Motivation: Prostate cancer is the most prevalent tumor in males and its incidence is expected to increase as the population ages. Prostate cancer is treatable by excision if detected at an early enough stage. The challenges of early diagnosis require the discovery of novel biomarkers and tools for prostate cancer management. Results: We developed a novel feature selection algorithm termed as associative voting (AV) for identifying biomarker candidates in prostate cancer data measured via targeted metabolite profiling MS/MS analysis. We benchmarked our algorithm against two standard entropy-based and correlation-based feature selection methods [Information Gain (IG) and ReliefF (RF)] and observed that, on a variety of classification tasks in prostate cancer diagnosis, our algorithm identified subsets of biomarker candidates that are both smaller and show higher discriminatory power than the subsets identified by IG and RF. A literature study confirms that the highest ranked biomarker candidates identified by AV have independently been identified as important factors in prostate cancer development. Availability: The algorithm can be downloaded from the following http://biomed.umit.at/page.cfm?pageid=516 Contact:melanie.osl@umit.at

Motivation: Alcoholic fatty liver disease (AFLD) and non-AFLD (NAFLD) can progress to severe liver diseases such as steatohepatitis, cirrhosis and cancer. Thus, the detection of early liver disease is essential; however, minimal invasive diagnostic methods in clinical hepatology still lack specificity. Results: Ion molecule reaction mass spectrometry (IMR-MS) was applied to a total of 126 human breath gas samples comprising 91 cases (AFLD, NAFLD and cirrhosis) and 35 healthy controls. A new feature selection modality termed Stacked Feature Ranking (SFR) was developed to identify potential liver disease marker candidates in breath gas samples, relying on the combination of different entropy- and correlation-based feature ranking methods including statistical hypothesis testing using a two-level architecture with a suggestion and a decision layer. We benchmarked SFR against four single feature selection methods, a wrapper and a recently described ensemble method, indicating a significantly higher discriminatory ability of up to 10–15% for the SFR selected gas compounds expressed by the area under the ROC curve (AUC) of 0.85–0.95. Using this approach, we were able to identify unexpected breath gas marker candidates in liver disease of high predictive value. A literature study further supports top-ranked markers to be associated with liver disease. We propose SFR as a powerful tool for biomarker search in breath gas and other biological samples using mass spectrometry. Availability: The algorithm SFR and IMR-MS datasets are available under http://biomed.umit.at/page.cfm?pageid=526 Contact:michalel.netzer@umit.at; christian.baumgartner@umit.at

In this paper, a cellular automaton framework for processing the spatiotemporal spread of infectious diseases is presented. The developed environment simulates and visualizes how infectious diseases might spread, and hence provides a powerful instrument for health care organizations to generate disease prevention and contingency plans. In this study, the outbreak of an avian flu like virus was modeled in the state of Tyrol, and various scenarios such as quarantine, effect of different medications on viral spread and changes of social behavior were simulated.The proposed framework is implemented using the programming language Java. The set up of the simulation environment requires specification of the disease parameters and the geographical information using a population density colored map, enriched with demographic data.The results of the numerical simulations and the analysis of the computed parameters will be used to get a deeper understanding of how the disease spreading mechanisms work, and how to protect the population from contracting the disease. Strategies for optimization of medical treatment and vaccination regimens will also be investigated using our cellular automaton framework.In this study, six different scenarios were simulated. It showed that geographical barriers may help to slow down the spread of an infectious disease, however, when an aggressive and deadly communicable disease spreads, only quarantine and controlled medical treatment are able to stop the outbreak, if at all.

Little is known about the effect of cardiac resynchronization therapy (CRT) on endo- and epicardial ventricular activation. Noninvasive imaging of cardiac electrophysiology (NICE) is a novel imaging tool for visualization of both epi- and endocardial ventricular electrical activation. NICE was performed in ten patients with congestive heart failure (CHF) undergoing CRT and in ten patients without structural heart disease (control group). NICE is a fusion of data from high-resolution ECG mapping with a model of the patient's individual cardiothoracic anatomy created from magnetic resonance imaging. Beat-to-beat endocardial and epicardial ventricular activation sequences were computed during native rhythm as well as during ventricular pacing using a bidomain theory-based heart model to solve the related inverse problem. During right ventricular (RV) pacing control patients showed a deterioration of the ventricular activation sequence similar to the intrinsic activation pattern of CHF patients. Left ventricular propagation velocities were significantly decreased in CHF patients as compared to the control group (1.6±0.4 versus 2.1±0.5 m/sec; p<0.05). CHF patients showed right-to-left septal activation with the latest activation epicardially in the lateral wall of the left ventricle. Biventricular pacing resulted in a resynchronization of the ventricular activation sequence and in a marked decrease of total LV activation duration as compared to intrinsic conduction and RV pacing (129±16 versus 157±28 and 173±25 ms; both p<0.05). Endocardial and epicardial ventricular activation can be visualized noninvasively by NICE. Identification of individual ventricular activation properties may help identify responders to CRT and to further improve response to CRT by facilitating a patient-specific lead placement and device programming.

Motivation: The discovery of new and unexpected biomarkers in cardiovascular disease is a highly data-driven process that requires the complementary power of modern metabolite profiling technologies, bioinformatics and biostatistics. Clinical biomarkers of early myocardial injury are lacking. A prospective biomarker cohort study was carried out to identify, categorize and profile kinetic patterns of early metabolic biomarkers of planned myocardial infarction (PMI) and spontaneous (SMI) myocardial infarction. We applied a targeted mass spectrometry (MS)-based metabolite profiling platform to serial blood samples drawn from carefully phenotyped patients undergoing alcohol septal ablation for hypertrophic obstructive cardiomyopathy serving as a human model of PMI. Patients with SMI and patients undergoing catheterization without induction of myocardial infarction served as positive and negative controls to assess generalizability of markers identified in PMI. Results: To identify metabolites of high predictive value in tandem mass spectrometry data, we introduced a new feature selection method for the categorization of metabolic signatures into three classes of weak, moderate and strong predictors, which can be easily applied to both paired and unpaired samples. Our paradigm outperformed standard null-hypothesis significance testing and other popular methods for feature selection in terms of the area under the receiver operating curve and the product of sensitivity and specificity. Our results emphasize that this new method was able to identify, classify and validate alterations of levels in multiple metabolites participating in pathways associated with myocardial injury as early as 10 min after PMI. Availability: The algorithm as well as supplementary material is available for download at: www.umit.at/page.cfm?vpath=departments/technik/iebe/tools/bi Contact:christian.baumgartner@umit.at Supplementary information: Supplementary data are available at Bioinformatics online.