Biomedical subjects

G Stocker

Publications and source records attributed to G Stocker.

3 recordsLinked to original sources

PubMed2005

A fully Bayesian model to cluster gene-expression profiles.

MOTIVATION: With cDNA or oligonucleotide chips, gene-expression levels of essentially all genes in a genome can be simultaneously monitored over a time-course or under different experimental conditions. After proper normalization of the data, genes are often classified into co-expressed classes (clusters) to identify subgroups of genes that share common regulatory elements, a common function or a common cellular origin. With most methods, e.g. k-means, the number of clusters needs to be specified in advance; results depend strongly on this choice. Even with likelihood-based methods, estimation of this number is difficult. Furthermore, missing values often cause problems and lead to the loss of data. RESULTS: We propose a fully probabilistic Bayesian model to cluster gene-expression profiles. The number of classes does not need to be specified in advance; instead it is adjusted dynamically using a Reversible Jump Markov Chain Monte Carlo sampler. Imputation of missing values is integrated into the model. With simulations, we determined the speed of convergence of the sampler as well as the accuracy of the inferred variables. Results were compared with the widely used k-means algorithm. With our method, biologically related co-expressed genes could be identified in a yeast transcriptome dataset, even when some values were missing. AVAILABILITY: The code is available at http://genome.tugraz.at/BayesianClustering/

Algorithms↗

PubMed1991

Effects of low and high dose oral contraceptives on blood coagulation and thrombogenesis induced by vascular subendothelium exposed to flowing human blood.

We investigated the effect of oral contraceptives with low and high estrogen concentration on blood coagulation and thrombogenesis, induced by vascular subendothelium of rabbit aorta exposed to flowing human blood. Twenty healthy women intending to take oral contraceptives were studied [1] before drug ingestion (control), and subsequently during the intake of oral contraceptives with [2] low estrogen content (20 micrograms ethinyl estradiol and 150 micrograms desogestrel per day) and [3] high estrogen content (50 micrograms ethinyl estradiol and 125 micrograms desogestrel per day). All experiments were performed between day 17 and 21 of the menstrual cycle and drug effects were studied during the third tablet cycle. Deposition of fibrin, platelets and platelet thrombi on vascular subendothelium was tested at a defined blood flow and wall shear rate (10 ml/min, 650 s-1) and was quantified by morphometrical techniques. Treatment with the low and high dose contraceptive increased the plasma levels of ethinyl estradiol (728 +/- 139 and 1438 +/- 212 vs. 0 fmol/l [low and high dose vs. control], means +/- SEM, P less than 0.001) and fibrinogen (2.3 +/- 0.1 and 2.6 +/- 0.1 vs. 2.0 +/- 0.1 g/l, P less than 0.05); and decreased antithrombin III activity (95 +/- 3 and 92 +/- 3 vs. 101 +/- 3 %, P less than 0.05). Fibrin deposition on vascular subendothelium was enhanced by the high dose contraceptive only (47 +/- 4 vs. 35 +/- 4 % coverage of the subendothelial surface with fibrin, high dose vs. control, P less than 0.05). The subendothelial deposition of platelets and platelet thrombi was not changed by contraceptive treatment. These results indicate that treatment with high dose contraceptives leads to an increase of fibrin-subendothelial interactions, whereas low dose contraceptives do not significantly alter the blood-subendothelium interactions. observed in this ex vivo model of thrombogenesis.

Adolescent↗

PubMedDate not supplied

Critical aspects related to the interpretation of the free-to-total PSA-ratio.

INTRODUCTION: The number of assays available for the measurement of total and free PSA is increasing. As different methods can determine different PSA concentrations as well as different free-to-total PSA ratios in identical serum samples, the cut-offvalue for the ratio still needs to be determined. METHODS: 114 sera from patients with histologically confirmed benign prostatic hyperplasia (BPH; n = 58) and cancer of the prostate (CaP; n = 56) were analyzed with two different assays. Free PSA (free), total PSA (total) and the free-to-total- PSA ratio (ratio) were determined employing Enzym-Test PSA und freies PSA (Boehringer Mannheim, Germany) and Immulite PSA und freies PSA (DPC Biermann, Bad Nauheim, Germany) RESULTS: The statistical results are tabulated below: [table: see text] CONCLUSION: Direct comparison of the two assays revealed a high statistical correlation (r = 0.94-0.99) for free and total PSA. In contrast, the ratio of the two assays was not as reproducible (r = 0.81-0.83). This result indicates that the reference range for the ratio is dependent on the assay employed and an that uncritical use of an applied reference range can be counter-productive.

Aged↗