Showing papers by "Jožef Stefan Institute published in 2006"
TL;DR: In this article, a review of the basic ideas and techniques of spectral density functional theory which are currently used in electronic structure calculations of strongly correlated materials where the one-dimensional electron description breaks down is presented.
Abstract: We present a review of the basic ideas and techniques of the spectral density functional theory which are currently used in electronic structure calculations of strongly{correlated materials where the one{electron description breaks down. We illustrate the method with several examples where interactions play a dominant role: systems near metal{insulator transition, systems near volume collapse transition, and systems with local moments.
1,921 citations
TL;DR: The status of human protease research and prospects for future protease-targeted drugs are reviewed, with reference to some key examples where protease drugs have succeeded or failed.
Abstract: Far from being simple degradative enzymes, proteases are now seen as key signalling molecules and desirable drug targets in several diseases. Turk discusses our success so far at targeting proteases and how these enzymes might be exploited therapeutically in the future. Until fairly recently, proteases were considered primarily to be protein-degrading enzymes. However, this view has dramatically changed and proteases are now seen as extremely important signalling molecules that are involved in numerous vital processes. Protease signalling pathways are strictly regulated, and the dysregulation of protease activity can lead to pathologies such as cardiovascular and inflammatory diseases, cancer, osteoporosis and neurological disorders. Several small-molecule drugs targeting proteases are already on the market and many more are in development. The status of human protease research and prospects for future protease-targeted drugs are reviewed here, with reference to some key examples where protease drugs have succeeded or failed.
1,233 citations
TL;DR: It is shown that colloidal particles confined to a few-micrometer-thick layer of a nematic liquid crystal form two-dimensional crystal structures that are bound by topological defects.
Abstract: The ability to generate regular spatial arrangements of particles is an important technological and fundamental aspect of colloidal science We showed that colloidal particles confined to a few-micrometer-thick layer of a nematic liquid crystal form two-dimensional crystal structures that are bound by topological defects Two basic crystalline structures were observed, depending on the ordering of the liquid crystal around the particle Colloids inducing quadrupolar order crystallize into weakly bound two-dimensional ordered structure, where the particle interaction is mediated by the sharing of localized topological defects Colloids inducing dipolar order are strongly bound into antiferroelectric-like two-dimensional crystallites of dipolar colloidal chains Self-assembly by topological defects could be applied to other systems with similar symmetry
699 citations
TL;DR: It is shown that on approaching the critical point, both the energy cost and the electric field necessary to induce ferroelectric polarization rotations decrease significantly, thus explaining the giant electromechanical response of these relaxors.
Abstract: The direct conversion of electrical energy to mechanical work by a material is relevant to a number of applications. This is illustrated by ferroelectric 'relaxors' such as Pb(Mg(1/3)Nb(2/3))O(3)-PbTiO(3) (PMN-PT; refs 5, 6): these materials exhibit a giant electromechanical (piezoelectric) response that is finding use in ultrasonic and medical applications, as well as in telecommunications. The origins of this effect are, however, still unclear. Here we show that the giant electromechanical response in PMN-PT (and potentially other ferroelectric relaxors) is the manifestation of critical points that define a line in the phase diagram of this system. Specifically, in the electric-field-temperature-composition phase diagram of PMN-PT (the composition being varied by changing the PT concentration), a first-order paraelectric-ferroelectric phase transition terminates in a line of critical points where the piezoelectric coefficient is maximum. Above this line, supercritical evolution is observed. On approaching the critical point, both the energy cost and the electric field necessary to induce ferroelectric polarization rotations decrease significantly, thus explaining the giant electromechanical response of these relaxors.
603 citations
TL;DR: Nyten et al. as discussed by the authors reported preparation and preliminary testing of Li 2 FeSiO 4, a representative of a new class of Li storage materials, and revealed partial occupation of alternate tetrahedral sites by Li and Mn.
433 citations
TL;DR: In this article, the porosity of porous LiMPO4/C composites with micro-sized particles was discussed in terms of qualitative results obtained from SEM micrographs and quantitative results from N2 adsorption isotherms.
263 citations
TL;DR: The hydrodynamic flow field generated far from a cilium which is attached to a surface and beats periodically is calculated and a state diagram where synchronized states occur as a function of the distance of cilia and the relative orientation of their beat is presented.
Abstract: We calculate the hydrodynamic flow field generated far from a cilium which is attached to a surface and beats periodically. In the case of two beating cilia, hydrodynamic interactions can lead to synchronization of the cilia, which are nonlinear oscillators. We present a state diagram where synchronized states occur as a function of the distance of cilia and the relative orientation of their beat. Synchronized states occur with different relative phases. In addition, asynchronous solutions exist. Our work could be relevant for the synchronized motion of cilia generating hydrodynamic flows on the surface of cells.
217 citations
TL;DR: PCR efficiency is the crucial parameter determining the reliability of quantitative results, therefore it was chosen as the primary criterion by which to evaluate the quality and performance on different matrixes and extraction techniques.
Abstract: Real-time PCR is the technique of choice for nucleic acid quantification. In the field of detection of genetically modified organisms (GMOs) quantification of biotech products may be required to fulfil legislative requirements. However, successful quantification depends crucially on the quality of the sample DNA analyzed. Methods for GMO detection are generally validated on certified reference materials that are in the form of powdered grain material, while detection in routine laboratories must be performed on a wide variety of sample matrixes. Due to food processing, the DNA in sample matrixes can be present in low amounts and also degraded. In addition, molecules of plant origin or from other sources that affect PCR amplification of samples will influence the reliability of the quantification. Further, the wide variety of sample matrixes presents a challenge for detection laboratories. The extraction method must ensure high yield and quality of the DNA obtained and must be carefully selected, since even components of DNA extraction solutions can influence PCR reactions. GMO quantification is based on a standard curve, therefore similarity of PCR efficiency for the sample and standard reference material is a prerequisite for exact quantification. Little information on the performance of real-time PCR on samples of different matrixes is available. Five commonly used DNA extraction techniques were compared and their suitability for quantitative analysis was assessed. The effect of sample matrix on nucleic acid quantification was assessed by comparing 4 maize and 4 soybean matrixes. In addition 205 maize and soybean samples from routine analysis were analyzed for PCR efficiency to assess variability of PCR performance within each sample matrix. Together with the amount of DNA needed for reliable quantification, PCR efficiency is the crucial parameter determining the reliability of quantitative results, therefore it was chosen as the primary criterion by which to evaluate the quality and performance on different matrixes and extraction techniques. The effect of PCR efficiency on the resulting GMO content is demonstrated. The crucial influence of extraction technique and sample matrix properties on the results of GMO quantification is demonstrated. Appropriate extraction techniques for each matrix need to be determined to achieve accurate DNA quantification. Nevertheless, as it is shown that in the area of food and feed testing matrix with certain specificities is impossible to define strict quality controls need to be introduced to monitor PCR. The results of our study are also applicable to other fields of quantitative testing by real-time PCR.
213 citations
TL;DR: It is concluded that, although there is no evidence to doubt the existence of the HP and HL pathways reciprocally inhibiting one another, it appears that such a mechanism is of little consequence when comparing the effects of nonthermal factors on the thermoregulatory system.
Abstract: The set point has been used to define the regulated level of body temperature, suggesting that displacements of core temperature from the set point initiate heat production (HP) and heat loss (HL) responses. Human and animal experiments have demonstrated that the responses of sweating and shivering do not coincide at a set point but rather establish a thermoeffector threshold zone. Neurophysiological studies have demonstrated that the sensor-to-effector pathways for HP and HL overlap and, in fact, mutually inhibit each other. This reciprocal inhibition theory, presumably reflecting the manner in which thermal factors contribute to homeothermy in humans, does not incorporate the effect of nonthermal factors on temperature regulation. The present review examines the actions of these nonthermal factors within the context of neuronal models of temperature regulation, suggesting that examination of these factors may provide further insights into the nature of temperature regulation. It is concluded that, although there is no evidence to doubt the existence of the HP and HL pathways reciprocally inhibiting one another, it appears that such a mechanism is of little consequence when comparing the effects of nonthermal factors on the thermoregulatory system, since most of these factors seem to exert their influence in the region after the reciprocal cross-inhibition. At any given moment, both thermal and several nonthermal factors will be acting on the thermoregulatory system. It may, therefore, not be appropriate to dismiss the contribution of either when discussing the regulation of body temperature in humans.
183 citations
TL;DR: Results suggest AM development in the metal hyperaccumulating T. praecox is favoured at elevated nutrient demands, e.g. during the reproductive period, and reduced heavy metal uptake, especially at higher soil metal contents, indicates a changed metal tolerance strategy in colonised T. Praecox plants.
178 citations
TL;DR: In this paper, the basic mechanism of low-temperature sintering called reactive liquid-phase Sintering has been explained in detail for the case of BaTiO 3, which was sintered to more than 95% of relative density in 15min at 820°C.
Abstract: We explain the basic mechanism of the low-temperature sintering called reactive liquid-phase sintering. The mechanism involves the presence of a low-temperature liquid phase that must be able to directly or indirectly accelerate a reaction with the matrix phase. The mechanism is explained in details for the case of the low-temperature sintering of BaTiO 3 , which was sintered to more than 95% of relative density in 15 min at 820 °C. We have applied reactive liquid-phase sintering to a number of different compounds with very different crystal-chemistry characteristics, and managed to sinter them as much as 400 °C below their original sintering temperatures. A thorough understanding of this sintering mechanism makes it possible to closely control the sintering behavior.
18 Sep 2006
TL;DR: In this paper, an empirical study of decision tree approaches to hierarchical multilabel classification (HMC) in the area of functional genomics is presented. And it turns out that HMC tree learning is more robust to overfitting than regular tree learning.
Abstract: Hierarchical multilabel classification (HMC) is a variant of classification where instances may belong to multiple classes organized in a hierarchy. The task is relevant for several application domains. This paper presents an empirical study of decision tree approaches to HMC in the area of functional genomics. We compare learning a single HMC tree (which makes predictions for all classes together) to learning a set of regular classification trees (one for each class). Interestingly, on all 12 datasets we use, the HMC tree wins on all fronts: it is faster to learn and to apply, easier to interpret, and has similar or better predictive performance than the set of regular trees. It turns out that HMC tree learning is more robust to overfitting than regular tree learning.
TL;DR: The authors used soft collinear effective theory (SCET) to predict unmeasured branching ratios, direct, and indirect $CP$ asymmetries in the decay amplitudes of pseudoscalars.
Abstract: Expressions for decay amplitudes of ${\overline{B}}^{0}$, ${B}^{\ensuremath{-}}$, and ${\overline{B}}_{s}^{0}$ mesons to two light pseudoscalar or vector mesons, including isosinglet mesons $\ensuremath{\eta}$, ${\ensuremath{\eta}}^{\ensuremath{'}}$, $\ensuremath{\omega}$, $\ensuremath{\phi}$, are obtained using soft collinear effective theory (SCET) at LO in $1/{m}_{b}$. These are then used to predict unmeasured branching ratios, direct, and indirect $CP$ asymmetries in ${\overline{B}}^{0}$, ${B}^{\ensuremath{-}}$, and ${\overline{B}}_{s}^{0}$ decays into two light pseudoscalars, following a determination of nonperturbative SCET parameters from existing data using a ${\ensuremath{\chi}}^{2}$-fit. A separate discussion of indirect $CP$ asymmetries in penguin dominated ${\overline{B}}^{0}\ensuremath{\rightarrow}{\ensuremath{\eta}}^{{(}^{\ensuremath{'}})}{K}_{S,L}$, ${\ensuremath{\pi}}^{0}{K}_{S,L}$ decays is given.
TL;DR: It may be recommended to replace up to 15 wt% of cement by BA and to use such binder where a low strength of concrete elements is required, although the aggregate used for low strength concrete need not be of a very good quality.
TL;DR: In this review, some specific functions of individual Cys cathepsins are covered and particularly those most relevant to the immune system are covered.
Abstract: Antigen (Ag) processing by major histocompatibility complex class II (MHC) class II molecules is tightly linked with the proteases of the endosomal/lysosomal system Cysteine (Cys) cathepsins, which constitute a major portion of this proteolytic system, have been found to have essential roles in both Ag processing and maturation of the MHC class II molecules In this review, we will cover some specific functions of individual Cys cathepsins and particularly those most relevant to the immune system
TL;DR: The experiences gained from a Matlab/Simulink implementation of ADM1 into the extended COST/IWA Benchmark Simulation Model (BSM2) are presented and the main conclusion is that if implemented properly, the ADm1 will also produce high-quality results in dynamic plant-wide simulations including noise, discrete sub-systems, etc. without imposing any major restrictions due to extensive computational efforts.
TL;DR: In this paper, the stable isotopic composition of hydrogen and oxygen (δ2H and δ18O) and tritium activity (3H) were monitored in monthly precipitation at two continental stations (Ljubljana, Zagreb) and six stations along the eastern Adriatic coasts of Slovenia and Croatia in the period 2001-2003.
TL;DR: Ketones were directly converted to their corresponding gem-dihydroperoxides using a "green" oxidant and a simple catalyst under neutral conditions in acetonitrile.
TL;DR: The aim of the present review was the analysis of data on cystatins from NCBI GEO database and the literature, and obtained in microarray and serial analysis of gene expression (SAGE) experiments, to discuss the expression of cystatin A, B, C, and F in macrophages, dendritic cells and natural killer cells of the immune system.
TL;DR: A pilot-survey study was performed by collecting samples (influent and effluent wastewaters, rivers and tap waters) from different locations in Europe and a detailed study of signal suppression evaluation for analysis of pharmaceutical residues in effluent wastewater is presented.
Abstract: A pilot-survey study was performed by collecting samples (influent and effluent wastewaters, rivers and tap waters) from different locations in Europe (Spain, Belgium, Germany and Slovenia). A solid-phase extraction (SPE) followed by liquid chromatography-tandem mass spectrometry method was applied for the determination of pharmaceuticals (ibuprofen, naproxen, ketoprofen, diclofenac and clofibric acid). Method detection limits and method quantification limits were at the parts-per-trillion level (7.5-75 ng/L). The recovery rates of the SPE from deionized water and effluent wastewater samples spiked at 100- and 1,000-ng/L levels ranged from 87 to 95%. Identification criteria in compliance with the EU regulation for confirmatory methods of organic residues were applied. A detailed study of signal suppression evaluation for analysis of pharmaceutical residues in effluent wastewaters is presented.
TL;DR: The system for maintaining the versions of the TAUOLA of tau-lepton decay and PHOTOS for radiative corrections in decays and documentation of the programs updates introduced over the last two years are presented.
TL;DR: In this article, the authors discuss the structure of the light Higgs and the role of the Peccei-Quinn symmetry for dark matter and the predictivity of the theory.
Abstract: We discuss the ordinary, nonsupersymmetric SO(10) as a theory of fermion masses and mixings. We construct two minimal versions of the Yukawa sector based on ${\overline{\mathbf{126}}}_{\mathbf{H}}$ and either ${\mathbf{10}}_{\mathbf{H}}$ or ${\mathbf{120}}_{\mathbf{H}}$. The latter case is of particular interest since it connects the absolute neutrino mass scale with the size of the atmospheric mixing angle ${\ensuremath{\theta}}_{A}$. It also relates the smallness of ${V}_{cb}$ with the largeness of ${\ensuremath{\theta}}_{A}$. These results are based on the analytic study of the second and third generations. Furthermore, we discuss the structure of the light Higgs and the role of the Peccei-Quinn symmetry for dark matter and the predictivity of the theory.
TL;DR: The second largest Hg mine in the world, the Idrija Mine, ceased operation in 1995, but still delivers large quantities of Hg downstream including into the northern Adriatic Sea, 100 kilometres away.
TL;DR: In this article, the effects of the type and quantity of metal ions in the ink, as determined by in-air PIXE method, pH of the ink on paper, grammage of paper, its absorptivity and the width of ink lines were evaluated against the extent of corrosion.
TL;DR: In this article, a configurable charge-coupled device (CCD) detector is used in a scanning transmission x-ray microscope to record the transmitted intensity distribution for every pixel in a raster scan of the sample.
Abstract: A configurable charge-coupled-device (CCD) detector is used in a scanning transmission x-ray microscope to record the transmitted intensity distribution for every pixel in a raster scan of the sample. Real-time processing of the CCD frames gives simultaneous absorption and phase contrast image signals from a single scan. The CCD combines fast frame-transfer readout with very high sensitivity and makes use of x-ray to visible-light coupling to allow operation over a wide range of photon energies, from the oxygen K edge upwards. Tests on the Twinmic end station at the Elettra synchrotron are reported.
TL;DR: In this paper, a large glass-forming domain was found for X=Ti, but no glass formation was evidenced for X =Zr within the Bi2O3-XO2-TeO2 (X =Ti, Zr) systems, and the Raman spectra of the glasses were interpreted in terms of the structural transformations produced by the modifiers.
TL;DR: Immunofluorescence experiments showed that both proteins change their subcellular localization during fresh human serum (FHS)-induced PCD migrating into the nucleus, suggesting that the metacaspases might be involved in PCD of the parasite.
Polish Academy of Sciences1, University of Tokyo2, University of Tsukuba3, Toyama National College of Maritime Technology4, University of Sydney5, University of Hawaii6, National Taiwan University7, Princeton University8, University of Melbourne9, Jožef Stefan Institute10, KEK11, Tokyo Institute of Technology12, Osaka University13, Niigata University14, Tohoku University15, Kanagawa University16, Lawrence Berkeley National Laboratory17
01 May 2006-Nuclear Instruments & Methods in Physics Research Section A-accelerators Spectrometers Detectors and Associated Equipment
TL;DR: In this paper, the authors presented a silicon vertex detector (SVD1) of the Belle detector, operating at the high-luminosity asymmetric energy e+e− collider KEKB.
Abstract: The old silicon vertex detector (SVD1) of the Belle detector, operating at the high-luminosity asymmetric energy e+e− collider KEKB, was replaced by an upgraded version (SVD2) in 2003. The new detector has modified geometry and redesigned readout electronics, providing a larger polar angle acceptance, better vertex resolution, improved radiation hardness and reduced dead time. The operation of the detector started successfully in October 2003. The basic concepts of the SVD2 design as well as its performance after 10 months of data taking are described in this paper.
TL;DR: In this article, the interaction of an Nd:YAG laser, operating at 1064 or 532-nm wavelength and pulse duration of 40ps, with titanium implant was studied.
TL;DR: In this article, the sedimentary sequences in three cores, ranging in length from 130 to 320 cm, were investigated through the variability in grain-size parameters, major (Al, Fe, S, N, Ca and Mg) and trace (Ti, Mn, Cr, Ni, Cu, Zn and Hg) elements, organic and inorganic C, δ 13 C and 14 C dating in order to obtain information on paleoenvironmental evolution and the historical development of heavy metal contamination.