最近のコクランレビューの約10%が文献検索式にアウトカムを含めており、結果が誇張された可能性がある: 研究の研究

京都大学新制・論文博士博士(医学)乙第13599号論医博第2309号京都大学大学院医学研究科社会健康医学系専攻(主査)教授 山本 洋介, 教授 近藤 尚己, 教授 西浦 博学位規則第4条第2項該当Doctor of Medical ScienceKyoto UniversityDFA

Application of a New Probabilistic Model for Mining Implicit Associated Cancer Genes from OMIM and Medline

An important issue in current medical science research is to find the genes that are strongly related to an inherited disease. A particular focus is placed on cancer-gene relations, since some types of cancers are inherited. As biomedical databases have grown speedily in recent years, an informatics approach to predict such relations from currently available databases should be developed. Our objective is to find implicit associated cancer-genes from biomedical databases including the literature database. Co-occurrence of biological entities has been shown to be a popular and efficient technique in biomedical text mining. We have applied a new probabilistic model, called mixture aspect model (MAM) [48], to combine different types of co-occurrences of genes and cancer derived from Medline and OMIM (Online Mendelian Inheritance in Man). We trained the probability parameters of MAM using a learning method based on an EM (Expectation and Maximization) algorithm. We examined the performance of MAM by predicting associated cancer gene pairs. Through cross-validation, prediction accuracy was shown to be improved by adding gene-gene co-occurrences from Medline to cancer-gene cooccurrences in OMIM. Further experiments showed that MAM found new cancer-gene relations which are unknown in the literature. Supplementary information can be found at http://www.bic.kyotou.ac.jp/pathway/zhusf/CancerInformatics/Supplemental2006.htm

Around ten percent of most recent Cochrane reviews included outcomes in their literature search strategy and were associated with potentially exaggerated results: A research-on-research study

[Objectives] To assess the proportion of the recent Cochrane reviews that included outcomes in their literature search strategy, how often they acknowledged these limitations, and how qualitatively different the results of outcomes included and not included in the search strategy were. [Design and Setting] We identified all the Cochrane reviews of the interventions published in 2020 that used a search strategy connecting outcome terms with “AND.” Reviews were defined as acknowledging the limitations of searching for outcomes if they mentioned them in the discussion. We compared the characteristics of outcomes included and not included in the search strategy. [Results] Of the 523 Cochrane reviews published in 2020, 51 (9.8%) included outcomes in their search strategy. Only one review acknowledged it as a limitation. Forty-seven (92%) assessed outcomes not included in the search strategy. Outcomes included in the search strategies tended to include a larger number of studies and show their effects in favor of the intervention. [Conclusions] Around ten percent of the recent Cochrane reviews included outcomes in their search, which may have resulted in more outcomes significantly in favor of the intervention. Reviewers should be more explicit in acknowledging the potential implications of searching for outcomes

The impact of continuity correction methods in Cochrane reviews with single-zero trials with rare events: A meta-epidemiological study.

Meta-analyses examining dichotomous outcomes often include single-zero studies, where no events occur in intervention or control groups. These pose challenges, and several methods have been proposed to address them. A fixed continuity correction method has been shown to bias estimates, but it is frequently used because sometimes software (e.g., RevMan software in Cochrane reviews) uses it as a default. We aimed to empirically compare results using the continuity correction with those using alternative models that do not require correction. To this aim, we reanalyzed the original data from 885 meta-analyses in Cochrane reviews using the following methods: (i) Mantel-Haenszel model with a fixed continuity correction, (ii) random effects inverse variance model with a fixed continuity correction, (iii) Peto method (the three models available in RevMan), (iv) random effects inverse variance model with the treatment arm continuity correction, (v) Mantel-Haenszel model without correction, (vi) logistic regression, and (vii) a Bayesian random effects model with binominal likelihood. For each meta-analysis we calculated ratios of odds ratios between all methods, to assess how the choice of method may impact results. Ratios of odds ratios <0.8 or <1.25 were seen in ~30% of the existing meta-analyses when comparing results between Mantel-Haenszel model with a fixed continuity correction and either Mantel-Haenszel model without correction or logistic regression. We concluded that injudicious use of the fixed continuity correction in existing Cochrane reviews may have substantially influenced effect estimates in some cases. Future updates of RevMan should incorporate less biased statistical methods

Association between Immediate Postoperative Radiographic Findings and Failed Internal Fixation for Trochanteric Fractures: Systematic Review and Meta-Analysis

Failed internal fixations for trochanteric fractures have a strong negative impact owing to increased postoperative mortality and high medical costs. However, evidence on the prognostic value of postoperative radiographic findings for failed internal fixations is limited. We aimed to clarify the association between comprehensive immediate postoperative radiographic findings and failed internal fixation using relative and absolute risk measures. We followed the meta-analysis of observational studies in epidemiology guidelines and the Cochrane handbook. We searched specific databases in November 2021. The outcomes of interest were failed internal fixation and cut-out. We pooled the odds ratios and 95% confidence intervals using a random-effects model and calculated the number needed to harm for each outcome. Thirty-six studies involving 8938 patients were included. The certainty of evidence in the association between postoperative radiographic findings and failed internal fixation or cut-out was mainly low or very low except for the association between intramedullary malreduction on the anteromedial cortex and failed internal fixation. Moderate certainty of evidence supported that intramedullary malreduction on the anteromedial cortex was associated with failed internal fixation. Most postoperative radiographic findings on immediate postoperative radiographs for trochanteric fractures were uncertain as prognostic factors for failed internal fixations

GEM-TREND: a web tool for gene expression data mining toward relevant network discovery

<p>Abstract</p> <p>Background</p> <p>DNA microarray technology provides us with a first step toward the goal of uncovering gene functions on a genomic scale. In recent years, vast amounts of gene expression data have been collected, much of which are available in public databases, such as the Gene Expression Omnibus (GEO). To date, most researchers have been manually retrieving data from databases through web browsers using accession numbers (IDs) or keywords, but gene-expression patterns are not considered when retrieving such data. The Connectivity Map was recently introduced to compare gene expression data by introducing gene-expression signatures (represented by a set of genes with up- or down-regulated labels according to their biological states) and is available as a web tool for detecting similar gene-expression signatures from a limited data set (approximately 7,000 expression profiles representing 1,309 compounds). In order to support researchers to utilize the public gene expression data more effectively, we developed a web tool for finding similar gene expression data and generating its co-expression networks from a publicly available database.</p> <p>Results</p> <p>GEM-TREND, a web tool for searching gene expression data, allows users to search data from GEO using gene-expression signatures or gene expression ratio data as a query and retrieve gene expression data by comparing gene-expression pattern between the query and GEO gene expression data. The comparison methods are based on the nonparametric, rank-based pattern matching approach of Lamb et al. (Science 2006) with the additional calculation of statistical significance. The web tool was tested using gene expression ratio data randomly extracted from the GEO and with in-house microarray data, respectively. The results validated the ability of GEM-TREND to retrieve gene expression entries biologically related to a query from GEO. For further analysis, a network visualization interface is also provided, whereby genes and gene annotations are dynamically linked to external data repositories.</p> <p>Conclusion</p> <p>GEM-TREND was developed to retrieve gene expression data by comparing query gene-expression pattern with those of GEO gene expression data. It could be a very useful resource for finding similar gene expression profiles and constructing its gene co-expression networks from a publicly available database. GEM-TREND was designed to be user-friendly and is expected to support knowledge discovery. GEM-TREND is freely available at <url>http://cgs.pharm.kyoto-u.ac.jp/services/network</url>.</p

Exercise can improve sleep quality: a systematic review and meta-analysis

Background Insomnia is common. However, no systematic reviews have examined the effect of exercise on patients with primary and secondary insomnia, defined as both sleep disruption and daytime impairment. This systematic review and meta-analysis aimed to examine the effectiveness/efficacy of exercise in patients with insomnia. Methods We searched the Cochrane Central Register of Controlled Trials, MEDLINE, Embase, PsycINFO, World Health Organization International Clinical Trials Registry Platform, and ClinicalTrials.gov to identify all randomized controlled trials that examined the effects of exercise on various sleep parameters in patients with insomnia. All participants were diagnosed with insomnia, using standard diagnostic criteria or predetermined criteria and standard measures. Data on outcome measures were subjected to meta-analyses using random-effects models. The Cochrane Risk of Bias Tool and Grading of Recommendations, Assessment, Development, and Evaluation approach were used to assess the quality of the individual studies and the body of evidence, respectively. Results We included nine studies with a total of 557 participants. According to the Pittsburgh Sleep Quality Index (mean difference [MD], 2.87 points lower in the intervention group; 95% confidence interval [CI], 3.95 points lower to 1.79 points lower; low-quality evidence) and the Insomnia Severity Index (MD, 3.22 points lower in the intervention group; 95% CI, 5.36 points lower to 1.07 points lower; very low-quality evidence), exercise was beneficial. However, exercise interventions were not associated with improved sleep efficiency (MD, 0.56% lower in the intervention group; 95% CI, 3.42% lower to 2.31% higher; moderate-quality evidence). Only four studies noted adverse effects. Most studies had a high or unclear risk of selection bias. Discussion Our findings suggest that exercise can improve sleep quality without notable adverse effects. Most trials had a high risk of selection bias. Higher quality research is needed

Retracted randomised controlled trials were cited and not corrected in systematic reviews and clinical practice guidelines

[Background and Objectives] To investigate whether and when the correction is done in Systematic Reviews (SRs) and Clinical Practice Guidelines (CPGs) when included Randomized Controlled Trials (RCTs) have been retracted. [Methods] In this meta-epidemiological study, we included SRs and CPGs citing the retracted RCTs from the Retraction Watch Database. We investigated how often the retracted RCTs were cited in SRs and CPGs. We also investigated whether and when such SRs and CPGs corrected themselves. [Results] We identified 587 articles (525 SRs and 62 CPGs) citing retracted RCTs. Among the 587 articles, 252 (43%) were published after retraction, and 335 (57%) were published before retraction. Among 127 articles published citing already retracted RCTs in their evidence synthesis without caution, none corrected themselves after publication. Of 335 articles published before retraction, 239 included RCTs that were later retracted in their evidence synthesis. Among them, only 5% of SRs (9/196) and 5% of CPGs (2/43) corrected or retracted their results. [Conclusion] Many SRs and CPGs included already or later retracted RCTs without caution. Most of them were never corrected. The scientific community, including publishers and researchers, should make systematic and concerted efforts to remove the impact of retracted RCTs

Characterization of gene expression profiles for different types of mast cells pooled from mouse stomach subregions by an RNA amplification method

<p>Abstract</p> <p>Background</p> <p>Mast cells (MCs) play pivotal roles in allergy and innate immunity and consist of heterogenous subclasses. However, the molecular basis determining the different characteristics of these multiple MC subclasses remains unclear.</p> <p>Results</p> <p>To approach this, we developed a method of RNA extraction/amplification for intact <it>in vivo </it>MCs pooled from frozen tissue sections, which enabled us to obtain the global gene expression pattern of pooled MCs belonging to the same subclass. MCs were isolated from the submucosa (sMCs) and mucosa (mMCs) of mouse stomach sections, respectively, 15 cells were pooled, and their RNA was extracted, amplified and subjected to microarray analysis. Known marker genes specific for mMCs and sMCs showed expected expression trends, indicating accuracy of the analysis.</p> <p>We identified 1,272 genes showing significantly different expression levels between sMCs and mMCs, and classified them into clusters on the basis of similarity of their expression profiles compared with bone marrow-derived MCs, which are the cultured MCs with so-called 'immature' properties. Among them, we found that several key genes such as <it>Notch4 </it>had sMC-biased expression and <it>Ptgr1 </it>had mMC-biased expression. Furthermore, there is a difference in the expression of several genes including extracellular matrix protein components, adhesion molecules, and cytoskeletal proteins between the two MC subclasses, which may reflect functional adaptation of each MC to the mucosal or submucosal environment in the stomach.</p> <p>Conclusion</p> <p>By using the method of RNA amplification from pooled intact MCs, we characterized the distinct gene expression profiles of sMCs and mMCs in the mouse stomach. Our findings offer insight into possible unidentified properties specific for each MC subclass.</p

Inhibitory effects of caffeine on allergic rhinitis symptoms in mice

We examined the effects of caffeine treatment on ovalbumin- and histamine-induced rhinitis mouse models and on corticosterone and catecholamine levels in mouse plasma. Treatment with caffeine decreased sneezing and nasal rubbing in both models, but direct nasal administration had no effect. Plasma levels of corticosterone and catecholamine, which have known anti-allergy effects, were increased by caffeine treatment. The increases in corticosterone and catecholamine may be associated with the suppression of rhinitis symptoms