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.     

The shape of human gene family phylogenies

Background  

The shape of phylogenetic trees has been used to make inferences about the evolutionary process by comparing the shapes of actual phylogenies with those expected under simple models of the speciation process. Previous studies have focused on speciation events, but gene duplication is another lineage splitting event, analogous to speciation, and gene loss or deletion is analogous to extinction. Measures of the shape of gene family phylogenies can thus be used to investigate the processes of gene duplication and loss. We make the first systematic attempt to use tree shape to study gene duplication using human gene phylogenies.     

Seasonal sex–specific energy expenditure in breeding and non-breeding Palestine sunbirds Nectarinia osea

The timing of the chick‐rearing phase is known to have a profound effect on the reproductive success of birds. However, little is known about the energetic costs faced by the parents during different periods of the breeding season. These costs may have vital consequences for both their survival and future reproduction. In most studies, daily energy expenditure (DEE) of breeding and non‐breeding birds has been compared, without controlling for the effect of season. In the present study, we examined the energy demands of breeding compared to non‐breeding Palestine sunbirds Nectarinia osea and whether there were sex‐specific differences in DEE within and between different seasons. We predicted that DEE would be elevated when birds rear chicks, especially at cooler ambient temperatures. Time‐energy budgets were constructed for pairs of sunbirds, rearing chicks, or not breeding, in spring and summer. There were significant seasonal differences in estimates of DEE in non‐breeders that were 21% higher in spring than in summer. We attributed these to increases in non‐flight metabolic rate rather than changes in time spent on different activities. Our estimates of DEE for the birds that were rearing chicks were higher than non‐breeding adults. In females the increase in DEE when breeding, compared to when not breeding, was similar in both spring and summer, while males increased their DEE much less when breeding in spring. The differences in estimated DEE, however, were not significant between male and female birds in any season. Between seasons, female breeders had 17.1% higher DEE in spring than in summer, while male breeders showed no difference in DEE when rearing chicks in different seasons. Accordingly, our initial prediction was supported, as DEE in chick‐rearing adults was higher than in non‐breeding adults. In addition, although temperatures are lower in spring, breeding in the spring is only more costly than breeding in summer for females. Apparently, males are more flexible in reallocating their time and energy spent on different activities.     

Quality determination and the repair of poor quality spots in array experiments

Background  

A common feature of microarray experiments is the occurence of missing gene expression data. These missing values occur for a variety of reasons, in particular, because of the filtering of poor quality spots and the removal of undefined values when a logarithmic transformation is applied to negative background-corrected intensities. The efficiency and power of an analysis performed can be substantially reduced by having an incomplete matrix of gene intensities. Additionally, most statistical methods require a complete intensity matrix. Furthermore, biases may be introduced into analyses through missing information on some genes. Thus methods for appropriately replacing (imputing) missing data and/or weighting poor quality spots are required.     

A Taxonomic Search Engine: Federating taxonomic databases using web services

Background  

The taxonomic name of an organism is a key link between different databases that store information on that organism. However, in the absence of a single, comprehensive database of organism names, individual databases lack an easy means of checking the correctness of a name. Furthermore, the same organism may have more than one name, and the same name may apply to more than one organism.     

Radiographic joint damage in rheumatoid arthritis is associated with differences in cartilage turnover and can be predicted by serum biomarkers: an evaluation from 1 to 4 years after diagnosis

Introduction  

The objective of this study was to determine whether serum biomarkers for degradation and synthesis of the extracellular matrix of cartilage are associated with, and can predict, radiographic damage in patients with rheumatoid arthritis (RA).     

Measuring energy expenditure in birds using bolus injections of 13C-labelled Na-bicarbonate

The ¹³C-labelled Na-bicarbonate technique uses stable isotopes to measure energy expenditure in birds. After administration, the isotopes reach equilibrium within the body's bicarbonate pools at a fast rate due to the small size of the bicarbonate pool in relation to CO₂ flux. This technique is therefore ideal for measuring energy expenditure over short-term activities. The major advantage of this technique is that it can be applied without the animal having to wear a respirometry mask or being enclosed in a respirometry chamber. Despite the technique's suitability for use in birds and other animals, there have been few studies that have used it to date and so its potential is not fully understood. Here we discuss the methodology and review previous applications.