a shrunk left amygdala, and enlarged white matter at the banks of the right superior temporal sulcus favor the progression. This is to date the largest retrospective study of SCD-to-MCI conversion with the longest follow-up, suggesting predictable far-future cognitive decline for the risky populations with baseline measures only. These findings provide valuable knowledge to the future neuropathological studies of AD in its prodromal phase.
COVID-19 is rapidly changing: Examining public perceptions and behaviors in response to this evolving pandemic
Authors: Seale H , Heywood AE , Leask J , Sheel M , Thomas S , Durrheim D.N , Bolsewicz K , Kaur R 
Published: May 2020

ABSTRACTBackgroundSince the emergence of SARS-CoV-2, the virus that causes coronavirus disease (COVID-19) in late 2019, communities have been required to rapidly adopt community mitigation strategies rarely used before, or only in limited settings. This study aimed to examine the attitudes and beliefs of Australian adults towards the COVID-19 pandemic, and willingness and capacity to engage with these mitigation measures. In addition, we aimed to explore the psychosocial and demographic factors that are associated with adoption of recommended hygiene-related and avoidance-related behaviors.MethodsA national cross-sectional online survey of 1420 Australian adults (18 years and older) was undertaken between the 18 and 24 March 2020. The statistical analysis of the data included univariate and multivariate logistic regression analysis.FindingsThe survey of 1420 respondents found 50% (710) of respondents felt COVID-19 would ‘somewhat’ affect their health if infected and 19% perceived their level of risk as high or very high. 84·9% had performed ≥1 of the three recommended hygiene-related behaviors and 93·4% performed ≥1 of six avoidance-related behaviors over the last one month. Adopting avoidance behaviors was associated with trust in government/authorities (aOR: 5·5, 95% CI 3-9·0), higher perceived rating of effectiveness of behaviors (aOR: 4·3, 95% CI: 2·8-6·9) and higher levels of perceived ability to adopt social distancing strategies (aOR: 1·8, 95% CI 1·1-3·0).InterpretationIn the last two months, members of the public have been inundated with messages about hygiene and social (physical) distancing. However, our results indicate that a continued focus on supporting community understanding of the rationale for these strategies, as well as instilling community confidence in their ability to adopt or sustain the recommendations is needed.FundingNone
Detailed and atypical HLA-E peptide binding motifs revealed by a novel peptide exchange binding assay
Authors: Walters Lucy C. , McMichael Andrew J. , Gillespie Geraldine M. 
Published: May 2020

AbstractDiverse SIV epitopes that bind the rhesus homologue of HLA-E, Mamu-E, have recently been identified in SIV-vaccine studies using a recombinant Rhesus cytomegalovirus (RhCMV 68-1) vector, where unprecedented protection against SIV challenge was achieved. Additionally, severalMycobacterialpeptides identified both algorithmically and following elution from infected cells, are presented to CD8+T cells by HLA-E in humans. Yet, a comparative and comprehensive analysis of relative HLA-E peptide binding strength via a reliable, high throughputin vitroassay is currently lacking. To address this we developed and optimised a novel, highly sensitive peptide exchange ELISA-based assay that relatively quantitates peptide binding to HLA-E. Using this approach we screened multiple peptides, including peptide panels derived from HIV, SIV and Mtb predicted to bind HLA-E. Our results indicate that although HLA-E preferentially accommodates canonical MHC class I leader peptides, many non-canonical, sequence diverse, pathogen-derived peptides also bind HLA-E, albeit generally with lower relative binding strength. Additionally, our screens demonstrate that the majority of peptides tested, including some key Mtb and SIV epitopes which have been shown to elicit strong Mamu-E-restricted T cell responses, either bind HLA-E extremely weakly or give signals that are indistinguishable from the negative, peptide-free controls.
SIGAR: Inferring features of genome architecture and DNA rearrangements by split read mapping
Authors: Feng Yi , Beh Leslie Y. , Chang Wei-Jen , Landweber Laura F. 
Published: May 2020

AbstractCiliates are microbial eukaryotes with distinct somatic and germline genomes. Post-zygotic development involves extensive remodeling of the germline genome to form somatic chromosomes. Ciliates therefore offer a valuable model for studying the architecture and evolution of programmed genome rearrangements. Current studies usually focus on a few model species, where rearrangement features are annotated by aligning reference germline and somatic genomes. While many high-quality somatic genomes have been assembled, a high quality germline genome assembly is difficult to obtain due to its smaller DNA content and abundance of repetitive sequences. To overcome these hurdles, we propose a new pipeline SIGAR (SplitreadInference ofGenomeArchitecture andRearrangements) to infer germline genome architecture and rearrangement features without a germline genome assembly, requiring only short germline DNA sequencing reads. As a proof of principle, 93% of rearrangement junctions identified by SIGAR in the ciliateOxytricha trifallaxwere validated by the existing germline assembly. We then applied SIGAR to six diverse ciliate species without germline genome assemblies, includingIchthyophthirius multifilii,a fish pathogen. Despite the high level of somatic DNA contamination in each sample, SIGAR successfully inferred rearrangement junctions, short eliminated sequences and potential scrambled genes in each species. This pipeline enables pilot surveys or exploration of DNA rearrangements in species with limited DNA material access, thereby providing new insights into the evolution of chromosome rearrangements.
Evidence for a behaviourally measurable perseverance trait
Authors: Määttänen Ilmari , Makkonen Emilia , Jokela Markus , Närväinen Johanna , Väliaho Julius , Seppälä Vilja , Kylmälä Julia , Henttonen Pentti 
Published: May 2020

AbstractThe aim of this exploratory study was to create a behavioural measure for trait(s) that reflect the ability and motivation to continue an unpleasant behaviour, i.e. perseverance or persistence, and to measure its correlates to several variables.We utilised six different tasks with 54 subjects to measure the perseverance-trait: cold pressor task, hand grip endurance task, impossible anagram task, impossible verbal reasoning task, thread and needle task and boring video task.According to our results, the task performances formed two perseverance factors that could be roughly described as “physical” and “mental” perseverance. Together, the two-factor solution is responsible for the common variance constituting 37.3 % of the total variance in the performances i.e. performance times. Excluding the impossible anagram task, the performance in any given task was better explained by performances in the other tasks (i.e. “trait”, η2range = 0.131–0.253) than by rank order variable (“depletion”, i.e. getting tired from the previous tasks, η2range = 0–0.096).HighlightsBehavioural perseverance of individuals can be measured behaviourallyBehavioural perseverance forms a two-factor structurePerseverance trait is better predictor of performance than depletion of individuals’ personal resources in a task
Anti-inflammatory dopamine- and serotonin-based endocannabinoid epoxides reciprocally regulate cannabinoid receptors and the TRPV1 channel
Authors: Arnold William R. , Carnevale Lauren N. , Xie Zili , Baylon Javier L. , Tajkhorshid Emad , Hu Hongzhen , Das Aditi 
Published: May 2020

ABSTRACTThe endocannabinoid (eCB) system is a promising target to mitigate pain as the eCBs are endogenous ligands of the pain-mediating receptors—cannabinoid receptors 1 and 2 (CB1 and CB2) and TRPV1. Here we report on a novel class of lipids formed by the epoxidation of N-arachidonoyl-dopamine (NADA) and N-arachidonoyl serotonin (NA5HT) by cytochrome P450 (CYP) epoxygenases. These epoxides (epoNADA and epoNA5HT) are dual-functional rheostat modulators (varying strength of agonism or antagonism) of the eCB-TRPV1 axis. In fact, epoNADA is a 6-fold stronger agonist of TRPV1 than NADA while epoNA5HT is a 30-fold stronger antagonist of TRPV1 than NA5HT and displays a significantly stronger inhibition on TRPV1-mediated responses in primary afferent neurons. Moreover, epoNA5HT is a full CB1 agonist. The epoxides reduce the pro-inflammatory biomarkers IL-6, IL-1β, TNF-α and nitrous oxide (NO) and raise anti-inflammatory IL-10 in activated microglial cells. The epoxides are spontaneously generated by activated microglia cells and their formation is potentiated in the presence of another eCB, anandamide (AEA). We provide evidence for the direct biochemical mechanism of this potentiation using human CYP2J2, a CYP epoxygenase in the human brain, using detailed kinetics studies and molecular dynamics simulations. Taken all together, inflammation leads to an increase in the metabolism of NADA, NA5HT and other eCBs by CYP epoxygenases to form the corresponding epoxides. The epoxide metabolites are bioactive lipids that are more potent, multi-faceted endogenous molecules, capable of influencing the activity of CB1, CB2 and TRPV1 receptors. The identification of these molecules will serve as templates for the synthesis of new multi-target therapeutics for the treatment of inflammatory pain.