Statistical modeling of biomedical corpora: mining the Caenorhabditis Genetic Center Bibliography for genes related to life span

Background  

The statistical modeling of biomedical corpora could yield integrated, coarse-to-fine views of biological phenomena that complement discoveries made from analysis of molecular sequence and profiling data. Here, the potential of such modeling is demonstrated by examining the 5,225 free-text items in the Caenorhabditis Genetic Center (CGC) Bibliography using techniques from statistical information retrieval. Items in the CGC biomedical text corpus were modeled using the Latent Dirichlet Allocation (LDA) model. LDA is a hierarchical Bayesian model which represents a document as a random mixture over latent topics; each topic is characterized by a distribution over words.     

'It's really a myriad of different signals, not just the textbook': the complexities of diagnosing depression in gay men in general practice

This paper reports on in-depth interviews with general practitioners (GPs) about their views and experiences of diagnosing depression in gay men - some of whom are living with HIV - and the broader social contexts in which such a diagnosis is located. This analysis is a key outcome of a collaboration between social researchers, primary healthcare researchers, GPs and community partners, to investigate the management of depression in gay men in primary care settings. As the qualitative component of this project, semi-structured in-depth interviews were conducted with 16 GPs with high caseloads of gay men, in three geographical settings in Australia: Sydney, Adelaide and a rural-coastal town. GPs considered the diagnosis and management of depression to be an integral part of primary care, especially in gay male patients. They had a heightened sense of awareness that depression was common in the group of patients they were seeing. Central to diagnosing depression was the ongoing, long-term relationship GPs had with their gay male patients. GPs were vigilant and proactively inquired about depression, taking into account somatic, social and psychological indicators. In their approach to diagnosing depression, GPs considered not only the life circumstances of individual patients but also the broader social context of stigma related to homosexuality, and the effects that the HIV epidemic has had on individuals, especially on gay men who have been living with HIV for a long time.     

Estimating the rate of evolution of the rate of molecular evolution

A simple model for the evolution of the rate of molecular evolution is presented. With a Bayesian approach, this model can serve as the basis for estimating dates of important evolutionary events even in the absence of the assumption of constant rates among evolutionary lineages. The method can be used in conjunction with any of the widely used models for nucleotide substitution or amino acid replacement. It is illustrated by analyzing a data set of rbcL protein sequences.      

Evaluation of a candidate International Standard for Meningococcal Group C polysaccharide

Meningococcal group C (MenC) plain polysaccharide (PS) and conjugate vaccines are primarily evaluated by physicochemical methods to ensure that batches are consistently manufactured. As different assays are employed to quantify the MenC PS content of final formulations and bulk intermediaries, there is a need for an International MenC PS Standard to calibrate internal references used in the different laboratories. Twelve laboratories from nine different countries participated in a collaborative study to determine the MenC PS content of a candidate International Standard MenC PS preparation (08/214) and to assess its suitability. On the basis of the results from this study the candidate standard 08/214 was established as an International Standard for the quantification of MenC PS content in vaccines and components. It has a content of 1.192 ± 0.192 mg MenC PS/ampoule (expanded uncertainty with coverage factor of k = 2.365 corresponding to a 95% level of confidence), as determined by the resorcinol assays carried out by eight of the participating laboratories. The standard is available from The National Institute of Biological Standards and Control who act as guardians and distributors of the material under the auspices of WHO.     

Ensemble attribute profile clustering: discovering and characterizing groups of genes with similar patterns of biological features

Background  

Ensemble attribute profile clustering is a novel, text-based strategy for analyzing a user-defined list of genes and/or proteins. The strategy exploits annotation data present in gene-centered corpora and utilizes ideas from statistical information retrieval to discover and characterize properties shared by subsets of the list. The practical utility of this method is demonstrated by employing it in a retrospective study of two non-overlapping sets of genes defined by a published investigation as markers for normal human breast luminal epithelial cells and myoepithelial cells.     

Australian Gay and Bisexual Men’s Attitudes to HIV Treatment as Prevention in Repeated,National Surveys, 2011-2013

Objective

Assess the acceptability of HIV treatment as prevention and early antiretroviral treatment among gay and bisexual men in Australia and any changes in attitudes over time.

Methods

National, online, cross-sectional surveys of gay and bisexual men were repeated in 2011 and 2013. Changes in attitudes to HIV treatment over time were assessed with multivariate analysis of variance. The characteristics of men who agreed that HIV treatment prevented transmission and thought that early treatment was necessary were identified with multivariate logistic regression.

Results

In total, 2599 HIV-negative, untested and HIV-positive men participated (n = 1283 in 2011 and n = 1316 in 2013). Attitudes changed little between 2011 and 2013; most participants remained sceptical about the preventative benefits of HIV treatment. In 2013, only 2.6% of men agreed that HIV treatment prevented transmission; agreement was associated with being HIV-positive, having an HIV-positive regular partner, and having received HIV post-exposure prophylaxis. In contrast, 71.8% agreed that early antiretroviral treatment is necessary; younger men were more likely and HIV-positive men and participants with HIV-positive partners were much less likely to agree with this.

Conclusions

Promoting the individual health benefits of HIV treatment rather than its preventative benefits remains more acceptable to Australian gay and bisexual men.     

Seeing without being seen: a removal experiment with mixed flocks of Willow and Crested Tits Parus montanus and cristatus

This paper tests the hypothesis that foraging site selection reflects a trade-off between the various needs for concealment from predators, to find food, and for the individual to maintain some view of its surroundings. After removal of Crested Tits Parus cristatus (the dominant species in mixed flocks), Willow Tits P. montanus did not decrease their foraging heights as expected but remained in the most exposed parts of young pines. In contrast, after removal of Willow Tits, Crested Tits increased their foraging height from the sheltered lower canopy to sites previously occupied by Willow Tits. When flock size was reduced, the birds maintained the same high levels of vigilance without concealing themselves in dense vegetation. I suggest that flock members may benefit from foraging in sites that afford good anti-predator vigilance.     

Rates of depression among men attending high-HIV-caseload general practices in Australia

This paper compares rates of current depression among men attending high-HIV-caseload general practices in New South Wales and South Australia. Current depression was assessed by the treating general practitioner (GP), using the nine-item Patient Health Questionnaire (PHQ-9), and by patient self-reporting. The study found that GPs, the PHQ-9 screening tool and patients were equally likely to identify current depression. High rates of depression were observed among the men attending general practice, with the highest rates among men with HIV and men who did not identify as either heterosexual or homosexual.     

Influence of Boar and Semen Parameters on Motility and Acrosome Integrity in Liquid Boar Semen Stored for Five Days

Ninety ejaculates from a total of 76 AI boars were extended in Beltsville Thawing Solution (BTS). Boar identity, breed, weight of the ejaculate and sperm concentration were registered. Motility and acrosome integrity were assessed after storage at 16–18°C for 6, 30, 54, 78, and 102 h. Storage time had a significant influence on both motility (p < 0.01) and acrosome integrity (p < 0.001). The Least Square Means for percentage of motility showed a small decline from 79.8% after 6 h of storage to 78.4% at 102 h. Motility at 78 and 102 h was significantly different from motility at 6 h (p < 0.05). The percentage of sperm cells with normal acrosomes declined throughout the experiment. The Least Square Means for 6, 30, 54, 78, and 102 h of storage were 93.9%, 90.6%, 88.0%, 84.8%, and 78.2%, respectively. The decrease in acrosome integrity from one storage time to the next was highly significant throughout the trial (p < 0.001). There was a significant influence of boar (p < 0.001) and sperm concentration (p < 0.01) on motility, while acrosome integrity was affected only by boar (p < 0.001). Breed of the boars and weight of the ejaculate did not influence the dependent variables.