Concept Based Knowledge Discovery from Biomedical Literature

Philosophiae Doctor - PhDThis thesis describes and introduces novel methods for knowledge discovery and presents a software system that is able to extract information from biomedical literature, review interesting connections between various biomedical concepts and in so doing, generates new hypotheses. The experimental results obtained by using methods described in this thesis, are compared to currently published results obtained by other methods and a number of case studies are described. This thesis shows how the technology, resented can be integrated with the researchers own knowledge, experimentation and observations for optimal progression of scientific research.South Afric

Loop Corrections in the Spectrum of 2D Hawking Radiation

We determine the one-loop and the two-loop back-reaction corrections in the spectrum of the Hawking radiation for the CGHS model of 2d dilaton gravity by evaluating the Bogoliubov coefficients for a massless scalar field propagating on the corresponding backgrounds. Since the back-reaction can induce a small shift in the position of the classical horizon, we find that a positive shift leads to a non-Planckian late-time spectrum, while a null or a negative shift leads to a Planckian late-time spectrum in the leading-order stationary-point approximation. In the one-loop case there are no corrections to the classical Hawking temperature, while in the two-loop case the temperature is three times greater than the classical value. We argue that these results are consistent with the behaviour of the Hawking flux obtained from the operator quantization only for the times which are not too late, in accordance with the limits of validity of the semiclassical approximation.Comment: 20 pages, latex, no figure

One-Loop Effective Action for Spherical Scalar Field Collapse

We calculate the complete one-loop effective action for a spherical scalar field collapse in the large radius approximation. This action gives the complete trace anomaly, which beside the matter loop contributions, receives a contribution from the graviton loops. Our result opens a possibility for a systematic study of the back-reaction effects for a real black hole.Comment: 14 pages, slightly expanded version to appear in Class. Quant. Gra

Modeling of thermoelectric module operation in inhomogeneous transient temperature field using finite element method

This paper is the result of research and operation modeling of the new systems for cooling of cutting tools based on thermoelectric module. A copper inlay with thermoelectric module on the back side was added to a standard turning tool for metal processing. For modeling and simulating the operation of thermoelectric module, finite element method was used as a method for successful solving the problems of inhomogeneous transient temperature field on the cutting tip of lathe knives. Developed mathematical model is implemented in the software package PAK-T through which numerical results are obtained. Experimental research was done in different conditions of thermoelectric module operation. Cooling of the hot module side was done by a heat exchanger based on fluid using automatic temperature regulator. After the calculation is done, numerical results are in good agreement with experimental. It can be concluded that developed mathe-matical model can be used successfully for modeling of cooling of cutting tools

INFLUENCE OF PHYSICAL TRAINING ON CARDIORESPIRATORY ENDURANCE IN PREADOLESCENT AGE

Cardiorespiratory or aerobic endurance is the ability of the whole body to sustain physical activity for an extended period of time, involving relatively large groups of muscles. The attitudes on the possible impact of training on cardiorespiratory endurance in preadolescents are contradictory. Our study enrolled 195 boys aged 11 to 12 years. Experimental group (n=92) consisted of the children who had been involved with planned and programmed water polo training for at least two years. Control group (n=103) consisted of schoolchildren who only had had regular physical education in schools. Our investigation protocol included standardized anthropometric measurements and tests, performed respecting the appropriate protocols. Statistical analysis of the results demonstrated that there were no significant differences in age and relative values of oxygen consumption (VO2peak). Body height and mass, as well as the skinfold thickness, were significantly higher in experimental group subjects. The values of absolute VO2peak, FVC and FEV1.0 were also significantly higher in the examinees involved with water polo training. These findings stress the importance of a systematic training process even in this early period of growth and development in order for the trainees to acquire important functional advantages. We believe that a properly planned and programmed physical training can significantly contribute to the development of cardiorespiratory endurance even as early as preadolescent age

Comparative study of Ag/ZnO nanopowders obtained by solvothermal and precipitation methods

Beside wide range of applications, zinc oxide is recently recognized as a promising photocatalyst mainly used to degrade organic water pollutants. The great advantage of ZnO over TiO2, which is the most common photocatalyst, is the absorption in wider solar spectrum, partly in the visible region [1]. Generally, the photocatalytic properties usually depend on the crystallinity and crystallite size, particle size, morphology and pore sizes, surface area, band gap energy, availability of active sites, number and nature of trapped sites, as well as on adsorption/desorption characteristics [2]. The modification of photocatalysts by noble metals can enhance their photocatalytic activity. This paper discuss the influence of synthetic method on photocatalytic activity of obtained powders. Solvothermal and precipitation methods were chosen for the preparation of Ag/ZnO nanopowders. For the first one, the Zn(CH3COO)2·2H2O with different AgNO3 content (0, 0.75, 1.5 and 3 mol.%) was solvothermally treated at 120 °C for 18 h in the presence of poly(vinyl pyrrolidone), ethylene-glycol and NaOH. The obtained samples were rinsed out with distilled water, centrifuged and dried at 105 °C for 3h. In precipitation method, Zn(CH3COO)2·2H2O was dissolved in ethylene-glycol in the presence of chitosan soluted in acetic acid, which was followed by addition of AgNO3 in the same quantity as used for the solvothermal synthesis. The obtained suspension was heated up to 150 °C for 2 h and then calcined at 400 °C for 1 h (Fig.1). The prepared samples were characterized by XRPD, FESEM, UV-vis techniques, while photocatalytic properties were tested on Reactive Orange 16 textile azo dye and compared to the commercial ZnO (the average particle size: 20 nm). 84 Based on XRPD, the predominant phase in all samples is ZnO with the weak reflections belonging to Ag for 0.75%Ag/ZnO, which become clearly visible for samples with 1.5 and 3% of Ag. The average crystallite size was calculated using Williamson-Hall method giving 20 ± 2 and 25 ± 2 nm for powders obtained by solvothermal and precipitation method, respectively. The calculated strains were insignificant probably due to low concentration of defects. On the other hand, this is not the case for commercial ZnO with strain of 0.25(3) %. This sample consists of nanoparticles with a slightly elongated spherical shape while all obtained ZnO nanopowders contain mutually similar nanoparticles with approximately spherical shape, which however create diverse forms of agglomerates. The average particle size was around 25 nm for solvothermally synthesized samples and approximately 30 nm for samples obtained by precipitation method. Comparing to both unmodified ZnO and commercial one, all prepared Ag/ZnO samples showed a broad band at 450 nm (visible region) which causes the narrowing of band gap. The existence of this band is the confirmation that metallic Ag particles were formed, as indicated by XRPD, since they can absorb visible light and activate photocatalyst in visible spectrum. The photocatalytic measurements showed that all synthesized nanopowders have higher adsorption power and photocatalytic activity than the commercial ZnO (Fig.1). This could be attributed to slightly elongated grains of commercial ZnO and the existence of significant strain. If compare the samples obtained by two different methods, Ag modified ZnO powders from solvothermal method are more efficient than the ones from precipitation method due to the smaller particles of silver.Larger Ag particles on ZnO could cause negative effects, such as light blocked, which result in the decrease of photocatalytic activity. The unmodified ZnO powders have the same efficiency regardless of the synthetic method. Comparing the photocatalytic activity of samples obtained by same method, the Ag distribution and its particle size seems to play the major role. Summary, no matter which procedure was used, 1.5% Ag/ZnO powders have performed the highest effciency in degradation of RO16. It means that the photocatalytic activity does not depend only on Ag content but the metal distribution is important as well. In this work, it is shown that the optimized content of Ag amounts about 1.5 mol.% regardless of synthetic method and it could be recommended for further research in terms of economy. References [1] B. Simović et al., J. Serb. Chem. Soc., 2014, 79, 1433. [2] B. Simović et al., Process. Appl. Ceram., 2017, 11, 27

Opportunities of Solid Renewable Fuels for (Co-)Combustion with Coal in Power Plants in Serbia

In the process of accession to the EU, Republic of Serbia will be obliged to achieve an appropriate share of renewable sources in primary energy consumption in addition to control the emission of carbon dioxide in order to comply with EUs energy policy. In this paper the potential of the production of the so called green electricity from biomass and waste in Republic of Serbia is shown with particular attention to the Electric Power Industry of Serbia, as the largest potential producer of electricity from renewable fuels. Based both on the available total quantity and heating value of non-hazardous solid waste material (municipal and industrial), the calculation of the total available energy potential of waste in Republic of Serbia (by regions) was performed for the state of the 2010th and the projections of waste quantity growth until 2020th. Also, for the same time period, the available amount of waste biomass suitable for (co-)combustion with coal was estimated, as the respective energy potential. The possible energy effects of (co-)combustion in power plants as well as reduced emissions of CO2 with significant financial impact are demonstrated. Actually, this paper demonstrates necessity and techno-economic justification (co-)combustion of renewable fuel with coal in thermal power plants in Serbia

DDESC: Dragon database for exploration of sodium channels in human

<p>Abstract</p> <p>Background</p> <p>Sodium channels are heteromultimeric, integral membrane proteins that belong to a superfamily of ion channels. The mutations in genes encoding for sodium channel proteins have been linked with several inherited genetic disorders such as febrile epilepsy, Brugada syndrome, ventricular fibrillation, long QT syndrome, or channelopathy associated insensitivity to pain. In spite of these significant effects that sodium channel proteins/genes could have on human health, there is no publicly available resource focused on sodium channels that would support exploration of the sodium channel related information.</p> <p>Results</p> <p>We report here Dragon Database for Exploration of Sodium Channels in Human (DDESC), which provides comprehensive information related to sodium channels regarding different entities, such as "genes and proteins", "metabolites and enzymes", "toxins", "chemicals with pharmacological effects", "disease concepts", "human anatomy", "pathways and pathway reactions" and their potential links. DDESC is compiled based on text- and data-mining. It allows users to explore potential associations between different entities related to sodium channels in human, as well as to automatically generate novel hypotheses.</p> <p>Conclusion</p> <p>DDESC is first publicly available resource where the information related to sodium channels in human can be explored at different levels. This database is freely accessible for academic and non-profit users via the worldwide web <url>http://apps.sanbi.ac.za/ddesc</url>.</p

DDEC: Dragon database of genes implicated in esophageal cancer

<p>Abstract</p> <p>Background</p> <p>Esophageal cancer ranks eighth in order of cancer occurrence. Its lethality primarily stems from inability to detect the disease during the early organ-confined stage and the lack of effective therapies for advanced-stage disease. Moreover, the understanding of molecular processes involved in esophageal cancer is not complete, hampering the development of efficient diagnostics and therapy. Efforts made by the scientific community to improve the survival rate of esophageal cancer have resulted in a wealth of scattered information that is difficult to find and not easily amendable to data-mining. To reduce this gap and to complement available cancer related bioinformatic resources, we have developed a comprehensive database (Dragon Database of Genes Implicated in Esophageal Cancer) with esophageal cancer related information, as an integrated knowledge database aimed at representing a gateway to esophageal cancer related data.</p> <p>Description</p> <p>Manually curated 529 genes differentially expressed in EC are contained in the database. We extracted and analyzed the promoter regions of these genes and complemented gene-related information with transcription factors that potentially control them. We further, precompiled text-mined and data-mined reports about each of these genes to allow for easy exploration of information about associations of EC-implicated genes with other human genes and proteins, metabolites and enzymes, toxins, chemicals with pharmacological effects, disease concepts and human anatomy. The resulting database, DDEC, has a useful feature to display potential associations that are rarely reported and thus difficult to identify. Moreover, DDEC enables inspection of potentially new 'association hypotheses' generated based on the precompiled reports.</p> <p>Conclusion</p> <p>We hope that this resource will serve as a useful complement to the existing public resources and as a good starting point for researchers and physicians interested in EC genetics. DDEC is freely accessible to academic and non-profit users at <url>http://apps.sanbi.ac.za/ddec/</url>. DDEC will be updated twice a year.</p