SciCombinator

Discover the most talked about and latest scientific content & concepts.

Concept: Analysis

156

Sensitivity analyses refer to investigations of the degree to which the results of a meta-analysis remain stable when conditions of the data or the analysis change. To the extent that results remain stable, one can refer to them as robust. Sensitivity analyses are rarely conducted in the organizational science literature. Despite conscientiousness being a valued predictor in employment selection, sensitivity analyses have not been conducted with respect to meta-analytic estimates of the correlation (i.e., validity) between conscientiousness and job performance.

Concepts: Scientific method, Mathematical analysis, Logic, Analysis, Sensitivity analysis

155

Gene set analysis methods, which consider predefined groups of genes in the analysis of genomic data, have been successfully applied for analyzing gene expression data in cross-sectional studies. The time-course gene set analysis (TcGSA) introduced here is an extension of gene set analysis to longitudinal data. The proposed method relies on random effects modeling with maximum likelihood estimates. It allows to use all available repeated measurements while dealing with unbalanced data due to missing at random (MAR) measurements. TcGSA is a hypothesis driven method that identifies a priori defined gene sets with significant expression variations over time, taking into account the potential heterogeneity of expression within gene sets. When biological conditions are compared, the method indicates if the time patterns of gene sets significantly differ according to these conditions. The interest of the method is illustrated by its application to two real life datasets: an HIV therapeutic vaccine trial (DALIA-1 trial), and data from a recent study on influenza and pneumococcal vaccines. In the DALIA-1 trial TcGSA revealed a significant change in gene expression over time within 69 gene sets during vaccination, while a standard univariate individual gene analysis corrected for multiple testing as well as a standard a Gene Set Enrichment Analysis (GSEA) for time series both failed to detect any significant pattern change over time. When applied to the second illustrative data set, TcGSA allowed the identification of 4 gene sets finally found to be linked with the influenza vaccine too although they were found to be associated to the pneumococcal vaccine only in previous analyses. In our simulation study TcGSA exhibits good statistical properties, and an increased power compared to other approaches for analyzing time-course expression patterns of gene sets. The method is made available for the community through an R package.

Concepts: Scientific method, Gene, Longitudinal study, Statistics, Vaccine, Vaccination, Influenza vaccine, Analysis

154

Open-ended questions eliciting free-text comments have been widely adopted in surveys of patient experience. Analysis of free text comments can provide deeper or new insight, identify areas for action, and initiate further investigation. Also, they may be a promising way to progress from documentation of patient experience to achieving quality improvement. The usual methods of analyzing free-text comments are known to be time and resource intensive. To efficiently deal with a large amount of free-text, new methods of rapidly summarizing and characterizing the text are being explored.

Concepts: Scientific method, Analysis, Full text search

149

Biologists generally interrogate genomics data using web-based genome browsers that have limited analytical potential. New generation genome browsers such as the Integrated Genome Browser (IGB) have largely overcome this limitation and permit customized analyses to be implemented using plugins. We illustrate the use of a plugin for IGB that exploits advanced visualization techniques to integrate the analysis of genomics data with network and structural approaches.

Concepts: Genetics, Greek loanwords, Analysis, Web browser, Plug-in, Genome browser

68

The purposes of this study were to evaluate the association between total testosterone (TT) deficiency and weakness on multimorbidity in men. Analyses were performed to examine the prevalence of multimobidity among young, middle-aged, and older men, with and without testosterone deficiency. Multivariate logistic models were also used to determine the association between age-specific TT tertiles and multimorbidity, adjusting for key sociodemographic variables, as well as a secondary analysis adjusted for grip strength. Multimorbidity was more prevalent among men with testosterone deficiency, compared to normal TT in the entire group (36.6% vs 55.2%; p < 0.001); however, differences were only seen within young (testosterone deficiency: 36.4%; normal TT: 13.5%; p < 0.001) and older men (testosterone deficiency: 75.0%; normal TT: 61.5%; p < 0.001). Robust associations were found between the age-specific low-TT (OR: 2.87; 95%CI: 2.14-3.83) and moderate-TT (OR: 1.67; 95%CI: 1.27-2.20) tertiles (reference high-TT) and multimorbidity. Secondary analysis demonstrated that both low TT (OR: 1.82; 95%CI: 1.29-2.55) and moderate-TT (OR: 1.31; 95%CI: 1.01-1.69) were associated with multimorbidity, even after adjusting for obesity (OR: 1.75; 95%CI: 1.07-2.87) and NGS (OR: 1.21 per 0.05 unit lower NGS). Low TT and weakness in men were independently associated with multimorbidity at all ages; however, multimorbidity was more prevalent among young and older men with testosterone deficiency.

Concepts: Incidence, Testosterone, The Association, Prevalence, Analysis, Logistic function, Grip strength

65

A combination of climate events (e.g., low precipitation and high temperatures) may cause a significant impact on the ecosystem and society, although individual events involved may not be severe extremes themselves. Analyzing historical changes in concurrent climate extremes is critical to preparing for and mitigating the negative effects of climatic change and variability. This study focuses on the changes in concurrences of heatwaves and meteorological droughts from 1960 to 2010. Despite an apparent hiatus in rising temperature and no significant trend in droughts, we show a substantial increase in concurrent droughts and heatwaves across most parts of the United States, and a statistically significant shift in the distribution of concurrent extremes. Although commonly used trend analysis methods do not show any trend in concurrent droughts and heatwaves, a unique statistical approach discussed in this study exhibits a statistically significant change in the distribution of the data.

Concepts: Statistics, United States, Precipitation, Climate, Weather, Climate change, Meteorology, Analysis

63

Serious and underappreciated sources of bias mean that extreme caution should be applied when using or interpreting functional enrichment analysis to validate findings from global RNA- or protein-expression analyses.

Concepts: Scientific method, Research methods, Critical thinking, Mathematical analysis, Analysis

62

Statistical analyses presented in general medical journals are becoming increasingly sophisticated. BMC Medicine relies on subject reviewers to indicate when a statistical review is required. We consider this policy and provide guidance on when to recommend a manuscript for statistical evaluation. Indicators for statistical review include insufficient detail in methods or results, some common statistical issues and interpretation not based on the presented evidence. Reviewers are required to ensure that the manuscript is methodologically sound and clearly written. Within that context, they are expected to provide constructive feedback and opinion on the statistical design, analysis, presentation and interpretation. If reviewers lack the appropriate background to positively confirm the appropriateness of any of the manuscript’s statistical aspects, they are encouraged to recommend it for expert statistical review.

Concepts: Medicine, Critical thinking, Statistics, Evaluation, Review, Morality, Analysis, Book review

47

Details about the type of analysis (e.g., intent to treat [ITT]) and definitions (i.e., criteria for including participants in the analysis) are necessary for interpreting a clinical trial’s findings. Our objective was to compare the description of types of analyses and criteria for including participants in the publication (i.e., what was reported) with descriptions in the corresponding internal company documents (i.e., what was planned and what was done). Trials were for off-label uses of gabapentin sponsored by Pfizer and Parke-Davis, and documents were obtained through litigation.

Concepts: Clinical trial, ClinicalTrials.gov, Report, Pfizer, Analysis, Gabapentin, Documents, Description logic

41

In this paper we estimate the minimum prevalence of grapheme-color synesthetes with letter-color matches learned from an external stimulus, by analyzing a large sample of English-speaking grapheme-color synesthetes. We find that at least 6% (400/6588 participants) of the total sample learned many of their matches from a widely available colored letter toy. Among those born in the decade after the toy began to be manufactured, the proportion of synesthetes with learned letter-color pairings approaches 15% for some 5-year periods. Among those born 5 years or more before it was manufactured, none have colors learned from the toy. Analysis of the letter-color matching data suggests the only difference between synesthetes with matches to the toy and those without is exposure to the stimulus. These data indicate learning of letter-color pairings from external contingencies can occur in a substantial fraction of synesthetes, and are consistent with the hypothesis that grapheme-color synesthesia is a kind of conditioned mental imagery.

Concepts: Scientific method, Sample size, Color, Learning, Analysis, Play, Match, Elementary arithmetic