Systematic reviews and meta-analyses on treatment of asthma: critical evaluation

ObjectiveTo evaluate the clinical, methodological, and reporting aspects of systematic reviews and meta-analyses on the treatment of asthma and to compare those published by the Cochrane Collaboration with those published in paper based journals.DesignAnalysis of studies identified from Medline, CINAHL, HealthSTAR, EMBASE, Cochrane Library, personal collections, and reference lists.StudiesArticles describing a systematic review or a meta-analysis of the treatment of asthma that were published as a full report, in any language or format, in a peer reviewed journal or the Cochrane Library.Results50 systematic reviews and meta-analyses were included. More than half were published in the past two years. Twelve reviews were published in the Cochrane Library and 38 were published in 22 peer reviewed journals. Forced expiratory volume in one second was the most frequently used outcome, but few reviews evaluated the effect of treatment on costs or patient preferences. Forty reviews were judged to have serious or extensive flaws. All six reviews associated with industry were in this group. Seven of the 10 most rigorous reviews were published in the Cochrane Library.ConclusionsMost reviews published in peer reviewed journals or funded by industry have serious methodological flaws that limit their value to guide decisions. Cochrane reviews are more rigorous and better reported than those published in peer reviewed journals.     

Transparency of Outcome Reporting and Trial Registration of Randomized Controlled Trials Published in the Journal of Consulting and Clinical Psychology

Background

Confidence that randomized controlled trial (RCT) results accurately reflect intervention effectiveness depends on proper trial conduct and the accuracy and completeness of published trial reports. The Journal of Consulting and Clinical Psychology (JCCP) is the primary trials journal amongst American Psychological Association (APA) journals. The objectives of this study were to review RCTs recently published in JCCP to evaluate (1) adequacy of primary outcome analysis definitions; (2) registration status; and, (3) among registered trials, adequacy of outcome registrations. Additionally, we compared results from JCCP to findings from a recent study of top psychosomatic and behavioral medicine journals.

Methods

Eligible RCTs were published in JCCP in 2013–2014. For each RCT, two investigators independently extracted data on (1) adequacy of outcome analysis definitions in the published report, (2) whether the RCT was registered prior to enrolling patients, and (3) adequacy of outcome registration.

Results

Of 70 RCTs reviewed, 12 (17.1%) adequately defined primary or secondary outcome analyses, whereas 58 (82.3%) had multiple primary outcome analyses without statistical adjustment or undefined outcome analyses. There were 39 (55.7%) registered trials. Only two trials registered prior to patient enrollment with a single primary outcome variable and time point of assessment. However, in one of the two trials, registered and published outcomes were discrepant. No studies were adequately registered as per Standard Protocol Items: Recommendation for Interventional Trials guidelines. Compared to psychosomatic and behavioral medicine journals, the proportion of published trials with adequate outcome analysis declarations was significantly lower in JCCP (17.1% versus 32.9%; p = 0.029). The proportion of registered trials in JCCP (55.7%) was comparable to behavioral medicine journals (52.6%; p = 0.709).

Conclusions

The quality of published outcome analysis definitions and trial registrations in JCCP is suboptimal. Greater attention to proper trial registration and outcome analysis definition in published reports is needed.     

An Assessment of the Methodological Quality of Published Network Meta-Analyses: A Systematic Review

ObjectiveTo assess the methodological quality of published network meta-analysis.DesignSystematic review.MethodsWe searched the medical literature for network meta-analyses of pharmaceuticals. We assessed general study characteristics, study transparency and reproducibility, methodological approach, and reporting of findings. We compared studies published in journals with lower impact factors with those published in journals with higher impact factors, studies published prior to January 1^st, 2013 with those published after that date, and studies supported financially by industry with those supported by non-profit institutions or that received no support.ResultsThe systematic literature search identified 854 citations. Three hundred and eighteen studies met our inclusion criteria. The number of network meta-analyses has grown rapidly, with 48% of studies published since January 2013. The majority of network meta-analyses were supported by a non-profit institution or received no support (68%). We found considerable inconsistencies among reviewed studies. Eighty percent reported search terms, 61% a network diagram, 65% sufficient data to replicate the analysis, and 90% the characteristics of included trials. Seventy percent performed a risk of bias assessment of included trials, 40% an assessment of model fit, and 56% a sensitivity analysis. Among studies with a closed loop, 69% examined the consistency of direct and indirect evidence. Sixty-four percent of studies presented the full matrix of head-to-head treatment comparisons. For Bayesian studies, 41% reported the probability that each treatment was best, 31% reported treatment ranking, and 16% included the model code or referenced publicly-available code. Network meta-analyses published in higher impact factors journals and those that did not receive industry support performed better across the assessment criteria. We found few differences between older and newer studies.ConclusionsThere is substantial variation in the network meta-analysis literature. Consensus among guidelines is needed improve the methodological quality, transparency, and consistency of study conduct and reporting.     

Publication delay of randomized trials on 2009 influenza A (H1N1) vaccination

Background

Randomized evidence for vaccine immunogenicity and safety is urgently needed in the setting of pandemics with new emerging infectious agents. We carried out an observational survey to evaluate how many randomized controlled trials testing 2009 H1N1 vaccines were published among those registered, and what was the time lag from their start to publication and from their completion to publication.

Methods

PubMed, EMBASE and 9 clinical trial registries were searched for eligible randomized controlled trials. The units of the analysis were single randomized trials on any individual receiving influenza vaccines in any setting.

Results

73 eligible trials were identified that had been registered in 2009–2010. By June 30, 2011 only 21 (29%) of these trials had been published, representing 38% of the randomized sample size (19905 of 52765). Trials starting later were published less rapidly (hazard ratio 0.42 per month; 95% Confidence Interval: 0.27 to 0.64; p<0.001). Similarly, trials completed later were published less rapidly (hazard ratio 0.43 per month; 95% CI: 0.27 to 0.67; p<0.001). Randomized controlled trials were completed promptly (median, 5 months from start to completion), but only a minority were subsequently published.

Conclusions

Most registered randomized trials on vaccines for the H1N1 pandemic are not published in the peer-reviewed literature.     

桃儿七属的命名学考订

桃儿七属（Sinopodophyllum）是中国-喜马拉雅地区特有的单型属,仅桃儿七（Shexandrum）一种。桃儿七的根茎和果实均具有较高的药用价值,人类的过度采挖和种群恢复较慢使其种群数量急剧下降,现已被列入《中国物种红色名录》。在近年来的一些研究论文中,学名Shexandrum和Semodi常被混用,这使得有必要考证桃儿七学名的命名学历史,确认正确的学名使用。查阅原始文献发现,Shexandrum的基名Podophyllum hexandrum Royle发表于1834年,而Semodi的基名Podophyllum emodi Wall. ex Honigberger到1852年才合格发表（大多数学者认为是Hooker和Thomson在1855年合格发表）,因此,名称Shexandrum比名称Semodi具有优先权。名称的混乱起于1979年应俊生建立桃儿七属时,他提出组合“Semodi (Wall.) Ying”作为桃儿七的学名。另外,由于他未引证Honigberger或Hooker和Thomson的文献信息,所以组合“Semodi”没有被合格发表（规则415）。随后,1985年出版的《西藏植物志》桃儿七属中,应俊生发现之前的错误并采用名称“Shexandrum”取代了“Semodi”。遗憾的是他虽然意识到该名称是新组合,但未引证基名Phexandrum合格发表的文献信息,使得组合“Shexandrum (Rolye) Ying”没有被合格发表。近年来出版的《云南植物志》、《青海植物志》、《中国植物》和《Flora of China》均未发现该错误,一直认为“Shexandrum (Rolye) Ying”合格发表时间是1985。实际上,在1993年由于编写格式要求,应俊生在王文采和武素功主编的《横断山区维管束植物》中引证了基名合格发表的文献信息。因此,该名称的合格发表时间是1993年,而不是常认为的1985年。     

Corrected sequence of the wheat plastid genome

Wheat is the most important cereal in the world in terms of acreage and productivity. We sequenced and assembled the plastid genome of one Egyptian wheat cultivar using next-generation sequence data. The size of the plastid genome is 133,873 bp, which is 672 bp smaller than the published plastid genome of “Chinese Spring” cultivar, due mainly to the presence of three sequences from the rice plastid genome. The difference in size between the previously published wheat plastid genome and the sequence reported here is due to contamination of the published genome with rice plastid DNA, most of which is present in three sequences of 332, 131 and 131 bp. The corrected plastid genome of wheat has been submitted to GenBank (accession number KJ592713) and can be used in future comparisons.     

Editorial Note: Change of Publisher and New Policies

The first volume of DNA Research was published in 1994, andsince then, it has been published as a leading journal in thefield. The online version of the journal was launched in 2000.From its launch, the online journal has been freely accessibleto all readers without charge. Though thorough analysis hasnot been performed to     

A formal classification of the extant cycads

My previously published provisional classification of the Cycadales is here formally published. This classification is based upon a cladistic analysis of characters ranging from gross morphology to phytochemistry. Encephalartos is lectotypified.     

CHROMOSOME NUMBERS IN UMBELLIFERAE. III

Chromosome numbers are reported for 156 collections representing 100 taxa of Umbelliferae. Approximately two thirds of the collections are from Mexico, Central and South America and indicate a high percentage of polyploid species in certain genera found in this area. Chromosome numbers for plants belonging to 78 taxa are published here for the first time, previously published chromosome numbers are verified for 18 taxa and chromosome numbers differing from those previously published are reported in seven instances. No chromosome counts have been previously published for nine of the genera included here. Further aneuploidy and polyploidy were found in Eryngium, and Lomatium columbianum has been found to be a high polyploid with 2n = 14x. Every chromosome count is referable to a cited herbarium specimen.     

Evidence for risk of bias in cluster randomised trials: review of recent trials published in three general medical journals

Objective To examine the prevalence of a risk of bias associated with the design and conduct of cluster randomised controlled trials among a sample of recently published studies.Design Retrospective review of cluster randomised trials published in the BMJ, Lancet, and New England Journal of Medicine from January 1997 to October 2002.Main outcome measures Prevalence of secure randomisation of clusters, identification of participants before randomisation (to avoid foreknowledge of allocation), differential recruitment between treatment arms, differential application of inclusion and exclusion criteria, and differential attrition.Results Of the 36 trials identified, 24 were published in the BMJ,11 in the Lancet, and a single trial in the New England Journal of Medicine. At the cluster level, 15 (42%) trials provided evidence for secure allocation and 25 (69%) used stratified allocation. Few trials showed evidence of imbalance at the cluster level. However, some evidence of susceptibility to risk of bias at the individual level existed in 14 (39%) studies.Conclusions Some recently published cluster randomised trials may not have taken adequate precautions to guard against threats to the internal validity of their design.     

Timing and Completeness of Trial Results Posted at ClinicalTrials.gov and Published in Journals

Background

The US Food and Drug Administration Amendments Act requires results from clinical trials of Food and Drug Administration–approved drugs to be posted at ClinicalTrials.gov within 1 y after trial completion. We compared the timing and completeness of results of drug trials posted at ClinicalTrials.gov and published in journals.

Methods and Findings

We searched ClinicalTrials.gov on March 27, 2012, for randomized controlled trials of drugs with posted results. For a random sample of these trials, we searched PubMed for corresponding publications. Data were extracted independently from ClinicalTrials.gov and from the published articles for trials with results both posted and published. We assessed the time to first public posting or publishing of results and compared the completeness of results posted at ClinicalTrials.gov versus published in journal articles. Completeness was defined as the reporting of all key elements, according to three experts, for the flow of participants, efficacy results, adverse events, and serious adverse events (e.g., for adverse events, reporting of the number of adverse events per arm, without restriction to statistically significant differences between arms for all randomized patients or for those who received at least one treatment dose).From the 600 trials with results posted at ClinicalTrials.gov, we randomly sampled 50% (n = 297) had no corresponding published article. For trials with both posted and published results (n = 202), the median time between primary completion date and first results publicly posted was 19 mo (first quartile = 14, third quartile = 30 mo), and the median time between primary completion date and journal publication was 21 mo (first quartile = 14, third quartile = 28 mo). Reporting was significantly more complete at ClinicalTrials.gov than in the published article for the flow of participants (64% versus 48% of trials, p<0.001), efficacy results (79% versus 69%, p = 0.02), adverse events (73% versus 45%, p<0.001), and serious adverse events (99% versus 63%, p<0.001).The main study limitation was that we considered only the publication describing the results for the primary outcomes.

Conclusions

Our results highlight the need to search ClinicalTrials.gov for both unpublished and published trials. Trial results, especially serious adverse events, are more completely reported at ClinicalTrials.gov than in the published article. Please see later in the article for the Editors'' Summary     

Reconsideration of the previously classified incompatibility groups of plasmids,IncP-1 and IncP-11

This study presents the reassessment of earlier published data with reference to the article published in Environmental Microbiology entitled ‘IncP-type plasmids carrying genes for antibiotic resistance or aromatic compound degradation are prevalent in sequenced Aromatoleum and Thauera strains’ by Lo et al. This correspondence clarifies misperceptions of plasmids classified under incompatibility (Inc) groups IncP-1 and IncP-11.     

Apparent alteration in properties of arl mutants of Escherichia coli

The published properties of lambda phages grown in Escherichia coli arl mutants, and plasmids maintained in them, included increased homologous recombination, decreased DNA-cytosine methylation, and increased sensitivity of DNA to nuclease S1. Some of these properties now appear altered; others remain approximately as published.     

Assessment of Adverse Events in Protocols,Clinical Study Reports,and Published Papers of Trials of Orlistat: A Document Analysis

BackgroundLittle is known about how adverse events are summarised and reported in trials, as detailed information is usually considered confidential. We have acquired clinical study reports (CSRs) from the European Medicines Agency through the Freedom of Information Act. The CSRs describe the results of studies conducted as part of the application for marketing authorisation for the slimming pill orlistat. The purpose of this study was to study how adverse events were summarised and reported in study protocols, CSRs, and published papers of orlistat trials.ConclusionsIn the orlistat trials, we identified important disparities in the reporting of adverse events between protocols, clinical study reports, and published papers. Reports of these trials seemed to have systematically understated adverse events. Based on these findings, systematic reviews of drugs might be improved by including protocols and CSRs in addition to published articles.     

Chromosome numbers in North and Central American Compositae

Chromosome numbers are reported for 364 collections representing 70 species and varieties in 16 genera. Of these, 35 species and varieties have not had counts published previously. Counts of 26 collections in 14 species differ from all previously published counts for the same species. One new combination,Stevia anadenotricha, and one new variety,Stevia subpubescens var.intermedia, are published.     

Diversity biases in terrestrial mammalian assemblages and quantifying the differences between museum collections and published accounts: A case study from the Miocene of Nevada

Understanding diversity through time in the fossil record has primarily relied on the raw count of species within a given time interval, or species richness. These estimates are often derived from published fossil data, and standardized for sample size or geographic area. However, most methods that standardize richness by sample size are sensitive to changes in evenness, which introduces a potential problem with relying on published records: published accounts could be more even than the museum collections from which they are drawn. We address this bias in the context of mammalian paleodiversity, comparing published and museum collections of the Hemphillian Thousand Creek fauna to those of the Barstovian Virgin Valley fauna. We rarified specimen data, both number of identified specimens (NISP) and minimum number of individuals (MNI), and presence/absence data to compare published and museum data within and between faunas. Within faunas, published numbers of specimens are more even than museum samples, but the difference for localities in Virgin Valley is not significant. Neither published nor museum numbers of specimens indicate a significant difference between faunas, but the diversity pattern is reversed between the two data sets. Presence/absence rarefactions show no differences between sources; here, published data adequately sample the underlying museum records. Specimen-based evenness is not accurate in the published sample, and therefore we suggest that future studies of diversity in terrestrial mammalian assemblages must assess unpublished collections. Additionally, NISP data for Thousand Creek are more even than MNI data, suggesting that relying solely on NISP for assessing species diversity can also be misleading. Because publication bias alters richness and evenness, diversity estimates using published data must be circumspect about data sources.     

Successful theory development in biology: A consideration of the theories of oxidative phosphorylation proposed by Davies and Krebs,Williams and Mitchell

The chemiosmotic theory is normally attributed to Peter Mitchell's formulation published in Nature in 1961. However, the essential elements of the theory were published 9 years earlier by Davies and Krebs. Why, then, was this earlier formulation overlooked? The success of Mitchell's theory is examined in comparison with those of Davies and Krebs and of Williams.     

Quantitative comparison of microarray experiments with published leukemia related gene expression signatures

Background  

Multiple gene expression signatures derived from microarray experiments have been published in the field of leukemia research. A comparison of these signatures with results from new experiments is useful for verification as well as for interpretation of the results obtained. Currently, the percentage of overlapping genes is frequently used to compare published gene signatures against a signature derived from a new experiment. However, it has been shown that the percentage of overlapping genes is of limited use for comparing two experiments due to the variability of gene signatures caused by different array platforms or assay-specific influencing parameters. Here, we present a robust approach for a systematic and quantitative comparison of published gene expression signatures with an exemplary query dataset.     

基于CiteSpace分析铜绿假单胞菌耐药性研究热点与趋势

【背景】铜绿假单胞菌(Pseudomonas aeruginosa)是临床引发感染的主要病原菌之一,对多种抗菌药物均有耐药性,临床治疗难度大,对该病原菌耐药性的研究一直备受关注。【目的】基于CiteSpace可视化功能,探究铜绿假单胞菌耐药性研究现状、热点与发展趋势。【方法】利用文献计量分析法,以2014–2021年中国知网(CNKI)、万方数据库(Wanfang)、Web of Science (WoS)共8 996篇铜绿假单胞菌耐药性的中英文文献为分析样本,运用Citespace软件对文献发文量、作者合作网络、国家和机构合作网络、文献共被引及期刊分析、关键词聚类、突现等方面进行分析,以探究该研究主题的研究热点及趋势。【结果】英文文献发文量增长速度高于中文文献;我国文献发文量仅次于美国、印度,在该领域科研成果贡献度较高,国际学术影响力较大;中英文文献中均对院内感染疾病和耐碳青霉烯类铜绿假单胞菌持高关注度。然而,中文文献较关注铜绿假单胞菌耐药性的临床防治问题,英文文献则较关注铜绿假单胞菌耐药性的基础研究。【结论】国内外铜绿假单胞菌耐药性研究对院内感染疾病及新型耐药菌的产生与防治关注度最高,暗示以上研究主题是该领域的研究热点与趋势。     

Ninety extra nucleotide inndhF gene of tobacco chloroplast DNA: a summary of revisions to the 1986 genome sequence

Corrections to the published sequence of the tobacco chloroplast genendhF are presented, including a 90 bpAlu I restriction enzyme fragment internal to the gene that was apparently missed during the original sequencing effort. A summary of the corrections to the published tobacco chloroplast DNA that have come to light since its original publication is included.