Impact of percutaneous coronary intervention on biomarker levels in patients in the subacute phase following myocardial infarction: the Occluded Artery Trial (OAT) biomarker ancillary study.

Background: The purpose of the Occluded Artery Trial (OAT) Biomarker substudy was to evaluate the impact of infarct related artery (IRA) revascularization on serial levels of N-terminal prohormone of brain natriuretic peptide (NT-proBNP) and dynamics of other biomarkers related to left ventricular remodeling, fibrosis and angiogenesis.

Methods: Patients were eligible for OAT-Biomarker based on the main OAT criteria. Of 70 patients (age 60.

Transcriptome profile of human colorectal adenomas.

Colorectal cancers are believed to arise predominantly from adenomas. Although these precancerous lesions have been subjected to extensive clinical, pathologic, and molecular analyses, little is currently known about the global gene expression changes accompanying their formation. To characterize the molecular processes underlying the transformation of normal colonic epithelium, we compared the transcriptomes of 32 prospectively collected adenomas with those of normal mucosa from the same individuals.

Treatment of acute ST-segment elevation myocardial infarction in West Pomerania province of Poland. Comparison between primary coronary intervention and thrombolytic therapy.

Introduction: The majority of randomised studies on reperfusion in acute ST-segment elevation myocardial infarction (STEMI) show the advantage of primary percutaneous coronary intervention (PCI) over thrombolysis. However, the real world registers' data are not so unequivocal.

Aim: To evaluate the way acute STEMI is treated in West Pomerania province with emphasis on comparison of two reperfusion strategies, primary PCI vs thrombolytic therapy, in early and long-term perspective.

[Anomalous pulmonary artery as a cause of wide, polycyclic pulmonary hilus--case report].

Changes of lymphatic system, vascular disease during pulmonary hypertension or aneurysms are very often considered to be a cause of wide pulmonary hilus. However, we should remember developmental anomaly of pulmonary artery, too. We present a case of a patient hospitalized very often due to necessity of diagnostic wide, polycyclic pulmonary hilus.

FRankenstein becomes a cyborg: the automatic recombination and realignment of fold recognition models in CASP6.

In the course of CASP6, we generated models for all targets using a new version of the "FRankenstein's monster approach." Previously (in CASP5) we were able to build many very accurate full-atom models by selection and recombination of well-folded fragments obtained from crude fold recognition (FR) results, followed by optimization of the sequence-structure fit and assessment of alternative alignments on the structural level. This procedure was however very arduous, as most of the steps required extensive visual and manual input from the human modeler.

[Resistance to activated protein C in a patient with multiple myocardial infarctions and stroke--a case report].

A case of a 49-year-old female with a history of two myocardial infarctions (MI) and ischaemic stroke is presented. The patient was admitted to the hospital due to a third acute MI. Laboratory investigations revealed resistance to activated protein C due to factor V Leiden mutation.

Probabilistic cross-link analysis and experiment planning for high-throughput elucidation of protein structure.

Emerging high-throughput techniques for the characterization of protein and protein-complex structures yield noisy data with sparse information content, placing a significant burden on computation to properly interpret the experimental data. One such technique uses cross-linking (chemical or by cysteine oxidation) to confirm or select among proposed structural models (e.g.

Phylogenomic identification of five new human homologs of the DNA repair enzyme AlkB.

Background: Combination of biochemical and bioinformatic analyses led to the discovery of oxidative demethylation - a novel DNA repair mechanism catalyzed by the Escherichia coli AlkB protein and its two human homologs, hABH2 and hABH3. This discovery was based on the prediction made by Aravind and Koonin that AlkB is a member of the 2OG-Fe2+ oxygenase superfamily.

Results: In this article, we report identification and sequence analysis of five human members of the (2OG-Fe2+) oxygenase superfamily designated here as hABH4 through hABH8.

A "FRankenstein's monster" approach to comparative modeling: merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation.

We applied a new multi-step protocol to predict the structures of all targets during CASP5, regardless of their potential category. 1) We used diverse fold-recognition (FR) methods to generate initial target-template alignments, which were converted into preliminary full-atom models by comparative modeling. All preliminary models were evaluated (scored) by VERIFY3D to identify well- and poorly-folded fragments.

STRUCLA: a WWW meta-server for protein structure comparison and evolutionary classification.

Motivation: Evolutionary relationships of proteins have long been derived from the alignment of protein sequences. But from the view of function, most restraints of evolutionary divergence operate at the level of tertiary structure. It has been demonstrated that quantitative measures of dissimilarity in families of structurally similar proteins can be applied to the construction of trees from a comparison of their three-dimensional structures.

GeneSilico protein structure prediction meta-server.

Rigorous assessments of protein structure prediction have demonstrated that fold recognition methods can identify remote similarities between proteins when standard sequence search methods fail. It has been shown that the accuracy of predictions is improved when refined multiple sequence alignments are used instead of single sequences and if different methods are combined to generate a consensus model. There are several meta-servers available that integrate protein structure predictions performed by various methods, but they do not allow for submission of user-defined multiple sequence alignments and they seldom offer confidentiality of the results.

Characterization of the cofactor-binding site in the SPOUT-fold methyltransferases by computational docking of S-adenosylmethionine to three crystal structures.

Background: There are several evolutionarily unrelated and structurally dissimilar superfamilies of S-adenosylmethionine (AdoMet)-dependent methyltransferases (MTases). A new superfamily (SPOUT) has been recently characterized on a sequence level and three structures of its members (1gz0, 1ipa, and 1k3r) have been solved. However, none of these structures include the cofactor or the substrate.