Showing papers by "Jožef Stefan Institute published in 2013"
Slovak Academy of Sciences1, Comenius University in Bratislava2, Bulgarian Academy of Sciences3, Spanish National Research Council4, University of Cagliari5, University of Lorraine6, Council of Scientific and Industrial Research7, Jožef Stefan Institute8, Keio University9, Russian Academy of Sciences10, Moscow Institute of Physics and Technology11
TL;DR: The aim of this review article is to provide a comprehensive overview of advances achieved in the field of atomistic processes, phase transformations, simple and multicomponent nanosystems and peculiarities of mechanochemistry.
Abstract: The aim of this review article on recent developments of mechanochemistry (nowadays established as a part of chemistry) is to provide a comprehensive overview of advances achieved in the field of atomistic processes, phase transformations, simple and multicomponent nanosystems and peculiarities of mechanochemical reactions. Industrial aspects with successful penetration into fields like materials engineering, heterogeneous catalysis and extractive metallurgy are also reviewed. The hallmarks of mechanochemistry include influencing reactivity of solids by the presence of solid-state defects, interphases and relaxation phenomena, enabling processes to take place under non-equilibrium conditions, creating a well-crystallized core of nanoparticles with disordered near-surface shell regions and performing simple dry time-convenient one-step syntheses. Underlying these hallmarks are technological consequences like preparing new nanomaterials with the desired properties or producing these materials in a reproducible way with high yield and under simple and easy operating conditions. The last but not least hallmark is enabling work under environmentally friendly and essentially waste-free conditions (822 references).
908 citations
TL;DR: A strategy to design self-assembling polypeptide nanostructured polyhedra, based on modularization using orthogonal dimerizing segments, which provides the basis for construction of new topological polyPEptide folds based on the set of Orthogonal interacting polypePTide segments.
Abstract: Protein structures evolved through a complex interplay of cooperative interactions, and it is still very challenging to design new protein folds de novo. Here we present a strategy to design self-assembling polypeptide nanostructured polyhedra based on modularization using orthogonal dimerizing segments. We designed and experimentally demonstrated the formation of the tetrahedron that self-assembles from a single polypeptide chain comprising 12 concatenated coiled coil-forming segments separated by flexible peptide hinges. The path of the polypeptide chain is guided by a defined order of segments that traverse each of the six edges of the tetrahedron exactly twice, forming coiled-coil dimers with their corresponding partners. The coincidence of the polypeptide termini in the same vertex is demonstrated by reconstituting a split fluorescent protein in the polypeptide with the correct tetrahedral topology. Polypeptides with a deleted or scrambled segment order fail to self-assemble correctly. This design platform provides a foundation for constructing new topological polypeptide folds based on the set of orthogonal interacting polypeptide segments.
283 citations
TL;DR: The AcerMC Monte Carlo generator is dedicated to the generation of Standard Model background processes which were recognised as critical for the searches at LHC, and generation of which was either unavailable or not straightforward so far.
268 citations
TL;DR: This paper develops methods for learning two types of ensembles (bagging and random forests) of predictive clustering trees for global and local predictions of different types of structured outputs, and proposes to build ensemble models consisting of predictive clustered trees, which generalize classification trees.
252 citations
TL;DR: N nanometre-sized ferromagnetic platelets suspended in a nematic liquid crystal can order ferromagnetically on quenching from the isotropic phase, and may find use in magneto-optic devices.
Abstract: More than four decades ago, Brochard and de Gennes proposed that colloidal suspensions of ferromagnetic particles in nematic (directionally ordered) liquid crystals could form macroscopic ferromagnetic phases at room temperature. The experimental realization of these predicted phases has hitherto proved elusive, with such systems showing enhanced paramagnetism but no spontaneous magnetization in the absence of an external magnetic field. Here we show that nanometre-sized ferromagnetic platelets suspended in a nematic liquid crystal can order ferromagnetically on quenching from the isotropic phase. Cooling in the absence of a magnetic field produces a polydomain sample exhibiting the two opposing states of magnetization, oriented parallel to the direction of nematic ordering. Cooling in the presence of a magnetic field yields a monodomain sample; magnetization can be switched by domain wall movement on reversal of the applied magnetic field. The ferromagnetic properties of this dipolar fluid are due to the interplay of the nematic elastic interaction (which depends critically on the shape of the particles) and the magnetic dipolar interaction. This ferromagnetic phase responds to very small magnetic fields and may find use in magneto-optic devices. The idea that magnetic particles suspended in a liquid crystal might spontaneously orient into a ferromagnetic state has hitherto not been confirmed experimentally, but such a state has now been realized using nanometre-sized ferromagnetic platelets in a nematic liquid crystal. The idea that magnetic particles suspended in a liquid crystal might spontaneously orient into a ferromagnetic state has been around for decades but had not been confirmed experimentally. Alenka Mertelj and colleagues have now realized such a state using nanosized ferromagnetic platelets in a nematic liquid crystal. The shape of the thin platelets is key to the development of ferromagnetic ordering. The resulting 'liquid magnet' phase responds to very small magnetic fields and may lead to new magneto–optic devices.
247 citations
TL;DR: To augment the removal of pharmaceuticals different conventional and alternative wastewater treatment processes and their combinations were investigated and optimal conditions for removal were established regarding the duration of cavitation, amount of added hydrogen peroxide and initial pressure, all of which influence the efficiency of the process.
218 citations
TL;DR: It is demonstrated that C-terminal ALS mutations disrupt the nuclear localizing signal (NLS) of FUS resulting in cytoplasmic accumulation in transfected cells and patient fibroblasts, and this findings support a two-hit hypothesis, whereby cytopLasmic mislocalization of F US protein, followed by cellular stress, contributes to the formation of cytopal aggregates that may sequester FUS, disrupt RNA processing and initiate motor neuron degeneration.
Abstract: Mutations in the gene encoding Fused in Sarcoma (FUS) cause amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disorder. FUS is a predominantly nuclear DNA- and RNA-binding protein that is involved in RNA processing. Large FUS-immunoreactive inclusions fill the perikaryon of surviving motor neurons of ALS patients carrying mutations at post-mortem. This sequestration of FUS is predicted to disrupt RNA processing and initiate neurodegeneration. Here, we demonstrate that C-terminal ALS mutations disrupt the nuclear localizing signal (NLS) of FUS resulting in cytoplasmic accumulation in transfected cells and patient fibroblasts. FUS mislocalization is rescued by the addition of the wild-type FUS NLS to mutant proteins. We also show that oxidative stress recruits mutant FUS to cytoplasmic stress granules where it is able to bind and sequester wild-type FUS. While FUS interacts with itself directly by protein–protein interaction, the recruitment of FUS to stress granules and interaction with PABP are RNA dependent. These findings support a two-hit hypothesis, whereby cytoplasmic mislocalization of FUS protein, followed by cellular stress, contributes to the formation of cytoplasmic aggregates that may sequester FUS, disrupt RNA processing and initiate motor neuron degeneration.
210 citations
TL;DR: Ecotoxicity was shown to increase in parallel with carbamazepine degradation indicating that the mixture of degradation products formed was more toxic than the parent compound, and all three ecotoxicity endpoints were still inhibited >60% relative to control populations upon dosing with 90+min UV-treated carbamazEPine solution.
175 citations
TL;DR: The scalar meson D*(s0)(2317) is found 37(17) MeV below the DK threshold in a lattice simulation of the J(P)=0(+) channel using, for the first time, both DK as well as s¯c interpolating fields.
Abstract: The scalar meson D*(s0)(2317) is found 37(17) MeV below the DK threshold in a lattice simulation of the J(P)=0(+) channel using, for the first time, both DK as well as s¯c interpolating fields. The simulation is done on N(f)=2+1 gauge configurations with m(π) is approximately equal to 156 MeV, and the resulting M(D*(s0))-1/4(M(D(s))+3M(D*(s)))=266(16) MeV is close to the experimental value 241.5(0.8) MeV. The energy level related to the scalar meson is accompanied by additional discrete levels due to DK scattering states. The levels near threshold lead to the negative DK scattering length a(0)=-1.33(20) fm that indicates the presence of a state below threshold.
169 citations
TL;DR: It is shown that quasiparticle excitations remain well defined above T(FL) and dominate transport throughout the intermediate regime T( FL) and T(MIR), and this pronounced particle-hole asymmetry has important consequences for the thermopower.
Abstract: We investigate transport in strongly correlated metals. Within dynamical mean-field theory, we calculate the resistivity, thermopower, optical conductivity and thermodynamic properties of a hole-doped Mott insulator. Two well-separated temperature scales are identified: ${T}_{\mathrm{FL}}$ below which Landau Fermi liquid behavior applies, and ${T}_{\mathrm{MIR}}$ above which the resistivity exceeds the Mott-Ioffe-Regel value and bad-metal behavior is found. We show that quasiparticle excitations remain well defined above ${T}_{\mathrm{FL}}$ and dominate transport throughout the intermediate regime ${T}_{\mathrm{FL}}\ensuremath{\lesssim}T\ensuremath{\lesssim}{T}_{\mathrm{MIR}}$. The lifetime of these resilient quasiparticles is longer for electronlike excitations and this pronounced particle-hole asymmetry has important consequences for the thermopower. The crossover into the bad-metal regime corresponds to the disappearance of these excitations and has clear signatures in optical spectroscopy.
168 citations
TL;DR: It is proposed that an imbalance between cathepsins and cystatins may attenuate immune cell functions and facilitate tumor cell invasion and tumorigenesis and metastasis.
Abstract: Cystatins comprise a large superfamily of related proteins with diverse biological activities. They were initially characterised as inhibitors of lysosomal cysteine proteases, however, in recent years some alternative functions for cystatins have been proposed. Cystatins possessing inhibitory function are members of three families, family I (stefins), family II (cystatins) and family III (kininogens). Stefin A is often linked to neoplastic changes in epithelium while another family I cystatin, stefin B is supposed to have a specific role in neuredegenerative diseases. Cystatin C, a typical type II cystatin, is expressed in a variety of human tissues and cells. On the other hand, expression of other type II cystatins is more specific. Cystatin F is an endo/lysosome targeted protease inhibitor, selectively expressed in immune cells, suggesting its role in processes related to immune response. Our recent work points on its role in regulation of dendritic cell maturation and in natural killer cells functional inactivation that may enhance tumor survival. Cystatin E/M expression is mainly restricted to the epithelia of the skin which emphasizes its prominent role in cutaneous biology. Here, we review the current knowledge on type I (stefins A and B) and type II cystatins (cystatins C, F and E/M) in pathologies, with particular emphasis on their suppressive vs. promotional function in the tumorigenesis and metastasis. We proposed that an imbalance between cathepsins and cystatins may attenuate immune cell functions and facilitate tumor cell invasion.
TL;DR: Fish consumption, the possible common source of As, Hg and Se intake, could explain the correlations between the elements determined in cord blood, mother's blood or breast milk and significant linear correlations were found between Hg, Se and As in blood, cord blood and breast milk.
TL;DR: The oil absorption properties of poplar seed hair fibers obtained from Populus nigra italica when tested with high-density motor oil and diesel fuel are reported, and they surpass all known natural absorbents.
TL;DR: The thermalization phenomenon and many-body quantum statistical properties are studied on the example of several observables in isolated spin-chain systems, both integrable and generic nonintegrable.
Abstract: The thermalization phenomenon and many-body quantum statistical properties are studied on the example of several observables in isolated spin-chain systems, both integrable and generic nonintegrable. While diagonal matrix elements for nonintegrable models comply with the eigenstate thermalization hypothesis, the integrable systems show evident deviations and similarity to properties of noninteracting many-fermion models. The finite-size scaling reveals that the crossover between the two regimes is given by a scale closely related to the scattering length. Low-frequency off-diagonal matrix elements related to dc transport quantities also follow in a generic system a behavior analogous to the eigenstate thermalization hypothesis, however, unrelated to one of the diagonal matrix elements.
TL;DR: The information presented here is needed by governments and NGO's in order to re-focus resources in making decisions regarding mitigation and remediation strategies on a global level.
TL;DR: A candidate for the charmonium(like) state X(3872) is found 11±7 MeV below the DD* threshold using dynamical N(f)=2 lattice simulation with J(PC)=1(++) and I=0.
Abstract: A candidate for the charmonium(like) state X(3872) is found 11±7 MeV below the DD* threshold using dynamical N(f)=2 lattice simulation with J(PC)=1(++) and I=0. This is the first lattice simulation that establishes a candidate for X(3872) in addition to the nearby scattering states DD* and J/ψω, which inevitably have to be present in dynamical QCD. We extract large and negative DD* scattering length a(0)(DD*)=-1.7±0.4 fm and the effective range r(0)(DD*)=0.5±0.1 fm, but their reliable determination will have to wait for a simulation on a larger volume. In I=1 channel, only the DD* and J/ψρ scattering states are found and no candidate for X(3872). This is in agreement with the interpretation that X(3872) is dominantly I=0, while its small I=1 component arises solely from the isospin breaking and is therefore absent in our simulation with m(u)=m(d).
TL;DR: In this article, a first exploratory lattice QCD simulation is presented, aimed at extracting the masses and widths of the broad scalar and the axial charm-light resonances, and the resonance parameters are extracted using a Breit-Wigner fit of the resulting phase shifts.
Abstract: A first exploratory lattice QCD simulation is presented, aimed at extracting the masses and widths of the broad scalar ${D}_{0}^{*}(2400)$ and the axial ${D}_{1}(2430)$ charm-light resonances. For that purpose $D\ensuremath{\pi}$ and ${D}^{*}\ensuremath{\pi}$ scattering are simulated, and the resonance parameters are extracted using a Breit-Wigner fit of the resulting phase shifts. We use a single two-flavor dynamical ensemble with ${m}_{\ensuremath{\pi}}\ensuremath{\approx}266\text{ }\text{ }\mathrm{MeV}$, $a\ensuremath{\simeq}0.124\text{ }\text{ }\mathrm{fm}$ and a rather small volume $V={16}^{3}\ifmmode\times\else\texttimes\fi{}32$. The resulting ${D}_{0}^{*}(2400)$ mass is $351\ifmmode\pm\else\textpm\fi{}21\text{ }\text{ }\mathrm{MeV}$ above the spin average $\frac{1}{4}({m}_{D}+3{m}_{{D}^{*}})$, in agreement with the experimental value of $347\ifmmode\pm\else\textpm\fi{}29\text{ }\text{ }\mathrm{MeV}$ above. The resulting ${D}_{0}^{*}\ensuremath{\rightarrow}D\ensuremath{\pi}$ coupling, ${g}^{\mathrm{lat}}=2.55\ifmmode\pm\else\textpm\fi{}0.21\text{ }\text{ }\mathrm{GeV}$, is close to the experimental value ${g}^{\mathrm{exp} }\ensuremath{\le}1.92\ifmmode\pm\else\textpm\fi{}0.14\text{ }\text{ }\mathrm{GeV}$, where $g$ parametrizes the width $\ensuremath{\Gamma}\ensuremath{\equiv}{g}^{2}{p}^{*}/s$. The resonance parameters for the broad ${D}_{1}(2430)$ are also found close to the experimental values; these are obtained by appealing to the heavy quark limit, where the neighboring resonance ${D}_{1}(2420)$ is narrow. The calculated $I=1/2$ scattering lengths are ${a}_{0}=0.81\ifmmode\pm\else\textpm\fi{}0.14\text{ }\text{ }\mathrm{fm}$ for $D\ensuremath{\pi}$ and ${a}_{0}=0.81\ifmmode\pm\else\textpm\fi{}0.17\text{ }\text{ }\mathrm{fm}$ for ${D}^{*}\ensuremath{\pi}$ scattering. The simulation of the scattering in these channels incorporates quark-antiquark as well as multihadron interpolators, and the distillation method is used for contractions. In addition, the ground and several excited charm-light and charmonium states with various ${J}^{P}$ are calculated using standard quark-antiquark interpolators.
TL;DR: In this paper, the main part of the paper is devoted to an assessment of the state-of-the-art materials, and the basic requirements for the target material are discussed in terms of the achieved properties.
Abstract: This article provides an overview of the main characteristics of SiCf/SiC that suggest the use of this SiC-based composite as a structural material for the blanket in future fusion reactors, a brief description of its structure and the role of its main constituents. The relevant fabrication processes and their ability to produce a material with the required properties are also summarised. The main part of the paper is devoted to an assessment of the state-of-the-art materials, and the basic requirements for the target material are discussed in terms of the achieved properties. The key issues and areas of uncertainty are described and suggestions for overcoming them are presented.
TL;DR: This work thoroughly investigated different solid phase extraction mechanisms (ion pair, ion exchange, reversed phase), sorbents and derivatisation agents to enable trace-level analysis of 5-FU based on GC-MS/MS in natural and wastewaters and concluded that alkylation was rejected in favour of silylation with MTBSTFA.
TL;DR: In this paper, the authors performed tunneling spectroscopy of a carbon nanotube quantum dot coupled to a metallic reservoir either in the normal or in the superconducting state.
Abstract: We performed tunneling spectroscopy of a carbon nanotube quantum dot (QD) coupled to a metallic reservoir either in the normal or in the superconducting state. We explore how the Kondo resonance, observed when the QD's occupancy is odd and the reservoir is normal, evolves towards Andreev bound states (ABS) in the superconducting state. Within this regime, the ABS spectrum observed is consistent with a quantum phase transition from a singlet to a degenerate magnetic doublet ground state, in quantitative agreement with a single-level Anderson model with superconducting leads.
TL;DR: It was shown that lysosomal proteases are not only able to initiate apoptotic signaling but can also amplify the apoptotic pathways initiated in other cellular compartments and the therapeutic potential of intervention in lysOSomal membrane permeabilization will be discussed.
Abstract: The endocytic pathway is a system specialized for the uptake of compounds from the cell microenvironment for their degradation. It contains an arsenal of hydrolases, including proteases, which are normally enclosed in membrane-bound organelles, but if released to the cytosol can initiate apoptosis signaling pathways. Endogenous and exogenous compounds have been identified that can mediate destabilization of lysosomal membranes, and it was shown that lysosomal proteases are not only able to initiate apoptotic signaling but can also amplify the apoptotic pathways initiated in other cellular compartments. The endocytic pathway also receives cargo destined for degradation via the autophagic pathway. By recycling energy and biosynthetic substrates, and by degrading damaged organelles and molecules, the endocytic system assists the autophagic system in resisting apoptotic stimuli. Steps leading to lysosomal membrane permeabilization and subsequent triggering of cell death as well as the therapeutic potential of intervention in lysosomal membrane permeabilization will be discussed.
TL;DR: Experiments show that the ruthenium complexes interact with DNA via intercalation and possible electrostatic interactions occur in the case of compound 4, which also shows the most pronounced rate of hydrolysis.
Abstract: Continuing the study of the physicochemical and biological properties of ruthenium-quinolone adducts, four novel complexes with the general formula [Ru([9]aneS3)(dmso-κS)(quinolonato-κ2O,O)](PF6), containing the quinolones levofloxacin (1), nalidixic acid (2), oxolinic acid (3), and cinoxacin (4), were prepared and characterized in solid state as well as in solution. Contrary to their organoruthenium analogues, these complexes are generally relatively stable in aqueous solution as substitution of the dimethylsulfoxide (dmso) ligand is slow and not quantitative, and a minor release of the quinolonato ligand is observed only in the case of 4. The complexes bind to serum proteins displaying relatively high binding constants. DNA binding was studied using UV–vis spectroscopy, cyclic voltammetry, and performing viscosity measurements of CT DNA solutions in the presence of complexes 1–4. These experiments show that the ruthenium complexes interact with DNA via intercalation. Possible electrostatic interactions ...
TL;DR: In this article, the photocatalytic degradation of the psychoactive substance caffeine was studied using composites prepared with multi-walled carbon nanotubes and three different TiO2 materials: one synthesized by a modified sol-gel method and two others obtained from Evonik and Sigma-Aldrich.
TL;DR: In this article, the properties of a quaternary Ti-20Nb-10Zr-5Ta alloy were investigated in relation to its use in biomedical applications and its microstructure was revealed by X-ray diffraction, and composition by energy dispersive Xray measurements.
TL;DR: The results show that after 6 months of use and 3600 working cycles the microreactor still exhibits 60% of its initial efficiency, and the longer-term stability of the TiO2 film is evaluated.
Abstract: A photocatalytic, TiO2-based microreactor is designed and fabricated on a metal–titanium foil. The microchannel is mechanically engraved in the substrate foil, and a double-layered TiO2 anatase film is immobilized on its inner walls with a two-step synthesis, which included anodization and a hydrothermal treatment. X-ray diffraction (XRD) and scanning electron microscopy (SEM) confirm the presence of an approximately 10-μm-thick layer of titania nanotubes and anatase nanoparticles. The SEM and transmission electron microscopy (TEM) of the cross sections show a dense interface between the titanium substrate and the TiO2 nanotubes. An additional layer of TiO2-anatase nanoparticles on the top of the film provides a large, photocatalytic surface area. The metal–titanium substrate with a functionalized serpentine channel is sealed with UV-transparent Plexiglas, and four 0.8-mW UV LEDs combined with a power controller on a small printed-circuit board are fixed over the substrate. The photocatalytic activity and...
TL;DR: In this article, the surface modification of cellulose fibres was performed with the use of low-pressure water vapour plasma, followed by the application of a pad-dry-cure sol-gel coating with the water- and oil-repellent organic-inorganic hybrid precursor fluoroalkyl-functional siloxane (FAS), with the aim of creating the "lotus effect" on the cotton fabric surface.
Abstract: The surface modification of cellulose fibres was performed with the use of low-pressure water vapour plasma, followed by the application of a pad-dry-cure sol-gel coating with the water- and oil-repellent organic-inorganic hybrid precursor fluoroalkyl-functional siloxane (FAS), with the aim of creating the “lotus effect” on the cotton fabric surface. The tailored “lotus effect” was confirmed by measurements of the contact angle of water (154°) and n-hexadecane (140°), as well as by measurements of the water sliding angle (7°), which were used to identify the super-hydrophobic, oleophobic and self-cleaning properties of the modified fibres. The chemical and morphological changes caused by modifications of the fibres were investigated by XPS, FTIR, AFM and SEM. The results show that the plasma pre-treatment simultaneously increased the surface polarity, average roughness, and surface area of the fabric. The application of the FAS coating after plasma pre-treatment caused only a slight increase in the surface roughness, accompanied by a decrease in the surface area, indicating that the architecture of the surface was significantly changed. This result suggests that the surface pattern affected the “lotus effect” more than the average surface roughness. The plasma pre-treatment increased the effective concentration of the FAS network on the fabric, which resulted in enhanced repellency before and after repetitive washing, compared with that of the FAS-coated fabric sample without the plasma pre-treatment. Despite the fact that the plasma pre-treatment increased the concentration of the oxygen-containing functional groups on the fabric surface, this phenomenon insignificantly contributed to the adhesion ability and, consequently, the washing fastness of the FAS coating.
TL;DR: In this paper, a rotors geometry of the cavitation generator, pressure in the treatment chamber, temperature of the liquid, amount of hydrogen peroxide and time of exposure to cavitation was investigated.
TL;DR: Any effort to mitigate the As exposure of the villagers in Bengal must consider the risk of As exposure from rice consumption together with drinking water, according to the estimates of exposure via dietary and drinking water routes.
Abstract: This study investigates the risk of arsenic (As) exposure to the communities in rural Bengal, even when they have been supplied with As safe drinking water. The estimates of exposure via dietary an ...
TL;DR: The features of MAIN and its tools for electron-density map calculations, model building, refinement in real and reciprocal space, and validation exploiting noncrystallographic symmetry in single and multiple crystal forms are presented.
Abstract: MAIN is software that has been designed to interactively perform the complex tasks of macromolecular crystal structure determination and validation. Using MAIN, it is possible to perform density modification, manual and semi-automated or automated model building and rebuilding, real- and reciprocal-space structure optimization and refinement, map calculations and various types of molecular structure validation. The prompt availability of various analytical tools and the immediate visualization of molecular and map objects allow a user to efficiently progress towards the completed refined structure. The extraordinary depth perception of molecular objects in three dimensions that is provided by MAIN is achieved by the clarity and contrast of colours and the smooth rotation of the displayed objects. MAIN allows simultaneous work on several molecular models and various crystal forms. The strength of MAIN lies in its manipulation of averaged density maps and molecular models when noncrystallographic symmetry (NCS) is present. Using MAIN, it is possible to optimize NCS parameters and envelopes and to refine the structure in single or multiple crystal forms.
TL;DR: In this paper, the association of prenatal mercury exposure from maternal fish consumption with child neurodevelopment in northern Italy was examined by using the Bayley Scales of Infant and Toddler Development, Third Edition (BSID-III).