Integration of molecular network data reconstructs Gene Ontology.

Motivation: Recently, a shift was made from using Gene Ontology (GO) to evaluate molecular network data to using these data to construct and evaluate GO. Dutkowski et al. provide the first evidence that a large part of GO can be reconstructed solely from topologies of molecular networks. Motivated by this work, we develop a novel data integration framework that integrates multiple types of molecular network data to reconstruct and update GO. We ask how much of GO can be recovered by integrating various molecular interaction data. Results: We introduce a computational framework for integration of various biological networks using penalized non-negative matrix tri-factorization (PNMTF). It takes all network data in a matrix form and performs simultaneous clustering of genes and GO terms, inducing new relations between genes and GO terms (annotations) and between GO terms themselves. To improve the accuracy of our predicted relations, we extend the integration methodology to include additional topological information represented as the similarity in wiring around non-interacting genes. Surprisingly, by integrating topologies of bakers’ yeasts protein–protein interaction, genetic interaction (GI) and co-expression networks, our method reports as related 96% of GO terms that are directly related in GO. The inclusion of the wiring similarity of non-interacting genes contributes 6% to this large GO term association capture. Furthermore, we use our method to infer new relationships between GO terms solely from the topologies of these networks and validate 44% of our predictions in the literature. In addition, our integration method reproduces 48% of cellular component, 41% of molecular function and 41% of biological process GO terms, outperforming the previous method in the former two domains of GO. Finally, we predict new GO annotations of yeast genes and validate our predictions through GIs profiling. Availability and implementation: Supplementary Tables of new GO term associations and predicted gene annotations are available at http://bio-nets.doc.ic.ac.uk/GO-Reconstruction/. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

Semantičko indeksiranje i klasifikacija dokumenata

Cilj ovog rada je klasifikacija proteina pomoću algoritma potpornih vektora i n-gramskog rječnika. Prvo su dani osnovni pojmovi iz linearne algebre, euklidskih prostora i teorije optimizacije, potrebni za lakše shvaćanje tema obrađenih u radu. Objašnjena je matematička pozadina načina rada algoritma, s posebnim naglaskom na jezgrene funkcije koje se koriste. Za analizu se koristi deset proteinskih familija, pri čemu je iz svake familije uzeto 300 proteina za trening i 100 proteina za testiranje. Nakon što je napravljen n-gramski rječnik, provedeni su testovi klasifikacije pomoću algoritma potpornih vektora te su uspoređivani rezultati za različite jezgrene funkcije u ovisnosti o parametrima.The aim of this work is to classify proteins using the support vector machine and the n-gram dictionary. First, we present some basic concepts from linear algebra, Euclidean spaces, and optimization theory that are needed later on. A mathematical background of the algorithm has been explained in detail, with a special emphasis on the kernel functions. Ten protein families were used for the analysis, using 300 protein for each family for training and 100 test proteins. After the n-gram vocabulary was made, classification tests were performed using the support vector machine, and comparisons were made for different kernel functions depending on the parameters

Echocardiographic Screening Parameters for Cardiac Resynchronization Therapy.

The application of diverse possibilities of treatment in ever greater number of patients with heart failure represents a significant progress in improvement of prognosis, quality of life and extension of life. Variables obtained on the basis of echocardiography may much more contribute to making indication for the implantation of biventricular pacemaker than what has been the case so far. In many diverse variables, it is necessary to define those applied in screening patients for implantation and monitoring symptomatic patients with implanted device, for the purpose of optimization of resynchronization system. The purpose of this article written following the debate by the participants of the 12th Croatian Symposium on Arrhythmias and Electrostimulation is to stimulate further constructive debate

Specificities of hand trauma in agriculture

Background/Aim. Hand injuries in agriculture are characterized by massive destruction of all tissues, frequent amputations of finger, hand and often the whole extremity. These injuries are mutilant and can cause death. The aim of this paper was to show the specificities of hand injuries in agriculture in regard to hand injuries of other etiology. Methods. We analyzed patients that were treated in the Department for Plastic and Reconstructive Surgery, Clinical Center Vojvodina, during a five-year period (2003-2007) because of hand injuries. Results. In a five-year period there were 366 patients hospitalized because of hand injuries, out of whom 36 injuries were related to agricultural machinery use. In both groups the number of patients trended to increased, with male gender being dominant. Most of the patients were young or middle-aged men. In agricultural injuries most of the patients were in the group of 41-50-year old (30%), while in the other group, the patients were younger (21-30-year old). Hand injuries in agriculture resulted in finger amputation in 92%, while in the other group that number was much smaller (13%). Skin defect reconstruction in agricultural injuries required complex methods of skin grafting or skin flaps in more than 71%, while this was necessary in only 10% of other hand injuries. Conclusion. Hand injuries in agriculture are very mutilant and often result in conquassation and finger amputation. A possibility to preserve tissue damaged in this way is very limited, and skin closer usually requires complex methods

Improving Students' Language Performance Through Consistent Use of E-Learning: An Empirical Study in Japanese, Korean, Hindi and Sanskrit

This paper describes the backing theories, methodology, and results of a two-semester long case study of the application of technology in teaching four Asian languages (Japanese, Korean, Hindi, and Sanskrit) to Croatian students. We have developed e-learning materials to follow the curriculum in Croatia and deployed them in Asian language classrooms. Students who agreed to participate in the study were tested before using the materials, and after each semester, and their progress was surveyed. In the case of Japanese students (N=53), we have thoroughly monitored their usage and compared the progress of students who have diligently studied vocabulary and grammar using our materials on Memrise, and those who have neglected their studies. This was measured through their scores on the Memrise, which shows the user's activity. Also, their progress was measured using standardized tests that were designed in such a manner to resemble Japanese Language Proficiency Test. We have found that frequent users progressed averagely 20,3% after each semester, while non-frequent users have progressed only 11,6%, proving this method to be related to stable and constant use of e-materials