A framework for identifying regional outbreak and spread of COVID-19 from one-minute population-wide surveys.
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ABSTRACT:
SUBMITTER: Rossman H
PROVIDER: S-EPMC7144578 | biostudies-literature | 2020 May
REPOSITORIES: biostudies-literature
Publications
A framework for identifying regional outbreak and spread of COVID-19 from one-minute population-wide surveys.
Rossman Hagai H Keshet Ayya A Shilo Smadar S Gavrieli Amir A Bauman Tal T Cohen Ori O Shelly Esti E Balicer Ran R Geiger Benjamin B Dor Yuval Y Segal Eran E
Nature medicine 20200501 5
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Project description:BackgroundContinuous education of clinicians improves quality of care. One Minute Wonder (OMW) summarize best practice knowledge on one page that can be hung on a wall and can be read during waiting times of just one minute. OMW are a fast, efficient and easy-to-adapt educational method and can easily be shared. Since 2018, an interprofessional network has been set up for OMW in German-speaking countries, but the benefits have not been evaluated yet.AimThe primary objective of this evaluation study was to examine whether and to what extent the members of the OMW network used OMW for training in different settings. Secondary objectives were subjective educational gain, OMW as a training method, and OMW-related structures and processes.MethodsAn online survey within the OMW network with 301 members over a period of 3 weeks in 2020 was conducted. Descriptive statistics were used for data analysis.ResultsResponse rate was 62.8% (n = 191). Most participants have used OMW for < 6 months (32.5%, n = 62), developed 1-10 OMW (42.4%, n = 81) by themselves and changed them infrequently (43.5%, n = 74). Topics were most often nursing interventions (79.6%, n = 152), diseases (71.2%, n = 136), drugs (64.4%, n = 123) and others. Participants reported that OMW extended professional knowledge, stimulated them to reflect on their work and are useful for sharing best practice knowledge. Authors of OMW were most often nurses (53.9%, n = 103), who were inspired by the OMW network or by questions of the team.ConclusionParticipants use OMW in practice to share best practice knowledge.
| S-EPMC8725639 | biostudies-literature
Project description:ObjectiveTo determine the minimum duration of electroencephalography (EEG) data necessary to differentiate EEG features of Lewy body dementia (LBD), that is, dementia with Lewy bodies and Parkinson disease dementia, from non-LBD patients, that is, Alzheimer disease and Parkinson disease.MethodsWe performed quantitative EEG analysis for 16 LBD and 14 non-LBD patients. After artifact removal, a fast Fourier transform was performed on 90, 60, and thirty 2-second epochs to derive dominant frequency; dominant frequency variability; and dominant frequency prevalence.ResultsIn LBD patients, there were no significant differences in EEG features derived from 90, 60, and thirty 2-second epochs (all P >0.05). There were no significant differences in EEG features derived from 3 different groups of thirty 2-second epochs (all P >0.05). When analyzing EEG features derived from ninety 2-second epochs, we found that LBD had significantly reduced dominant frequency, reduced dominant frequency variability, and reduced dominant frequency prevalence alpha compared with the non-LBD group (all P <0.05). These same differences were observed between the LBD and non-LBD groups when analyzing thirty 2-second epochs.ConclusionsThere were no differences in EEG features derived from 1 minute versus 3 minutes of EEG data, and both durations of EEG data equally differentiated LBD from non-LBD.
| S-EPMC9974530 | biostudies-literature
Project description:IntroductionThe one-minute sit to stand test (1min-STST) is a field test used to assess functional capacity. It is easily implementable and of significant clinical utility; however, no reference values are currently available for the Chilean population. The objective of this study was to establish reference values for the 1min-STST in a healthy Chilean population.MethodsA multicenter cross-sectional study involving data collection from six locations in Chile was conducted. Healthy adults between 18 and 80 years of age were recruited. The anthropometric variables, levels of physical activity, smoking status, Borg scale ratings, and number of repetitions during the 1min-STST were recorded. Reference values were determined according to sex and age range.ResultsFour hundred ninety-nine healthy subjects (57.5% women, n = 287; median height, 1.63 (0.14) m; weight, 72.8 (20) kg; average BMI, 27.3 ± 4.1 kg/m2) were included in the study. The median (and the lower limit of normality (LLN) values) for the 1min-STST in men ranged from 18-29 years, with 38 (LLN 27) repetitions and 23 (LLN 15) repetitions for 70-80 years. For women aged 18-29 years, 38 (LLN 28) repetitions were performed, and for women aged 70-80 years, 24 (LLN 17) repetitions were performed.ConclusionsThis study established reference values for the healthy adult Chilean population.
| S-EPMC11778653 | biostudies-literature
Project description: Not available
| S-EPMC9553205 | biostudies-literature
Project description:ObjectiveMonitoring health outcomes disaggregated by socioeconomic position (SEP) is crucial to ensure no one is left behind in efforts to achieve universal health coverage. In eye health planning, rapid population surveys are most commonly implemented; these need an SEP measure that is feasible to collect within the constraints of a streamlined examination protocol. We aimed to assess whether each of four SEP measures identified inequality-an underserved group or socioeconomic gradient-in key eye health outcomes.DesignPopulation-based cross-sectional survey.ParticipantsA subset of 4020 adults 50 years and older from a nationally representative sample of 9188 adults aged 35 years and older in The Gambia.Outcome measuresBlindness (presenting visual acuity (PVA) <3/60), any vision impairment (VI) (PVA <6/12), cataract surgical coverage (CSC) and effective cataract surgical coverage (eCSC) at two operable cataract thresholds (<6/12 and <6/60) analysed by one objective asset-based measure (EquityTool) and three subjective measures of relative SEP (a self-reported economic ladder question and self-reported household food adequacy and income sufficiency).ResultsSubjective household food adequacy and income sufficiency demonstrated a socioeconomic gradient (queuing pattern) in point estimates of any VI and CSC and eCSC at both operable cataract thresholds. Any VI, CSC <6/60 and eCSC <6/60 were worse among people who reported inadequate household food compared with those with just adequate food. Any VI and CSC <6/60 were worse among people who reported not enough household income compared with those with just enough income. Neither the subjective economic ladder question nor the objective asset-wealth measure demonstrated any socioeconomic gradient or pattern of inequality in any of the eye health outcomes.ConclusionWe recommend pilot-testing self-reported food adequacy and income sufficiency as SEP variables in vision and eye health surveys in other locations, including assessing the acceptability, reliability and repeatability of each question.
| S-EPMC10008479 | biostudies-literature
Project description:For the COVID-19 pandemic, viral transmission has been documented in many historical and geographical contexts. Nevertheless, few studies have explicitly modeled the spatiotemporal flow based on genetic sequences, to develop mitigation strategies. Additionally, thousands of SARS-CoV-2 genomes have been sequenced with associated records, potentially providing a rich source for such spatiotemporal analysis, an unprecedented amount during a single outbreak. Here, in a case study of seven states, we model the first wave of the outbreak by determining regional connectivity from phylogenetic sequence information (i.e. "genetic connectivity"), in addition to traditional epidemiologic and demographic parameters. Our study shows nearly all of the initial outbreak can be traced to a few lineages, rather than disconnected outbreaks, indicative of a mostly continuous initial viral flow. While the geographic distance from hotspots is initially important in the modeling, genetic connectivity becomes increasingly significant later in the first wave. Moreover, our model predicts that isolated local strategies (e.g. relying on herd immunity) can negatively impact neighboring regions, suggesting more efficient mitigation is possible with unified, cross-border interventions. Finally, our results suggest that a few targeted interventions based on connectivity can have an effect similar to that of an overall lockdown. They also suggest that while successful lockdowns are very effective in mitigating an outbreak, less disciplined lockdowns quickly decrease in effectiveness. Our study provides a framework for combining phylodynamic and computational methods to identify targeted interventions.
| S-EPMC10209930 | biostudies-literature
Project description:ObjectivesWe investigated the associations between Apgar scores at 1 and 5 min, across the entire range of score values, and child developmental health at 5 years of age.SettingBritish Columbia, Canada PARTICIPANTS: All singleton term infants without major congenital anomalies born between 1993 and 2009, who had a developmental assessment in kindergarten between 1999 and 2014.Main outcomes and measuresDevelopmental vulnerability on one or more domains of the Early Development Instrument and special needs requirements. Adjusted rate ratios (aRRs) and 95% CIs were estimated using log-linear regression.ResultsOf the 150 081 children in the study, 45 334 (30.2%) were developmentally vulnerable and 3644 (2.5%) had special needs. There was an increasing trend in developmental vulnerability and special needs with decreasing 1 min and 5 min Apgar scores. Compared with children with an Apgar score of 10 at 5 min, the aRR for developmental vulnerability increased steadily with decreasing Apgar score from 1.02 (95% CI 1.00 to 1.04) for an Apgar score of 9 to 1.57 (95% CI 1.03 to 2.39) for an Apgar score of 2. Among children with 1 min Apgar scores in the 7-10 range, changes in Apgar scores between 1 and 5 min were associated with significant differences in developmental vulnerability. Compared with children who had an Apgar score of 9 at 1 min and 10 at 5 min, children with an Apgar score of 9 at both 1 and 5 min had higher rates of developmental vulnerability (aRR 1.03, 95% CI 1.01 to 1.05). Compared with infants with an Apgar of 10 at both 1 and 5 min, infants with a 1 min score of 10 and a 5 min score of <10 had higher rates of developmental vulnerability (aRR 1.53, 95% CI 1.08 to 2.17).ConclusionRisks of adverse developmental health and having special needs at 5 years of age are inversely associated with 1 min and 5 min Apgar scores across their entire range.
| S-EPMC6528022 | biostudies-literature
Project description:Population stratification or confounding by genetic ancestry is a potential cause of false associations in genetic association studies. Estimation of and adjustment for genetic ancestry has become common practice thanks in part to the availability of ancestry informative markers on genome-wide association study (GWAS) arrays. While array data is now widespread, these data are not ubiquitous as several large epidemiologic and clinic-based studies lack genome-wide data. One such large epidemiologic-based study lacking genome-wide data accessible to investigators is the National Health and Nutrition Examination Surveys (NHANES), population-based cross-sectional surveys of Americans linked to demographic, health, and lifestyle data conducted by the Centers for Disease Control and Prevention. DNA samples (n = 14,998) were extracted from biospecimens from consented NHANES participants between 1991-1994 (NHANES III, phase 2) and 1999-2002 and represent three major self-identified racial/ethnic groups: non-Hispanic whites (n = 6,634), non-Hispanic blacks (n = 3,458), and Mexican Americans (n = 3,950). We as the Epidemiologic Architecture for Genes Linked to Environment study genotyped candidate gene and GWAS-identified index variants in NHANES as part of the larger Population Architecture using Genomics and Epidemiology I study for collaborative genetic association studies. To enable basic quality control such as estimation of genetic ancestry to control for population stratification in NHANES san genome-wide data, we outline here strategies that use limited genetic data to identify the markers optimal for characterizing genetic ancestry. From among 411 and 295 autosomal SNPs available in NHANES III and NHANES 1999-2002, we demonstrate that markers with ancestry information can be identified to estimate global ancestry. Despite limited resolution, global genetic ancestry is highly correlated with self-identified race for the majority of participants, although less so for ethnicity. Overall, the strategies outlined here for a large epidemiologic study can be applied to other datasets accessible for genotype-phenotype studies but are sans genome-wide data.
| S-EPMC4858524 | biostudies-literature
Project description:MotivationRecent technological advances in high-throughput sequencing and genotyping have facilitated an improved understanding of genomic structure and disease-associated genetic factors. In this context, simulation models can play a critical role in revealing various evolutionary and demographic effects on genomic variation, enabling researchers to assess existing and design novel analytical approaches. Although various simulation frameworks have been suggested, they do not account for natural selection in admixture processes. Most are tailored to a single chromosome or a genomic region, very few capture large-scale genomic data, and most are not accessible for genomic communities.ResultsHere we develop a multi-scenario genome-wide medical population genetics simulation framework called 'FractalSIM'. FractalSIM has the capability to accurately mimic and generate genome-wide data under various genetic models on genetic diversity, genomic variation affecting diseases and DNA sequence patterns of admixed and/or homogeneous populations. Moreover, the framework accounts for natural selection in both homogeneous and admixture processes. The outputs of FractalSIM have been assessed using popular tools, and the results demonstrated its capability to accurately mimic real scenarios. They can be used to evaluate the performance of a range of genomic tools from ancestry inference to genome-wide association studies.Availability and implementationThe FractalSIM package is available at http://www.cbio.uct.ac.za/FractalSIM.Contactemile.chimusa@uct.ac.za.Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC5870573 | biostudies-literature
Project description:Quantitative structure-activity relationships (QSAR) models are often seen as a "black box" because they are considered difficult to interpret. Meanwhile, qualitative approaches, e.g., structural alerts (SA) or read-across, provide mechanistic insight, which is preferred for regulatory purposes, but predictive accuracy of such approaches is often low. Herein, we introduce the chemistry-wide association study (CWAS) approach, a novel framework that both addresses such deficiencies and combines advantages of statistical QSAR and alert-based approaches. The CWAS framework consists of the following steps: (i) QSAR model building for an end point of interest, (ii) identification of key chemical features, (iii) determination of communities of such features disproportionately co-occurring more frequently in the active than in the inactive class, and (iv) assembling these communities to form larger (and not necessarily chemically connected) novel structural alerts with high specificity. As a proof-of-concept, we have applied CWAS to model Ames mutagenicity and Stevens-Johnson Syndrome (SJS). For the well-studied Ames mutagenicity data set, we identified 76 important individual fragments and assembled co-occurring fragments into SA both replicative of known as well as representing novel mutagenicity alerts. For the SJS data set, we identified 29 important fragments and assembled co-occurring communities into SA including both known and novel alerts. In summary, we demonstrate that CWAS provides a new framework to interpret predictive QSAR models and derive refined structural alerts for more effective design and safety assessment of drugs and drug candidates.
| S-EPMC6831087 | biostudies-literature