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- Imanishi, T., et al.
(author)
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Integrative annotation of 21,037 human genes validated by full-length cDNA clones
- 2004
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In: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 2:6, s. 856-875
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Journal article (peer-reviewed)abstract
- The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology.
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- Shiba, K., et al.
(author)
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Estimating the Impact of Sustained Social Participation on Depressive Symptoms in Older Adults
- 2021
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In: Epidemiology. - : Ovid Technologies (Wolters Kluwer Health). - 1044-3983. ; 32:6, s. 886-895
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Journal article (peer-reviewed)abstract
- Background: Social participation has been suggested as a means to prevent depressive symptoms. However, it remains unclear whether a one-time boost suffices or whether participation needs to be sustained over time for long-term prevention. We estimated the impacts of alternative hypothetical interventions in social participation on subsequent depressive symptoms among older adults. Methods: Data were from a nationwide prospective cohort study of Japanese older adults >= 65 years of age (n = 32,748). We analyzed social participation (1) as a baseline exposure from 2010 (approximating a one-time boost intervention) and (2) as a time-varying exposure from 2010 and 2013 (approximating a sustained intervention). We defined binary depressive symptoms in 2016 using the Geriatric Depression Scale. We used the doubly robust targeted maximum likelihood estimation to address time-dependent confounding. Results: The magnitude of the association between sustained participation and the lower prevalence of depressive symptoms was larger than the association observed for baseline participation only (e.g., prevalence ratio [PR] for participation in any activity = 0.83 [95% confidence interval = 0.79, 0.88] vs. 0.90 [0.87, 0.94]). For activities with a lower proportion of consistent participation over time (e.g., senior clubs), there was little evidence of an association between baseline participation and subsequent depressive symptoms, while an association for sustained participation was evident (e.g., PR for senior clubs = 0.96 [0.90, 1.02] vs. 0.88 [0.79, 0.97]). Participation at baseline but withholding participation in 2013 was not associated with subsequent depressive symptoms. Conclusions: Sustained social participation may be more strongly associated with fewer depressive symptoms among older adults.
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