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.     

Treatment of fruit waste leachate using microbial fuel cell: Preservation of agricultural environment

A microbial fuel cell (MFC) was conceived to low electric power production in parallel to valorization of industrial wastes and environment preservation. It consisted of two compartments separated by polymer Nafion membrane, platinum grid as cathode catalyst and graphite rod inoculated with fruit leachate as bio-anode. Owing to its bio-compatibity with bacterial inoculum and chemical stability, Graphite Carbon (GC) was tested as carrier of biofilm using fruit waste inoculum. The maximum power density harvested with this electrode was about 20 mW.m^?2 much greater than that obtained previously with a garden compost inoculum (i.e. 7 mW.m^?2). The difference between the two values may be attributed to the bacterial nature of inoculum utilized. Impressively, upon the addition of 6 mL of fuel (sucrose), the soft porous graphite felt GF yielded voltage (260 mV) which was significantly higher than that of the hard smooth solid GC (i.e. 140 mV). This result makes in evidence the effect of adsorption of the electro-active biofilm onto the surface of the electrode. We ascribe therefore the enhanced power density to a more uniform spread out of the electro-active biofilm within the GF matrix, as verified by higher conductivity obtained with four probe method. The results reported herein highlight the importance of assessing the bio-catalytic activity towards the oxidation of the organic substrate to yield renewable low energy. The experimental data and the differences between the bio-anodes GC and GF were discussed in term of electrochemical techniques such as cyclic voltammetry, impedance spectroscopy and four-probe conductivity. Whatever the nature of the bio-anodes, the overall bacterial colonization still yields low values of clean electric energy compared to highly polluted energy obtained with an alkaline fuel cell.     

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.      

Characterization of the PCR inhibitory effect of bile to optimize real-time PCR detection of Helicobacter species

The inhibitory effect of human and porcine bile samples to detect Helicobacter DNA was studied by adding different concentrations of bile samples to PCR mixtures of six thermostable DNA polymerases containing cagA specific primers and Helicobacter pylori DNA. PCR products were amplified by using the Rotorgene system and SYBR Green I. Among the six DNA polymerases tested, rTth had the lowest sensitivity to bile inhibitors, whereas Taq and Tfl had the highest sensitivity. Bile proteins did not inhibit AmpliTaq DNA polymerase, whereas the fraction containing mainly bile acids and their salts inhibited the amplification capacity of AmpliTaq. Heating human bile at 98 degrees C and adding casein and formamide to the reaction mixture reduced the PCR inhibitory effect of bile. Therefore, a pre-PCR treatment based on dilution and heating of bile, adding casein and formamide to the reaction mixture of rTth DNA polymerase was found efficient to amplify DNA directly in bile.     

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.     

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.     

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.