Showing papers by "University of Ljubljana published in 2001"

Radiation hard silicon detectors—developments by the RD48 (ROSE) collaboration

Abstract: The RD48 (ROSE) collaboration has succeeded to develop radiation hard silicon detectors, capable to withstand the harsh hadron fluences in the tracking areas of LHC experiments. In order to reach this objective, a defect engineering technique was employed resulting in the development of Oxygen enriched FZ silicon (DOFZ), ensuring the necessary O-enrichment of about 2×1017 O/cm3 in the normal detector processing. Systematic investigations have been carried out on various standard and oxygenated silicon diodes with neutron, proton and pion irradiation up to a fluence of 5×1014 cm−2 (1 MeV neutron equivalent). Major focus is on the changes of the effective doping concentration (depletion voltage). Other aspects (reverse current, charge collection) are covered too and the appreciable benefits obtained with DOFZ silicon in radiation tolerance for charged hadrons are outlined. The results are reliably described by the “Hamburg model”: its application to LHC experimental conditions is shown, demonstrating the superiority of the defect engineered silicon. Microscopic aspects of damage effects are also discussed, including differences due to charged and neutral hadron irradiation.

EDTA enhanced heavy metal phytoextraction: metal accumulation, leaching and toxicity

Abstract: Synthetic chelates such as ethylene diamine tetraacetic acid (EDTA) have been shown to enhance phytoextraction of some heavy metals from contaminated soil. In a soil column study, we examined the effect of EDTA on the uptake of Pb, Zn and Cd by Chinese cabbage (Brassica rapa), mobilization and leaching of heavy metals and the toxicity effects of EDTA additions on plants. The most effective was a single dose of 10 mmol EDTA kg−1 soil where we detected Pb, Zn and Cd concentrations that were 104.6, 3.2 and 2.3-times higher in the aboveground plant biomass compared to the control treatments. The same EDTA addition decreased the concentration of Pb, Zn and Cd in roots of tested plants by 41, 71 and 69%, respectively compared to concentrations in the roots of control plants. In columns treated with 10 mmol kg−1 EDTA, up to 37.9, 10.4 and 56.3% of initial total Pb, Zn and Cd in soil were leached down the soil profile, suggesting high solubility of heavy metals-EDTA complexes. EDTA treatment had a strong phytotoxic effect on the red clover (Trifolium pratense) in bioassay experiment. Moreover, the high dose EDTA additions inhibited the development of arbuscular mycorrhiza. The results of phospholipid fatty acid analyses indicated toxic effects of EDTA on soil fungi and increased environmental stress of soil microfauna.

Retrospective correction of MR intensity inhomogeneity by information minimization

Abstract: In this paper, the problem of retrospective correction of intensity inhomogeneity in magnetic resonance (MR) images is addressed. A novel model-based correction method is proposed, based on the assumption that an image corrupted by intensity inhomogeneity contains more information than the corresponding uncorrupted image. The image degradation process is described by a linear model, consisting of a multiplicative and an additive component which are modeled by a combination of smoothly varying basis functions. The degraded image is corrected by the inverse of the image degradation model. The parameters of this model are optimized such that the information of the corrected image is minimized while the global intensity statistic is preserved. The method was quantitatively evaluated and compared to other methods on a number of simulated and real MR images and proved to be effective, reliable, and computationally attractive. The method can be widely applied to different types of MR images because it solely uses the information that is naturally present in an image, without making assumptions on its spatial and intensity distribution. Besides, the method requires no preprocessing, parameter setting, nor user interaction. Consequently, the proposed method may be a valuable tool in MR image analysis.

Measurement of residual stress by load and depth sensing indentation with spherical indenters

Abstract: A new experimental technique is presented for making measurements of biaxial residual stress using load and depth sensing indentation (nanoindentation). The technique is based on spherical indentation, which, in certain deformation regimes, can be much more sensitive to residual stress than indentation with sharp pyramidal indenters like the Berkovich. Two different methods of analysis were developed: one requiring an independent measure of the material's yield strength and the other a reference specimen in the unstressed state or other known reference condition. Experiments conducted on aluminum alloys to which controlled biaxial bending stresses were applied showed that the methods are capable of measuring the residual stress to within 10-20% of the specimen yield stress. Because the methods do not require imaging of the hardness impressions, they are potentially useful for making localized measurements of residual stress, as in thin films or small volumes, or for characterization of point-to-point spatial variations of the surface stress.

Bacteriophage latent-period evolution as a response to resource availability.

Abstract: Bacteriophages (phages) modify microbial communities by lysing hosts, transferring genetic material, and effecting lysogenic conversion. To understand how natural communities are affected it is important to develop predictive models. Here we consider how variation between models—in eclipse period, latent period, adsorption constant, burst size, the handling of differences in host quantity and host quality, and in modeling strategy—can affect predictions. First we compare two published models of phage growth, which differ primarily in terms of how they model the kinetics of phage adsorption; one is a computer simulation and the other is an explicit calculation. At higher host quantities (∼108 cells/ml), both models closely predict experimentally determined phage population growth rates. At lower host quantities (107 cells/ml), the computer simulation continues to closely predict phage growth rates, but the explicit model does not. Next we concentrate on predictions of latent-period optima. A latent-period optimum is the latent period that maximizes the population growth of a specific phage growing in the presence of a specific quantity and quality of host cells. Both models predict similar latent-period optima at higher host densities (e.g., 17 min at 108 cells/ml). At lower host densities, however, the computer simulation predicts latent-period optima that are much shorter than those suggested by explicit calculations (e.g., 90 versus 1,250 min at 105 cells/ml). Finally, we consider the impact of host quality on phage latent-period evolution. By taking care to differentiate latent-period phenotypic plasticity from latent-period evolution, we argue that the impact of host quality on phage latent-period evolution may be relatively small.

Nutritional Properties of Starch in Buckwheat Products: Studies in Vitro and in Vivo

Abstract: The nutritional characteristics of buckwheat starch were studied to identify the possibility for reduced postmeal metabolic responses to various buckwheat products. The in vitro rate of starch hydrolysis and resistant starch (RS) formation in boiled buckwheat groats and in a series of breads, baked with 30-70% of buckwheat flour (BWF) or groats (BWG), respectively, were evaluated in vitro. In parallel, postprandial glucose and insulin responses and also the satiety score to BWG and wheat bread with 50% BWG as compared with the reference white wheat bread (WWB) were studied in healthy humans. The highest concentration of RS was found in boiled BWG (6% total starch basis). The RS level in bread products based on different proportions of BWF or BWG (30-70%) varied from 0.9 to 4.4%. The rate of in vitro amylolysis was significantly lower (P < 0.05) in all buckwheat products in comparison with the reference WWB. The calculated hydrolysis indices (HI) were lowest in boiled BWG (HI = 50) and in bread with 70% BWG (HI = 54). Consumption of boiled BWG or bread based on wheat flour and 50% BWG induced significantly lower postprandial blood glucose and insulin responses compared with the WWB. The calculated glycemic and insulinemic indices (GI and II) for boiled BWG were 61 and 53 and for the buckwheat bread, 66 and 74, respectively. The highest satiety score was found with boiled BWG. It is concluded that buckwheat has potential use in the design of foods with lower GI properties.

Evaluation of the ability to make non-invasive estimation of muscle contractile properties on the basis of the muscle belly response.

Abstract: The histochemical and biomechanical relationships of limb muscles are examined in two groups of 15 men aged between 17 and 40 years. Seven muscles are chosen: biceps brachii, triceps brachii (TB), flexor digitorum superficialis, extensor digitorum, biceps femoris, tibialis anterior and gastrocnemius caput mediale (GCM). The aim of the preliminary study is to evaluate an alternative method based on a tensiomyographic (TMG) non-invasive measurement technique. The percentage of type I muscle fibres obtained with the histochemical method is 2.2 times higher for the slowest measured muscle (GCM) than for the fastest (TB). The contraction time of a muscle belly twitch response measured by TMG is 1.9 times higher for GCM than for TB. Statistical analysis of the data obtained by tensiomyographic and histochemical techniques shows a significant correlation between the contraction time of muscle response measured by TMG and the percentage of type I muscle fibres (correlation coefficient equals 0.93). Results of the study suggest using the TMG measuring technique as a basis for the estimation of the percentage of type I muscle fibres.

Soft storey effects in uniformly infilled reinforced concrete frames

Abstract: A large number of multi-storey reinforced concrete frame buildings with masonry infill walls, which were uniformly distributed over the height of the building, collapsed in the 1999 Kocaeli (Turkey) earthquake, due to complete failure of the first storey or the bottom two stories. In the paper it is demonstrated that a soft storey mechanism is formed in such structural systems if the intensity of ground motion is above a certain level. It is likely that collapse will occur if the global ductilities of the bare frames, as well as the ductilities of the structural elements, are low, and if the infill walls are relatively weak and brittle.

Comparison of toxinotyping and PCR ribotyping of Clostridium difficile strains and description of novel toxinotypes

Abstract: Toxinotyping and PCR ribotyping are two methods that have been used to type Clostridium difficile isolates. Toxinotyping is based on PCR-RFLP analysis of a 19 kb region encompassing the C. difficile pathogenicity locus. PCR ribotyping is based on comparison of patterns of PCR products of the 16S-23S rRNA intergenic spacer region. Representative strains (101) from a C. difficile PCR ribotype library and 22 strains from previously described toxinotypes were analysed to compare ribotyping with toxinotyping. Within this panel of strains all 11 toxinotypes (0-X) described previously and an additional 5 novel toxinotypes (XI-XV) were observed. PCR ribotyping and toxinotyping correlated well and usually all strains within a given ribotype had similar changes in toxin genes. The new toxinotype XI comprises strains that did not express toxins TcdA or TcdB at detectable levels, but contained part of the tcdA gene. Strains of toxinotype XII exhibit changes only in the 5' end of the tcdB gene. Toxinotype XIV is composed of strains that have a large insertion at the beginning of the tcdA gene. A total of 25 of the 89 tested PCR ribotypes of C. difficile contained variant strains. It was estimated that they represent 7.7% of the total number of strains in the Anaerobe Reference Unit collection.

Upper limb motion analysis using haptic interface

Abstract: An objective test for evaluating the functional studies of the upper limbs (UL) in patients with neurological diseases (ND) is presented. The method allows assessment of kinematic and dynamic motor abilities of UL. Our methodology is based on creating a virtual environment, using a computer display for visual information and a PHANTOM haptic interface. The haptic interface is used as a kinematic measuring device and for providing tactile feedback to the patient. In virtual environment, a labyrinth in patient's frontal plane was created at the start of each test. By moving the haptic interface control stick the patient was able to move the pointer (a ball) through the labyrinth in three dimensions and to feel the reactive forces of the wall. The new test offers a wide range of numerical and graphic results. It has so far been applied to 13 subjects with various forms of ND (e.g., Friedreich Ataxia, Parkinson's disease, Multiple Sclerosis) as well as to healthy subjects. The comparison in performance between right and left UL has been carried out in healthy subjects.

Supporting discovery in medicine by association rule mining in Medline and UMLS.

Abstract: The paper presents an interactive discovery support system for the field of medicine. The intended users of the system are medical researchers. The goal of the system is: for a given starting concept of interest, discover new, potentially meaningful relations with other concepts that have not been published in the medical literature before. The known relations between the medical concepts come from the Medline bibliographic database and the UMLS. We use association rules for discovering the relationship between medical concepts. We evaluated the system by testing how successfully it predicted future discoveries (new relations between concepts). We first divided the Medline database into two segments (older and newer) using the publication date. Then we calculated how many of the new relations found by the system in the older segment become known relations in the newer segment. We found out with statistical significance that the system predicts new relations better then someone predicting randomly. The evaluation showed that our approach for supporting discovery in medicine is successful, but also that some improvements are needed, especially on limiting the number of potential discoveries the system generates.

Specificity and genetic polymorphism of the Bacillus competence quorum-sensing system.

Abstract: A quorum-sensing mechanism involving the pheromone ComX and the ComP-ComA two-component system controls natural competence in Bacillus subtilis. ComX is expressed as a cytoplasmic inactive precursor that is released into the extracellular medium as a cleaved, modified decapeptide. This process requires the product of comQ. In the presence of ComX, the membrane-localized ComP histidine kinase activates the response regulator ComA. We compared the sequences of the quorum-sensing genes from four closely related bacilli, and we report extensive genetic polymorphism extending through comQ, comX, and the 5′ two-thirds of comP. This part of ComP encodes the membrane-localized and linker domains of the sensor protein. We also determined the sequences of the comX genes of four additional wild-type bacilli and tested the in vivo activities of all eight pheromones on isogenic strains containing four different ComP receptor proteins. A striking pattern of specificity was discovered, providing strong evidence that the pheromone contacts ComP directly. Furthermore, we show that coexpression of comQ and comX in Escherichia coli leads to the production of active pheromone in the medium, demonstrating that comQ is the only dedicated protein required for the processing, modification, and release of active competence pheromone. Some of the implications of these findings for the evolution and the mechanism of the quorum-sensing system are discussed.

Diversity of Babesia Infecting European Sheep Ticks (Ixodes ricinus)

Abstract: Questing Ixodes ricinus (Acari: Ixodidae) adult and nymphal ticks collected in various parts of Slovenia were tested for the presence of babesial parasites with a PCR assay based on the nuclear small subunit rRNA gene (nss-ribosomal DNA [rDNA]). Thirteen of 135 ticks were found to contain babesial DNA. Sequence determination and analysis of amplified portions of nss-rDNA revealed their identity with Babesia microti and a high degree of homology with Babesia odocoilei and Babesia divergens. The results of this study represent the first genetic evidence of B. microti and B. divergens-like parasites in I. ricinus ticks in Europe.

DNS of Turbulent Heat Transfer in Channel Flow With Heat Conduction in the Solid Wall

Abstract: The Direct Numerical Simulation (DNS) of the fully developed velocity and temperature fields in the two-dimensional turbulent channel flow coupled with the unsteady conduction in the heated walls was carried out. Simulations were performed at constant friction Reynolds number 150 and Prandtl numbers between 0.71 and 7 considering the fluid temperature as a passive scalar. The obtained statistical quantities like root-mean-square temperature fluctuations and turbulent heat fluxes were verified with existing DNS studies obtained with ideal thermal boundary conditions. Results of the present study were compared to the findings of Polyakov (1974), who made a similar study with linearization of the fluid equations in the viscous sublayer that allowed analytical approach and results of Kasagi et al. (1989), who performed similar calculation with deterministic near-wall turbulence model and numerical approach. The present DNS results pointed to the main weakness of the previous studies, which underestimated the values of the wall temperature fluctuations for the limiting cases of the ideal-isoflux boundary conditions. With the results of the present DNS it can be decided, which behavior has to be expected in a real fluid-solid system and which one of the limiting boundary conditions is valid for calculation, or whether more expensive conjugate heat transfer calculation is required. @DOI: 10.1115/1.1389060#