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Search Results: 1 - 10 of 1792 matches for " Tomas Salkus "
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Electrical and Dielectric Characterization of Na0.5Li0.5Zr2(PO4)3  [PDF]
Umaru Ahmadu, Abubakar Ohinoyi Musa, Tomas Salkus, Kasim Uthman Isah
Open Journal of Physical Chemistry (OJPC) , 2011, DOI: 10.4236/ojpc.2011.13013
Abstract: Na0.5Li0.5Zr2(PO4)3has been synthesized by solid state reaction and characterized by thermogravimetry/ differential thermal analyses (TGA/DTA) in the temperature range 300 - 1573 K. X-ray diffraction measure- ments have been carried out to determine the phase of the composition and scanning electron microscopy (SEM) for microstructure evaluation. Impedance spectroscopy at different temperatures (310 - 600 K) and frequencies (300 kHz - 1 GHz) have been carried out and the dielectric relaxation behaviour was determined under the same conditions. A dc conductivity maximum value of 0.25 S/m at 580 K was observed. However, the mixed alkali effect was not observed. The material exhibited relaxation behaviour with a peak in the dielectric permitivity at 469 K. There were no structural transformations observed.
Seasonal Differences in Visitor Perceptions: A Comparative Study of Three Mountainous National Parks in Central Europe  [PDF]
Tomas Gorner, Martin Cihar
Journal of Environmental Protection (JEP) , 2011, DOI: 10.4236/jep.2011.28120
Abstract: This paper compares the views and attitudes of visitors to three key mountain national parks and Biosphere Reserves: Sumava National Park (Sumava NP, Czech Republic), Krkonose National Park (KRNAP, Czech Republic) and Karkonoski Park Narodowy (KPN, Poland). A large numbers of people visit these destinations both in the summer (e.g. hikers and cyclists) and in the winter (e.g. hikers and skiers), which threatens sustainability and creates problems regarding the management of these areas. A comprehensive understanding of visitor use, including visitors’ attitudes and perceptions, is fundamental for effective park management. Most research in these national parks is carried out during the summer season, therefore different results in the winter season are expected. Using a standardised socio-environmental survey we attempt to find seasonal differences between visitors and their opinions. A total of 2252 questionnaires were gathered. There were 13 common questions for these three national parks, three of them yielded significantly different results between the two seasons (visitors’ nationality, type of accommodation and financial costs). Other differences were detected in one or two national parks.
House Dust Mite Allergy Models—Reliability for Research of Airway Defensive Mechanisms  [PDF]
Tomas Buday, Jana Plevkova
Open Journal of Molecular and Integrative Physiology (OJMIP) , 2014, DOI: 10.4236/ojmip.2014.43004
Extensive research of respiratory physiology and diseases of the airways and lungs provides better understanding of mechanisms of diseases and it is a source of new data with potential clinical application. The majority of the data in the field of airway defensive reflexes were obtained from guinea pig model, as the most convenient one. Neurophysiology and neuropharma-cology of the cough reflex—which is exclusively mediated by the vagus nerve, share close similarities between guinea pigs and humans. The models used to study pathological processes and their influence on airway-defensive reflexes use sensitization with ovalbumin—the protein from chicken egg, which does not mimic allergies within human respiratory system. House dust mites (HDM) (Dermatophagoides pteronyssius and Dermatophagoides farinae) represent frequent human aeroallergens, however the HDM models are used considerably less than ovalbumin models. The primary objective of this review is to focus on already validated models of HDM-induced airway diseases to see, whether some of them are suitable to study mechanisms of peripheral cough plasticity in a condition of HDM-induced pathological processes. The main purpose of future use and validation of HDM model is to produce higher ability to translate the results obtained in animal models to human cough research.
Sphingoid Base Metabolism in Yeast: Mapping Gene Expression Patterns Into Qualitative Metabolite Time Course Predictions
Tomas Radivoyevitch
Comparative and Functional Genomics , 2001, DOI: 10.1002/cfg.106
Abstract: Can qualitative metabolite time course predictions be inferred from measured mRNA expression patterns? Speaking against this possibility is the large number of ‘decoupling’ control points that lie between these variables, i.e. translation, protein degradation, enzyme inhibition and enzyme activation. Speaking for it is the notion that these control points might be coordinately regulated such that action exerted on the mRNA level is informative of action exerted on the protein and metabolite levels. A simple kinetic model of sphingoid base metabolism in yeast is postulated. When the enzyme activities in this model are modulated proportional to mRNA expression levels measured in heat shocked yeast, the model yields a transient rise and fall in sphingoid bases followed by a permanent rise in ceramide. This finding is in qualitative agreement with experiments and is thus consistent with the aforementioned coordinated control system hypothesis.
Simulation Study of Building Integrated Solar Liquid PV-T Collectors
Tomas Matuska
International Journal of Photoenergy , 2012, DOI: 10.1155/2012/686393
Abstract: Influence of building integration of polycrystalline PV modules on their performance and potential for use of active liquid cooling by use of BIPV-T collectors has been investigated by simulation analysis with a detailed model. Integration of PV modules into building envelope could reduce the annual production of electricity by a rate above 5% and negatively influence lifetime due to thermal stresses induced by high operation temperatures above 100°C in the case of warm climate and above 90°C in moderate climate. Two configurations of unglazed PV-T collectors (low-tech, high-tech) and their ability to eliminate overheating of BIPV module have been discussed. Simulation study on combined heat and electricity production from given BIPV-T collectors has been presented for three typical applications (5°C: primary circuits of heat pumps; 15°C: cold water preheating; 25°C: pool water preheating). Thermal output of unglazed BIPV-T collectors is up to 10 times higher than electricity. Electricity production could be up to 25% higher than BIPV (without cooling) for warm climate and up to 15% in moderate climate. 1. Introduction Utilization of solar energy being a scarce energy source needs a large area of south-facing collecting surfaces. Rational use of building envelopes for the collection of solar energy and its conversion to required energy carrier results into integration of active solar devices into the building envelope structure and leads to multifunctional or hybrid solar collector configurations combining several purposes (heat and electricity generation, daylighting, and air-liquid) in a single unit [1]. The integration of solar collectors into building envelope instead of separate installation represents a transition from the concept of envelope considered as an energy loss to envelope being an energy source—energy active envelope—which actually means a way to solar active buildings. As photovoltaic modules are getting more and more common in sustainable buildings in order to compensate the electricity consumption by electricity production on site, the combination of photovoltaic and solar thermal technology in hybrid PV-T collectors could represent a step further with combined heat and power production (solar cogeneration). Standard commercial PV modules cannot convert more than 15% of incident solar radiation to electricity, the rest of energy is converted to waste heat which increases temperature of PV cell. The rise of PV cell temperature affects negatively the efficiency of photovoltaic solar/electricity conversion. Aesthetically preferred
Purification of Tropomyosin, Paramyosin, Actin, Tubulin, Troponin and Kinases for Chemiproteomics and Its Application to Different Scientific Fields
Tomas Erban
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0022860
Abstract: Background p-aminobenzamidine (p-ABA) is used as a ligand in the purification of many serine proteases and in their removal from heterogeneous samples. Moreover, p-ABA has a potent ability to bind Ca2+-binding proteins. The binding ability and use of p-ABA in purification processes is still not fully understood. Methodology/Principal Findings A p-Aminobenzamidine (p-ABA) ligand enabled the purification of the panallergenic proteins tropomyosin and paramyosin, as well as actin, tubulin, troponin and several kinases and annexins, with variable specificity depending on the tissue source and slight modifications to the purification process. The high affinity of p-ABA to tropomyosin, paramyosin, actin, troponin and myosin is calcium-dependent, since calcium regulates the function of these proteins. In addition, p-ABA probably simulates phosphorylated serine and therefore purified appropriate kinases. Because p-ABA binds to calcium-dependent proteins, and probably those with binding sites containing serine, it is not a suitable inhibitor of proteolysis during the purification of such proteins. p-ABA is widely used to inhibit proteases during protein purification processes, but it is used in columns here to purify non-protease proteins. Two strategies were applied; the first was the inactivation of proteases that were not of interest using protease inhibitors. The second strategy employed was the use of a Ca2+ wash solution to remove calcium-dependent proteins. The removal of calcium-dependent proteins from rabbit hind muscle pointed out even more selective purification. It is possible to obtain two purified samples: a) calcium dependent proteins and b) calcium independent proteins. Moreover, p-ABA may be useful as a model to study processes involving the phosphorylation of serine. Conclusion A p-Aminobenzamidine (p-ABA) ligand enabled the purification of non-protease proteins, with variable specificity depending on the tissue source and slight modifications to the purification process. The method is applicable to various scientific branches, but is especially practical for medicinal applications.
Mass action models versus the Hill model: An analysis of tetrameric human thymidine kinase 1 positive cooperativity
Tomas Radivoyevitch
Biology Direct , 2009, DOI: 10.1186/1745-6150-4-49
Abstract: Mass action models of tetrameric human thymidine kinase 1 (TK1) activity data were formed as pairs of plausible hypotheses that per site activities and binary dissociation constants are equal within contiguous stretches of the number of substrates bound. Of these, six 3-parameter models were fitted to 5 different datasets. Akaike's Information Criterion was then used to form model probability weighted averages. The literature average of the 5 model averages was K = (0.85, 0.69, 0.65, 0.51) μM and k = (3.3, 3.9, 4.1, 4.1) sec-1 where K and k are per-site binary dissociation constants and activities indexed by the number of substrates bound to the tetrameric enzyme.The TK1 model presented supports both K and k positive cooperativity. Three-parameter mass action models can and should replace the 3-parameter Hill model.This article was reviewed by Philip Hahnfeldt, Fangping Mu (nominated by William Hlavacek) and Rainer Sachs.The Hill model [1] characterizes cooperativity with a single number, but it cannot discriminate cooperativity mediated by enzyme activity changes versus substrate binding affinity changes. In contrast, models based on the equilibrium concept of mass action (Eqs. 2-4 below) accomplish this, but to be used, methods that deal with multiple models and models that are over-parameterized [2] need to be developed.This paper yields a literature model of tetrameric human thymidine kinase 1 (TK1) activity data [3-7] that could be used in network models of dNTP supply [8]. TK1 is important because it rate-limits the absorption of thymidine and analogs such as the cancer imaging marker 3'-18 F-fluoro-3'-deoxy-fluorothymidine (FLT) [9,10].The empirical Hill model of the average activity of an enzyme per catalytic site as a function of the total substrate concentration [ST] iswhere kmax is the maximum activity obtained in the limit of high/saturating substrate concentrations, S50 is the total substrate concentration at k = 1/2kmax, and if the Hill coefficient h i
Automated mass action model space generation and analysis methods for two-reactant combinatorially complex equilibriums: An analysis of ATP-induced ribonucleotide reductase R1 hexamerization data
Tomas Radivoyevitch
Biology Direct , 2009, DOI: 10.1186/1745-6150-4-50
Abstract: Thousands of ATP-induced R1 hexamerization models with up to three (s, a and h) ATP binding sites per R1 subunit were automatically generated via hypotheses that complete dissociation constants are infinite and/or that binary dissociation constants are equal. To limit the model space size, it was assumed that s-sites are always filled in oligomers and never filled in monomers, and to interpret model terms it was assumed that a-sites fill before h-sites. The models were fitted to published dynamic light scattering data. As the lowest Akaike Information Criterion (AIC) of the 3-parameter models was greater than the lowest of the 2-parameter models, only models with up to 3 parameters were fitted. Models with sums of squared errors less than twice the minimum were then partitioned into two groups: those that contained no occupied h-site terms (508 models) and those that contained at least one (1580 models). Normalized AIC densities of these two groups of models differed significantly in favor of models that did not include an h-site term (Kolmogorov-Smirnov p < 1 × 10-15); consistent with this, 28 of the top 30 models (ranked by AICs) did not include an h-site term and 28/30 > 508/2088 with p < 2 × 10-15. Finally, 99 of the 2088 models did not have any terms with ATP/R1 ratios >1.5, but of the top 30, there were 14 such models (14/30 > 99/2088 with p < 3 × 10-16), i.e. the existence of R1 hexamers with >3 a-sites occupied by ATP is also not supported by this dataset.The analysis presented suggests that three a-sites may not be occupied by ATP in R1 hexamers under the conditions of the data analyzed. If a-sites fill before h-sites, this implies that the dataset analyzed can be explained without the existence of an h-site.This article was reviewed by Ossama Kashlan (nominated by Philip Hahnfeldt), Bin Hu (nominated by William Hlavacek) and Rainer Sachs.The dNTP supply system produces dNTPs at rates that match those demanded by DNA replication and repair. With respect to
A two-way interface between limited Systems Biology Markup Language and R
Tomas Radivoyevitch
BMC Bioinformatics , 2004, DOI: 10.1186/1471-2105-5-190
Abstract: A model structure that parallels SBML to a limited degree is defined in R. An interface between this structure and SBML is provided through two function definitions: write.SBML() which maps this R model structure to SBML level 2, and read.SBML() which maps a limited range of SBML level 2 files back to R. A published model of purine metabolism is provided in this SBML-like format and used to test the interface. The model reproduces published time course responses before and after its mapping through SBML.List infrastructure preexisting in R makes it well-suited for manipulating SBML models. Further developments of this SBML-R interface seem to be warranted.Systems biology markup language (SBML) is a standard for representing dynamical systems of biological interest [1,2]. Interfaces between SBML and high level computational environments are currently being developed for Mathematica [3] and Matlab [4], but to the author's knowledge, no such efforts are being carried forth for R/S-plus. This brief paper presents the author's initial developments toward a two-way SBML-R interface. The interface is currently limited in the range of SBML input files that it can handle. For example, it only handles SBML level 2 and does not handle "Events" and "FunctionDefinitions." The interface can nevertheless be used for some models, examples [5,6] of which are included under "demo" in the SBMLR package [7]. This paper provides an explicit example of one approach to an SBML-R interface. It is assumed throughout that the reader is already quite familiar with both SBML [8] and R [9].The software exists completely in R. It is comprised of four functions and is currently being distributed as a developmental package called "SBMLR" through Bioconductor [10]. The software was written subject to two constraints: 1) models expressed in SBML-like R must be exchangeable with a range of SBML models; and 2) models must be amenable to simulation in R. The first subsection that follows defines an SBM
Equilibrium model selection: dTTP induced R1 dimerization
Tomas Radivoyevitch
BMC Systems Biology , 2008, DOI: 10.1186/1752-0509-2-15
Abstract: A framework is presented in which equilibriums are modeled as pairs (g, h) where g = 0 maps total reactant concentrations (system inputs) into free reactant concentrations (system states) which h then maps into expected values of measurements (system outputs). By letting dissociation constants Kd be either freely estimated, infinity, zero, or equal to other Kd, and by letting undamaged protein fractions be either freely estimated or 1, many g models are formed. A standard space of g models for ligand-induced protein dimerization equilibria is given. Coupled to an h model, the resulting (g, h) were fitted to dTTP induced R1 dimerization data (R1 is the large subunit of ribonucleotide reductase). Models with the fewest parameters were fitted first. Thereafter, upon fitting a batch, the next batch of models (with one more parameter) was fitted only if the current batch yielded a model that was better (based on the Akaike Information Criterion) than the best model in the previous batch (with one less parameter). Within batches models were fitted in parallel. This semi-exhaustive approach yielded the same best models as an exhaustive model space fit, but in approximately one-fifth the time.Comprehensive model space based biochemical equilibrium model selection methods are realizable. Their significance to systems biology as mappings of data into mathematical models warrants their development.Ribonucleotide reductase (RNR) has a small subunit R2 that exists almost exclusively as a dimer, and a large subunit R1 that dimerizes when dTTP, dGTP, dATP, or ATP binds to its specificity site, and hexamerizes when dATP or ATP binds to its activity site [1-6]. Thus, R1 is the backbone of a biochemical equilibrium network that contains a large number of R1 complexes. This network has more dissociation constants (Kd) than can be estimated from currently available data, so assumptions must be made to reduce the number of independent Kd. These assumptions come in two forms: those that
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