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Biomedical subjects

A Zell

Publications and source records attributed to A Zell.

12 recordsLinked to original sources
PubMed2006

JCell--a Java-based framework for inferring regulatory networks from time series data.

MOTIVATION: JCell is a Java-based application for reconstructing gene regulatory networks from experimental data. The framework provides several algorithms to identify genetic and metabolic dependencies based on experimental data conjoint with mathematical models to describe and simulate regulatory systems. Owing to the modular structure, researchers can easily implement new methods. JCell is a pure Java application with additional scripting capabilities and thus widely usable, e.g. on parallel or cluster computers. AVAILABILITY: The software is freely available for download at http://www-ra.informatik.uni-tuebingen.de/software/JCell.

Algorithms↗
PubMed2004

ParSeq: searching motifs with structural and biochemical properties.

SUMMARY: Searches for variable motifs such as protein-binding sites or promoter regions are more complex than the search for casual motifs. For example, in amino acid sequences comparing motifs alone mostly proves to be insufficient to detect regions that represent proteins with a special function, because the function depends on biochemical properties of individual amino acids (such as polarity or hydrophobicity). Pure string matching programs are not able to find these motifs; hence, we developed ParSeq, a program that combines the search for motifs with certain structural properties, the verification of biochemical properties, an approximate search mechanism and a stepwise creation of the motif description by allowing to search on previously obtained results. AVAILABILITY: http://www-pr.informatik.uni-tuebingen.de/parseq

Algorithms↗
PubMed2004

Gene expression patterns of epithelial cells modulated by pathogenicity factors of Yersinia enterocolitica.

Epithelial cells express genes whose products signal the presence of pathogenic microorganisms to the immune system. Pathogenicity factors of enteric bacteria modulate host cell gene expression. Using microarray technology we have profiled epithelial cell gene expression upon interaction with Yersinia enterocolitica. Yersinia enterocolitica wild-type and isogenic mutant strains were used to identify host genes modulated by invasin protein (Inv), which is involved in enteroinvasion, and Yersinia outer protein P (YopP) which inhibits innate immune responses. Among 22 283 probesets (14,239 unique genes), we found 193 probesets (165 genes) to be regulated by Yersinia infection. The majority of these genes were induced by Inv, whose recognition leads to expression of NF-kappa B-regulated factors such as cytokines and adhesion molecules. Yersinia virulence plasmid (pYV)-encoded factors counter regulated Inv-induced gene expression. Thus, YopP repressed Inv-induced NF-kappa B regulated genes at 2 h post infection whereas other pYV-encoded factors repressed host cell genes at 4 and 8 h post infection. Chromosomally encoded factors of Yersinia, other than Inv, induced expression of genes known to be induced by TGF-beta receptor signalling. These genes were also repressed by pYV-encoded factors. Only a few host genes were exclusively induced by pYV-encoded factors. We hypothesize that some of these genes may contribute to pYV-mediated silencing of host cells. In conclusion, the data demonstrates that epithelial cells express a limited number of genes upon interaction with enteric Yersinia. Both Inv and YopP appear to modulate gene expression in order to subvert epithelial cell functions involved in innate immunity.

Adhesins, Bacterial↗
PubMed2001

[Bilateral kidney tumor. Therapy management and histopathological results with long-term follow-up of 66 patients].

Bilateral renal cell carcinoma is detected at an incidence rate of 1.6-6% of all renal tumors. The management, histopathological results and the long-term follow-up of 66 patients with bilateral renal cell carcinoma (29 synchronous, 37 asynchronous tumors) are presented in this issue. The incidence rate of bilateral renal cell carcinoma (RCC) at our hospital was 3.5%. Nephron-sparing surgery should be used first for the smaller and favourably located tumor when radical nephrectomy of the contralateral tumor is necessary. Thus, the patients can be spared dialysis. The histopathological results showed a significantly higher incidence rate of chromophil RCCs in cases of synchronous bilateral renal tumors (36%). The 5-year survival rate was 82%. Patients with asynchronous renal cell carcinomas were significantly younger than those with synchronous RCCs (median age: 60.2 years). The histopathological results were similar to unilateral renal cell carcinomas. Clear cell carcinoma was detected in 70% of cases. The 5-year survival rate was 61% and lower than that of synchronous tumors (82%). There was no significant difference because of the small number of cases. Current standardised techniques of nephron-sparing surgery achieve good survival rates, therefore making bilateral nephrectomy only necessary in very poor cases. In cases of chromophil renal cell carcinomas, the contralateral kidney should always be carefully examined, because these tumors were significantly more often detected to be bilateral. The risk of also developing a tumor in the contralateral kidney increases with decreasing age at first manifestation (< 55 years, 6%). Especially in those younger than 55 years, partial nephrectomy seems to be recommended for unilateral renal tumors in patients with a normal contralateral kidney (tumor size < 4 cm in diameter).

Adenocarcinoma, Clear Cell↗
PubMed1998

Bioelectronic noses: a status report. Part II.

The present state of the art to record or to mimic electronically the human senses of olfaction and taste is characterized. In this part II, strategies are outlined to utilize chemical and biological structures with their different complexities which serve as sensor elements in (bio-) electronic noses. Finally a survey is given on the computer-science aspects of odor recognition based on these elements.

Animals↗
PubMed1995

A parallel neural network simulator on the connection machine CM-5.

We here present a parallel implementation of artificial neural networks on the connection machine CM-5 and compare it with other parallel implementations on SIMD and MIMD architectures. This parallel implementation was developed with the goal of efficiently training large neural networks with huge training pattern sets for applications in molecular biology, in particular the prediction of coding regions in DNA sequences. The implementation uses training pattern parallelism and makes use of the parallel I/O facilities of the CM-5 and its efficient reduction operations available within the control network to achieve a high scalability. The parallel simulator obtains a maximum speed of 149.25 MCUPS for training feedforward networks with backpropagation on a 512 processor CM-5 system without using the CM-5 vector facility. The implementation poses no restriction on the type of network topology and works with different batch training algorithms like BP. Quickprop and Rprop.

Algorithms↗
PubMed1985

Model for calcium binding to gamma-carboxyglutamic acid residues of proteins: crystal structure of calcium alpha-ethylmalonate.

The crystal structure of a Ca2+ salt of alpha-ethylmalonic acid was determined from three-dimensional X-ray diffraction data. The dicarboxylate anion represents the functional side chain of gamma-carboxyglutamic acid (Gla) residues, which are implicated as essential calcium-binding ligands in a variety of proteins. The alpha-ethylmalonate ion chelates the Ca2+ ion in a bidentate manner that involves an O atom from each of the two malonate carboxylate groups. This type of binding arises from the constrained arrangement of carboxylate ligands in the malonate group and may be of significance to the calcium-binding properties of Gla-containing sites in proteins. The Ca2+-malonate chelation forms a six-membered ring, which is stabilized by interactions that are consistent with the preferred stereochemistries of both calcium-carboxylate and metal-malonate complexes. No other interactions are observed between Ca2+ ions and alpha-ethylmalonate ions that depend upon the malonate juxtaposition of two carboxylate groups. The potential for this type of binding distinguishes Gla residues from the monocarboxylate residues, aspartate and glutamate, and confers a novel calcium-chelation ability upon Gla-containing sites in proteins.

Calcium↗
PubMed1981

[Ocular scanning modalities in dyslexic children (author's transl)].

Voluntary and reflex ocular scanning has been investigated in 55 dyslexic children, aged from 8 to 14 years 3 months, by means of potentiometric electrooculography with multiple monocular electrodes. Results are expressed in terms of amplitude, frequency, shape of movements and ocular congruence. A comparison between the oculomotor behaviour of dyslexic and normal children with no reading problem shows the same types of ocular movements as observed in normal schoolchildren, but they differ in their distribution according to age. Moreover, the evolution of oblique movements, described in normal children and correlated with the degree of schooling, is not the same in dyslexic children, where it instead seems to follow particular patterns. Finally, in stereotyped ocular scanning simulating reading movements, the dyslexics are characterized by the absence of two important stages leading to ocular congruence: scanning with random alternate monocular predominance and scanning with selected alternate monocular predominance.

Adolescent↗
PubMed1978

Cleidocranial dysostosis: a multidisciplinary approach to treatment.

To ensure eruption of the dentition in patients with cleidocranial dysostosis, close collatoration between the oral surgeon and the orthodontist is essential to determine the sequence of extraction, the teeth to be ligated, the preferred technique of ligation, and the approach for surgical exposure.

Child↗
PubMedDate not supplied

Locating biologically active compounds in medium-sized heterogeneous datasets by topological autocorrelation vectors: dopamine and benzodiazepine agonists.

Electronic properties located on the atoms of a molecule such as partial atomic charges as well as electronegativity and polarizability values are encoded by an autocorrelation vector accounting for the constitution of a molecule. This encoding procedure is able to distinguish between compounds being dopamine agonists and those being benzodiazepine receptor agonists even after projection into a two-dimensional self-organizing network. The two types of compounds can still be distinguished if they are buried in a dataset of 8323 compounds of a chemical supplier catalog comprising a wide structural variety. The maps obtained by this sequence of events, calculation of empirical physicochemical effects, encoding in a topological autocorrelation vector, and projection by a self-organizing neural network, can thus be used for searching for structural similarity, and, in particular, for finding new lead structures with biological activity.

Databases, Factual↗