A 4DVar PIV-data assimilation for flow spatio-temporal reconstruction

[Departement_IRSTEA]Ecotechnologies [TR1_IRSTEA]SPEEInternational audienceA variational data assimilation technique (4DVar) was used to reconstruct turbulent flows (Gronskis et al., 2013). The problem consists in recovering a flow by modifying the initial and inflow conditions of a system composed of a DNS code coupled with some noisy and possibly incomplete PIV measurements. In the present study the ability of the technique to reconstruct flow in gappy PIV data was investigated

Prevalence and Characteristics of Autism Spectrum Disorder Among Children Aged 4 Years - Early Autism and Developmental Disabilities Monitoring Network, Seven Sites, United States, 2010, 2012, and 2014

Problem/Condition: Autism spectrum disorder (ASD) is estimated to affect up to 3% of children in the United States. Public health surveillance for ASD among children aged 4 years provides information about trends in prevalence, characteristics of children with ASD, and progress made toward decreasing the age of identification of ASD so that evidence-based interventions can begin as early as possible. Period Covered: 2010, 2012, and 2014. Description of System: The Early Autism and Developmental Disabilities Monitoring (Early ADDM) Network is an active surveillance system that provides biennial estimates of the prevalence and characteristics of ASD among children aged 4 years whose parents or guardians lived within designated sites. During surveillance years 2010, 2012, or 2014, data were collected in seven sites: Arizona, Colorado, Missouri, New Jersey, North Carolina, Utah, and Wisconsin. The Early ADDM Network is a subset of the broader ADDM Network (which included 13 total sites over the same period) that has been conducting ASD surveillance among children aged 8 years since 2000. Each Early ADDM site covers a smaller geographic area than the broader ADDM Network. Early ADDM ASD surveillance is conducted in two phases using the same methods and project staff members as the ADDM Network. The first phase consists of reviewing and abstracting data from children's records, including comprehensive evaluations performed by community professionals. Sources for these evaluations include general pediatric health clinics and specialized programs for children with developmental disabilities. In addition, special education records (for children aged >= 3 years) were reviewed for Arizona, Colorado, New Jersey, North Carolina, and Utah, and early intervention records (for children aged 0 to = 60% data on cognitive test scores (Arizona, New Jersey, North Carolina, and Utah), the frequency of co-occurring intellectual disabilities was significantly higher among children aged 4 years than among those aged 8 years for each site in each surveillance year except Arizona in 2010. The percentage of children with ASD who had a first evaluation by age 36 months ranged from 48.8% in Missouri in 2012 to 88.9% in Wisconsin in 2014. The percentage of children with a previous ASD diagnosis from a community provider varied by site, ranging from 43.0% for Arizona in 2012 to 86.5% for Missouri in 2012. The median age at earliest known ASD diagnosis varied from 28 months in North Carolina in 2014 to 39.0 months in Missouri and Wisconsin in 2012. In 2014, the ASD prevalence based on the DSM-IV-TR case definition was 20% higher than the prevalence based on the DSM-5 (17.0 versus 14.1 per 1,000, respectively). Trends in ASD prevalence and characteristics among children aged 4 years during the study period were assessed for the three sites with data for all 3 years and consistent data sources (Arizona, Missouri, and New Jersey) using the DSM-IV-TR case definition; prevalence was higher in 2014 than in 2010 among children aged 4 years in New Jersey and was stable in Arizona and Missouri. In Missouri, ASD prevalence was higher among children aged 8 years than among children aged 4 years. The percentage of children with ASD who had a comprehensive evaluation by age 36 months was stable in Arizona and Missouri and decreased in New Jersey. In the three sites, no change occurred in the age at earliest known ASD diagnosis during 2010-2014. Interpretation: The findings suggest that ASD prevalence among children aged 4 years was higher in 2014 than in 2010 in one site and remained stable in others. Among children with ASD, the frequency of cognitive impairment was higher among children aged 4 years than among those aged 8 years and suggests that surveillance at age 4 years might more often include children with more severe symptoms or those with co-occurring conditions such as intellectual disability. In the sites with data for all years and consistent data sources, no change in the age at earliest known ASD diagnosis was found, and children received their first developmental evaluation at the same or a later age in 2014 compared with 2010. Delays in the initiation of a first developmental evaluation might adversely affect children by delaying access to treatment and special services that can improve outcomes for children with ASD. Public Health Action: Efforts to increase awareness of ASD and improve the identification of ASD by community providers can facilitate early diagnosis of children with ASD. Heterogeneity of results across sites suggests that community-level differences in evaluation and diagnostic services as well as access to data sources might affect estimates of ASD prevalence and age of identification. Continuing improvements in providing developmental evaluations to children as soon as developmental concerns are identified might result in earlier ASD diagnoses and earlier receipt of services, which might improve developmental outcomes.This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Measures of Parent-Infant Interaction

Increasingly, programs for handicapped infants and toddlers are including in their intervention activities objectives related to the quality of parent-child interaction. As a consequence, it has become necessary for programs to assess the impact of these intervention efforts on parent behaviors. This article considers tools available for assessing parent-child interaction for program planning and evaluation. Lastly, recommendations are offered to guide the selection of a measure of parent-child interactions.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/69100/2/10.1177_027112148600600204.pd

Autism Spectrum Disorder Symptoms Among Children Enrolled in the Study to Explore Early Development (SEED)

This study examined the phenotypic profiles of children aged 30–68 months in the Study to Explore Early Development (SEED). Children classified as autism spectrum disorder (ASD), developmental delay (DD) with ASD symptoms, DD without ASD symptoms, and population comparison (POP) differed significantly from each other on cognitive, adaptive, behavioral, and social functioning and the presence of parent-reported conditions. Children with ASD and DD with ASD symptoms had mild to severe ASD risk on several measures compared to children with other DD and POP who had little ASD risk across measures. We conclude that children in SEED have varying degrees of ASD impairment and associated deficits. SEED thus provides a valuable sample to explore ASD phenotypes and inform risk factor analyses

The Study to Explore Early Development (SEED): A Multisite Epidemiologic Study of Autism by the Centers for Autism and Developmental Disabilities Research and Epidemiology (CADDRE) Network

The Study to Explore Early Development (SEED), a multisite investigation addressing knowledge gaps in autism phenotype and etiology, aims to: (1) characterize the autism behavioral phenotype and associated developmental, medical, and behavioral conditions and (2) investigate genetic and environmental risks with emphasis on immunologic, hormonal, gastrointestinal, and sociodemographic characteristics. SEED uses a case–control design with population-based ascertainment of children aged 2–5 years with an autism spectrum disorder (ASD) and children in two control groups—one from the general population and one with non-ASD developmental problems. Data from parent-completed questionnaires, interviews, clinical evaluations, biospecimen sampling, and medical record abstraction focus on the prenatal and early postnatal periods. SEED is a valuable resource for testing hypotheses regarding ASD characteristics and causes

Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel

Imputing genotypes from reference panels created by whole-genome sequencing (WGS) provides a cost-effective strategy for augmenting the single-nucleotide polymorphism (SNP) content of genome-wide arrays. The UK10K Cohorts project has generated a data set of 3,781 whole genomes sequenced at low depth (average 7x), aiming to exhaustively characterize genetic variation down to 0.1% minor allele frequency in the British population. Here we demonstrate the value of this resource for improving imputation accuracy at rare and low-frequency variants in both a UK and an Italian population. We show that large increases in imputation accuracy can be achieved by re-phasing WGS reference panels after initial genotype calling. We also present a method for combining WGS panels to improve variant coverage and downstream imputation accuracy, which we illustrate by integrating 7,562 WGS haplotypes from the UK10K project with 2,184 haplotypes from the 1000 Genomes Project. Finally, we introduce a novel approximation that maintains speed without sacrificing imputation accuracy for rare variants

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

Adjunctive rifampicin for Staphylococcus aureus bacteraemia (ARREST): a multicentre, randomised, double-blind, placebo-controlled trial.

BACKGROUND: Staphylococcus aureus bacteraemia is a common cause of severe community-acquired and hospital-acquired infection worldwide. We tested the hypothesis that adjunctive rifampicin would reduce bacteriologically confirmed treatment failure or disease recurrence, or death, by enhancing early S aureus killing, sterilising infected foci and blood faster, and reducing risks of dissemination and metastatic infection. METHODS: In this multicentre, randomised, double-blind, placebo-controlled trial, adults (≥18 years) with S aureus bacteraemia who had received ≤96 h of active antibiotic therapy were recruited from 29 UK hospitals. Patients were randomly assigned (1:1) via a computer-generated sequential randomisation list to receive 2 weeks of adjunctive rifampicin (600 mg or 900 mg per day according to weight, oral or intravenous) versus identical placebo, together with standard antibiotic therapy. Randomisation was stratified by centre. Patients, investigators, and those caring for the patients were masked to group allocation. The primary outcome was time to bacteriologically confirmed treatment failure or disease recurrence, or death (all-cause), from randomisation to 12 weeks, adjudicated by an independent review committee masked to the treatment. Analysis was intention to treat. This trial was registered, number ISRCTN37666216, and is closed to new participants. FINDINGS: Between Dec 10, 2012, and Oct 25, 2016, 758 eligible participants were randomly assigned: 370 to rifampicin and 388 to placebo. 485 (64%) participants had community-acquired S aureus infections, and 132 (17%) had nosocomial S aureus infections. 47 (6%) had meticillin-resistant infections. 301 (40%) participants had an initial deep infection focus. Standard antibiotics were given for 29 (IQR 18-45) days; 619 (82%) participants received flucloxacillin. By week 12, 62 (17%) of participants who received rifampicin versus 71 (18%) who received placebo experienced treatment failure or disease recurrence, or died (absolute risk difference -1·4%, 95% CI -7·0 to 4·3; hazard ratio 0·96, 0·68-1·35, p=0·81). From randomisation to 12 weeks, no evidence of differences in serious (p=0·17) or grade 3-4 (p=0·36) adverse events were observed; however, 63 (17%) participants in the rifampicin group versus 39 (10%) in the placebo group had antibiotic or trial drug-modifying adverse events (p=0·004), and 24 (6%) versus six (2%) had drug interactions (p=0·0005). INTERPRETATION: Adjunctive rifampicin provided no overall benefit over standard antibiotic therapy in adults with S aureus bacteraemia. FUNDING: UK National Institute for Health Research Health Technology Assessment

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant

SARS-CoV-2 infections were rising during early summer 2021 in many countries associated with the Delta variant. We assessed RT-PCR swab-positivity in the REal-time Assessment of Community Transmission-1 (REACT-1) study in England. We observed sustained exponential growth with average doubling time (June-July 2021) of 25 days driven by complete replacement of Alpha variant by Delta, and by high prevalence at younger less-vaccinated ages. Unvaccinated people were three times more likely than double-vaccinated people to test positive. However, after adjusting for age and other variables, vaccine effectiveness for double-vaccinated people was estimated at between ~50% and ~60% during this period in England. Increased social mixing in the presence of Delta had the potential to generate sustained growth in infections, even at high levels of vaccination