Extraction of Transcript Diversity from Scientific Literature

Transcript diversity generated by alternative splicing and associated mechanisms contributes heavily to the functional complexity of biological systems. The numerous examples of the mechanisms and functional implications of these events are scattered throughout the scientific literature. Thus, it is crucial to have a tool that can automatically extract the relevant facts and collect them in a knowledge base that can aid the interpretation of data from high-throughput methods. We have developed and applied a composite text-mining method for extracting information on transcript diversity from the entire MEDLINE database in order to create a database of genes with alternative transcripts. It contains information on tissue specificity, number of isoforms, causative mechanisms, functional implications, and experimental methods used for detection. We have mined this resource to identify 959 instances of tissue-specific splicing. Our results in combination with those from EST-based methods suggest that alternative splicing is the preferred mechanism for generating transcript diversity in the nervous system. We provide new annotations for 1,860 genes with the potential for generating transcript diversity. We assign the MeSH term “alternative splicing” to 1,536 additional abstracts in the MEDLINE database and suggest new MeSH terms for other events. We have successfully extracted information about transcript diversity and semiautomatically generated a database, LSAT, that can provide a quantitative understanding of the mechanisms behind tissue-specific gene expression. LSAT (Literature Support for Alternative Transcripts) is publicly available at http://www.bork.embl.de/LSAT/

Histomorphology of the Hypothalamo – Neurosecretory System of the Indian Scad, Decapterus tabl (Berry)

Hypothalamo-neurosecretory complex of Decapterus fabl consists mainly of the nucleus preopticus (NPO), nucleus lateral is tuberis (NL T) and their zonal tracts. The neurosecretory cells of NPO are generally bipolar and stain readily with aldehyde fuchsin (AF) and chrom-alum -hematoxylin-phloxine (CAPH) but they are also positive to acid fuchsin in Mallory's triple stain. NPO is a paired structure situated on either side of the third ventricle antero-dorsal to the optic chiasma. It is highly vascularized structure and looks inverted L.-shape in the sagittal section

Rejection of Cowbird Eggs by Mourning Doves: A Manifestation of Nest Usurpation? Brian D. Peer and Eric K. Bollinger

This article was printed in The Auk, Volume 115, No.4 (1998)

EXPLANATIONS FOR THE INFREQUENT COWBIRD PARASITISM ON COMMON GRACKLES

We determined the factors responsible for the lack of parasitism on Common Grackles (Quiscalus quiscula) by Brown-headed Cowbirds (Molothrus ater). We found no evidence of parasitism on the 401 grackle nests we monitored in east-central Illinois. By the time cowbirds began laying eggs, 88.5% of all grackle nests were beyond the point of successful parasitism. Grackles rejected cowbird eggs more frequently during the prelaying stage of the nesting cycle (38.2%) compared to later stages (12.3%). Thirty-three cowbird eggs and nestlings were cross-fostered into grackle nests. Data were collected on 15 cowbird nestlings, of which three fledged. The cross-fostered cowbird eggs that did not hatch appeared to have been incubated ineffectively. These eggs were in clutches that contained four to six eggs, whereas the cowbird eggs that hatched were in clutches of three eggs or less. Grackles also responded more aggressively toward female cowbird models than to Fox Sparrow (Passerella iliaca) models in five of seven response categories. Cowbirds avoid parasitizing grackles even though the opportunity existed. Nest abandonment and infestation of grackle nests with ectoparasitic mites may decrease the suitability of grackles as hosts; however the primary reason for the infrequent cowbird parasitism on grackles appears to be past rejection behavior. Grackles likely rejected cowbird eggs at a higher frequency in the past and as a consequence grackles were avoided by cowbirds. Rejection apparently decreased in the absence of parasitism due to the high degree of intraclutch egg variability exhibited by grackles whiwhich would increase the chances of them mistakenly rejecting their own discordant eggs

Branchial, renal and hepatic lesions in an estuarine mullet, Liza parsia Hamilton - Buchanan, induced by sublethal exposure to BHC

Gill of Liza parsia exposed to sublethal concentration (0.5 ppm) of BHC responded initially with the copious secretion of mucus followed by oedematous separation of epithelial lining cells from the basement membrane. Fusion of secondary gill lamellae, tissue hyperplasia and multiple telangiectases (aneurysms) were noticed on day 10 of the exposure. By day 15, the entire interlamellar spaces became filled with the hyperplastic epithelium. Kidney revealed an initial hypertrophy of the cells lining proximal convoluted tubules followed by shrinkage in the glomerular tufts resulting in the increase of Bowman's space and oedema. Tubulonecrosis, hyperemia and fibrosis were noticed in the reneal tissue after day 19 of BHC intoxication. Exposure to BHC elicited an initial dilation of bile canaliculi, enhanced secretion of bile and cellular hypertophy on day 4. Necrotic changes like excessive vacuolation, and karyorrhexis and karyolysis were seen on day 8. By day 10 and 15, complete vacuolation of hepatocytes, pycnosis of nuclei and focal necrosis were noticed

A Multi-Factor User Interface Components Layout Problem

This paper presents a multi-factor layout model which combines the qualitative and quantitative factors for the facilities layout problem.  The proposed model is applied to the design of the user interface in order to obtain the best layout of the facilities in which the closeness rating scores are evaluated by using the Goals, Operators, Methods, and Selection (GOMS) technique. The results of the proposed model are compared with that of an existing model to obtain the layouts of user interface components. The model developed here has significant relevance for facility layout design in achieving an optimal interface by structuring the layout of a building to enhance and support production. The user interface model provides support for quick response to changes in customer demand and inventory planning particularly in such an area where timely transfer of information is crucial

Layout design of user interface components with multiple objectives

A multi-goal layout problem may be formulated as a Quadratic Assignment model, considering multiple goals (or factors), both qualitative and quantitative in the objective function. The facilities layout problem, in general, varies from the location and layout of facilities in manufacturing plant to the location and layout of textual and graphical user interface components in the human–computer interface. In this paper, we propose two alternate mathematical approaches to the single-objective layout model. The first one presents a multi-goal user interface component layout problem, considering the distance-weighted sum of congruent objectives of closeness relationships and the interactions. The second one considers the distance-weighted sum of congruent objectives of normalized weighted closeness relationships and normalized weighted interactions. The results of first approach are compared with that of an existing single objective model for example task under consideration. Then, the results of first approach and second approach of the proposed model are compared for the example task under consideration

A Multi-Factor User Interface Components Layout Problem

This paper presents a multi-factor layout model which combines the qualitative and quantitative factors for the facilities layout problem.  The proposed model is applied to the design of the user interface in order to obtain the best layout of the facilities in which the closeness rating scores are evaluated by using the Goals, Operators, Methods, and Selection (GOMS) technique. The results of the proposed model are compared with that of an existing model to obtain the layouts of user interface components. The model developed here has significant relevance for facility layout design in achieving an optimal interface by structuring the layout of a building to enhance and support production. The user interface model provides support for quick response to changes in customer demand and inventory planning particularly in such an area where timely transfer of information is crucial

Cortisol administration enhances the coupling of midfrontal delta and beta oscillations

Wetensch. publ. refereedFaculteit der Sociale Wetenschappe