This paper explores the statistical properties of microfragment recovery techniques used on NTFS filesystems in the use of digital forensics. A microfragment is the remnant file-data existing in the cluster slack after this file has been overwritten. The total amount of cluster slack is related to the size distribution of the overwriting files as well as to the size of cluster. Experiments have been performed by varying the size distributions of the overwriting files as well as the cluster sizes of the partition. These results are then compared with existing analytical models. / FIVES

Mycobacterium tuberculosis (Mtb), a deadly pathogen, has scourged mankind for many centuries and has remained a major threat to global world health. Tuberculosis, the disease caused by this bacterium, is a major cause of death in developing nations and there is potential for its re-emergence in developed countries. An alarming rise in cases of multidrug-resistant and extremely-drug resistant tuberculosis (MDR-TB and XDR-TB) that do not respond to the customary first-line antibiotics necessitates the urgent need for development of new anti-TB drugs. Mtb becomes engulfed in human macrophages post infection of the host, but persists in the harsh environment of the human lungs by utilization of host cholesterol as a carbon source. The P450s CYP125A1, CYP142A1 and CYP124A1 are responsible for catalysing the side-chain degradation of cholesterol, which is critical for cholesterol to be used in the Mtb β-oxidation pathway for energy production. This PhD thesis focuses on understanding the structure/mechanism of the Mtb cholesterol 27-oxidases with the aim of facilitating the development of novel inhibitors of these P450s, which are crucial for Mtb to infect the host and to sustain infection. CYP142A1 and CYP124A1 were purified through three chromatographic steps with contaminating proteins successfully removed to give highly pure forms of these enzymes following the final purification step. Spectrophotometric titrations indicate that CYP142A1 and CYP124A1 bind tightly to cholesterol and cholestenone (and also to branched-chain methyl lipids for CYP124A1), highlighting their physiological roles in sterol and fatty acid metabolism, respectively. Binding analyses with a range of azole antibiotics revealed tight binding to bifonazole, clotrimazole, miconazole and econazole, and weak binding to fluconazole. Studies with compounds from a fragment screening library revealed weak binding to fragment hits for the cholesterol oxidases, but much tighter binding to these enzymes was found for ‘elaborated’ hits from a previous fragment screen on the Mtb cyclodipeptide oxidase CYP121A1, indicative of improved ligand potency achieved via ‘fragment merging’ strategies, and of structural similarities between these diverse Mtb P450s. Light scattering data indicate that CYP142A1 exists in dimeric form in solution, but becomes monomeric when treated with DTT; while CYP124A1 is completely monomeric. Crystal structures of CYP142A1 and CYP124A1 in complex with cholestenone, econazole and fragment library hits were determined. CYP142A1 crystal structures with econazole and fragment hits revealed heme coordination via the heterocyclic nitrogen in an azole group, and provide important data towards design of superior inhibitor drugs. The binding of cholestenone within the active site channels of CYP124A1 and CYP142A1 revealed an alignment favourable for C27 hydroxylation of the cholestenone side chain, which supports the physiological roles of CYP142A1 and CYP124A1 (as well as CYP125A1) in host cholesterol catabolism.

The biological diversity of the planet is at great risk as a direct result of an ever-expanding human population and its associated activities. Landscape transformation to accommodate such activities leads to habitat loss and habitat fragmentation, often creating patches of relatively undisturbed habitat within a matrix of transformed areas that are often too small too support most species previously occupying the area and as a result loses its ecological integrity. A century ago the escarpment region of Mpumalanga consisted of large open plains covered with montane grassland dissected by montane forests and riparian vegetation alongside mountain streams. Today the grasslands and forests have almost disappeared from the area, the remaining patches mostly small fragments within a matrix of exotic tree plantations which have also dried up many of the rivers and streams in the area. The natural grassland areas persisting in the region are unique in habitat characteristics and floral species composition. It is also high in plant species richness, diversity and endemicity. The high degree of isolation experienced by these floral communities poses serious threats to both the floral and faunal species that currently exits within these isolated ‘islands’, many of which are endemic to the area and at great risk of extinction. These risks call for serious collaboration between the land owners (mostly forestry companies) and conservationists to assure the practical and necessary preservation and management of this unique and crucially valuable natural resource. This study aims to provide the first step into understanding the ecological principles associated with habitat fragmentation related specifically to the mountain grassland fragments within the afforestation matrix of the escarpment region of Mpumalanga, and to create a platform for the process of collaboration between land owners and conservation agencies to assess and manage these grassland patches. The aims of Chapter 2 included: 1 To determine if any marked human-induced disturbance to the plant communities in the grassland fragments has occurred. I do this in three ways: a) To compare the plant community composition of eighteen fragments with those of six control plots outside of the plantations where no marked disturbance to the grassland can be observed. b) To determine whether the plant assemblages in the fragments can be assigned to any of the natural and intact plant communities that Matthews (1993) described from a large-scale survey of undisturbed mountain areas. c) To determine the presence of any known intruder plant species within the fragments. 2 To assign conservation priorities to the remaining grassland fragments. The results obtained from the TWINSPAN analysis revealed six alliances of plant communities grouped hierarchically into four orders and two major classes of montane grassland. The DECORANA supported these results, indicating clear differences between communities 1.1 (Eriosema salignum – Loudetia simplex grassland of the wetter North region), 1.2 (Lobelia erinus – Panicum natalense grassland of the Transitional region), 2.1 (Parinari capensis – Eragrostis racemosa grassland) and 2.2 (Helichrysum rugulosum – Eragrostis racemosa grassland). Different plant communities revealed different combinations of geological characteristics, slope, aspect and elevation. The sample plots of isolated grassland fragments and those of large unfragmented areas compare well with each other - the species richness of experimental and control plots do not differ significantly. Also, the species composition of plots from the Wetter North, Transitional and Drier South regions show more variation than is evident between experimental and control plots. There was also good qualitative comparisons (quantitative comparisons were not possible as a results of sampling and analytic discrepancies) between the sample plots used in this study and the plant communities described by Graham Deall and Wayne Matthews. Some evidence of exotic invader plants was found within the sample plots, notably Pteridium aquilinum. Fortunately such species were localized in their distribution and restricted to community 1.1.2.2. The aims of Chapter 3 included the following: 1. To compare the faunal biodiversity in grassland fragments within afforested areas to that of control plots in large, relatively undisturbed grassland areas. 2. To determine to which degree the Coleoptera, Orthoptera, Lepidoptera and bird communities reflect recognized plant communities, and are restricted to specific plant communities. 3. To compare the habitat specificity (degree of stenotopy) of the different taxonomic groups and trophic levels of animals. 4. To make recommendations for the conservation of the Afromontane grassland fauna in the remaining grassland fragments in afforested areas. The sampling of 15602 beetles, grasshoppers and crickets were collected, with an average of 3900 per sampling period, revealed unique combinations of animal species linked to the different plant communities mentioned above. Significant differences were evident from the one-way analyses of similarity (ANOSIM) used to compare the faunal community structures of sample plots of the Wetter North, Transitional and Dryer South regions. The faunal community structures of the experimental and control plots of the Wetter North and Transitional regions did not differ significantly. The indexes of habitat specificity (fractions of species constricted to certain plant communities) indicated that the plants and butterflies were more habitat-specific than the Coleoptera, Orthoptera and Birds. The carnivorous insects showed a surprisingly high level of habitat specificity compared to the relatively low level of the phytophagous insects. This surprising trend was also evident in various insect families – Acrididae, Scarabaeidae and Nymphalidae had relatively high levels of habitat specificity compared to that of the Curculionidae and the Chrysomelidae. Chapter 4 has the following aims: 1. To quantify the effect of several environmental characteristics (slope, rainfall, geology, etc) on the faunal community structure of the grassland fragments. 2. To quantify the effects of degree of isolation on species richness, species diversity and assemblage structure of plants, insects and birds in grassland remnants. 3. To test for the effects of edges on the extant insect biodiversity in the grassland fragments inside plantations. 4. To quantify the effects of fragment size on species richness, species diversity and assemblage structure of plants, insects and birds. 5. To rank the grassland fragments in an order of conservation importance using factors such as biodiversity and uniqueness of the floral community. No clear relationship between fragment size and area sampled and species richness and/or – diversity was evident from the results. Indeed, the smallest area sampled had the fourth highest species richness and the largest area sampled had the fourth lowest species richness and species diversity. Regressions results did not show any significant effects of the geographical area sampled on the biodiversity estimates of the fragments. Therefore I assume that the estimates arrived at for the area sampled within each fragment is representative of that of the complete fragment. The Detrended correspondence analysis (DCA - using square root transformed abundance data) used, indicated the need to perform a gradient analysis using a redundancy analysis (RDA). The permutation test resulting from this analysis revealed a non-significant value for the first canonical axis, but a significant value for the first four canonical axes together. The ten species contributing the most to above-mentioned result include two Scarabs (Scarabaeidae – Aphodius sp 1 and Melolonthinae sp 2), two weevils (Curculionidae – Eudraces sp 1 and Curculionidae sp 42), one leaf beetle (Chrysomelidae – Asbecesta near capensis), one darkling beetle (Tenebrionidae – Lagria sp 1), one longhorn beetle (Cerambycidae – Anubis scalaris), one jewel beetle (Buprestidae – Buprestidae sp 1), one ladybird (Coccinellidae – Coccinellidae sp 4) and one Dor beetle (Bolboceratidae – Mimobolbus maculicollis). Of these ten beetles only three are not restricted to the Drier South Region (Anubis scalaris – Wetter North and Drier South, Lagria sp 1 – throughout and Eudraces sp 1 – throughout). The associated stepwise multivariate regression showed distance to the nearest grassland to be the only environmental characteristic to significantly influence the faunal community structure of the fragments. Slope was the environmental characteristic with the smallest effect. In contrast with the results from redundancy analysis, the analysis of similarity (ANOSIM) and t-tests did not reveal significant differences in the faunal community structure of fragments closer to – and further than one kilometre from the nearest grassland neighbour. This trend was the most evident for fragments of the Transitional region and the least obvious for the fragments of the study area as a whole. The SIMPER analysis showed that of the ten species contributing most to the dissimilarity between insect communities of fragments closer/further than one kilometre from the nearest grassland neighbour, eight were also in the group of ten species characterizing the faunal communities of either/both groups (contributing towards similarity). The insect communities found at 10, 20 and 50 metres from the edge of the grassland fragments did not differ significantly, nor did an ANOSIM performed separately for each of the three major plant communities reveal any significant edge-related differences. The ANOVA results for the individual species revealed only one (of 57 - in the Transitional region) having a distribution that differs significantly with respect to distance from the habitat edge:Eremnus sp. 2 was only found at 10 metres from the edge of the fragment, close to the plantations. Of all the groups, only bird diversity, bird richness and general faunal diversity showed significant relationships with fragment size. There was a non-significant trend for insects to biodiversity to be reduced in very small fragments. Most of the botanical data exhibited no significant relationship with fragment size. The species composition of control sites were not found to be significantly different from that of experimental fragments for all the faunal groups pooled together or for the fragments of the Transitional Region and the Wetter North Region. Using the four separate scores for birds, butterflies, beetles and grasshoppers, each fragment was assigned a total conservation score. The twenty-four fragments were then ranked in order of conservation importance. Fragments of the Wetter North had an average score of 65.3, fragments of The Transitional Region 66.6 and fragments of the Drier South 52.3. The results relating to this study has lead to the following conclusions: o It is concluded that afforestation and habitat fragmentation have not significantly impacted on the flora of the montane grassland of the study area since many of the grassland fragments surrounded by plantations are still easily identifiable as natural communities, described by Matthews and Deall in broader-scale surveys in the past. Also, no obvious invader – or disturbed plant communities are discernible even though some of them have been isolated for as long as 40 years. o The plant communities of conservation importance described by Matthews coincide with the important communities recognized in this study. Rare and endangered plant species, as well as species endemic to the region, are more often than not found on the scarce Black Reef quartzite of the region, which is more evident to the Northern part of the study area. Communities 1.1 and 1.2.2 are therefore of particular conservation importance, not only as a result of their scare geological base, but also because of the high risk associated with the few grassland examples left of these communities. o The high levels of habitat specificity of many of the taxonomic and trophic faunal groups indicate that many of the invertebrate taxa are probably endemic to the region, and that the plant endemicity encountered in the Afromontane grasslands is reflected by a similar degree of animal endemicity. o The similarity in faunal assemblages and diversity between isolated fragments and large areas of grassland emphasizes the conservation importance of the fragments, even when smaller than 5 Ha in extent. o Appropriate management of the grassland fragments within the plantations is therefore important for the conservation of the plant and animal taxa encountered there. Experimental management involving grazing, mechanical cutting, grazing and burning is needed to decide on an efficient management regime, so that the grassland biodiversity can be conserved in a planned way. Such work will also allow empirical testing the efficiency of the indicator species suggested above. o Isolated grassland fragments in this study represent largely unaffected natural plant and insect communities, differing little from large unfragmented grasslands in the study area. o Fragments found within afforested areas therefore have a high conservation importance, since they represent ‘natural’ grassland areas and are often the only representative of a particular plant community left in the area. o No significant edge effects on the faunal communities 10, 20 and 50 metres from the fragments’ edges exist as a result of afforestation in the area. o Birds (and probably other vertebrates in these grasslands) are affected by fragment size, while invertebrates are much less affected and plants do not show any measurable effect of fragment size. o Fragments in the wetter northern part of the study area, characterized by high levels of plant endemicity, have a higher conservation importance as judged by faunal biodiversity. / Dissertation (MSc (Zoology and Entomology))--University of Pretoria, 2005. / Zoology and Entomology / unrestricted

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This diploma thesis deals with two assumptions - the necessity of physiological and material aspects for human life - Food and Shelter. It is an immersive installation, which is created through the formal deconstruction of architecture and food. The artwork has the ambition to reflect a certain form of everydayness, in relation to the existence of the individual.

This thesis deals with implementation of a debugging and development tool for GLSL shader programming. In the text, you will find design of the application and it's implementation in Qt library. The thesis also includes performance testing with GLSL shaders. Experiments were focused on commands of application control flow in GLSL and texturing commands used in shaders. In the thesis, you will find explanation of the functionality of some shaders used in OpenGL. Application developed in this thesis, is meant to help with implementation of graphic programs programmed in OpenGL 3.3 or higher.

Charles University in Prague Faculty of Pharmacy in Hradec Králové Department of Biophysic and Physical Chemistry Candidate: Bc. Martina Dvořáková Supervisor: Doc. Ing. Alice Lázníčková, CSc. Consultant: Mgr. Martina Hermannová, Ph.D. Title of diploma thesis: Optimization of preparative LC-MS method for fractionation of oligosaccharides of hyaluronanu This diploma thesis deals with optimization of LC-MS method for analysis of hyaluronan oligosaccharides in preparative mode. The theoretical part summarizes available information about biological and chemical properties of hyaluronic acid. Hyaluronic acid is easily enzymatically degradable by mammalian hyaluronidases that produce hyaluronan oligosaccharides. The biological function of these degradation products depend on their molecular weight. High-performance liquid chromatography is mainly used for separation and purification of hyaluronan oligosaccharides. A new method for the determination of hyaluronan oligosaccharides is based on a combination of separation techniques and mass spectrometry. The experimental part deals with optimization of ionisation conditions for electrospray ionization mass spectrometry in positive and negative ion mode. In the first step, we focused on setting of capillary voltage, cone voltage, desolvation temperature, flow...

Die Tonscherbe mit der Inventarnummer 1270 ist das zentrale Stück der Vitrine im Schriftenraum, das im Ägyptischen Museum der Universität Leipzig die demotische Sprache und Schrift repräsentiert. Sie ist neben knapp 20 weiteren Objekten Zeuge dieser Sprachstufe des Ägyptischen, die zwischen dem siebten vorchristlichen und fünften nachchristlichen Jahrhundert in Ägypten geschrieben und gesprochen wurde, so zum Beispiel zur Zeit Kleopatras VII. Es handelt sich dabei um eine komplizierte, von rechts nach links zu lesende Kursive. Nur wenige Forscher weltweit sind in der Lage, die Zeichen zu entziffern, die stark durch individuelle Handschriften geprägt sind. In Demotisch liegen uns neben großen Werken der Weltliteratur wie die Setna-Romane oder magische Handbücher auch Zeugnisse des Alltagslebens vor. Darunter sind Schülerübungen, Einkaufslisten, Ehe- und Scheidungsurkunden oder auch komplexe Gerichtsdokumente zu nennen. Diese geben uns einen Einblick in Wirtschaft, Recht und Verwaltung in die Lebensweise der Bevölkerung Ägyptens vor 2000 Jahren.

Domain-specific languages (DSLs) are useful tools for coping with complexity in software development. DSLs provide developers with appropriate constructs for specifying and solving the problems they are faced with. While the exact definition of DSLs can vary, they can roughly be divided into two categories: embedded and non-embedded. Embedded DSLs (E-DSLs) are integrated into general-purpose host languages (e.g. Java), while non-embedded DSLs (NE-DSLs) are standalone languages with their own tooling (e.g. compilers or interpreters). NE-DSLs can for example be found on the Semantic Web where they are used for querying or describing shared domain models (ontologies). A common theme with DSLs is naturally their support of focused expressive power. However, in many cases they do not support non–domain-specific component-oriented constructs that can be useful for developers. Such constructs are standard in general-purpose languages (procedures, methods, packages, libraries etc.). While E-DSLs have access to such constructs via their host languages, NE-DSLs do not have this opportunity. Instead, to support such notions, each of these languages have to be extended and their tooling updated accordingly. Such modifications can be costly and must be done individually for each language. A solution method for one language cannot easily be reused for another. There currently exist no appropriate technology for tackling this problem in a general manner. Apart from identifying the need for a general approach to address this issue, we extend existing composition technology to provide a language-inclusive solution. We build upon fragment-based composition techniques and make them applicable to arbitrary (context-free) languages. We call this process for the composition techniques’ universalization. The techniques are called fragment-based since their view of components— reusable software units with interfaces—are pieces of source code that conform to an underlying (context-free) language grammar. The universalization process is grammar-driven: given a base language grammar and a description of the compositional needs wrt. the composition techniques, an adapted grammar is created that corresponds to the specified needs. The result is thus an adapted grammar that forms the foundation for allowing to define and compose the desired fragments. We further build upon this grammar-driven universalization approach to allow developers to define the non–domain-specific component-oriented constructs that are needed for NE-DSLs. Developers are able to define both what those constructs should be, and how they are to be interpreted (via composition). Thus, developers can effectively define language extensions and their semantics. This solution is presented in a framework that can be reused for different languages, even if their notion of ‘components’ differ. To demonstrate the approach and show its applicability, we apply it to two Semantic Web related NE-DSLs that are in need of component-oriented constructs. We introduce modules to the rule-based Web query language Xcerpt and role models to the Web Ontology Language OWL.

<div> <div> <div> <p>The Effective Fragment Potential (EFP) is a quantum-mechanical based model potential for accurate calculations of non-covalent interactions between molecules. It can be coupled with ab initio methods in so-called QM/EFP models to explore the electronic properties of extended molecular systems by providing rigorous description of surrounding environments. The current EFP formulation is, however, not well suited for large-scale simulations due to its inherent limitation of representing effective fragments as rigid structures. The process of utilizing EFP method for the molecular systems with flexible degrees of freedom entails multiple sets of parameter calculations requiring intensive computational resources. This work presents development of the EFP method for describing flexible molecular systems, so-called Flexible EFP. To validate the applicability of the Flexible EFP method, extensive benchmark studies on the amino acid interactions, binding energies, and electronic properties of flavin chromophore of the cryptochrome protein have been demonstrated. In addition to methodological developments, excitonic properties of the Fenna-Matthews-Olson (FMO) photosynthetic pigment-protein complex are explored. In biological systems where intermolecular interactions span a broad range from non-polar to polar and ionic forces, EFP is superior to the classical force fields. In the present study, we demonstrate excellent performance of the QM/EFP model for predicting excitonic interactions and spectral characteristics of the FMO wildtype complex. We characterize the key factors for accurate modeling of electronic properties of bacteriochlrophyll a (BChl a) photosynthetic pigments and suggest a robust computational protocol that can be applied for modeling other photosynthetic systems. Developed computational procedures were also successfully utilized to elucidate photostability and triplet dynamics in the FMO complex and spectroscopic effects of single-point mutagenesis in FMO. A combination of polarizable EFP molecular dynamics and QM/EFP vibrational frequency calculations were also applied to understanding and interpreting structures and Raman spectroscopy of tert-butyl alcohol solutions. </p> </div> </div> </div>