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Search Results: 1 - 10 of 1834 matches for " Rok Ga?pari? "
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Miocene pteropods from Poli ki Vrh in Slovenske gorice, northeast Slovenia
Vasja Miku?,Rok Gapari,Milo? Bartol,Aleksander Horvat
Geologija , 2012,
Abstract: In the paper relatively modestly preserved but very numerous pteropod remains from Middle Miocene – Badenianmicaceous marlstones of Poli~ki Vrh locality in Slovenske gorice, northeastern part of Slovenia are described.The fossils were attributed to the pteropod family Cliidae Jeffreys, 1869, respectively the species Clio pedemontana(Mayer, 1868). They represent the first documented finds of this species in Slovenia, and so far also the southernmostoccurrence of the pteropods belonging to this species in Neogene beds of the Styrian basin in the Central Paratethys.
Comparison of different real-time PCR chemistries and their suitability for detection and quantification of genetically modified organisms
Meti Buh Gapari, Katarina Cankar, Jana ?el, Kristina Gruden
BMC Biotechnology , 2008, DOI: 10.1186/1472-6750-8-26
Abstract: Amplicons were designed on the maize invertase gene and the 5'-junction of inserted transgene and plant genomic DNA in MON 810 event. Real-time assays were subsequently compared for their efficiency in PCR amplification, limits of detection and quantification, repeatability and accuracy to test the performance of the assays. Additionally, the specificity of established assays was checked on various transgenic and non-transgenic plant species. The overall applicability of the designed assays was evaluated, adding practicability and costs issues to the performance characteristics.Although none of the chemistries significantly outperformed the others, there are certain characteristics that suggest that LNA? technology is an alternative to TaqMan? when designing assays for quantitative analysis. Because LNA? probes are much shorter they might be especially appropriate when high specificity is required and where the design of a common TaqMan? probe is difficult or even impossible due to sequence characteristics. Plexor? on the other hand might be a method of choice for qualitative analysis when sensitivity, low cost and simplicity of use prevail.Real-time quantitative PCR (Q-PCR) is the state-of-the-art technology for the quantification of nucleic acids, both in gene expression analysis and in routine DNA quantification, and is becoming ubiquitous in research and diagnostics of various fields. Because of its prominence, several new Q-PCR detection chemistries were developed, reaching approximately 20 different at present [1]. Of all TaqMan? and/or SYBR? Green chemistries are being the most widely used [2]. The reason could lie in the numerous data available on the performance of these two methods, while only a few comparisons of the performance of alternative chemistries have been published [3-5].The detection of genetically modified (GM) components is a challenging application of Q-PCR since exact quantification and the ability to detect trace amounts of GM material in
Corporate identity in wood processing and furniture manufacturing in the Republic of Croatia
Kristina Bi?ani?,Denis Jela?i?,Vanja Gapari,Vesna Carev-La?karin
Drvna Industrija , 2009,
Abstract: Corporate identity was defined differently by different authors and its unique definition was not established, but it is most certainly the soul of each enterprise that is based on history, environment, previous development and recognition on the market. This paper deals with the perception of corporate identity in wood processing and furniture manufacturing companies in the Republic of Croatia. Research was conducted as a survey using questionnaires containing general information about the enterprise and 10 questions regarding the perception of corporate identity. 210 enterprises for wood processing and furniture manufacturing were surveyed and 43 (20.47 %) of them answered to all the questions, of which 35 (16.67 %) were taken into consideration. The given data were analyzed statistically using X2-test. The results showed that corporate identity in Croatian wood processing and furniture manufacturing companies was mostly defined by and identified with the company’s visual presentation, image and recognizability and differentiation in the market. At the same time, most surveyees thought that corporate identity is mostly made of the company’s design, company’s external communication and its philosophy.
Computational Protein Engineering: Bridging the Gap between Rational Design and Laboratory Evolution
Alexandre Barrozo,Rok Borstnar,Ga?l Marloie,Shina Caroline Lynn Kamerlin
International Journal of Molecular Sciences , 2012, DOI: 10.3390/ijms131012428
Abstract: Enzymes are tremendously proficient catalysts, which can be used as extracellular catalysts for a whole host of processes, from chemical synthesis to the generation of novel biofuels. For them to be more amenable to the needs of biotechnology, however, it is often necessary to be able to manipulate their physico-chemical properties in an efficient and streamlined manner, and, ideally, to be able to train them to catalyze completely new reactions. Recent years have seen an explosion of interest in different approaches to achieve this, both in the laboratory, and in silico. There remains, however, a gap between current approaches to computational enzyme design, which have primarily focused on the early stages of the design process, and laboratory evolution, which is an extremely powerful tool for enzyme redesign, but will always be limited by the vastness of sequence space combined with the low frequency for desirable mutations. This review discusses different approaches towards computational enzyme design and demonstrates how combining newly developed screening approaches that can rapidly predict potential mutation “hotspots” with approaches that can quantitatively and reliably dissect the catalytic step can bridge the gap that currently exists between computational enzyme design and laboratory evolution studies.
Insertion of a Specific Fungal 3′-phosphoadenosine-5′-phosphatase Motif into a Plant Homologue Improves Halotolerance and Drought Tolerance of Plants
Meti Buh Gapari, Metka Lenassi, Cene Gostin?ar, Ana Rotter, Ana Plemenita?, Nina Gunde-Cimerman, Kristina Gruden, Jana ?el
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0081872
Abstract: Soil salinity and drought are among the most serious agricultural and environmental problems of today. Therefore, investigations of plant resistance to abiotic stress have received a lot of attention in recent years. In this study, we identified the complete coding sequence of a 3′-phosphoadenosine-5′-phosphatase protein, ApHal2, from the halotolerant yeast Aureobasidium pullulans. Expression of the ApHAL2 gene in a Saccharomyces cerevisiae hal2 mutant complemented the mutant auxotrophy for methionine, and rescued the growth of the hal2 mutant in media with high NaCl concentrations. A 21-amino-acids-long region of the ApHal2 enzyme was inserted into the Arabidopsis thaliana homologue of Hal2, the SAL1 phosphatase. The inserted sequence included the META motif, which has previously been implicated in increased sodium tolerance of the Hal2 homologue from a related fungal species. Transgenic Arabidopsis plants overexpressing this modified SAL1 (mSAL1) showed improved halotolerance and drought tolerance. In a medium with an elevated salt concentration, mSAL1-expressing plants were twice as likely to have roots in a higher length category in comparison with the wild-type Arabidopsis and with plants overexpressing the native SAL1, and had 5% to 10% larger leaf surface area under moderate and severe salt stress, respectively. Similarly, after moderate drought exposure, the mSAL1-expressing plants showed 14% increased dry weight after revitalisation, with no increase in dry weight of the wild-type plants. With severe drought, plants overexpressing native SAL1 had the worst rehydration success, consistent with the recently proposed role of SAL1 in severe drought. This was not observed for plants expressing mSAL1. Therefore, the presence of this fungal META motif sequence is beneficial under conditions of increased salinity and moderate drought, and shows no drawbacks for plant survival under severe drought. This demonstrates that adaptations of extremotolerant fungi should be considered as a valuable resource for improving stress-tolerance in plant breeding in the future.
An Optimization Prototype for Distribution Planning
Rok Strasek
Lecture Notes in Engineering and Computer Science , 2011,
Kondo screening in high-spin side-coupled two-impurity clusters
Rok Zitko
Physics , 2009, DOI: 10.1088/0953-8984/22/2/026002
Abstract: We study the system of two magnetic impurities described by a two-impurity Kondo model where only the first impurity couples directly to the conduction band, while the second impurity interacts with the first through Heisenberg exchange coupling in a "side-coupled" configuration. We consider various choices of the impurity spins (S_1S_2) and we contrast the regimes where the inter-impurity exchange coupling J is either lower or higher than the Kondo temperature T_K^(0) of the first impurity in the absence of the second. This model is a high-spin generalization of the two-impurity model for side-coupled double quantum dots which corresponds to the simplest S_1=S_2=1/2 case, where the moments are Kondo screened successively in two stages for J= S_1. For S_1 >= 1, the second Kondo temperature T_K^(2) is not exponentially reduced, as for S_1 = 1/2, but is approximately a power-law function of the coupling J. Furthermore, for S_1 >=1 1 all three scales (T_K^(0), J, T_K^(2)) explicitly appear in the temperature-dependence of the thermodynamic properties. For S_1 > S_2, there is no second stage of screening for JT_K^(0) the Kondo screening of the effective spin S_1-S_2 is found.
NRG calculations of the ground-state energy: application to the correlation effects in the adsorption of magnetic impurities on metal surfaces
Rok Zitko
Physics , 2009, DOI: 10.1103/PhysRevB.79.233105
Abstract: The ground-state energy of a quantum impurity model can be calculated using the numerical renormalization group with a modified discretization scheme, with sufficient accuracy to reliably extract physical information about the system. The approach is applied to study binding of magnetic adsorbates modeled by the Anderson-Newns model for chemisorption on metal surfaces. The correlation energy is largest in the valence-fluctuation regime; in the strong-coupling (Kondo) regime the Kondo-singlet formation energy is found to be only a minor contribution. As an application of the method to more difficult surface-science problems, we study the binding energy of a magnetic atom adsorbed near a step edge on a surface with a strongly modulated surface-state electron density. The zero-temperature magnetic susceptibility is determined from the field dependence of the binding energy, thereby providing an independent result for the Kondo temperature TK, which agrees very well with the TK extracted from a thermodynamic calculation.
Convergence acceleration and stabilization for dynamical-mean-field-theory calculations
Rok Zitko
Physics , 2009, DOI: 10.1103/PhysRevB.80.125125
Abstract: The convergence to the self-consistency in the dynamical-mean-field-theory (DMFT) calculations for models of correlated electron systems can be significantly accelerated by using an appropriate mixing of hybridization functions which are used as the input to the impurity solver. It is shown that the techniques and the past experience with the mixing of input charge densities in the density-functional-theory (DFT) calculations are also effective in DMFT. As an example, the increase of the computational requirements near the Mott metal-insulator transition in the Hubbard model due to critical slowing down can be strongly reduced by using the modified Broyden's method to numerically solve the non-linear self-consistency equation. Speed-up factors as high as 3 were observed in practical calculations even for this relatively well behaved problem. Furthermore, the convergence can be achieved in difficult cases where simple linear mixing is either not effective or even leads to divergence. Unstable and metastable solutions can also be obtained. We also determine the linear response of the system with respect to the variations of the hybridization function, which is related to the propagation of the information between the different energy scales during the iteration.
Adaptive logarithmic discretization for numerical renormalization group methods
Rok Zitko
Physics , 2009, DOI: 10.1016/j.cpc.2009.02.007
Abstract: The problem of the logarithmic discretization of an arbitrary positive function (such as the density of states) is studied in general terms. Logarithmic discretization has arbitrary high resolution around some chosen point (such as Fermi level) and it finds application, for example, in the numerical renormalization group (NRG) approach to quantum impurity problems (Kondo model), where the continuum of the conduction band states needs to be reduced to a finite number of levels with good sampling near the Fermi level. The discretization schemes under discussion are required to reproduce the original function after averaging over different interleaved discretization meshes, thus systematic deviations which appear in the conventional logarithmic discretization are eliminated. An improved scheme is proposed in which the discretization-mesh points themselves are determined in an adaptive way; they are denser in the regions where the function has higher values. Such schemes help in reducing the residual numeric artefacts in NRG calculations in situations where the density of states approaches zero over extended intervals. A reference implementation of the solver for the differential equations which determine the full set of discretization coefficients is also described.
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