Launch of the Sao Paulo Wellcome Trust-funded multidisciplinary research program on optimising antimicrobial use in highly populated urban environments
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ABSTRACT:
SUBMITTER: Levin A
PROVIDER: S-EPMC10460985 | biostudies-literature | 2023 Aug
REPOSITORIES: biostudies-literature
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Project description:Lately, the Indian research ecosystem has seen an upward trend in scientists showing interest in communicating their science and engaging with non-scientific audiences; however, the number and variety of science communication or public engagement activities undertaken formally by scientists remains low in the country. There could be many contributing factors for this trend. To explore this further, the science funding public charity in India, DBT/Wellcome Trust India Alliance (India Alliance), in a first of its kind of study by a funding agency in India, surveyed its 243 research grantees in November 2020 requesting their views on public engagement with science in India through an online survey. The survey included both quantitative as well as open-ended questions to assess the understanding of, participation in, and attitude of India Alliance Fellows/Grantees towards public engagement with research, identify the enablers, challenges, and barriers to public engagement for India Alliance Fellows/Grantees, understand the specific needs (training/capacity-building, funding, etc.) and develop recommendations for India Alliance as well as for the larger scientific ecosystem in the country. The survey showed that India Alliance grantees are largely motivated to engage with the public about science or their research but lack professional recognition and incentives, training and structural support to undertake public engagement activities.
| S-EPMC9021671 | biostudies-literature
Project description:Introduction Periodic follow-up appointments are important to ensure long-term effectiveness of rehabilitation with hearing aids. However, not all users are able to maintain adherence to recommendations prescribed during the fitting process and some do not attend those appointments, which compromises the effectiveness of treatment. Objective Compare hearing aid use after 1 year between subjects who did not attend a follow-up evaluation appointment at a publicly-funded health service (nonattenders) and those who attended the appointment (attenders). Reasons for nonuse of hearing aids and unscheduled appointments were also analyzed. Methods Prospective observational cross-sectional study. Nonattenders and attenders in a follow-up evaluation appointment were interviewed by telephone about hearing aid use, reasons for nonuse, and unscheduled appointments. Results The nonattenders group consisted of 108 subjects and the attenders group had 200 subjects; in both groups, most users kept bilateral use but the nonuse rate was higher in nonattenders. The main reason for nonuse of hearing aids among nonattenders was health problems; fitting problems was the main reason for nonuse in the attenders group. Health problems and issues like unavailable companion and transportation difficulties were the reasons for unscheduled follow-up appointments. Conclusion Nonattenders had a greater nonuse rate and were more likely to abandon hearing aid use. Measures to increase hearing aid use and adherence to prescribed recommendations are also necessary to ensure long-term effectiveness of rehabilitation with hearing aids.
| S-EPMC4490920 | biostudies-other
Project description:We applied a recently developed multilocus association testing method (localized haplotype clustering) to Wellcome Trust Case Control Consortium data (14,000 cases of seven common diseases and 3,000 shared controls genotyped on the Affymetrix 500 K array). After rigorous data quality filtering, we identified three disease-associated loci with strong statistical support from localized haplotype cluster tests but with only marginal significance in single marker tests. These loci are chromosomes 10p15.1 with type 1 diabetes (p = 5.1 x 10(-9)), 12q15 with type 2 diabetes (p = 1.9 x 10(-7)) and 15q26.2 with hypertension (p = 2.8 x 10(-8)). We also detected the association of chromosome 9p21.3 with type 2 diabetes (p = 2.8 x 10(-8)), although this locus did not pass our stringent genotype quality filters. The association of 10p15.1 with type 1 diabetes and 9p21.3 with type 2 diabetes have both been replicated in other studies using independent data sets. Overall, localized haplotype cluster analysis had better success detecting disease associated variants than a previous single-marker analysis of imputed HapMap SNPs. We found that stringent application of quality score thresholds to genotype data substantially reduced false-positive results arising from genotype error. In addition, we demonstrate that it is possible to simultaneously phase 16,000 individuals genotyped on genome-wide data (450 K markers) using the Beagle software package.
| S-EPMC2384233 | biostudies-literature
Project description: Not available
| S-EPMC8492019 | biostudies-literature
Project description:We present an approach for genome-wide association analysis with improved power on the Wellcome Trust data consisting of seven common phenotypes and shared controls. We achieved improved power by expanding the control set to include other disease cohorts, multiple races, and closely related individuals. Within this setting, we conducted exhaustive univariate and epistatic interaction association analyses. Use of the expanded control set identified more known associations with Crohn's disease and potential new biology, including several plausible epistatic interactions in several diseases. Our work suggests that carefully combining data from large repositories could reveal many new biological insights through increased power. As a community resource, all results have been made available through an interactive web server.
| S-EPMC3551227 | biostudies-literature
Project description:Candidatus Liberibacter americanus str. Sao Paulo Genome sequencing
| PRJNA181147 | ENA
Project description:To estimate the prevalence of one month psychotropic drug use in São Paulo, Brazil, and to assess the gap treatment between the presence of mental disorders and psychotropic drug users.A probabilistic sample of non-institutionalized individuals from the general population of São Paulo (n = 2336; turnout: 84.5%) who were 15 years or older were interviewed by a trained research staff, applying the Composite International Diagnostic Interview 2.1 (CIDI WHO) (depression, anxiety-phobia, OCD\PTSD, alcoholism sections), and an inventory investigating psychotropic drug use during the 12-month and one-month periods immediately preceding the interview. Logistic models were fitted to investigate associations between psychotropic drug use as well as socio-demographic and clinical variables.The one month prevalence of psychotropic drug use in São Paulo was 5.89%, the most commonly used drugs were antidepressants (3.15%) and tranquilizers (2.67%). A higher consumption of psychotropic drugs (overall, antidepressants and tranquilizers) was observed among women (OR:2.42), older individuals (OR:1.04), individuals with higher levels of formal education (1.06), and individuals with a family (OR:2.29) or personal history of mental illness (OR:3.27). The main psychotropic drug prescribers were psychiatrists (41%), followed by general practitioners (30%); 60% of psychotropic drugs were obtained through a government-run dispensing program. Most individuals who obtained a positive diagnosis on the CIDI 2.1 during the previous month were not using psychotropic medication (85%). Among individuals with a diagnosis of moderate to severe depression, 67.5% were not on any pharmacological treatment.There is a change in the type of psychotropic more often used in São Paulo, from benzodiazepines to antidepressants, this event is observed in different cultures. The prevalence of use is similar to other developing countries. Most of the patients presenting a psychiatric illness in the month prior to testing were not receiving any sort of psychiatric medication. This may be explained by a failure to identify cases in primary care, which could be improved (and access to treatment could be facilitated) if professionals received more specialized training in managing cases with mental health problems.
| S-EPMC4529275 | biostudies-other
Project description:Transmission of herpesvirus between humans and non-human primates represents a serious potential threat to human health and endangered species conservation. This study aimed to identify herpesvirus genomes in samples of neotropical primates (NTPs) in the state of São Paulo, Brazil. A total of 242 NTPs, including Callithrix sp., Alouatta sp., Sapajus sp., and Callicebus sp., were evaluated by pan-herpesvirus polymerase chain reaction (PCR) and sequencing. Sixty-two (25.6%) samples containing genome segments representative of members of the family Herpesviridae, including 16.1% for Callitrichine gammaherpesvirus 3, 6.1% for Human alphaherpesvirus 1, 2.1% for Alouatta macconnelli cytomegalovirus, and 0.83% for Cebus albifrons lymphocryptovirus 1. No co-infections were detected. The detection of herpesvirus genomes was significantly higher among adult animals (p = 0.033) and those kept under human care (p = 0.008671). These findings confirm the importance of monitoring the occurrence of herpesviruses in NTP populations in epizootic events.
| S-EPMC10689701 | biostudies-literature
Project description:The Hepeviridae comprise single-stranded positive-sense RNA viruses classified into two genera, Orthohepevirus and Piscihepevirus. Orthohepeviruses have a wide host range that includes rodents, but previous studies had been restricted to rodents of the Muridae family. In this study, we applied a high-throughput sequencing approach to examine the presence of orthohepeviruses in rodents from São Paulo State, Brazil. We also used RT-PCR to determine the frequency of orthohepeviruses in our sampled population. We identified novel orthohepeviruses in blood samples derived from Necromys lasiurus (1.19%) and Calomys tener (3.66%). Therefore, our results expand the host range and viral diversity of the Hepeviridae family.
| S-EPMC5998382 | biostudies-literature
Project description:BackgroundIncreasingly large amounts of DNA sequencing data are being generated within the Wellcome Trust Sanger Institute (WTSI). The traditional file system struggles to handle these increasing amounts of sequence data. A good data management system therefore needs to be implemented and integrated into the current WTSI infrastructure. Such a system enables good management of the IT infrastructure of the sequencing pipeline and allows biologists to track their data.ResultsWe have chosen a data grid system, iRODS (Rule-Oriented Data management systems), to act as the data management system for the WTSI. iRODS provides a rule-based system management approach which makes data replication much easier and provides extra data protection. Unlike the metadata provided by traditional file systems, the metadata system of iRODS is comprehensive and allows users to customize their own application level metadata. Users and IT experts in the WTSI can then query the metadata to find and track data.The aim of this paper is to describe how we designed and used (from both system and user viewpoints) iRODS as a data management system. Details are given about the problems faced and the solutions found when iRODS was implemented. A simple use case describing how users within the WTSI use iRODS is also introduced.ConclusionsiRODS has been implemented and works as the production system for the sequencing pipeline of the WTSI. Both biologists and IT experts can now track and manage data, which could not previously be achieved. This novel approach allows biologists to define their own metadata and query the genomic data using those metadata.
| S-EPMC3228552 | biostudies-literature