Interactive text mining with Pipeline Pilot: a bibliographic web-based tool for PubMed.

Text mining has become an integral part of all research in the medical field. Many text analysis software platforms support particular use cases and only those. We show an example of a bibliographic tool that can be used to support virtually any use case in an agile manner. Here we focus on a Pipeline Pilot web-based application that interactively analyzes and reports on PubMed search results. This will be of interest to any scientist to help identify the most relevant papers in a topical area more quickly and to evaluate the results of query refinement. Links with Entrez databases help both the biologist and the chemist alike. We illustrate this application with Leishmaniasis, a neglected tropical disease, as a case study.

Massive mortality of common carp (Cyprinus carpio carpio) in the St. Lawrence River in 2001: diagnostic investigation and experimental induction of lymphocytic encephalitis.

A massive fish kill affecting exclusively common carp (Cyprinus carpio carpio) in the St. Lawrence River, Québec, Canada, during the summer of 2001 was investigated by use of laboratory diagnostic methods and by an attempt to experimentally induce the disease. The ultimate causes of mortality were opportunistic bacterial infections with Aeromonas hydrophila and Flavobacterium sp. secondary to immunosuppression induced by physiologic (i.e., spawning) and environmental (i.e., high temperatures and low water levels) stressors, and possibly enhanced by an infection causing lymphocytic encephalitis observed in 9 of 18 (50%) fish examined. Experimental induction of disease was attempted in captured wild carp by administration of crude and filtered (particulate <0.22 microm) inocula prepared from a homogenate of tissues from carp affected by the natural outbreak. Although significant clinical disease or mortality was not induced by experimental challenge, lymphocytic encephalitis similar to the one observed in naturally affected carp was induced in four of seven (57%) fish administered crude inoculum and four of seven (57%) fish administered filtered inoculum. None of the control fish inoculated with sterile phosphate-buffered saline (n = 6) were affected by encephalitis. The cause of the encephalitis observed in carp from the natural outbreak and in experimentally inoculated fish could not be determined by use of virus isolation and transmission electron microscopy.

Non-additivity in protein-DNA binding.

MOTIVATION: Localizing protein binding sites within genomic DNA is of considerable importance, but remains difficult for protein families, such as transcription factors, which have loosely defined target sequences. It is generally assumed that protein affinity for DNA involves additive contributions from successive nucleotide pairs within the target sequence. This is not necessarily true, and non-additive effects have already been experimentally demonstrated in a small number of cases. The principal origin of non-additivity involves the so-called indirect component of protein-DNA recognition which is related to the sequence dependence of DNA deformation induced during complex formation. Non-additive effects are difficult to study because they require the identification of many more binding sequences than are normally necessary for describing additive specificity (typically via the construction of weight matrices). RESULTS: In the present work we will use theoretically estimated binding energies as a basis for overcoming this problem. Our approach enables us to study the full combinatorial set of sequences for a variety of DNA-binding proteins, make a detailed analysis of non-additive effects and exploit this information to improve binding site predictions using either weight matrices or support vector machines. The results underline the fact that, even in the presence of significant deformation, non-additive effects may involve only a limited number of dinucleotide steps. This information helps to reduce the number of binding sites which need to be identified for successful predictions and to avoid problems of over-fitting. AVAILABILITY: The SVM software is available upon request from the authors.

Pattern of cadmium contamination in the liver and kidneys of moose and white-tailed deer in Québec.

Samples of moose (N = 431) and white-tailed deer (N = 225) liver and kidneys were collected during the 1985 hunting season from 14 zones south of the 50 degree latitude in Québec. Regional differences in cadmium level in the liver were detected and three homogeneous areas were delineated for each species. Uptake was greater for moose than for deer: in the liver, mean concentrations were 2.9-15.9 mg kg-1 (dry weight) for moose and 0.8-2.6 for deer, depending on the area and sex; in kidneys, means ranged between 31.8-100.5 and 20.9-39.0 mg kg-1, respectively. Female moose had lower levels than bulls. Less affected moose, in eastern Québec, contained cadmium concentrations comparable to the highest values measured in Scandinavia. Cadmium uptake in deer was on the same level or higher than in the United States. Our results indicate a widespread presence of this heavy metal in the environment that may be linked to acid precipitation. We do not recommend consuming wild cervid liver or kidneys in Québec for the moment. Further research is needed on the overall mechanisms involved in the cadmium contamination of the environment and on the actual intake of this metal in the human diet.