Šiame darbe tirtas gramteigiamųjų ir gramneigiamųjų bakterijų atsakas į natyvaus ir katalitiškai neaktyvaus lizocimo bei jo 9 aminorūgščių katijoninio peptido sukeltus ląstelės apvalkalo pažeidimus. Panaudojant potenciometrinius metodus, buvo nustatyta, kad šie junginiai sukelia viduląstelinio K+ ištekėjimą iš L. lactis, B. subtilis ir P. aeruginosa ląstelių ir dalinę jų citoplazminės membranos depoliarizaciją, tačiau natyvus, kaitintas lizocimas ir 9a peptidas skirtingai veikia L. lactis apvalkalėlio laidumą. Peptidas bei kaitintas lizocimas sukelia staigesnį K+ jonų ištekėjimą ir membranos įtampos sumažėjimą nei natyvus lizocimas. Peptido sukeliamas K+ jonų ištekėjimas yra grįžtamas. Taip pat buvo įvertintas įvairių mutantinių L. lactis padermių jautrumas lizocimui. Pastebėta, kad kuo padermė atsparesnė lizocimui, tuo vėliau prasideda K+ jonų ištekėjimas iš šios padermės ląstelių. Pasitelkus DNR mikrogardelių metodą, buvo tiriamas lizocimo bei peptido poveikis L. lactis MG1363 bei ΔoppA ląstelių genų raiškos pokyčiams. Nustatyta, jog peptidu ir lizocimu veiktose ląstelėse iššaukiama dvikomponentės valdymo sistemos CesSR raiška ir sukeliamas nuo SpxB priklausomas ląstelių atsparumas lizocimui. Gauti rezultatai rodo, jog lizocimas ir 9a peptidas sukelia kiek skirtingus L. lactis transkriptomo pokyčius: lizocimas savitai skatina nuo N-deacetilazės priklausomo atsparumo mechanizmo įsijungimą, taip pat skiriasi OpuA sistemą koduojančių genų raiška. / We used potenciometric measurments to investigate the response of Gram-positive and Gram-negative bacteria to cell envelope stress, caused by native and heat-inactivated lysozyme and lysozyme-derived 9 amino acid peptide. It was found that these antimicrobial compounds induce leakage of K+ outside the cells of L. lactis, B. subtilis and P. aeruginosa and cause partial depolarization of bacterial cytoplasmic membrane. We observed different response of L. lactis cells to these compounds – peptide and heat-inactivated lysozyme cause more rapid efflux of K+ ions than native lysozyme. Peptide has a reversible effect on K+ leakage. Sensitivity of different mutant strains of L. lactis to lysozyme was studied. It was shown that more resistant the strain is, the later the leakage of K+ ions is induced by lysozyme. To investigate the genome-wide response of L. lactis MG1363 and ΔoppA strains to lysozyme and 9 a.a. peptide, changes of gene expression after challenging cells with these antimicrobial compounds were analysed using DNA microarrays. It was estimated, that lysozyme and lysozyme-derived 9a.a. peptide induce CesSR system and SpxB-mediated response. It was also shown that L. lactis response to 9a.a. peptide and lysozyme differs. Lysozyme specifically induces PgdA-mediated resistance mechanism. Changes of expression of OpuA system in lysozyme and peptide treated cells are also different.

A continuum plasticity yield function is developed that captures tension/compression asymmetry and its evolution as exhibited by HCP materials such as magnesium alloy sheet. The model, referred to herein as “CPB06ex3ev”, is based upon the CPB06 [1] yield surface which is extended in this research to consider evolution of asymmetry and anisotropy under monotonic loading. The model is further modified to incorporate thermal softening and strain rate effects. Mechanical characterization experiments are performed to acquire uniaxial tensile and compressive stress-strain data along a range of in-plane and through-thickness loading orientations. Experiments are performed for a range of strain rates (0.001-1s-1) and temperatures (23-250°C). A strong, evolving asymmetry is observed at room temperature when comparing tensile and compressive flow stresses and r-values, while asymmetry and anisotropy are reduced dramatically as temperature is increased. AZ31B exhibits moderate strain rate sensitivity at room temperature, however, the rate sensitivity increases with temperature. The CPB06ex3ev model is applied to simulate AZ31B magnesium alloy sheet. An error minimization scheme is used to fit the yield function and evolution coefficients over the entire data set. The calibrated model is shown to capture the evolving asymmetric/anisotropic response of both flow stresses and r-values in tension and compression, while also fitting the flow stress at the biaxial tension and pure shear locations on the yield locus. The model, which uses three stress transformations, is implemented within a user defined material model (UMAT) and linked to the commercial finite element software LS-DYNA. In order to assess the finite element implementation of the CPB06ex3ev model, a series of validation experiments were performed and corresponding finite element models were developed: (i) room temperature three-point bending; (ii) elevated temperature (250°C) limiting dome height experiments; and, (iii) warm cup drawing experiments. The three point bend simulations demonstrated the importance of capturing material asymmetry and the associated shift in neutral axis. Comparison between the warm forming experiments and models revealed qualitative agreement between the predicted punch load-displacement and strain distributions. The CPB06ex3ev formulation was able to capture the anisotropy trends in terms of the differences in strains measured along the sheet rolling versus transverse directions. Beyond the constitutive characterization and modeling effort, the cup draw formability experiments have provided interesting insight into the effect of temperature and temperature distribution within the AZ31B sheet. The current work has served to show the existence of a process window in which the blank center temperature must lie below the die temperature but above the temperature for activation of non-basal slip systems (to avoid low temperature fracture). Two modes of failure have been identified at the process window boundaries in which the cup either fractures due to low temperature (brittle) failure or a high temperature (necking) failure.

HIV-1 genetic diversity is a major obstacle for developing an effective vaccine. My hypothesis is that HIV-1 genetic diversity can be characterized and that cross-clade immunogens can be predicted at the population level. I systematically investigated positive selection (PS) pressures on HIV-1 Env and Gag proteins based on the analysis of the sequences collected from the Los Alamos Sequence Database. I identified PS sites, investigated PS patterns, correlated PS with the known functional sites of the two proteins, calculated frequencies of HLA alleles targeting CTL epitopes, and compared PS patterns among major subtypes. The results showed that PS pressure was widely dispersed across the entire regions of both HIV-1 Env and Gag proteins, suggesting the conserved regions are under host immune response pressure. The neutralizing antibody, non-neutralizing antibody, and CTL responses were found to be the major forces driving genetic diversity of HIV-1 env and gag genes at population level. However, PS pressures on both Env and Gag proteins remain stable over time, suggesting genetic diversity of HIV-1 driven by host immune responses changed very little over the last 29 years. Furthermore, the results also demonstrated that up to 70% PS sites were shared among the major HIV-1 clades, implying the existence of cross-clade immunogenicity. A number of potential cross-clades immunogens were predicted to elicit CTL or neutralizing antibody responses from Env and Gag proteins. I also detected a significant correlation between HLA allele frequencies and host CTL responses elicited by Accessory/Regulator’s proteins at population level. Moreover, I detected an association between the frequency of HLA-B7 supertype and the number of identified optimal CTL epitopes. The results suggest HLA class I allele frequencies in a population influence the evolution of HIV-1. I also systematically evaluated the utility of ultra-deep pyrosequencing to characterize genetic diversity of HIV-1 gag genes within quasispecies. The results showed that ultra-deep pyrosequencing of amplified HIV genes is a better method than the traditional Sanger-clone-based method in the comprehensive characterization of genetic diversity of HIV-1 quasispecies, especially in detecting low frequency variations. In conclusion, my thesis provides important information for rational design of an effective HIV-1 vaccine.

Synthesis of polycrystalline, vs. single-crystalline porous materials, such as metal-organic frameworks (MOFs), is usually beneficial due to shorter synthetic time and higher yields. However, the structural characterization of these materials by X-ray powder diffraction can be complicated. Even more difficult, is to track structural changes of MOFs by in situ experiments. Hence, we designed several successful techniques for the structural investigation of porous MOFs. These methods utilize the Structure Envelope (SE) density maps. SEs are surfaces which describing the pore system with the framework. It was shown that these maps can be easily generated from the structure factors of a few (1 to 10) of the most intense low index reflections. Application of SE in Charge Flipping calculations shortens and simplifies structure determination of MOF materials. This method provides excellent MOF models which can be used as a good starting point for their refinement. However, the most interesting results have been found by using Difference Envelope Density (DED) analysis. DED plots are made by taking the difference between observed and calculated SE densities. This allows us to study guest related issues of MOFs such as, location of guest molecules in the pores, tracking activation of MOFs and gas loading, etc. We also have shown that, DED created from routine powder diffraction patterns might provide very important information about MOF structure itself. In fact DED can be used for study of interpenetration, substituents locations and effects conformational changes in the MOF ligands. Generation and analysis of SEs and DEDs are easy and straightforward. It provides the information needed to explain major deviations in structure-property relationship in MOFs. In our opinion, this method might become one of the important and routine techniques for MOFs structural analysis.

In this study, the energy conservation potential of selected retrofitting interventions on an office building were investigated, on the basis of which some rational strategies for the improvement of building envelopes in terms of energy, environment and comfort design were proposed. Examined were various measures on envelope constructions that can be retrofitted to existing buildings. By using simulation techniques, the effectiveness of such measures in reducing energy consumption and environmental threat were also assessed. Effects of glazing types, effect of insulation and thermal mass were analyzed as energy efficient retrofit measures to the Engineering Building (MM building) situated on Middle East Technical University Campus, Ankara. The Energy-10 computer program was used for the modeling and simulation of the energy flows through the envelope to examine measures for reducing thermal load. Within this framework, the energy conservation potential of single and combined retrofitting actions was investigated. Based on results from the evaluation model, it was found that a saving of 161.20 MWh in the annual heating load could result, depending on the glazing type. The evaluation showed that thermal insulation is the most effective factor in thermal performance when placed as an exterior layer on walls. The study showed thermal mass has significant impact on increasing the duration, where highest temperatures were achieved, under passive mode. The study also revealed that applying a combination of retrofitting measures which responded to the challenges and opportunities presented by different fa&ccedil / ade orientations, a saving of 52.41% can be achieved in annual heating energy use in case study building.

The structured arrangement of sounds in musical pieces, results in the unique creation of complex acoustic mixtures. The analysis of these mixtures, with the objective of estimating the individual sounds which constitute them, is known as musical instrument sound source separation, and has applications in audio coding, audio restoration, music production, music information retrieval and music education. This thesis principally addresses the issues related to the separation of harmonic musical instrument sound sources in single-channel mixtures. The contributions presented in this work include novel separation methods which exploit the characteristic structure and inherent correlations of pitched sound sources; as well as an exploration of the musical timbre space, for the development of an objective distortion metric to evaluate the perceptual quality of separated sources. The separation methods presented in this work address the concordant nature of musical mixtures using a model-based paradigm. Model parameters are estimated for each source, beginning with a novel, computationally efficient algorithm for the refinement of frequency estimates of the detected harmonics. Harmonic tracks are formed, and overlapping components are resolved by exploiting spectro-temporal intra-instrument dependencies, integrating the spectral and temporal approaches which are currently employed in a mutually exclusive manner in existing systems. Subsequent to the harmonic magnitude extraction using this method, a unique, closed-loop approach to source synthesis is presented, separating sources by iteratively minimizing the aggregate error of the sources, constraining the minimization to a set of estimated parameters. The proposed methods are evaluated independently, and then are placed within the context of a source separation system, which is evaluated using objective and subjective measures. The evaluation of music source separation systems is presently limited by the simplicity of objective measures, and the extensive effort required to conduct subjective evaluations. To contribute to the development of perceptually relevant evaluations, three psychoacoustic experiments are also presented, exploring the perceptual sensitivity of timbre for the development of an objective distortion metric for timbre. The experiments investigate spectral envelope sensitivity, spectral envelope morphing and noise sensitivity.

The limiter is a commonly used device in communication receiving systems to remove the amplitude variations of the received signal, but it is usually observed that limiter degrades the envelope detection performance of a single tone. In this thesis, it is demonstrated that the limiter-generated third harmonic can be used to improve the envelope detection performance of a single tone over that of the linearly processed fundamental. Differences in the probability distributions of the limiter-generated harmonics cause differences in their detection probabilities, which lead to differences in the performance of subsequent envelope detection. Comparison of the envelope detection performance of the limiter-generated third harmonic and the input to the limiter shows a maximum detection probability gain of 1.12 and also error probability gain of 2.4 in linear scale, whereas the fundamental harmonic does not show any practically significant gain. The envelope detection performance of the vector sum of the limiter-generated fundamental and third harmonics is also evaluated. This combination provides better performance than do the individual harmonics, especially for a large clipping parameter of the limiter. The combined harmonics shows a maximum detetction probability gain of 1.15 and error probability gain of 14, over that of the envelope detection performance of a tone without limiter. It is also observed that the envelope detection performance of a tone with limiter-generated higher harmonics shows non-monotonic behaviour as functions of either noise or the limiter-clipping parameter, which is a signature of stochastic resonance. The theoretical results from earlier research on the envelope detection of a single tone embedded in additive white Gaussian noise, both with and without a limiter, are presented and shown to match our simulation results. In previous work when a limiter was used in the envelope detection of a single tone, only the envelope of the fundamental harmonic was considered under very specific conditions. By contrast we also take notice of the limiter-generated higher harmonics and obtain improved envelope detection performance in the detection of a single tone.

The structured arrangement of sounds in musical pieces, results in the unique creation of complex acoustic mixtures. The analysis of these mixtures, with the objective of estimating the individual sounds which constitute them, is known as musical instrument sound source separation, and has applications in audio coding, audio restoration, music production, music information retrieval and music education. This thesis principally addresses the issues related to the separation of harmonic musical instrument sound sources in single-channel mixtures. The contributions presented in this work include novel separation methods which exploit the characteristic structure and inherent correlations of pitched sound sources; as well as an exploration of the musical timbre space, for the development of an objective distortion metric to evaluate the perceptual quality of separated sources. The separation methods presented in this work address the concordant nature of musical mixtures using a model-based paradigm. Model parameters are estimated for each source, beginning with a novel, computationally efficient algorithm for the refinement of frequency estimates of the detected harmonics. Harmonic tracks are formed, and overlapping components are resolved by exploiting spectro-temporal intra-instrument dependencies, integrating the spectral and temporal approaches which are currently employed in a mutually exclusive manner in existing systems. Subsequent to the harmonic magnitude extraction using this method, a unique, closed-loop approach to source synthesis is presented, separating sources by iteratively minimizing the aggregate error of the sources, constraining the minimization to a set of estimated parameters. The proposed methods are evaluated independently, and then are placed within the context of a source separation system, which is evaluated using objective and subjective measures. The evaluation of music source separation systems is presently limited by the simplicity of objective measures, and the extensive effort required to conduct subjective evaluations. To contribute to the development of perceptually relevant evaluations, three psychoacoustic experiments are also presented, exploring the perceptual sensitivity of timbre for the development of an objective distortion metric for timbre. The experiments investigate spectral envelope sensitivity, spectral envelope morphing and noise sensitivity.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2006. / Härtill 3 uppsatser.

Thesis (Ph.D. in Microbiology) -- University of Colorado Denver, 2008. / Typescript. Includes bibliographical references (leaves 161-183). Free to UCD Anschutz Medical Campus. Online version available via ProQuest Digital Dissertations;