Contemporary prostate cancer management - introduction

W pracy przedstawiono zarys historyczny postępowania u chorych z rakiem gruczołu krokowego oraz istniejące wątpliwości związane z leczeniem, które należy wyjaśnić w dalszych badaniach klinicznych.The paper presents historical outline of the management in prostate cancer and current questions concerning the treatment that awaits answering in future clinical trials

The High Throughput Sequence Annotation Service (HT-SAS) – the shortcut from sequence to true Medline words

<p>Abstract</p> <p>Background</p> <p>Advances in high-throughput technologies available to modern biology have created an increasing flood of experimentally determined facts. Ordering, managing and describing these raw results is the first step which allows facts to become knowledge. Currently there are limited ways to automatically annotate such data, especially utilizing information deposited in published literature.</p> <p>Results</p> <p>To aid researchers in describing results from high-throughput experiments we developed HT-SAS, a web service for automatic annotation of proteins using general English words. For each protein a poll of Medline abstracts connected to homologous proteins is gathered using the UniProt-Medline link. Overrepresented words are detected using binomial statistics approximation. We tested our automatic approach with a protein test set from SGD to determine the accuracy and usefulness of our approach. We also applied the automatic annotation service to improve annotations of proteins from <it>Plasmodium bergei </it>expressed exclusively during the blood stage.</p> <p>Conclusion</p> <p>Using HT-SAS we created new, or enriched already established annotations for over 20% of proteins from <it>Plasmodium bergei </it>expressed in the blood stage, deposited in PlasmoDB. Our tests show this approach to information extraction provides highly specific keywords, often also when the number of abstracts is limited. Our service should be useful for manual curators, as a complement to manually curated information sources and for researchers working with protein datasets, especially from poorly characterized organisms.</p

DeCAF—Discrimination, Comparison, Alignment Tool for 2D PHarmacophores

Comparison of small molecules is a common component of many cheminformatics workflows, including the design of new compounds and libraries as well as side-effect predictions and drug repurposing. Currently, large-scale comparison methods rely mostly on simple fingerprint representation of molecules, which take into account the structural similarities of compounds. Methods that utilize 3D information depend on multiple conformer generation steps, which are computationally expensive and can greatly influence their results. The aim of this study was to augment molecule representation with spatial and physicochemical properties while simultaneously avoiding conformer generation. To achieve this goal, we describe a molecule as an undirected graph in which the nodes correspond to atoms with pharmacophoric properties and the edges of the graph represent the distances between features. This approach combines the benefits of a conformation-free representation of a molecule with additional spatial information. We implemented our approach as an open-source Python module called DeCAF (Discrimination, Comparison, Alignment tool for 2D PHarmacophores), freely available at http://bitbucket.org/marta-sd/decaf. We show DeCAF’s strengths and weaknesses with usage examples and thorough statistical evaluation. Additionally, we show that our method can be manually tweaked to further improve the results for specific tasks. The full dataset on which DeCAF was evaluated and all scripts used to calculate and analyze the results are also provided

Downstream and Intermediate Interactions of Synovial Sarcoma-Associated Fusion Oncoproteins and Their Implication for Targeted Therapy

Synovial sarcoma (SS), an aggressive type of soft tissue tumor, occurs mostly in adolescents and young adults. The origin and molecular mechanism of the development of SS remain only partially known. Over 90% of SS cases are characterized by the t(X;18)(p11.2;q11.2) translocation, which results mainly in the formation of SS18-SSX1 or SS18-SSX2 fusion genes. In recent years, several reports describing direct and indirect interactions of SS18-SSX1/SSX2 oncoproteins have been published. These reports suggest that the fusion proteins particularly affect the cell growth, cell proliferation, TP53 pathway, and chromatin remodeling mechanisms, contributing to SS oncogenesis. Additional research efforts are required to fully explore the protein-protein interactions of SS18-SSX oncoproteins and the pathways that are regulated by these partnerships for the development of effective targeted therapy

e-LiSe--an online tool for finding needles in the '(Medline) haystack'.

UNLABELLED Using literature databases one can find not only known and true relations between processes but also less studied, non-obvious associations. The main problem with discovering such type of relevant biological information is 'selection'. The ability to distinguish between a true correlation (e.g. between different types of biological processes) and random chance that this correlation is statistically significant is crucial for any bio-medical research, literature mining being no exception. This problem is especially visible when searching for information which has not been studied and described in many publications. Therefore, a novel bio-linguistic statistical method is required, capable of 'selecting' true correlations, even when they are low-frequency associations. In this article, we present such statistical approach based on Z-score and implemented in a web-based application 'e-LiSe'. AVAILABILITY The software is available at http://miron.ibb.waw.pl/elise

One‑year survival of ambulatory patients with end‑stage heart failure : the analysis of prognostic factors

Introduction An increasing number of ambulatory patients are placed on orthotopic heart transplantation (OHT) waiting lists, which results in an extended waiting time and a higher mortality rate. Objectives The aim of this study was to identify the factors associated with reduced survival during a 1‑year follow‑up in patients with end‑stage heart failure listed for an OHT. Patients and methods We retrospectively analyzed the data of 221 adult patients, who were accepted for OHT in our institution over a 2‑year period between 2013 and 2014. Results The mean (SD) age of the patients was 54.7 (9.6) years, and 90.1% of them were male. The mortality rate during the follow‑up period was 43.3%. The modified Model for End‑Stage Liver Disease (modMELD) score (odds ratio [OR], 1.70; P <0.001), as well as the plasma levels of high‑sensitivity C‑reactive protein (hs‑CRP; OR, 1.10; P <0.01), sodium (OR, 0.74; P <0.001), and uric acid (UA; OR, 1.003; P <0.05) were independent factors affecting death. The receiver‑operating characteristic (ROC) analysis indicated that a modMELD cut‑off of 10 (area under the ROC curve [AUC], 0.868; P <0.001), hs‑CRP cut‑off of 5.6 mg/l (AUC, 0.674; P <0.001), plasma sodium level cut‑off of 135 mmol/l (AUC, 0.778; P <0.001), and a plasma UA cut‑off of 488 μmol/l (AUC, 0.634; P <0.001) were the most accurate factors affecting death. Conclusions In conclusion, although limited to a single center, our study demonstrated that an elevated modMELD score, incorporating a combination of renal and hepatic laboratory parameters, as well as plasma sodium, UA, and hs‑CRP levels at the time of listing are associated with reduced survival in ambulatory patients with end‑stage heart failure, accepted for OHT