Biological Literature (biological + literature)

Distribution by Scientific Domains

Selected Abstracts

The Candida Genome Database: Facilitating research on Candida albicans molecular biology

Maria C. Costanzo
Abstract The Candida Genome Database (CGD; is a resource for information about the Candida albicans genomic sequence and the molecular biology of its encoded gene products. CGD collects and organizes data from the biological literature concerning C. albicans, and provides tools for viewing, searching, analysing, and downloading these data. CGD also serves as an organizing centre for the C. albicans research community, providing a gene-name registry, contact information, and research community news. This article describes the information contained in CGD and how to access it, either from the perspective of a bench scientist interested in the function of one or a few genes, or from the perspective of a biologist or bioinformatician interpreting large-scale functional genomic datasets. [source]

Contributions of ethnobiology to the conservation of tropical rivers and streams

R.A.M. Silvano
Abstract 1.This study aimed to link basic ethnobiological research on local ecological knowledge (LEK) to the conservation of Brazilian streams, based on two case studies: original data on LEK of fishermen about freshwater fish in the Negro River, Amazon, and previously published data about LEK of farmers on the ecological relationship between forest and streams in the Macabuzinho catchment, Atlantic Forest. 2.Information was obtained from fishermen through interviews using standard questionnaires containing open-ended questions. Informants for interview were selected either following some defined criteria or applying the ,snowball' method. 3.Fishermen's LEK about the diets and habitats of 14 fish species in the Negro River provided new biological information on plant species that are eaten by fish, in addition to confirming some ecological patterns from the biological literature, such as dependence of fish on forests as food sources. 4.In the Atlantic Forest, a comparison between farmers' LEK and a rapid stream assessment in the farmers' properties indicated that farmers tended to overestimate the ecological integrity of their streams. Farmers recognized at least 11 forest attributes that correspond to the scientific concept of ecosystem services. Such information may be useful to promote or enhance dialogue among farmers, scientists and managers. 5.These results may contribute to the devising of ecosystem management measures in the Negro River, aimed to conserve both rivers and their associated floodplain forests, involving local fishermen. In the Atlantic Forest, we proposed some initiatives, such as to allow direct economic use of their forests to conciliate conflicting perceptions of farmers about ecological benefits versus economic losses from reforestation. Despite their cultural, environmental and geographical differences, the two study cases are complementary and cost-effective and promising approaches to including LEK in the design of ecological research. Copyright 2007 John Wiley & Sons, Ltd. [source]

Publication bias in ecology and evolution: an empirical assessment using the ,trim and fill' method

ABSTRACT Recent reviews of specific topics, such as the relationship between male attractiveness to females and fluctuating asymmetry or attractiveness and the expression of secondary sexual characters, suggest that publication bias might be a problem in ecology and evolution. In these cases, there is a significant negative correlation between the sample size of published studies and the magnitude or strength of the research findings (formally the ,effect size'). If all studies that are conducted are equally likely to be published, irrespective of their findings, there should not be a directional relationship between effect size and sample size; only a decrease in the variance in effect size as sample size increases due to a reduction in sampling error. One interpretation of these reports of negative correlations is that studies with small sample sizes and weaker findings (smaller effect sizes) are less likely to be published. If the biological literature is systematically biased this could undermine the attempts of reviewers to summarise actual biology relationships by inflating estimates of average effect sizes. But how common is this problem? And does it really effect the general conclusions of literature reviews? Here, we examine data sets of effect sizes extracted from 40 peer-reviewed, published meta-analyses. We estimate how many studies are missing using the newly developed ,trim and fill' method. This method uses asymmetry in plots of effect size against sample size (,funnel plots') to detect ,missing' studies. For random-effect models of meta-analysis 38% (15/40) of data sets had a significant number of ,missing' studies. After correcting for potential publication bias, 21% (8/38) of weighted mean effects were no longer significantly greater than zero, and 15% (5/34) were no longer statistically robust when we used random-effects models in a weighted meta-analysis. The mean correlation between sample size and the magnitude of standardised effect size was also significantly negative (rs=-0.20, P < 0-0001). Individual correlations were significantly negative (P < 0.10) in 35% (14/40) of cases. Publication bias may therefore effect the main conclusions of at least 15,21% of meta-analyses. We suggest that future literature reviews assess the robustness of their main conclusions by correcting for potential publication bias using the ,trim and fill' method. [source]

Should amenorrhea be a diagnostic criterion for anorexia nervosa?

Evelyn Attia MD
Abstract Objective: The removal of the amenorrhea criterion for anorexia nervosa (AN) is being considered for the fifth edition of The Diagnostic and Statistical Manual (DSM-V). This article presents and discusses the arguments for maintaining as well as those for removing the criterion. Method: The psychological and biological literatures on the utility of amenorrhea as a distinguishing diagnostic criterion for AN and as an indicator of illness severity are reviewed. Results: The findings suggest that the majority of differences among patients with AN who do and do not meet the amenorrhea criterion appear largely to reflect nutritional status. Overall, the two groups have few psychological differences. There are mixed findings regarding biological differences between those with AN who do and do not menstruate and the relationship between amenorrhea and bone health among patients with AN. Discussion: Based on these findings, one option is to describe amenorrhea in DSM-V as a frequent occurrence among individuals with AN that may provide important information about clinical severity, but should not be maintained as a core diagnostic feature. The possibilities of retaining the criterion or eliminating it altogether are discussed. 2009 American Psychiatric Association. Int J Eat Disord 2009 [source]