共查询到20条相似文献，搜索用时 296 毫秒
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Xiaopei Shen Shan Li Lin Zhang Hongdong Li Guini Hong XianXiao Zhou Tingting Zheng Wenjing Zhang Chunxiang Hao Tongwei Shi Chunyang Liu Zheng Guo 《PloS one》2013,8(4)
Background
Cancer cells typically exhibit large-scale aberrant methylation of gene promoters. Some of the genes with promoter methylation alterations play “driver” roles in tumorigenesis, whereas others are only “passengers”.Results
Based on the assumption that promoter methylation alteration of a driver gene may lead to expression alternation of a set of genes associated with cancer pathways, we developed a computational framework for integrating promoter methylation and gene expression data to identify driver methylation aberrations of cancer. Applying this approach to breast cancer data, we identified many novel cancer driver genes and found that some of the identified driver genes were subtype-specific for basal-like, luminal-A and HER2+ subtypes of breast cancer.Conclusion
The proposed framework proved effective in identifying cancer driver genes from genome-wide gene methylation and expression data of cancer. These results may provide new molecular targets for potential targeted and selective epigenetic therapy. 相似文献7.
Genome Wide Association for Addiction: Replicated Results and Comparisons of Two Analytic Approaches
Tomas Drgon Ping-Wu Zhang Catherine Johnson Donna Walther Judith Hess Michelle Nino George R. Uhl 《PloS one》2010,5(1)
Background
Vulnerabilities to dependence on addictive substances are substantially heritable complex disorders whose underlying genetic architecture is likely to be polygenic, with modest contributions from variants in many individual genes. “Nontemplate” genome wide association (GWA) approaches can identity groups of chromosomal regions and genes that, taken together, are much more likely to contain allelic variants that alter vulnerability to substance dependence than expected by chance.Methodology/Principal Findings
We report pooled “nontemplate” genome-wide association studies of two independent samples of substance dependent vs control research volunteers (n = 1620), one European-American and the other African-American using 1 million SNP (single nucleotide polymorphism) Affymetrix genotyping arrays. We assess convergence between results from these two samples using two related methods that seek clustering of nominally-positive results and assess significance levels with Monte Carlo and permutation approaches. Both “converge then cluster” and “cluster then converge” analyses document convergence between the results obtained from these two independent datasets in ways that are virtually never found by chance. The genes identified in this fashion are also identified by individually-genotyped dbGAP data that compare allele frequencies in cocaine dependent vs control individuals.Conclusions/Significance
These overlapping results identify small chromosomal regions that are also identified by genome wide data from studies of other relevant samples to extents much greater than chance. These chromosomal regions contain more genes related to “cell adhesion” processes than expected by chance. They also contain a number of genes that encode potential targets for anti-addiction pharmacotherapeutics. “Nontemplate” GWA approaches that seek chromosomal regions in which nominally-positive associations are found in multiple independent samples are likely to complement classical, “template” GWA approaches in which “genome wide” levels of significance are sought for SNP data from single case vs control comparisons. 相似文献8.
David Patrick Kateete Fred Ashaba Katabazi Alfred Okeng Moses Okee Conrad Musinguzi Benon Byamugisha Asiimwe Samuel Kyobe Jeniffer Asiimwe W. Henry Boom Moses Lutaakome Joloba 《PloS one》2012,7(9)
Background
Rhomboids are ubiquitous proteins with unknown roles in mycobacteria. However, bioinformatics suggested putative roles in DNA replication pathways and metabolite transport. Here, mycobacterial rhomboid-encoding genes were characterized; first, using the Providencia stuartii null-rhomboid mutant and then deleted from Mycobacterium smegmatis for additional insight in mycobacteria.Methodology/Principal Findings
Using in silico analysis we identified in M. tuberculosis genome the genes encoding two putative rhomboid proteins; Rv0110 (referred to as “rhomboid protease 1”) and Rv1337 (“rhomboid protease 2”). Genes encoding orthologs of these proteins are widely represented in all mycobacterial species. When transformed into P. stuartii null-rhomboid mutant (ΔaarA), genes encoding mycobacterial orthologs of “rhomboid protease 2” fully restored AarA activity (AarA is the rhomboid protein of P. stuartii). However, most genes encoding mycobacterial “rhomboid protease 1” orthologs did not. Furthermore, upon gene deletion in M. smegmatis, the ΔMSMEG_4904 single mutant (which lost the gene encoding MSMEG_4904, orthologous to Rv1337, “rhomboid protease 2”) formed the least biofilms and was also more susceptible to ciprofloxacin and novobiocin, antimicrobials that inhibit DNA gyrase. However, the ΔMSMEG_5036 single mutant (which lost the gene encoding MSMEG_5036, orthologous to Rv0110, “rhomboid protease 1”) was not as susceptible. Surprisingly, the double rhomboid mutant ΔMSMEG_4904–ΔMSMEG_5036 (which lost genes encoding both homologs) was also not as susceptible suggesting compensatory effects following deletion of both rhomboid-encoding genes. Indeed, transforming the double mutant with a plasmid encoding MSMEG_5036 produced phenotypes of the ΔMSMEG_4904 single mutant (i.e. susceptibility to ciprofloxacin and novobiocin).Conclusions/Significance
Mycobacterial rhomboid-encoding genes exhibit differences in complementing aarA whereby it''s only genes encoding “rhomboid protease 2” orthologs that fully restore AarA activity. Additionally, gene deletion data suggests inhibition of DNA gyrase by MSMEG_4904; however, the ameliorated effect in the double mutant suggests occurrence of compensatory mechanisms following deletion of genes encoding both rhomboids. 相似文献9.
Background
After the publication of the CONSORT 2010 statement, few studies have been conducted to assess the reporting quality of randomized clinical trials (RCTs) on treatment of diabetes mellitus with Traditional Chinese Medicine (TCM) published in Chinese journals.Objective
To investigate the current situation of the reporting quality of RCTs in leading medical journals in China with the CONSORT 2010 statement as criteria.Methods
The China National Knowledge Infrastructure (CNKI) electronic database was searched for RCTs on the treatment of diabetes mellitus with TCM published in the Journal of Traditional Chinese Medicine, Chinese Journal of Integrated Traditional & Western Medicine, and the China Journal of Chinese Materia Medica from January to December 2011. We excluded trials reported as “animal studies”, “in vitro studies”, “case studies”, or “systematic reviews”. The CONSORT checklist was applied by two independent raters to evaluate the reporting quality of all eligible trials after discussing and comprehending the items thoroughly. Each item in the checklist was graded as either “yes” or “no” depending on whether it had been reported by the authors.Results
We identified 27 RCTs. According to the 37 items in the CONSORT checklist, the average reporting percentage was 45.0%, in which the average reporting percentage for the “title and abstract”, the “introduction”, the “methods”, the “results”, the “discussion” and the “other information” was 33.3%, 88.9%, 36.4%, 54.4%, 71.6% and 14.8%, respectively. In the Journal of Traditional Chinese Medicine, Chinese Journal of Integrated Traditional & Western Medicine, and the China Journal of Chinese Materia Medica the average reporting percentage was 42.2%, 56.8%, and 46.0%, respectively.Conclusions
The reporting quality of RCTs in these three journals was insufficient to allow readers to assess the validity of the trials. We recommend that editors require authors to use the CONSORT statement when reporting their trial results as a condition of publication. 相似文献10.
Objective
Given the importance of high sodium diets as a risk factor for disease burden (ranked 11th in importance in the Global Burden of Disease Study 2010), we aimed to determine the feasibility of low-sodium diets that were also low-cost, nutritious and (for some scenarios) included familiar meals.Methods
The mathematical technique of “linear programming” was used to model eight optimized daily diets (some with uncertainty), including some diets that contained “familiar meals” for New Zealanders or were Mediterranean-, Asian- and Pacific-style diets. Data inputs included nutrients in foods, food prices and food wastage.Findings
Using nutrient recommendations for men and a cost constraint of <NZ$9/d (US$6.84), the sodium intake levels in the eight optimized daily diets were all well below the 2300 mg/d (5.8 g salt/d) recommended maximum. The only diet to not consistently fall below the recommended “target” upper limit of 1600 mg/d included an evening meal with sausages (median = 1640 mg/d, 95% simulation interval: 1551–1735 mg/d). Many additional nutritional aspects of these optimized low-sodium diets suggest that they would reduce cardiovascular disease risk in other ways (e.g., improved polyunsaturated to saturated fat ratio) and also reduce risk of cancer and other chronic diseases (e.g., via higher intakes of vegetables, fruits and dietary fiber). Even healthier diets (e.g., with higher intakes of fruit) occurred when the cost constraint was relaxed to $NZ15/d (US$11.40). Similar results were obtained when the modeling considered diets for women.Conclusions
These results provide some reassurance for the feasibility of substantially reducing population sodium intake given currently available low-cost foods and while maintaining some level of familiar meals. Policy makers could consider ways to promote such optimized diets and foods, including regulations on maximum salt levels in processed foods, and taxes on alternative foods that are high in salt, sugar and saturated fat. 相似文献11.
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Background
Relationships between the neighborhood environment and children’s physical activity have been well documented in Western countries but are less investigated in ultra-dense Asian cities. The aim of this study was to identify the environmental facilitators and barriers of physical activity behaviors among Hong Kong Chinese children using nominal group technique.Methods
Five nominal groups were conducted among 34 children aged 10–11 years from four types of neighborhoods varying in socio-economic status and walkability in Hong Kong. Environmental factors were generated by children in response to the question “What neighborhood environments do you think would increase or decrease your willingness to do physical activity?” Factors were prioritized in order of their importance to children’s physical activity.Results
Sixteen unique environmental factors, which were perceived as the most important to children’s physical activity, were identified. Factors perceived as physical activity-facilitators included “Sufficient lighting”, “Bridge or tunnel”, “Few cars on roads”, “Convenient transportation”, “Subway station”, “Recreation grounds”, “Shopping malls with air conditioning”, “Fresh air”, “Interesting animals”, and “Perfume shop”. Factors perceived as physical activity-barriers included “People who make me feel unsafe”, “Crimes nearby”, “Afraid of being taken or hurt at night”, “Hard to find toilet in shopping mall”, “Too much noise”, and “Too many people in recreation grounds”.Conclusions
Specific physical activity-related environmental facilitators and barriers, which are unique in an ultra-dense city, were identified by Hong Kong children. These initial findings can inform future examinations of the physical activity-environment relationship among children in Hong Kong and similar Asian cities. 相似文献14.
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Background
A significant U-shaped association between sleep duration and several morbidity (obesity, diabetes or cardiovascular disease) and mortality risks has been regularly reported. However, although the physiological pathways and risks associated with “too short sleep” (<5 hours/day) have been well demonstrated, little is known about “too much sleeping”.Purpose
To explore socio-demographic characteristics and comorbidities of “long sleepers” (over 10 hours/day) from a nationally representative sample of adults.Methods
A cross-sectional nationally representative sample of 24,671 subjects from 15 to 85-year-old. An estimated total sleep time (TST) on non-leisure days was calculated based on a specifically designed sleep log which allows to distinguish “long sleepers” from “short sleepers” (<5 hours/day). Insomnia was assessed according to the International classification of sleep disorders (ICSD-2).Results
The average TST was 7 hours and 13 minutes (+/− 17 minutes). Six hundred and twelve subjects were “long sleepers” (2.7%) and 1969 “short sleepers” (7.5%). Compared to the whole group, “long sleepers” were more often female, younger (15–25 year-old) or older (above 65 year-old), with no academic degree, mostly clerks and blue collar workers. “Long sleepers” were significantly more likely to have psychiatric diseases and a greater body mass index (BMI). However, long sleep was not significantly associated with the presence of any other chronic medical disease assessed. Conversely, short sleep duration was significantly associated with almost all the other chronic diseases assessed.Conclusions
In the general population, sleeping too much was associated with psychiatric diseases and higher BMI, but not with other chronic medical diseases. 相似文献16.
T?res Theorell Anna Nyberg Constanze Leineweber Linda L. Magnusson Hanson Gabriel Oxenstierna Hugo Westerlund 《PloS one》2012,7(9)
Background
The way in which leadership is experienced in different socioeconomic strata is of interest per se, as well as how it relates to employee mental health.Methods
Three waves of SLOSH (Swedish Longitudinal Occupational Survey of Health, a questionnaire survey on a sample of the Swedish working population) were used, 2006, 2008 and 2010 (n = 5141). The leadership variables were: “Non-listening leadership” (one question: “Does your manager listen to you?” - four response categories), “Self centered leadership” (sum of three five-graded questions – “non-participating”, “asocial” and “loner”). The socioeconomic factors were education and income. Emotional exhaustion and depressive symptoms were used as indicators of mental health.Results
Non-listening leadership was associated with low income and low education whereas self-centered leadership showed a weaker relationship with education and no association at all with income. Both leadership variables were significantly associated with emotional exhaustion and depressive symptoms. “Self centered” as well as “non-listening” leadership in 2006 significantly predicted employee depressive symptoms in 2008 after adjustment for demographic variables. These predictions became non-significant when adjustment was made for job conditions (demands and decision latitude) in the “non-listening” leadership analyses, whereas predictions of depressive symptoms remained significant after these adjustments in the “self-centered leadership” analyses.Conclusions
Our results show that the leadership variables are associated with socioeconomic status and employee mental health. “Non-listening” scores were more sensitive to societal change and more strongly related to socioeconomic factors and job conditions than “self-centered” scores. 相似文献17.
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Bipin P. Kulkarni Sona B. Nair Manasi Vijapurkar Leenam Mota Sharda Shanbhag Shehnaz Ali Shrimati D. Shetty Kanjaksha Ghosh 《PloS one》2014,9(10)
Background
Though rare in occurrence, patients with rare bleeding disorders (RBDs) are highly heterogeneous and may manifest with severe bleeding diathesis. Due to the high rate of consanguinity in many caste groups, these autosomal recessive bleeding disorders which are of rare occurrence in populations across the world, may not be as rare in India.Objectives
To comprehensively analyze the frequency and nature of mutations in Indian patients with RBDs.Methods
Pubmed search was used (www.pubmed.com) to explore the published literature from India on RBDs using the key words “rare bleeding disorders”, “mutations”, “India”, “fibrinogen”, “afibrinogenemia”, “factor II deficiency”, “prothrombin” “factor VII deficiency”, “factor V deficiency”, “factor X deficiency”, “factor XI deficiency”, “combined factor V and VIII deficiency”, “factor XIII deficiency”, “Bernard Soulier syndrome” and “Glanzmanns thrombasthenia” in different combinations. A total of 60 relevant articles could be retrieved. The distribution of mutations from India was compared with that of the world literature by referring to the Human Gene Mutation Database (HGMD) (www.hgmd.org).Results
Taken together, 181 mutations in 270 patients with different RBDs have been reported from India. Though the types of mutations reported from India and their percentage distribution with respect to the world data are largely similar, yet much higher percentage of small deletions, duplication mutations, insertions, indels were observed in this analysis. Besides the identification of novel mutations and polymorphisms, several common mutations have also been reported, which will allow to develop a strategy for mutation screening in Indian patients with RBDs.Conclusion
There is a need for a consortium of Institutions working on the molecular pathology of RBDs in India. This will facilitate a quicker and cheaper diagnosis of RBDs besides its utility in first trimester prenatal diagnosis of the affected families. 相似文献19.
Background
Statistical simulations have consistently demonstrated that new dose-escalation designs such as accelerated titration design (ATD) and continual reassessment method (CRM)-type designs outperform the standard “3+3” design in phase I cancer clinical trials.Methods
We evaluated the actual efficiency of different dose escalation methods employed in first-in-human phase I clinical trials of targeted agents administered as single agents published over the last decade.Results
Forty-nine per cent of the 84 retrieved trials used the standard “3+3” design. Newer designs used included ATD in 42%, modified CRM [mCRM] in 7%, and pharmacologically guided dose escalation in 1%. The median numbers of dose levels explored in trials using “3+3”, ATD and mCRM designs were 6, 8 and 10, respectively. More strikingly, the mean MTD to starting dose ratio appeared to be at least twice as high for trials using mCRM or ATD designs as for trials using a standard “3+3” design. Despite this, the mean number of patients exposed to a dose below the MTD was similar in trials using “3+3”, ATD and mCRM designs.Conclusion
Our results support a more extensive implementation of innovative dose escalation designs such as mCRM and ATD in phase I cancer clinical trials of molecularly targeted agents. 相似文献20.
Rohina Joshi Mohammed Alim Andre Pascal Kengne Stephen Jan Pallab K. Maulik David Peiris Anushka A. Patel 《PloS one》2014,9(8)