Enhancing the sample diversity of snowball samples: Recommendations from a research project on anti-dam movements in Southeast Asia.
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ABSTRACT:
SUBMITTER: Kirchherr J
PROVIDER: S-EPMC6104950 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Affymetrix single nucleotide polymorphism (SNP) array data were collected to study genome-wide patterns of genomic variation across a broad geographical range of Island Southeast Asian populations. This region has experienced an extremely complex admixture history. Initially settled ~50,000 years ago, Island Southeast Asia has since been the recipient of multiple waves of population movements, most recently by Austronesian-speaking groups ultimately from Neolithic mainland Asia and later arrivals during the historic era from India and the Middle East. We have genotyped SNPs in ~500 individuals from 30 populations spanning this entire geographical region, from communities close to mainland Asia through to New Guinea. Particular attention has been paid to genomic data that are informative for population history, including the role of recent arrivals during the historic era and admixture with archaic hominins.
2017-08-02 | GSE80534 | GEO
Project description:Shotgun sequencing of Southeast Asia mammals
| PRJNA361218 | ENA
Project description:The Association of Southeast Asian Nations (ASEAN) is a diverse region that is experiencing economic growth and increased non-communicable disease burden. This paper aims to evaluate the current regulations, dietary recommendations and research related to whole grains in this region. To do this, a systematic literature review was carried out and information was collected on regulations and dietary recommendations from each member state. The majority of publications on whole grains from the region (99 of 147) were in the area of food science and technology, with few observational studies (n = 13) and human intervention studies (n = 10) related to whole grains being apparent. Information from six countries (Indonesia, Malaysia, The Philippines, Singapore, Thailand and Vietnam) was available. Wholegrain food-labelling regulations were only noted in Malaysia and Singapore. Public health recommendation related to whole grains were apparent in four countries (Indonesia, Malaysia, The Philippines, Singapore), while recent intake data from whole grains was only apparent from Malaysia, The Philippines and Singapore. In all cases, consumption of whole grains appeared to be very low. These findings highlight a need for further monitoring of dietary intake in the region and further strategies targeted at increasing the intake of whole grains.
| S-EPMC6024883 | biostudies-other
Project description:BackgroundEncephalitis is a worldwide public health issue, with a substantially high burden among children in southeast Asia. We aimed to determine the causes of encephalitis in children admitted to hospitals across the Greater Mekong region by implementing a comprehensive state-of-the-art diagnostic procedure harmonised across all centres, and identifying clinical characteristics related to patients' conditions.MethodsIn this multicentre, observational, prospective study of childhood encephalitis, four referral hospitals in Cambodia, Vietnam, Laos, and Myanmar recruited children (aged 28 days to 16 years) who presented with altered mental status lasting more than 24 h and two of the following minor criteria: fever (within the 72 h before or after presentation), one or more generalised or partial seizures (excluding febrile seizures), a new-onset focal neurological deficit, cerebrospinal fluid (CSF) white blood cell count of 5 per mL or higher, or brain imaging (CT or MRI) suggestive of lesions of encephalitis. Comprehensive diagnostic procedures were harmonised across all centres, with first-line testing was done on samples taken at inclusion and results delivered within 24 h of inclusion for main treatable causes of disease and second-line testing was done thereafter for mostly non-treatable causes. An independent expert medical panel reviewed the charts and attribution of causes of all the included children. Using multivariate analyses, we assessed risk factors associated with unfavourable outcomes (ie, severe neurological sequelae and death) at discharge using data from baseline and day 2 after inclusion. This study is registered with ClinicalTrials.gov, NCT04089436, and is now complete.FindingsBetween July 28, 2014, and Dec 31, 2017, 664 children with encephalitis were enrolled. Median age was 4·3 years (1·8-8·8), 295 (44%) children were female, and 369 (56%) were male. A confirmed or probable cause of encephalitis was identified in 425 (64%) patients: 216 (33%) of 664 cases were due to Japanese encephalitis virus, 27 (4%) were due to dengue virus, 26 (4%) were due to influenza virus, 24 (4%) were due to herpes simplex virus 1, 18 (3%) were due to Mycobacterium tuberculosis, 17 (3%) were due to Streptococcus pneumoniae, 17 (3%) were due to enterovirus A71, 74 (9%) were due to other pathogens, and six (1%) were due to autoimmune encephalitis. Diagnosis was made within 24 h of admission to hospital for 83 (13%) of 664 children. 119 (18%) children had treatable conditions and 276 (42%) had conditions that could have been preventable by vaccination. At time of discharge, 153 (23%) of 664 children had severe neurological sequelae and 83 (13%) had died. In multivariate analyses, risk factors for unfavourable outcome were diagnosis of M tuberculosis infection upon admission (odds ratio 3·23 [95% CI 1·04-10·03]), coma on day 2 (2·90 [1·78-4·72]), supplementary oxygen requirement (1·89 [1·25-2·86]), and more than 1 week duration between symptom onset and admission to hospital (3·03 [1·68-5·48]). At 1 year after inclusion, of 432 children who were discharged alive from hospital with follow-up data, 24 (5%) had died, 129 (30%) had neurological sequelae, and 279 (65%) had completely recovered.InterpretationIn southeast Asia, most causes of childhood encephalitis are either preventable or treatable, with Japanese encephalitis virus being the most common cause. We provide crucial information that could guide public health policy to improve diagnostic, vaccination, and early therapeutic guidelines on childhood encephalitis in the Greater Mekong region.FundingInstitut Pasteur, Institut Pasteur International Network, Fondation Merieux, Aviesan Sud, INSERM, Wellcome Trust, Institut de Recherche pour le Développement (IRD), and Fondation Total.
| S-EPMC9210261 | biostudies-literature
Project description:The Prehistoric Peopling of Southeast Asia
| PRJEB26721 | ENA
Project description:Island Southeast Asia (ISEA) was first colonized by modern humans at least 45,000 years ago, but the extent to which the modern inhabitants trace their ancestry to the first settlers is a matter of debate. It is widely held, in both archaeology and linguistics, that they are largely descended from a second wave of dispersal, proto-Austronesian-speaking agriculturalists who originated in China and spread to Taiwan approximately 5,500 years ago. From there, they are thought to have dispersed into ISEA approximately 4,000 years ago, assimilating the indigenous populations. Here, we demonstrate that mitochondrial DNA diversity in the region is extremely high and includes a large number of indigenous clades. Only a fraction of these date back to the time of first settlement, and the majority appear to mark dispersals in the late-Pleistocene or early-Holocene epoch most likely triggered by postglacial flooding. There are much closer genetic links to Taiwan than to the mainland, but most of these probably predated the mid-Holocene "Out of Taiwan" event as traditionally envisioned. Only approximately 20% at most of modern mitochondrial DNAs in ISEA could be linked to such an event, suggesting that, if an agriculturalist migration did take place, it was demographically minor, at least with regard to the involvement of women.
| S-EPMC1876738 | biostudies-other
Project description: Not available
| S-EPMC3647655 | biostudies-literature
Project description:ObjectivesThis study aimed to assess the rate of concordance, and to investigate sources of non-concordance of recommendations in the management of hypertension across CPGs in Southeast Asia, with internationally reputable clinical practice guidelines (CPGs).MethodsCPGs for the management of hypertension in Southeast Asia were retrieved from the websites of the Ministry of Health or cardiovascular specialty societies of the individual countries of Southeast Asia during November to December 2020. The recommendations for the management of hypertension specified in the 2017 American College of Cardiology (ACC)/American Heart Association (AHA) guideline and the 2018 European Society of Cardiology (ESC)/European Society of Hypertension (ESH) guideline were selected to be the reference standards; the recommendations concerning the management of hypertension in the included CPGs in Southeast Asia were assessed if they were concordant with the reference recommendations generated from both the 2017 ACC/AHA guideline and the 2018 ESC/ESH guideline, using the population (P)-intervention (I)-comparison (C) combinations approach.ResultsA total of 59 reference recommendations with unique and unambiguous P-I-C specifications was generated from the 2017 ACC/AHA guideline. In addition, a total of 51 reference recommendations with unique and unambiguous P-I-C specifications was generated from the 2018 ESC/ESH guideline. Considering the six included CPGs from Southeast Asia, concordance was observed for 30 reference recommendations (50.8%) out of 59 reference recommendations generated from the 2017 ACC/AHA guideline and for 31 reference recommendations (69.8%) out of 51 reference recommendations derived from the 2018 ESC/ESH guideline.ConclusionsHypertension represents a significant issue that places health and economic strains in Southeast Asia and demands guideline-based care, yet CPGs in Southeast Asia have a high rate of non-concordance with internationally reputable CPGs. Concordant recommendations could perhaps be considered a standard of care for hypertension management in the Southeast Asia region.
| S-EPMC8317337 | biostudies-literature
Project description:Genetic differences between populations are potentially an important contributor to health disparities around the globe. As differences in gene frequencies influence study design, it is important to have a thorough understanding of the natural variation of the genetic variant(s) of interest. Along these lines, we characterized the variation of the 5HTTLPR and rs25531 polymorphisms in six samples from North America, Southeast Asia, and Africa (Cameroon) that differ in their racial and ethnic composition. Allele and genotype frequencies were determined for 24,066 participants. Results indicated higher frequencies of the rs25531 G-allele among Black and African populations as compared with White, Hispanic and Asian populations. Further, we observed a greater number of 'extra-long' ('XL') 5HTTLPR alleles than have previously been reported. Extra-long alleles occurred almost entirely among Asian, Black and Non-White Hispanic populations as compared with White and Native American populations where they were completely absent. Lastly, when considered jointly, we observed between sample differences in the genotype frequencies within racial and ethnic populations. Taken together, these data underscore the importance of characterizing the L-G allele to avoid misclassification of participants by genotype and for further studies of the impact XL alleles may have on the transcriptional efficiency of SLC6A4.
| S-EPMC4348250 | biostudies-literature
Project description:For centuries swidden was an important farming practice found across the girth of Southeast Asia. Today, however, these systems are changing and sometimes disappearing at a pace never before experienced. In order to explain the demise or transitioning of swidden we need to understand the rapid and massive changes that have and are occurring in the political and economic environment in which these farmers operate. Swidden farming has always been characterized by change, but since the onset of modern independent nation states, governments and markets in Southeast Asia have transformed the terms of swiddeners' everyday lives to a degree that is significantly different from that ever experienced before. In this paper we identified six factors that have contributed to the demise or transformation of swidden systems, and support these arguments with examples from China (Xishuangbanna), Laos, Thailand, Malaysia, and Indonesia. These trends include classifying swiddeners as ethnic minorities within nation-states, dividing the landscape into forest and permanent agriculture, expansion of forest departments and the rise of conservation, resettlement, privatization and commoditization of land and land-based production, and expansion of market infrastructure and the promotion of industrial agriculture. In addition we note a growing trend toward a transition from rural to urban livelihoods and expanding urban-labor markets.
| S-EPMC2709851 | biostudies-other