A systematic comparison of software dedicated to meta-analysis of causal studies

<p>Abstract</p> <p>Background</p> <p>Our objective was to systematically assess the differences in features, results, and usability of currently available meta-analysis programs.</p> <p>Methods</p> <p>Systematic review of software. We did an extensive search on the internet (Google, Yahoo, Altavista, and MSN) for specialized meta-analysis software. We included six programs in our review: Comprehensive Meta-analysis (CMA), MetAnalysis, MetaWin, MIX, RevMan, and WEasyMA. Two investigators compared the features of the software and their results. Thirty independent researchers evaluated the programs on their usability while analyzing one data set.</p> <p>Results</p> <p>The programs differed substantially in features, ease-of-use, and price. Although most results from the programs were identical, we did find some minor numerical inconsistencies. CMA and MIX scored highest on usability and these programs also have the most complete set of analytical features.</p> <p>Conclusion</p> <p>In consideration of differences in numerical results, we believe the user community would benefit from openly available and systematically updated information about the procedures and results of each program's validation. The most suitable program for a meta-analysis will depend on the user's needs and preferences and this report provides an overview that should be helpful in making a substantiated choice.</p

Families with infants: a general approach to solve hard partition problems

We introduce a general approach for solving partition problems where the goal is to represent a given set as a union (either disjoint or not) of subsets satisfying certain properties. Many NP-hard problems can be naturally stated as such partition problems. We show that if one can find a large enough system of so-called families with infants for a given problem, then this problem can be solved faster than by a straightforward algorithm. We use this approach to improve known bounds for several NP-hard problems as well as to simplify the proofs of several known results. For the chromatic number problem we present an algorithm with $O^*((2-\varepsilon(d))^n)$ time and exponential space for graphs of average degree $d$. This improves the algorithm by Bj\"{o}rklund et al. [Theory Comput. Syst. 2010] that works for graphs of bounded maximum (as opposed to average) degree and closes an open problem stated by Cygan and Pilipczuk [ICALP 2013]. For the traveling salesman problem we give an algorithm working in $O^*((2-\varepsilon(d))^n)$ time and polynomial space for graphs of average degree $d$. The previously known results of this kind is a polyspace algorithm by Bj\"{o}rklund et al. [ICALP 2008] for graphs of bounded maximum degree and an exponential space algorithm for bounded average degree by Cygan and Pilipczuk [ICALP 2013]. For counting perfect matching in graphs of average degree~$d$ we present an algorithm with running time $O^*((2-\varepsilon(d))^{n/2})$ and polynomial space. Recent algorithms of this kind due to Cygan, Pilipczuk [ICALP 2013] and Izumi, Wadayama [FOCS 2012] (for bipartite graphs only) use exponential space.Comment: 18 pages, a revised version of this paper is available at http://arxiv.org/abs/1410.220

Development and validation of MIX: comprehensive free software for meta-analysis of causal research data

BACKGROUND: Meta-analysis has become a well-known method for synthesis of quantitative data from previously conducted research in applied health sciences. So far, meta-analysis has been particularly useful in evaluating and comparing therapies and in assessing causes of disease. Consequently, the number of software packages that can perform meta-analysis has increased over the years. Unfortunately, it can take a substantial amount of time to get acquainted with some of these programs and most contain little or no interactive educational material. We set out to create and validate an easy-to-use and comprehensive meta-analysis package that would be simple enough programming-wise to remain available as a free download. We specifically aimed at students and researchers who are new to meta-analysis, with important parts of the development oriented towards creating internal interactive tutoring tools and designing features that would facilitate usage of the software as a companion to existing books on meta-analysis. RESULTS: We took an unconventional approach and created a program that uses Excel as a calculation and programming platform. The main programming language was Visual Basic, as implemented in Visual Basic 6 and Visual Basic for Applications in Excel 2000 and higher. The development took approximately two years and resulted in the 'MIX' program, which can be downloaded from the program's website free of charge. Next, we set out to validate the MIX output with two major software packages as reference standards, namely STATA (metan, metabias, and metatrim) and Comprehensive Meta-Analysis Version 2. Eight meta-analyses that had been published in major journals were used as data sources. All numerical and graphical results from analyses with MIX were identical to their counterparts in STATA and CMA. The MIX program distinguishes itself from most other programs by the extensive graphical output, the click-and-go (Excel) interface, and the educational features. CONCLUSION: The MIX program is a valid tool for performing meta-analysis and may be particularly useful in educational environments. It can be downloaded free of charge via or

Excluding venous thromboembolism using point of care D-dimer tests in outpatients: a diagnostic meta-analysis

Objective To review the evidence on the diagnostic accuracy of the currently available point of care D-dimer tests for excluding venous thromboembolism

Safety and Efficacy of Erythrocyte Encapsulated Thymidine Phosphorylase in Mitochondrial Neurogastrointestinal Encephalomyopathy.

Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is an ultra-rare autosomal recessive disorder of nucleoside metabolism that is caused by mutations in the nuclear thymidine phosphorylase gene (TYMP) gene, encoding for the enzyme thymidine phosphorylase. There are currently no approved treatments for MNGIE. The aim of this study was to investigate the safety, tolerability, and efficacy of an enzyme replacement therapy for the treatment of MNGIE. In this single centre study, three adult patients with MNGIE received intravenous escalating doses of erythrocyte encapsulated thymidine phosphorylase (EE-TP; dose range: 4 to 108 U/kg/4 weeks). EE-TP was well tolerated and reductions in the disease-associated plasma metabolites, thymidine, and deoxyuridine were observed in all three patients. Clinical improvements, including weight gain and improved disease scores, were observed in two patients, suggesting that EE-TP is able to reverse some aspects of the disease pathology. Transient, non-serious adverse events were observed in two of the three patients; these did not lead to therapy discontinuation and they were managed with pre-medication prior to infusion of EE-TP. To conclude, enzyme replacement therapy with EE-TP demonstrated biochemical and clinical therapeutic efficacy with an acceptable clinical safety profile

Early Detection of Prostate Cancer: The Role of Scent

Prostate cancer (PCa) represents the cause of the second highest number of cancer-related deaths worldwide, and its clinical presentation can range from slow-growing to rapidly spreading metastatic disease. As the characteristics of most cases of PCa remains incompletely understood, it is crucial to identify new biomarkers that can aid in early detection. Despite the prostate-specific antigen serum (PSA) levels, prostate biopsy, and imaging representing the actual gold-standard for diagnosing PCa, analyzing volatile organic compounds (VOCs) has emerged as a promising new frontier. We and other authors have reported that highly trained dogs can recognize specific VOCs associated with PCa with high accuracy. However, using dogs in clinical practice has several limitations. To exploit the potential of VOCs, an electronic nose (eNose) that mimics the dog olfactory system and can potentially be used in clinical practice was designed. To explore the eNose as an alternative to dogs in diagnosing PCa, we conducted a systematic literature review and meta-analysis of available studies. PRISMA guidelines were used for the identification, screening, eligibility, and selection process. We included six studies that employed trained dogs and found that the pooled diagnostic sensitivity was 0.87 (95% CI 0.86–0.89; I2, 98.6%), the diagnostic specificity was 0.83 (95% CI 0.80–0.85; I2, 98.1%), and the area under the summary receiver operating characteristic curve (sROC) was 0.64 (standard error, 0.25). We also analyzed five studies that used an eNose to diagnose PCa and found that the pooled diagnostic sensitivity was 0.84 (95% CI, 0.80–0.88; I2, 57.1%), the diagnostic specificity was 0.88 (95% CI, 0.84–0.91; I2, 66%), and the area under the sROC was 0.93 (standard error, 0.03). These pooled results suggest that while highly trained dogs have the potentiality to diagnose PCa, the ability is primarily related to olfactory physiology and training methodology. The adoption of advanced analytical techniques, such as eNose, poses a significant challenge in the field of clinical practice due to their growing effectiveness. Nevertheless, the presence of limitations and the requirement for meticulous study design continue to present challenges when employing eNoses for the diagnosis of PCa

Meta-analyses and Forest plots using a microsoft excel spreadsheet: step-by-step guide focusing on descriptive data analysis

<p>Abstract</p> <p>Background</p> <p>Meta-analyses are necessary to synthesize data obtained from primary research, and in many situations reviews of observational studies are the only available alternative. General purpose statistical packages can meta-analyze data, but usually require external macros or coding. Commercial specialist software is available, but may be expensive and focused in a particular type of primary data. Most available softwares have limitations in dealing with descriptive data, and the graphical display of summary statistics such as incidence and prevalence is unsatisfactory. Analyses can be conducted using Microsoft Excel, but there was no previous guide available.</p> <p>Findings</p> <p>We constructed a step-by-step guide to perform a meta-analysis in a Microsoft Excel spreadsheet, using either fixed-effect or random-effects models. We have also developed a second spreadsheet capable of producing customized forest plots.</p> <p>Conclusions</p> <p>It is possible to conduct a meta-analysis using only Microsoft Excel. More important, to our knowledge this is the first description of a method for producing a statistically adequate but graphically appealing forest plot summarizing descriptive data, using widely available software.</p