Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is ~32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene

Burden of Total and Cause-Specific Mortality Related to Tobacco Smoking among Adults Aged ≥45 Years in Asia: A Pooled Analysis of 21 Cohorts

Background:Tobacco smoking is a major risk factor for many diseases. We sought to quantify the burden of tobacco-smoking-related deaths in Asia, in parts of which men's smoking prevalence is among the world's highest.Methods and Findings:We performed pooled analyses of data from 1,049,929 participants in 21 cohorts in Asia to quantify the risks of total and cause-specific mortality associated with tobacco smoking using adjusted hazard ratios and their 95% confidence intervals. We then estimated smoking-related deaths among adults aged ≥45 y in 2004 in Bangladesh, India, mainland China, Japan, Republic of Korea, Singapore, and Taiwan-accounting for ∼71% of Asia's total population. An approximately 1.44-fold (95% CI = 1.37-1.51) and 1.48-fold (1.38-1.58) elevated risk of death from any cause was found in male and female ever-smokers, respectively. In 2004, active tobacco smoking accounted for approximately 15.8% (95% CI = 14.3%-17.2%) and 3.3% (2.6%-4.0%) of deaths, respectively, in men and women aged ≥45 y in the seven countries/regions combined, with a total number of estimated deaths of ∼1,575,500 (95% CI = 1,398,000-1,744,700). Among men, approximately 11.4%, 30.5%, and 19.8% of deaths due to cardiovascular diseases, cancer, and respiratory diseases, respectively, were attributable to tobacco smoking. Corresponding proportions for East Asian women were 3.7%, 4.6%, and 1.7%, respectively. The strongest association with tobacco smoking was found for lung cancer: A 3- to 4-fold elevated risk, accounting for 60.5% and 16.7% of lung cancer deaths, respectively, in Asian men and East Asian women aged ≥45 y.Conclusions:Tobacco smoking is associated with a substantially elevated risk of mortality, accounting for approximately 2 million deaths in adults aged ≥45 y throughout Asia in 2004. It is likely that smoking-related deaths in Asia will continue to rise over the next few decades if no effective smoking control programs are implemented.Please see later in the article for the Editors' Summary. © 2014 Zheng et al

Behavioural Risk Factors in Mid-Life Associated with Successful Ageing, Disability, Dementia and Frailty in Later Life: A Rapid Systematic Review.

BACKGROUND: Smoking, alcohol consumption, poor diet and low levels of physical activity significantly contribute to the burden of illness in developed countries. Whilst the links between specific and multiple risk behaviours and individual chronic conditions are well documented, the impact of these behaviours in mid-life across a range of later life outcomes has yet to be comprehensively assessed. This review aimed to provide an overview of behavioural risk factors in mid-life that are associated with successful ageing and the primary prevention or delay of disability, dementia, frailty and non-communicable chronic conditions. METHODS: A literature search was conducted to identify cohort studies published in English since 2000 up to Dec 2014. Multivariate analyses and a minimum follow-up of five years were required for inclusion. Two reviewers screened titles, abstracts and papers independently. Studies were assessed for quality. Evidence was synthesised by mid-life behavioural risk for a range of late life outcomes. FINDINGS: This search located 10,338 individual references, of which 164 are included in this review. Follow-up data ranged from five years to 36 years. Outcomes include dementia, frailty, disability and cardiovascular disease. There is consistent evidence of beneficial associations between mid-life physical activity, healthy ageing and disease outcomes. Across all populations studied there is consistent evidence that mid-life smoking has a detrimental effect on health. Evidence specific to alcohol consumption was mixed. Limited, but supportive, evidence was available relating specifically to mid-life diet, leisure and social activities or health inequalities. CONCLUSIONS: There is consistent evidence of associations between mid-life behaviours and a range of late life outcomes. The promotion of physical activity, healthy diet and smoking cessation in all mid-life populations should be encouraged for successful ageing and the prevention of disability and chronic disease.This work was funded by the National Institute for Health and Care Excellence (NICE), invitation to tender reference DDER 42013, and supported by the National Institute for Health Research School for Public Health Research. The scope of the work was defined by NICE and the protocol was agreed with NICE prior to the start of work. The funders had no role in data analysis, preparation of the manuscript or decision to publish.This is the final version of the article. It first appeared from PLOS via http://dx.doi.org/10.1371/journal.pone.014440

Education level and physical functional limitations among Japanese community residents-gender difference in prognosis from stroke

<p>Abstract</p> <p>Background</p> <p>Little research has been conducted to examine the relationship between education level and functional limitations among Japanese community residents. We sought to examine the association between education level and physical functional limitations among Japanese men and women, and whether that association was modified by gender and history of stroke.</p> <p>Methods</p> <p>We examined prevalence of physical functional limitation by educational level using the data from a total of 29,134 Japanese men and women aged 50–69 years living in communities in 2000. The information of educational level (junior high school graduates, senior high school graduates, college and/or higher education) and physical functional limitations (no need for assistance, need for assistance when going outdoors, and need for assistance to carry out indoor activities) were obtained by self-administrated questionnaire.</p> <p>Results</p> <p>The proportions of the subjects reported their highest level of schooling were 48% for junior high school, 39% for high school, and 13% for college. Three hundred and twenty eight subjects (1% of total subjects) reported having some physical functional limitations. Multinomial logistic regression analyses showed that the odds ratio of needing assistance to carry out indoor activities were 4.84(95%CI:3.61,6.50) for lowest education level group and 2.21(95%CI:1.00,4.86) for middle education level group compared to highest education level group. The corresponding odds ratios of needing assistance when going outdoors were 2.36(95%CI: 2.03,2.72) and 1.08(95%CI:0.73,1.60), respectively. Further, the significant excess prevalence of having functional limitations associated with the low education level was identified for men regardless of history of stroke and for women without history of stroke.</p> <p>Conclusion</p> <p>Low education level was associated with the higher prevalence of physical functional limitations for both genders. That association among persons with history of stroke was observed for men but not for women probably due to gender differences in stroke subtypes and social support.</p

Sleep Duration and Stress Level in the Risk of Gastric Cancer: A Pooled Analysis of Case-Control Studies in the Stomach Cancer Pooling (StoP) Project

The association between sleep and stress and cancer is underinvestigated. We evaluated these factors in association with gastric cancer (GC). Five case-control studies from the Stomach Cancer Pooling (StoP) Project were included. We calculated the odds ratios (ORs) and the corresponding 95% confidence intervals (CIs) for sleep duration and stress level in association with GC through multiple logistic regression models adjusted for several lifestyle factors. The analysis included 1293 cases and 4439 controls, 215 cardia and 919 noncardia GC, and 353 diffuse and 619 intestinal types. Sleep duration of =9 h was associated with GC (OR =1.57, 95% CI = 1.23-2.00) compared to 8 h. This was confirmed when stratifying by subsite (noncardia OR = 1.59, 95% CI = 1.22-2.08, and cardia OR = 1.63, 95% CI = 0.97-2.72) and histological type (diffuse OR = 1.65, 95% CI = 1.14-2.40 and intestinal OR = 1.24, 95% CI = 0.91-1.67). Stress was associated with GC (OR = 1.33, 95% CI = 1.18-1.50, continuous). This relationship was selectively related to noncardia GC (OR = 1.28, 95% 1.12-1.46, continuous). The risk of diffuse (OR = 1.32, 95% CI = 1.11-1.58) and intestinal type (OR = 1.23, 95% CI = 1.07-1.42) were higher when stress was reported. Results for the association between increasing level of stress and GC were heterogeneous by smoking and socioeconomic status (p for heterogeneity = 0.02 and <0.001, respectively). In conclusion, long sleep duration (=9 h) was associated with GC and its subtype categories. Stress linearly increased the risk of GC and was related to noncardia GC.The authors thank the European Cancer Prevention (ECP) Organization for providing support for the StoP Project meetings.This study was supported by the Fondazione AIRC, Associazione Italianaper la Ricerca sul Cancro, Project no. 21378 (Investigator Grant)

Exploring the interactions between Helicobacter pylori (Hp) infection and other risk factors of gastric cancer: A pooled analysis in the Stomach cancer Pooling (StoP) Project

Helicobacter pylori (Hp) is crucial in gastric carcinogenesis, but infection alone is not a sufficient cause, and the interaction between Hp infection and other risk factors has not been adequately studied. We conducted a pooled analysis of seven case-control studies from the Stomach cancer Pooling (StoP) Project, comprising 1377 cases and 2470 controls, to explore the interaction among Hp infection and tobacco smoking, alcohol drinking, socioeconomic status (SES) and dietary salt intake on the risk of gastric cancer. We estimated summary odds ratios (ORs) and the corresponding 95% confidence intervals (CIs) by multivariate unconditional logistic regression. The analysis showed no consistent interaction between Hp infection and cigarette smoking, while interaction was more than multiplicative for alcohol drinking (OR = 1.38, 95% CI: 1.07-1.77, P-interaction 0.02) and high intake of salt (OR = 2.62, 95% CI: 1.88-3.65, P-interaction = 0.04). The interaction with SES followed the multiplicative model (P = 0.49), resulting in a weakening among infected individuals of the protective effect of high SES among observed Hp-negative individuals. The interactions found were more pronounced in subjects with history of peptic ulcer. The interactions with Hp infection were stronger for cigarette smoking and dietary salt in the case of noncardia cancer, and for alcohol and SES in the case of cardia cancer. No differences were found when stratifying for histologic type. This large-scale study aimed to quantify the interaction between Hp infection and other modifiable risk factors of gastric cancer revealed that the benefit of combined Hp eradication and lifestyle modification on gastric cancer prevention may be larger than commonly appreciated.This study was supported by the Associazione Italiana per la Ricerca sul Cancro (AIRC), Project no. 21378 (Investigator Grant), and by the Italian League for the Fight Against Cancer (LILT). The authors thank the European Cancer Prevention (ECP) Organization for providing support for the StoP meetings

Salt intake and gastric cancer risk according to Helicobacter pylori infection, smoking, tumour site and histological type

Background:Although salt intake is considered a probable risk factor for gastric cancer, relevant studies have provided heterogeneous results, and the magnitude of the association has not been accurately quantified.Methods:To quantify gastric cancer risk in relation to dietary salt exposure according to Helicobacter pylori infection status and virulence, smoking, tumour site, and histological type, we evaluated 422 gastric cancer cases and 649 community controls. Salt exposure was estimated in the year before the onset of symptoms through: sodium intake (estimated by a food frequency questionnaire (FFQ)); main food items/groups contributing to dietary sodium intake; visual analogical scale for salt intake preference; use of table salt; and duration of refrigerator ownership.Results:Comparing subjects with the highest with those with the lowest salt exposure (3rd vs 1st third), sodium intake (OR2.01, 95% CI: 1.16-3.46), consumption of food items with high contribution to sodium intake (OR2.54, 95% CI: 1.56-4.14) and salt intake evaluated by visual analogical scale (OR1.83, 95% CI: 1.28-2.63) were associated with an increased gastric cancer risk. Subjects owning a refrigerator for 50 years had a lower risk for gastric cancer (OR0.28, 95% CI: 0.14-0.57). These associations were observed regardless of H. pylori infection status and virulence, smoking, tumour site or histological type.Conclusion:Our results support the view that salt intake is an important dietary risk factor for gastric cancer, and confirms the evidence of no differences in risk according to H. pylori infection and virulence, smoking, tumour site and histological type. © 2011 Cancer Research UK All rights reserved.This work was performed using grants from Fundac¸ão para a Ciência e a Tecnologia (POCTI/SAU-ESP/56126/2004, POCTI/ SAU-ESP/61685/2004, PTDC/SAU-ESA/71517/2006) and Agência Portuguesa de Seguranc¸a Alimentar. This work, presented at the GRELL Meeting 2010 in Toledo, was awarded the ‘Enrico Anglesio’ Prize, offered by the ‘Anglesio Moroni Foundation’, Turin, Italy

Use of vitamin supplements and risk of total cancer and cardiovascular disease among the Japanese general population: A population-based survey

<p>Abstract</p> <p>Background</p> <p>Despite the popular use of vitamin supplements and several prospective cohort studies investigating their effect on cancer incidence and cardiovascular disease (CVD), scientific data supporting their benefits remain controversial. Inconsistent results may be partly explained by the fact that use of supplements is an inconsistent behavior in individuals. We examined whether vitamin supplement use patterns affect cancer and CVD risk in a population-based cohort study in Japan.</p> <p>Methods</p> <p>A total of 28,903 men and 33,726 women in the Japan Public Health Center-based Prospective Study cohort, who answered questions about vitamin supplement use in the first survey from 1990-1994 and the second survey from 1995-1998, were categorized into four groups (never use, past use, recent use, and consistent use) and followed to the end of 2006 for cancer and 2005 for CVD. Sex-specific hazard ratios (HRs) and 95% confidence intervals (95% CIs) were used to describe the relative risks of cancer and CVD associated with vitamin supplement use.</p> <p>Results</p> <p>During follow-up, 4501 cancer and 1858 CVD cases were identified. Multivariate adjusted analysis revealed no association of any pattern of vitamin supplement use with the risk of cancer and CVD in men. In women, consistent use was associated with lower risk of CVD (HR 0.60, 95% CI 0.41-0.89), whereas past (HR 1.17, 95% CI 1.02-1.33) and recent use (HR 1.24, 95% CI 1.01-1.52) were associated with higher risk of cancer.</p> <p>Conclusions</p> <p>To our knowledge, this is the first prospective cohort study to examine simultaneously the associations between vitamin supplement use patterns and risk of cancer and CVD. This prospective cohort study demonstrated that vitamin supplement use has little effect on the risk of cancer or CVD in men. In women, however, consistent vitamin supplement use might reduce the risk of CVD. Elevated risk of cancer associated with past and recent use of vitamin supplements in women may be partly explained by preexisting diseases or unhealthy background, but we could not totally control for this in our study.</p

Dietary intake of folate, vitamin B6, and vitamin B12, genetic polymorphism of related enzymes, and risk of breast cancer: a case-control study in Brazilian women

<p>Abstract</p> <p>Background</p> <p>Several studies have determined that dietary intake of B vitamins may be associated with breast cancer risk as a result of interactions between <it>5,10-methylenetetrahydrofolate reductase (MTHFR) </it>and <it>methionine synthase </it>(<it>MTR</it>) in the one-carbon metabolism pathway. However, the association between B vitamin intake and breast cancer risk in Brazilian women in particular has not yet been investigated.</p> <p>Methods</p> <p>A case-control study was conducted in São Paulo, Brazil, with 458 age-matched pairs of Brazilian women. Energy-adjusted intakes of folate, vitamin B₆, and vitamin B₁₂were derived from a validated Food Frequency Questionnaire (FFQ). Genotyping was completed for <it>MTHFR </it>A1298C and C677T, and <it>MTR </it>A2756G polymorphisms. A logistical regression model was used to calculate odds ratios (ORs) and 95% confidence intervals (95% CIs).</p> <p>Results</p> <p>Neither dietary intake of folate, vitamin B₆, or vitamin B₁₂nor <it>MTHFR </it>polymorphisms were independently associated with breast cancer risk. Analysis stratified by menopausal status showed a significant association between placement in the highest tertile of folate intake and risk of breast cancer in premenopausal women (OR = 2.17, 95% CI: 1.23–3.83; <it>P</it>_{<it>trend </it>}= 0.010). The <it>MTR </it>2756GG genotype was associated with a higher risk of breast cancer than the 2756AA genotype (OR = 1.99, 95% CI = 1.01–3.92; <it>P</it>_{<it>trend </it>}= 0.801), and statistically significant interactions with regard to risk were observed between the <it>MTHFR </it>A1298C polymorphism and folate (P = 0.024) or vitamin B₆(P = 0.043), and between the <it>MTHFR </it>C677T polymorphism and folate (P = 0.043) or vitamin B₁₂(P = 0.022).</p> <p>Conclusion</p> <p><it>MTHFR </it>polymorphisms and dietary intake of folate, vitamin B₆, and vitamin B₁₂had no overall association with breast cancer risk. However, increased risk was observed in total women with the <it>MTR </it>2756GG genotype and in premenopausal women with high folate intake. These findings, as well as significant interactions between <it>MTHFR </it>polymorphisms and B vitamins, warrant further investigation.</p

Association of Sleep Duration with All- And Major-Cause Mortality among Adults in Japan, China, Singapore, and Korea

open28siImportance: The association between long sleep duration and mortality appears stronger in East Asian populations than in North American or European populations. Objectives: To assess the sex-specific association between sleep duration and all-cause and major-cause mortality in a pooled longitudinal cohort and to stratify the association by age and body mass index. Design, Setting, and Participants: This cohort study of individual-level data from 9 cohorts in the Asia Cohort Consortium was performed from January 1, 1984, to December 31, 2002. The final population included participants from Japan, China, Singapore, and Korea. Mean (SD) follow-up time was 14.0 (5.0) years for men and 13.4 (5.3) years for women. Data analysis was performed from August 1, 2018, to May 31, 2021. Exposures: Self-reported sleep duration, with 7 hours as the reference category. Main Outcomes and Measures: Mortality, including deaths from all causes, cardiovascular disease, cancer, and other causes. Sex-specific hazard ratios (HRs) and 95% CIs were estimated using Cox proportional hazards regression with shared frailty models adjusted for age and the key self-reported covariates of marital status, body mass index, smoking status, alcohol consumption, physical activity, history of diabetes and hypertension, and menopausal status (for women). Results: For 322721 participants (mean [SD] age, 54.5 [9.2] years; 178542 [55.3%] female), 19419 deaths occurred among men (mean [SD] age of men, 53.6 [9.0] years) and 13768 deaths among women (mean [SD] age of women, 55.3 [9.2] years). A sleep duration of 7 hours was the nadir for associations with all-cause, cardiovascular disease, and other-cause mortality in both men and women, whereas 8 hours was the mode sleep duration among men and the second most common sleep duration among women. The association between sleep duration and all-cause mortality was J-shaped for both men and women. The greatest association for all-cause mortality was with sleep durations of 10 hours or longer for both men (hazard ratio [HR], 1.34; 95% CI, 1.26-1.44) and women (HR, 1.48; 95% CI, 1.36-1.61). Sex was a significant modifier of the association between sleep duration and mortality from cardiovascular disease (χ25= 13.47, P =.02), cancer (χ25= 16.04, P =.007), and other causes (χ25= 12.79, P =.03). Age was a significant modifier of the associations among men only (all-cause mortality: χ25= 41.49, P &lt;.001; cancer: χ25= 27.94, P &lt;.001; other-cause mortality: χ25= 24.51, P &lt;.001). Conclusions and Relevance: The findings of this cohort study suggest that sleep duration is a behavioral risk factor for mortality in both men and women. Age was a modifier of the association between sleep duration in men but not in women. Sleep duration recommendations in these populations may need to be considered in the context of sex and age.noneSvensson T.; Saito E.; Svensson A.K.; Melander O.; Orho-Melander M.; Mimura M.; Rahman S.; Sawada N.; Koh W.-P.; Shu X.-O.; Tsuji I.; Kanemura S.; Park S.K.; Nagata C.; Tsugane S.; Cai H.; Yuan J.-M.; Matsuyama S.; Sugawara Y.; Wada K.; Yoo K.-Y.; Chia K.S.; Boffetta P.; Ahsan H.; Zheng W.; Kang D.; Potter J.D.; Inoue M.Svensson T.; Saito E.; Svensson A.K.; Melander O.; Orho-Melander M.; Mimura M.; Rahman S.; Sawada N.; Koh W.-P.; Shu X.-O.; Tsuji I.; Kanemura S.; Park S.K.; Nagata C.; Tsugane S.; Cai H.; Yuan J.-M.; Matsuyama S.; Sugawara Y.; Wada K.; Yoo K.-Y.; Chia K.S.; Boffetta P.; Ahsan H.; Zheng W.; Kang D.; Potter J.D.; Inoue M