bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seroprevalence of anti-SARS-CoV-2 antibodies in Iquitos, Loreto, Peru
Authors: Álvarez-Antonio Carlos , Meza-Sánchez Graciela , Calampa Carlos , Casanova Wilma , Carey Cristiam , Alava Freddy , Rodríguez-Ferrucci Hugo , Quispe Antonio M. 
Published: January 2021

SummaryBackgroundDetection of SARS-CoV-2 antibodies among people at risk is critical for understanding both the prior transmission of COVID-19 and vulnerability of the population to the continuing transmission and, when done serially, the intensity of ongoing transmission over an interval in a community. In this study, we estimated the seroprevalence of COVID-19 in a representative population-based cohort of Iquitos, one of the regions with the highest mortality rates from COVID-19 in Peru, where a devastating number of cases occurred in March 2020.MethodsWe conducted a population-based study of transmission tested each participant using the COVID-19 IgG/IgM Rapid Test from Orient Gene Biotech and used survey analysis methods to estimate seroprevalence accounting for the sampling design effect and test performance characteristics. Here we report results from the baseline (13 to 18 July 2020) and the first month of follow-up (13 to 18 August 2020) study.FindingsWe enrolled a total of 716 participants and estimated seroprevalence of 70.0% (95% CI: 67.0%–73.4%), a test-re-test positivity of 65% (95% CI: 61.0%–68.3%), and an incidence of new exposures of 1.8% (95% CI: 0.9%–3.2%) data that suggest that transmission is ongoing but is occurring at low levels. We observed significant differences in the seroprevalence between age groups, with participants 18 to 29 years of age having lower seroprevalence than children <12 years of age (Prevalence ratio =0.85 [PR]; 95% CI: 0.73 – 0.98), suggesting that children were not refractory to infection in this setting.InterpretationIquitos demonstrates one of the highest rates of seroprevalence of COVID-19 worldwide. Current data shows a limited case burden in Iquitos for the past seven months and suggests that these levels are sufficient to provide significant but incomplete herd immunity.FundingDirección Regional de Salud de Loreto, DIRESA, Loreto, Peru
Sleeping under the waves: a longitudinal study across the contagion peaks of COVID-19 pandemic in Italy
Authors: Salfi Federico , D’Atri Aurora , Tempesta Daniela , Ferrara Michele 
Published: January 2021

AbstractAfter the March–April 2020 COVID-19 outbreak, a second contagion wave afflicted Europe in autumn. This study aimed to evaluate sleep health/patterns of Italians during this further challenging situation.A total of 2013 Italians longitudinally participated in a web-based survey during the two contagion peaks of the COVID-19 outbreak. We investigated the risk factors for sleep disturbances during the second wave, and we compared sleep quality and psychological well-being between the two assessments (March–April and November–December 2020). Female gender, low education, evening chronotype, being at high-risk for COVID-19 infection, reporting negative social or economic impact, and evening smartphone overuse predicted a higher risk of poor sleep and insomnia symptoms during the second wave. Advanced age, living with high-risk subjects for COVID-19 infection, and having a relative/friend infected with COVID-19 before the prior two weeks were risk categories for poor sleep quality. Living with children, having contracted COVID-19 before the prior two weeks, being pessimistic on the vaccine, and working in healthcare were risk factors for insomnia symptoms. The follow-up assessment highlighted reduced insomnia symptoms and anxiety. Nevertheless, we showed reduced sleep duration, higher daytime dysfunction and sleep medication use, and advanced sleep phase, confirming the alarming prevalence of poor sleepers (∼60%) and severe depression (∼20%) in a context of increased perceived stress.This study demonstrated a persistent impact of the COVID-19 pandemic on sleep and mental health. Large-scale interventions to counteract the chronicity and exacerbation of sleep and psychological disturbances are necessary, especially for the risk categories.
Optimizing SARS-CoV-2 vaccination strategies in France: Results from a stochastic agent-based model
Authors: Hoertel Nicolas , Blachier Martin , Limosin Frédéric , Sánchez-Rico Marina , Blanco Carlos , Olfson Mark , Luchini Stéphane , Schwarzinger Michaël , Leleu Henri 
Published: January 2021

AbstractThe COVID-19 pandemic is a major global societal, economic and health threat. The availability of COVID-19 vaccines has raised hopes for a decline in the pandemic. We built upon a stochastic agent-based microsimulation model of the COVID-19 epidemic in France. We examined the potential impact of different vaccination strategies, defined according to the age, medical conditions, and expected vaccination acceptance of the target non-immunized adult population, on disease cumulative incidence, mortality, and number of hospital admissions. Specifically, we examined whether these vaccination strategies would allow to lift all non-pharmacological interventions (NPIs), based on a sufficiently low cumulative mortality and number of hospital admissions. While vaccinating the full adult non-immunized population, if performed immediately, would be highly effective in reducing incidence, mortality and hospital-bed occupancy, and would allow discontinuing all NPIs, this strategy would require a large number of vaccine doses. Vaccinating only adults at higher risk for severe SARS-CoV-2 infection, i.e. those aged over 65 years or with medical conditions, would be insufficient to lift NPIs. Immediately vaccinating only adults aged over 45 years, or only adults aged over 55 years with mandatory vaccination of those aged over 65 years, would enable lifting all NPIs with a substantially lower number of vaccine doses, particularly with the latter vaccination strategy. Benefits of these strategies would be markedly reduced if the vaccination was delayed, was less effective than expected on virus transmission or in preventing COVID-19 among older adults, or was not widely accepted.
Population-based seroprevalence of SARS-CoV-2 antibodies in a high-altitude setting in Peru
Authors: Huamaní Charles , Velásquez Lucio , Montes Sonia , Mayanga-Herrera Ana , Bernabé-Ortiz Antonio 
Published: January 2021

ABSTRACTBackgroundLittle evidence exists about the prevalence of COVID-19 infection at high altitude. We aimed to estimate the population-based seroprevalence of COVID-19 in Cusco at the end of the first wave.MethodsA population-based survey was conducted in September 2020 in three settings in Cusco: (1) Cusco city at 3300 meters above the sea level (m.a.s.l.), (2) the periphery of Cusco (Santiago, San Jerónimo, San Sebastián, and Wanchaq) at 3300 m.a.s.l., and (3) Quillabamba city, located at 1050 m.a.s.l. People aged ≥18 years within a family unit were included. The diagnosis of COVID-19 infection was based on identifying total antibodies (IgM and IgG) anti-SARS-CoV-2 in serum using the Elecsys Anti-SARS-CoV-2 chemiluminescence test.FindingsWe enrolled 1924 participants from 712 families. Of the total, 637 participants were COVID-19 seropositive. Seroprevalence was 38·8% (95%CI: 33·4%-44·9%) in Cusco city, 34·9% (95%CI: 30·4%-40·1%) in the periphery of Cusco, and 20·3% (95%CI: 16·2%-25·6%) in Quillabamba. In 141 families (19·8%; 95%CI: 17·0%-22·8%) the whole members were positive to the test. Living with more than three persons in the same house, a positive COVID-19 case at home, and a member who died in the last five months were factors associated with COVID-19 positivity. The smell/taste alteration was the symptom most associated with seropositivity (aOR= 14·27, 95% CI: 8·24-24·70); whereas always wearing a face shield (aOR= 0·62; 95% CI: 0·46-0·84) or a facial mask (aOR= 0·65, 95% CI: 0·47-0·88) reduced that probability.InterpretationSeroprevalence of COVID-19 in Cusco was high, with significant differences between settings. Wearing masks and face shields were associated with lower rate of infection; however, efforts must be made to sustain them over time since there is still a high proportion of susceptible people.FundingFondo Nacional de Desarrollo Científico, Tecnológico y de Innovación Tecnológica (FONDECYT – Perú) and Universidad Andina del Cusco.
Comprehensive mapping of SARS-CoV-2 interactions in vivo reveals functional virus-host interactions
Authors: Yang Siwy Ling , DeFalco Louis , Anderson Danielle E. , Zhang Yu , Aw Ashley J , Lim Su Ying , Ni Lim Xin , Tan Kiat Yee , Zhang Tong , Chawla Tanu , Su Yan , Lezhava Alexander , de Sessions Paola , Merits Andres , Wang Lin-Fa , Huber Roland G. , Wan Yue 
Published: January 2021

AbstractSARS-CoV-2 has emerged as a major threat to global public health, resulting in global societal and economic disruptions. Here, we investigate the intramolecular and intermolecular RNA interactions of wildtype (WT) and a mutant (Δ382) SARS-CoV-2 virus in cells using high throughput structure probing on Illumina and Nanopore platforms. We identified twelve potentially functional structural elements within the SARS-CoV-2 genome, observed that identical sequences can fold into divergent structures on different subgenomic RNAs, and that WT and Δ382 virus genomes can fold differently. Proximity ligation sequencing experiments identified hundreds of intramolecular and intermolecular pair-wise interactions within the virus genome and between virus and host RNAs. SARS-CoV-2 binds strongly to mitochondrial and small nucleolar RNAs and is extensively 2’-O-methylated. 2’-O-methylation sites in the virus genome are enriched in the untranslated regions and are associated with increased pair-wise interactions. SARS-CoV-2 infection results in a global decrease of 2’-O-methylation sites on host mRNAs, suggesting that binding to snoRNAs could be a pro-viral mechanism to sequester methylation machinery from host RNAs towards the virus genome. Collectively, these studies deepen our understanding of the molecular basis of SARS-CoV-2 pathogenicity, cellular factors important during infection and provide a platform for targeted therapy.
Measurements of acoustic radiation force of ultrahigh frequency ultrasonic transducers using model-based approach
Authors: Kim Sangnam , Moon Sunho , Rho Sunghoon , Yoon Sangpil 
Published: January 2021

AbstractEven though ultrahigh frequency ultrasonic transducers over 60 MHz have been used for single cell level manipulation such as intracellular delivery, acoustic tweezers, and stimulation to investigate cell phenotype and cell mechanics, no techniques have been available to measure actual acoustic radiation force (ARF) applied to target cells. Therefore, we have developed an approach to measure ARF of ultrahigh frequency ultrasonic transducers using theoretical model of the dynamics of a solid sphere in a gelatin phantom. To estimate ARF at the focus of 130 MHz transducer, we matched measured maximum displacements of a solid sphere with theoretical calculations. We selected appropriate ranges of input voltages and pulse durations for single cell applications and estimated ARF were in the range of tens of pN to nN. FRET live cell imaging was demonstrated to visualize calcium transport between cells after a target single cell was stimulated by the developed ultrasonic transducer.
The unapparent effect of climate forcing on urban amoebiasis in Mexico City
Authors: Baeza Andres , Santos-Vega Mauricio , Escalante Ana E. , Eakin Hallie 
Published: January 2021

AbstractDespite advances in the provision of sanitation infrastructure in cities, diarrheal-related illnesses continue to be a global burden. In cities of the developing world, explanations for the persistence of diarrheal-related diseases revolve around the role of sanitation, poverty, and individual behavior. Less is known about the role of climate in forcing the inter-annual variability of transmission. We quantified the contribution of rainfall to the transmission of a diarrhoeal disease caused by the protozoan Entamoeba histolytica. We formulated a process-based model of the population dynamics of Entamoeba histolytica in 6 municipalities of Mexico City, and we reconstructed the interannual variability of the observed cases of amebiasis between 2005 and 2012. Using inference methods for non-linear systems, we estimated that 10% of the susceptible individuals were infected in early 2005 and 90% of those infections were causally related to the exposure to the environmental stage of the pathogen after rainfall events. The magnitude of these results underscores the importance of considering the interaction between climate forcing and water management as ecological determinants of health in megacities.
Comparative and Stability Study of Glucose Concentrations Measured in both Sodium Fluoride and Serum Separator tubes
Authors: Dibbasey Mustapha , Price Cathy , Lawal Bolarinde , Umukoro Solomon 
Published: January 2021

AbstractIntroductionSodium fluoride/potassium oxalate (NaF/KOx) tubes were once regarded as the gold-standard tubes for glucose analysis. Even though their ineffectiveness in immediately inhibiting glycolysis has been reported in several studies especially in the first 1–4hours, they are still used in our clinical Biochemistry laboratory for glucose measurement. However in its absence, only SSTs are employed for glucose measurement.AimTo determine whether SSTs can replace NaF/KOx tubes for laboratory-based measurement of blood glucose and to assess the stability of glucose concentrations for 3 days periodMethodsDuring the study period (1 March to 11 April, 2015), a total of 50 paired samples collected separately in NaF/KOx tubes and SSTs from healthy adult participants in the Gambia Adults Reference Intervals Study (GARIS) project were used as the project sample size. The samples were analysed within 2hours, and at 24hours, 42hours and 72hours time-points following blood collection and separation using Vitros 350 dry chemistry analyser. The GARIS samples were treated as clinical samples.ResultsThere was no significant difference in the mean glucose concentrations between the two tubes (Mean difference= 0.06mmol/L; P=0.38) recorded in the different time-points. Using growth trajectory and mixed effects model, the study data showed no significant change in the glucose concentrations (p=0.25) for three days period.ConclusionsThe study confirms that SSTs can produce similar glucose results when employed in the absence of NaF/KOx tubes. Besides, the glucose concentrations were stable in both tubes for three days when the samples were separated within two hours and refrigerated in 2-8°C.
Predicting spatial and seasonal patterns of wildlife-vehicle collisions in high-risk areas
Authors: Nguyen Hanh K.D. , Buettel Jessie C. , Fielding Matthew W. , Brook Barry W. 
Published: January 2021

AbstractContextVehicle collisions with wildlife can injure or kill animals, threaten human safety, and threaten the viability of rare species. This has led to a focus in road-ecology research on identifying the key predictors of ‘road-kill’ risk, with the goal of guiding management to mitigate its impact. However, because of the complex and context-dependent nature of the causes of risk exposure, modelling road-kill data in ways that yield consistent recommendations has proven challenging.AimHere we used a novel multi-model machine-learning approach to identify the spatio-temporal predictors, such as traffic volume, road shape, surrounding vegetation and distance to human settlements, associated with road-kill risk.MethodsWe collected data on the location, identity and size of each road mortality across four seasons along eight roads in southern Tasmania – a ‘road-kill hotspot’ of management concern. We focused on three large-bodied and frequently impacted crepuscular Australian marsupial herbivore species, the rufous-bellied pademelon (Thylogale billardierii), Bennett’s wallaby (Macropus rufogriseus) and the bare-nosed wombat (Vombatus ursinus). We fit the point-location data using ‘lasso-regularization’ of a logistic generalized linear model (LL-GLM) and out-of-bag optimization of a decision-tree-based ‘random forests’ (RF) algorithm.ResultsThe RF model, with high-level feature interactions, yielded superior results to the linear additive model, with a RF classification accuracy of 84.8% for the 871 road-kill observations and a true skill statistic of 0.708, compared to 61.2% and 0.205 for the LL-GLM.ConclusionsForested areas with no roadside barrier fence along curved sections of road posed the highest risk to animals. Seasonally, the frequency of wildlife-vehicle collisions increased notably for females during oestrus, when they were more dispersive and so had a higher encounter rate with roads.ImplicationsThese findings illustrate the value of using data-driven approaches to predictive modelling, as well as offering a guide to practical management interventions that can mitigate road-related hazards.
Initial Clinical Outcomes from NOCD Digital Behavioral Health Treatment of Obsessive-Compulsive Disorder Using Exposure and Response Prevention
Authors: Feusner Jamie D. , McGrath Patrick B. , Faneuff Ted , Lonsway Stephanie , Mohideen Reza , Trusky Larry , Smith Stephen M. 
Published: January 2021

AbstractEffective first-line treatments for obsessive-compulsive disorder (OCD) include exposure and response prevention (ERP) therapy. Despite extensive evidence of its efficacy in clinical studies and real-world samples, ERP is still underutilized as a treatment, likely due to access to care barriers such as the availability of adequately trained ERP therapists, geographical location, time, and cost. NOCD has created a digital behavioral health treatment for OCD using ERP delivered via teletherapy and between-session support. We examined preliminary treatment outcomes in a large naturalistic sample of 2069 adults, children, and adolescents with a primary OCD diagnosis. Treatment consisted of twice-weekly live teletherapy ERP for three weeks, followed by six weeks of once-weekly brief teletherapy check-ins. Assessments were conducted at baseline, after completion of three weeks of twice-weekly sessions, and at the end of the six weeks of brief check-ins. Treatment resulted in significant improvements, with a 45% mean reduction in OCD symptoms and a 71% response rate (≥35% reduction in OCD symptoms).Treatment also resulted in a significant, 43% reduction in depression, a 49% reduction in anxiety, and a 35% reduction in stress symptoms. Quality of life improved by a mean of 35%. The mean duration of treatment was approximately 11 weeks, and the total therapist time was approximately 11 hours, which is less than half the total time compared with standard once-weekly outpatient treatment. In sum, in this preliminary sample, NOCD’s treatment model for OCD, delivered in a readily-accessible format for patients, has demonstrated to be effective and efficient.
Viral dispersion in open air
Authors: Machado Gabriella Trombini , de Carvalho Pinto Claudia Ramos , da Fonseca Luisa Andrea Villanueva , dos Santos Ramos Taissa Cristina , Pereira Paggi Tuanny Fernanda , Spira Beny 
Published: January 2021

ABSTRACTThe SARS-CoV-2 pandemic has revived the debate about the routes of virus transmission and their likelihoods. It is of utmost importance to assess the risks of contamination of susceptible people by infectious individuals and to evaluate the level of viral transmission in the community. Most countries have imposed non-pharmaceutical measures to contain SARS-CoV-2 transmission, including social distancing and mask wearing. Here we evaluated the spreading of viruses in open air using harmless Escherichia coli bacteriophages as a surrogate. Phages were sprayed towards Petri dishes seeded with bacteria at different lengths and angles. Median droplets size was 127 µm, similar to those produced by sneeze. Our results showed that the transmission rate decreased exponentially with distance. The highest recorded transmission rate was 9 × 10−6 PFU/plate when phages were sprayed from a 1 m distance, suggesting that the probability of transmission of a single virus at a 1 m distance is 1:100,000. These results agree with the WHO recommendation that face mask protection in an uncrowded well-ventilated space is not required.
Association between polygenic propensity for a psychiatric disorder and nutrient intake
Authors: Hunjan Avina K. , Hübel Christopher , Lin Yuhao , Eley Thalia C. , Breen Gerome 
Published: January 2021

AbstractBackgroundDespite the observed associations between psychiatric disorders and nutrient intake, genetic studies are limited.AimsWe examined whether polygenic scores for psychiatric disorders, including anorexia nervosa, major depressive disorder and schizophrenia, are associated with self-reported nutrient intake.MethodsWe used data obtained by the UK Biobank ‘Diet by 24-hour recall’ questionnaire (N=163,619). Association was assessed using linear mixed models for the analysis of data with repeated measures.ResultsWe find polygenic scores for psychiatric disorders are differentially associated with nutrient intake, with attention-deficit/hyperactivity disorder, bipolar disorder and schizophrenia showing the strongest associations, whilst autism spectrum disorder showed no association. Expressed as the effect of a one standard deviation higher polygenic score, anorexia nervosa polygenic score was associated with higher intake of fibre (0.06 g), folate (0.93 μg), iron (0.03 mg) and vitamin C (0.92 μg). Similarly, a higher major depressive disorder polygenic score was associated with 0.04 mg lower iron and 1.13 μg lower vitamin C intake per day, and a greater obsessive-compulsive disorder polygenic score with 0.06 g higher fibre intake. These associations were predominantly driven by socioeconomic status and educational attainment. However, a higher alcohol dependence polygenic score was associated with higher alcohol intake and individuals with higher persistent thinness polygenic scores reported their food to weigh 8.61 g less, both independent of socioeconomic status.ConclusionsOur findings suggest that polygenic propensity for a psychiatric disorder is associated with dietary behaviour. The nutrient intake is based on self-reported data and findings must therefore be interpreted mindfully.Declaration of interestNone.
Emergence of a novel SARS-CoV-2 strain in Southern California, USA
Authors: Zhang Wenjuan , Davis Brian D , Chen Stephanie S , Martinez Jorge M Sincuir , Plummer Jasmine T , Vail Eric 
Published: January 2021

AbstractSince October 2020, novel strains of SARS-CoV-2 including B.1.1.7, have been identified to be of global significance from an infection and surveillance perspective. While this strain (B.1.1.7) may play an important role in increased COVID rates in the UK, there are still no reported strains to account for the spike of cases in Los Angeles (LA) and California as a whole, which currently has some of the highest absolute and per-capita COVID transmission rates in the country. From the early days of the pandemic when LA only had a single viral genome uploaded onto GISAID we have been at the forefront of generating and analyzing the SARS-CoV-2 sequencing data from the LA region. We report a novel strain emerging in Southern California. Most current cases in the catchment population in LA fall into two distinct subclades: 1) 20G (24% of total) is the predominant subclade currently in the United States 2) a relatively novel strain in clade 20C, CAL.20C strain (∼36% of total) is defined by five concurrent mutations. After an analysis of all of the publicly available data and a comparison to our recent sequences, we see a dramatic growth in the relative percentage of the CAL.20C strain beginning in November of 2020. The predominance of this strain coincides with the increased positivity rate seen in this region. Unlike 20G, this novel strain CAL.20C is defined by multiple mutations in the S protein, a characteristic it shares with both the UK and South African strains, both of which are of significant clinical and scientific interest