Haplotype‐resolved DNA methylome of African cassava genome

ISSN:1467-7644ISSN:1467-765

MODIFIED YUPINGFENG FORMULA FOR THE TREATMENT OF STABLE CHRONIC OBSTRUCTIVE PULMONARY DISEASE: A SYSTEMATIC REVIEW OF RANDOMIZED CONTROLLED TRIALS

Background: Chronic obstructive pulmonary disease (COPD), is a very common disease of respiratory system. An increasing number of clinical trials on Yupingfeng formula in the management of stable COPD have been performed. However, the evidence base for it remains unknown. This review aims at assessing the efficacy, and safety of modified Yupingfeng formula in the treatment of stable COPD through a systematic review of all available randomized controlled trials. Materials and Methods: Literature retrieval was conducted using four English databases (CENTRAL, PubMed, EMBASE, and ISI Web of Science), and four Chinese databases (CBM, CNKI, VIP, and WANFANG), from respective inception to January 2013, and supplemented with a manual search. Review authors independently extracted the trial data, and assessed the quality of each trial. Methodological quality was assessed by Cochrane risk of bias and Jadad’s scale. The following outcomes were evaluated: (1) lung function; (2) 6-minute walk distance (6MWD); (3) effective rate; (4) serum levels of IgA, IgG and IgE; and (5) adverse events. Data were analyzed using STATA 12.0 software. Results: A total of nine studies involving 660, stable COPD patients were identified. Patients from all studies included in this review were randomized to receive Yupingfeng formula combined with Western medications in comparison with Western medications. In general, the methodological quality of the included trials was poor. The results of this systematic review indicates that, compared with Western medications alone, the use of Yupingfeng formula, if combined with Western medications could significantly improve FEV1 (WMD = 0.30L; 95%CI: 0.19, 0.42), FEV1/FVC ratio (SMD = 0.69; 95%CI: 0.48, 0.91), 6MWD (WMD = 31.73m; 95% CI: 19.29, 44.17), and effective rate (RR = 1.24; 95% CI: 1.10, 1.41), and increase the serum levels of IgA (WMD = 0.25; 95%CI: 0.16, 0.34) and IgG (WMD = 1.10; 95%CI: 0.53, 1.68), but no difference was found in the serum IgE levels (WMD = 0.47; 95%CI: -0.32, 1.27) between the two groups. No serious adverse events were reported. Conclusions: Within the limitations of this systematic review, we may conclude that compared with Western medications alone, Yupingfeng formula, when combined with Western medications can provide more benefits for patients with stable COPD, without any serious adverse reactions being identified. However, these benefits need to be further confirmed through high-quality prospective placebo-controlled trials that should be strictly conducted in accordance with methodological principles and procedures

The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies

Reproducibility is a fundamental requirement in scientific experiments and clinical contexts. Recent publications raise concerns about the reliability of microarray technology because of the apparent lack of agreement between lists of differentially expressed genes (DEGs). In this study we demonstrate that (1) such discordance may stem from ranking and selecting DEGs solely by statistical significance (P) derived from widely used simple t-tests; (2) when fold change (FC) is used as the ranking criterion, the lists become much more reproducible, especially when fewer genes are selected; and (3) the instability of short DEG lists based on P cutoffs is an expected mathematical consequence of the high variability of the t-values. We recommend the use of FC ranking plus a non-stringent P cutoff as a baseline practice in order to generate more reproducible DEG lists. The FC criterion enhances reproducibility while the P criterion balances sensitivity and specificity

The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies

<p>Abstract</p> <p>Background</p> <p>Reproducibility is a fundamental requirement in scientific experiments. Some recent publications have claimed that microarrays are unreliable because lists of differentially expressed genes (DEGs) are not reproducible in similar experiments. Meanwhile, new statistical methods for identifying DEGs continue to appear in the scientific literature. The resultant variety of existing and emerging methods exacerbates confusion and continuing debate in the microarray community on the appropriate choice of methods for identifying reliable DEG lists.</p> <p>Results</p> <p>Using the data sets generated by the MicroArray Quality Control (MAQC) project, we investigated the impact on the reproducibility of DEG lists of a few widely used gene selection procedures. We present comprehensive results from inter-site comparisons using the same microarray platform, cross-platform comparisons using multiple microarray platforms, and comparisons between microarray results and those from TaqMan – the widely regarded "standard" gene expression platform. Our results demonstrate that (1) previously reported discordance between DEG lists could simply result from ranking and selecting DEGs solely by statistical significance (<it>P</it>) derived from widely used simple <it>t</it>-tests; (2) when fold change (FC) is used as the ranking criterion with a non-stringent <it>P</it>-value cutoff filtering, the DEG lists become much more reproducible, especially when fewer genes are selected as differentially expressed, as is the case in most microarray studies; and (3) the instability of short DEG lists solely based on <it>P</it>-value ranking is an expected mathematical consequence of the high variability of the <it>t</it>-values; the more stringent the <it>P</it>-value threshold, the less reproducible the DEG list is. These observations are also consistent with results from extensive simulation calculations.</p> <p>Conclusion</p> <p>We recommend the use of FC-ranking plus a non-stringent <it>P </it>cutoff as a straightforward and baseline practice in order to generate more reproducible DEG lists. Specifically, the <it>P</it>-value cutoff should not be stringent (too small) and FC should be as large as possible. Our results provide practical guidance to choose the appropriate FC and <it>P</it>-value cutoffs when selecting a given number of DEGs. The FC criterion enhances reproducibility, whereas the <it>P </it>criterion balances sensitivity and specificity.</p

Analysis of serum syphilis screening results of 364 MSM patients: Based on the results of serum test and mobile app

Objective To investigate the prevalence and risk factors of syphilis in MSM patients in Guangzhou. Methods Yang Cheng Yi Fang smart application integrated a set of assessment questionnaire for syphilis infection risk was developed for MSM to self-evaluate the risk of syphilis at voluntary counseling and testing (VCT) clinic in the study. The syphilis risk is classified into high-, middle- and low-risk levels. Subjects with middle to high risk were automatically referred to a STD prevention institution or general hospital for further screen for syphilis and HIV. The individuals′ test results and their respective questionnaire were analyzed. Results Among the 364 evaluated MSM individuals, individuals at low-, middle- and high-risk accounted for 6.04% (22/364), 81.32% (296/364) and 12.64% (46/364), respectively. The positive rates of syphilis and HIV were 9.07% (33/364) and 3.02% (11/364), respectively. The positive rates of syphilis did not differ significantly between middle- and high-risk groups (9.12% vs 13.04%,χ2=0.33,P=0.569). The risk of syphilis was higher in individuals who occasionally or never or often used condom than in those who always used condom (χ2=7.06,P=0.030). Moreover, the risk of syphilis was higher in subjects whose sexual partner had syphilis than in those whose sexual partner did not have syphilis (χ2=36.27, P<0.001). Conclusions The rate of syphilis infections is higher in MSM individuals in Guangzhou. Online assessment of the risk of syphilis infections and referral, followed by serum test can be helpful to precisely prevent and control syphilis infections in MSM individuals

Quality of reporting of two-group parallel randomized controlled clinical trials of multi-herb formulae: a survey of reports indexed in the Science Citation Index Expanded

Introduction: An increasing number of trials of multi-herb formula interventions are being published in relatively high-ranked medical journals indexed in the Science Citation Index Expanded (SCIE). The aim of the study was to evaluate the quality of reporting of two-group parallel randomized controlled clinical trials (indexed in SCIE) of multi-herb formulae. Methods: Computerized literature searches were performed in SCIE from 1996 to November 2010. Two reviewers independently assessed the included trials using the modified Consolidated Standard of Reporting Trials (CONSORT) 2010 checklist and additional items reflecting the basic characteristics of traditional Chinese medicine (TCM). The number and proportion of reports describing each of the 38 modified CONSORT items and 6 additional TCM items were calculated. We also performed stratified analyses according to whether reports had or had not adopted the CONSORT statement, or according to Chinese reports (conducted in Mainland China, Hong Kong and Taiwan) or non-Chinese reports. Results: The reporting of the items recommended by the CONSORT 2010 statement was suboptimal as only 5 items were described in more than 80% of the 153 included reports. For the recommended CONSORT items, adherence was higher in CONSORT-adopters, and more items were reported in non-Chinese reports. The reporting of the TCM items was considered inadequate in the included studies, particularly in non-Chinese reports. Conclusions: The present study shows that the quality of reporting of these trials is suboptimal. We recommend all journals endorse the CONSORT statement, which would help researchers to improve the reporting of future randomized controlled trials. In addition, the reporting of the TCM items was considered inadequate in the included studies. All TCM practitioners should pay attention to the unique characteristics of TCM and improve the reporting of the recommended TCM items

Modified Yupinfeng formula for the traetment of stable chronic obstructive pulmonary disease: a systematic review of randomized controlled trials

Background: Chronic obstructive pulmonary disease (COPD), is a very common disease of respiratory system. An increasing number of clinical trials on Yupingfeng formula in the management of stable COPD have been performed. However, the evidence base for it remains unknown. This review aims at assessing the efficacy, and safety of modified Yupingfeng formula in the treatment of stable COPD through a systematic review of all available randomized controlled trials. Materials and Methods: Literature retrieval was conducted using four English databases (CENTRAL, PubMed, BASEMAN, and ISI Web of Science), and four Chinese databases (CBM, CNKI, VIP, and WANFANG), from respective inception to January 2013, and supplemented with a manual search. Review authors independently extracted the trial data, and assessed the quality of each trial. Methodological quality was assessed by Cochrane risk of bias and Jadad’s scale. The following outcomes were evaluated: (1) lung function; (2) 6-minute walk distance (6MWD); (3) effective rate; (4) serum levels of IgA, IgG and IgE; and (5) adverse events. Data were analyzed using STATA 12.0 software. Results: A total of nine studies involving 660, stable COPD patients were identified. Patients from all studies included in this review were randomized to receive Yupingfeng formula combined with Western medications in comparison with Western medications. In general, the methodological quality of the included trials was poor. The results of this systematic review indicates that, compared with Western medications alone, the use of Yupingfeng formula, if combined with Western medications could significantly improve FEV1 (WMD = 0.30L; 95%CI: 0.19, 0.42), FEV1/FVC ratio (SMD = 0.69; 95%CI: 0.48, 0.91), 6MWD (WMD = 31.73m; 95% CI: 19.29, 44.17), and effective rate (RR = 1.24; 95% CI: 1.10, 1.41), and increase the serum levels of IgA (WMD = 0.25; 95%CI: 0.16, 0.34) and IgG (WMD = 1.10; 95%CI: 0.53, 1.68), but no difference was found in the serum IgE levels (WMD = 0.47; 95%CI: －0.32, 1.27) between the two groups. No serious adverse events were reported. Conclusions: Within the limitations of this systematic review, we may conclude that compared with Western medications alone, Yupingfeng formula, when combined with Western medications can provide more benefits for patients with stable COPD, without any serious adverse reactions being identified. However, these benefits need to be further confirmed through high-quality prospective placebo-controlled trials that should be strictly conducted in accordance with methodological principles and procedures