In this article, we present CoPub 5.0, a publicly available text mining system, which uses Medline abstracts to calculate robust statistics for keyword co-occurrences. CoPub was initially developed for the analysis of microarray data, but we broadened the scope by implementing new technology and new thesauri. In CoPub 5.0, we integrated existing CoPub technology with new features, and provided a new advanced interface, which can be used to answer a variety of biological questions. CoPub 5.0 allows searching for keywords of interest and its relations to curated thesauri and provides highlighting and sorting mechanisms, using its statistics, to retrieve the most important abstracts in which the terms co-occur. It also provides a way to search for indirect relations between genes, drugs, pathways and diseases, following an ABC principle, in which A and C have no direct connection but are connected via shared B intermediates. With CoPub 5.0, it is possible to create, annotate and analyze networks using the layout and highlight options of Cytoscape web, allowing for literature based systems biology. Finally, operations of the CoPub 5.0 Web service enable to implement the CoPub technology in bioinformatics workflows. CoPub 5.0 can be accessed through the CoPub portal http://www.copub.org. © 2011 The Author(s).
To gain insight into changes of scholarly journals’ recommendations, we conducted a systematic review of studies that analysed journals’ Instructions to Authors (ItAs). We summarised results of 153 studies, and meta-analysed how often ItAs addressed: 1) authorship, 2) conflicts of interest, 3) data sharing, 4) ethics approval, 5) funding disclosure, and 6) International Committee of Medical Journal Editors’ Uniform Requirements for Manuscripts. For each topic we found large between-study heterogeneity. Here, we show six factors that explained most of that heterogeneity: 1) time (addressing of topics generally increased over time), 2) country (large differences found between countries), 3) database indexation (large differences found between databases), 4) impact factor (topics were more often addressed in highest than in lowest impact factor journals), 5) discipline (topics were more often addressed in Health Sciences than in other disciplines), and 6) sub-discipline (topics were more often addressed in general than in sub-disciplinary journals).
Rationale: A higher protein intake is suggested to preserve muscle mass during aging, and may therefore reduce the risk for sarcopenia. We explored whether the amount, type (animal/vegetable) and essential amino acid (EAA) composition of protein intake were associated with 5-year change in mid-thigh muscle cross-sectional area (CSA) in older adults.Methods: Protein intake was assessed at year 2 by a Block food frequency questionnaire in 2,597 participants of the Health ABC study, aged 70–79 y. At year 1 and year 6 mid-thigh muscle CSA (cm2) was measured by computed tomography. Multiple linear regression analysis was used to examine the association between energy adjusted protein residuals (total, animal and vegetable protein) and muscle CSA at year 6, adjusted for muscle CSA at year 1 and potential confounders including prevalent health conditions, physical activity and 5-year change in fat mass. EAAintake was expressed as percentage of total protein intake.Results: Mean protein intake was 0.90 (SD 0.36) g/kg/d and mean 5-year change in muscle CSA was −9.8 (17.0) cm2 (n = 1,561). No association was observed between energy adjusted total (β = −0.00 cm2 ; SE = 0.03; P = 0.98), animal (β = −0.00 cm2; SE = 0.03; P = 0.92), and plant (β = +0.07 cm2; SE = 0.07; P = 0.291) protein intake and muscle CSA at year 6, adjusted for baseline mid-thigh muscle area and potential confounders. No associations were observed for the EAAs.Conclusion: A higher total, animal or vegetable protein intake was not associated with 5 year change in mid-thigh cross sectional area in older adults. This conclusion contradicts some, but not all previous research, therefore optimal protein intake for older adults is currently not known.
