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.     

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.     

Multislice spiral computed tomography in the planning of transcatheter aortic valve replacement

Surgical treatment for aortic valve (AV) pathology is an urgent and important problem of modern medicine. The prevalence of valve disease is great and remains steadily high in the population. Due to a large number of patients who cannot undergo open AV surgery, alternative hybrid treatments are recently being actively improved. Multislice spiral computed tomography (MSCT) is mandatory prior to transcatheter AV replacement as the examination results determine if a hybrid treatment can be performed and the access is transfemoral or transapical. MSCT provides the data necessary to determine the sizes and types of AV prostheses. The application of the current systems of 320-640 spiral tomographs will further improve MSCT as the method of choice in examining patients before transcatheter AV replacement.     

Capacities of multidetector spiral computed tomography in the planning and postoperative examination of patients undergoing coronary artery bypass surgery

Multiple investigations show that multidetector spiral computed tomography (MSCT) bypass grafting becomes an alternative to invasive coronary angiography in detecting coronary graft stenoses and occlusions. The investigation retrospectively estimated the patency of aortocoronary and mammary coronary artery anastomoses by MSCT bypass grafting. Examinations were made in 85 (326 anastomoses) patients who had undergone aortocoronary and mammary coronary artery bypass surgery and had MSCT bypass grafting within 3 years after the surgery. In the first year following the surgery, 18 patients with graft stenotic changes, as evidenced by MSCT, underwent intervention coronary angiography, the sensitivity and specificity of which was 100%. The results of clinical and instrumental examinations were also compared with graft incompetence, as shown on MSCT that revealed that MSCT bypass grafting was the only noninvasive technique to evaluate early coronary graft closure both in the absence of clear signs of myocardial ischemia according to the data of exercise tests and in the presence of recurrent angina pectoris.     

Cryopreservation of hemopoietic tissue aimed at reducing immunological reactivity

A method has been developed of decreasing immunologic activity of lymphocytes from spleen, lymph nodes, and bone marrow (freshly collected or frozen) with a high percentage of intact stem cells. In experiments in vivo on lethally irradiated mice, it was demonstrated that during combined transplantation to the recipients of preserved bone marrow from two genetically different donors, a rapid decrease or absence of the effect of inactivation of hemopoietic stem cells under the influence of allogeneic lymphocytes was observed in the mixed graft. When it is necessary to transplant large quantities of bone marrow from several genetically different donors, the use of cryopreserved bone marrow is preferable to freshly drawn marrow due to the higher proliferative activity and the decreased risk in the development of immunological reactions.     

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.