We have developed novel fluorescence bio-imaging based automated models to screen for novel candidate targets involved in prostate cancer metastasis. Utilizing these models and adopting a... Show moreWe have developed novel fluorescence bio-imaging based automated models to screen for novel candidate targets involved in prostate cancer metastasis. Utilizing these models and adopting a functional genomics based approach; we identified SYK as a novel regulator of prostate cancer progression. We also identified functional involvement of MST1R in regulating the progression of prostate cancer. For both of these targets, there is supporting human clinical data to validate our results in prostate cancer. Show less
In this thesis, nanochannels as well as nanofluidic phenomena are used to provide new and miniaturized bioanalytical tools for the life sciences. Isotachophoresis performed in nanochannels showed... Show moreIn this thesis, nanochannels as well as nanofluidic phenomena are used to provide new and miniaturized bioanalytical tools for the life sciences. Isotachophoresis performed in nanochannels showed the focusing and separation of analytes in a 0.4 picoliter volume, which is a volume in the order of a sample from a single cell. Depletion zone isotachophoresis (dzITP) is demonstrated which uses a nanofluidic phenomenon, concentration polarization, to enable isotachophoresis in a microchannel while using only a single electrolyte. A concept for surface enhanced Raman spectroscopy (SERS) sensor (SERSOR) is explored; a coating protecting the SERS surface from irreversible adsorption may enable dynamic measurements of biomolecules in solution in minute volumes. Working with nanochannels has led to the discovery of new unexpected fundamental phenomena: the very high surface to volume ratio in nanochannels causes acidification of solutions introduced in them, despite the presence of up to 1 mol/L of buffer. Also, extreme pressures of more than a 1000 bar may be induced in a nanochannel by what we named electrocavitation, an effects shown to impose a limit on further downscaling of ITP. Show less
We develop a new technique for Run-time Checking for two object-oriented languages: Java and the Abstract Behavioral Specification language ABS. In object-oriented languages, objects communicate by... Show moreWe develop a new technique for Run-time Checking for two object-oriented languages: Java and the Abstract Behavioral Specification language ABS. In object-oriented languages, objects communicate by sending each other messages. Assuming encapsulation, the behavior of objects is completely determined by the order of the messages, and their content. Traditional methods for Run-time Checking focus either exclusively on the description and testing of the order of the messages (Monitoring), or they focus on specifying and testing the content of those messages (Run-time Assertion Checking). Our method combines Monitoring with Run-time Assertion Checking.The basic idea behind our technique is that the behavior of objects can be described formally by means of an attribute grammar extended with assertions. The underlying (context-free) grammar specifies the valid orderings of the messages, the attributes define properties of the contents of the messages, and assertions specify the desired values of those properties. We develop a new Run-time Checker for attribute grammars in the form of a meta-program in the language Rascal and applied the Run-time Checker to an industrial case of the e-commerce company Fredhopper. We also investigated the efficiency of the run-time checker, and successfully discovered and solved several bugs in the Fredhopper software. Show less
In this thesis, patterns of variation in plant metabolomes and insect communities were described in GM and non-GM potato plants in both laboratory and field experiments. Differences between plant... Show moreIn this thesis, patterns of variation in plant metabolomes and insect communities were described in GM and non-GM potato plants in both laboratory and field experiments. Differences between plant genotypes in insect abundances were small when compared to year-to-year differences, location effects and differences between developmental stages of plants. Standardized effect sizes are discussed as an alternative scale for measuring effects. Leaf age, aphid infestation and virus infection were found to cause significant alterations in leaf metabolism in a laboratory study as measured by 1H NMR. However, these changes were similar in quantity and quality in both GM and non-GM plants. Furthermore, 1H NMR metabolomic profiles of potato plants were measured in a 2-year field study. Large changes in metabolomic profiles occurred across years and locations, and throughout the growth period of plants within years. Only weak relationships were found between metabolomics data and insect abundances on the same experimental fields. GxE interactions imply that conclusions from field trials are not valid outside the range of tested environments. This emphasizes the need for a careful choice of representative geographical zones for risk assessment studies. However, it also shows that a residual level of uncertainty in NTO safety is unavoidable. Show less
In this thesis the thermal- and photo-substitution behavior of polypyridyl ruthenium complexes is described at the surface of lipid bilayers and in homogeneous solutions. It is shown that the... Show moreIn this thesis the thermal- and photo-substitution behavior of polypyridyl ruthenium complexes is described at the surface of lipid bilayers and in homogeneous solutions. It is shown that the successive thermal binding and light-induced unbinding of the cationic ruthenium complex at the surface of the lipid bilayer requires negatively charged liposomes and ruthenium complexes containing moderately hindered N-N bidentate ligands. Our results in homogeneous solution show that changing the steric hindrance of the bidentate ligand influences both the photo- and thermal reactivities of these complexes, by altering the mechanism of the Ru-S bond formation. It is also shown that the Ru-S bond formation at the surface of negative lipid bilayers is faster than the same reaction in homogenous aqueous solutions, and a two-steps mechanism is proposed for the thermal coordination of ruthenium aqua complexes at membrane-embedded ligands. Furthermore, the application of ruthenium-functionalized liposomes in drug delivery is discussed. In vitro tests on cancer cell lines show that neutral liposomes functionalized with ruthenium compounds are more readily taken up by cancer cells than ruthenium-free liposomes. The liposome samples with ruthenium compounds are shown to be poorly cytotoxic in the dark. After light irradiation, the cytotoxicity increased at least up to five times for ruthenium complexes supported on non-PEGylated liposomes. Finally, the photoactivation of polypyridyl complexes with low-energy photons was studied using a photosensitization approach. A photosubstitution reaction was made faster upon yellow light irradiation than upon blue light irradiation by covalently linking a rhodamine B dye to the ruthenium complex. Show less
A system-level design methodology such as Daedalus provides designers with a forward synthesis flow for automated design, programming, and implementation of multiprocessor systems-on-chip. Daedalus... Show moreA system-level design methodology such as Daedalus provides designers with a forward synthesis flow for automated design, programming, and implementation of multiprocessor systems-on-chip. Daedalus employs the polyhedral process network model of computation to represent applications. These networks are automatically derived from sequential C code. A forward synthesis flow greatly increases designer productivity. Still, the designer needs to perform a time-consuming forward synthesis step to learn if a network satisfies his performance constraints. Furthermore, it is not trivial to select a set of transformations and transformation parameters for a network such that performance requirements are met. A forward synthesis flow thus solves only part of a design problem, as it does not provide fast feedback on the transformations a designer should apply to meet his performance constraints. This dissertation intro duces different performance estimation techniques for polyhedral process networks. The most promising technique is the profiling-based cprof technique that works directly on the sequential application code. This makes cprof an easy-to-use, robust, and fast technique, without the need to derive a polyhedral process network. This dissertation then discusses four transformations and analyzes factors that affect the efficacy of each transformation. Show less
The aim of this thesis is to introduce the readers to the importance of bio-based products and their potential applications in chemical industries. Alternative routes to the widely used nylon... Show moreThe aim of this thesis is to introduce the readers to the importance of bio-based products and their potential applications in chemical industries. Alternative routes to the widely used nylon precursor caprolactam are discussed and compared with the current fossil-based synthesis. Furthermore, the aim of the research - the development of a novel synthesis route to caprolactam based on biomass - is reported; the envisaged reaction sequence includes the development of new catalytic chemistry, namely reductive amidation and hydroamidomethylation. Show less
The main goal of this work is to develop a method that, operating on top of an Evolutionary Algorithm, increases its likeliness of finding innovative solutions. This likeliness is laid out to be... Show moreThe main goal of this work is to develop a method that, operating on top of an Evolutionary Algorithm, increases its likeliness of finding innovative solutions. This likeliness is laid out to be increased with the diversity of the solutions found, provided that they are of sufficient quality. The developed method needs to be applicable in a scenario in which the search is required to be started from a single, fixed solution. Therefore, a scheme is envisioned in which the search is performed in a sequential fashion, zooming in on a locally-optimal solution, and then exploring for a new potentially high-quality region based on a memory of solutions encountered earlier in the search. Two exploration criteria, one using an archive of earlier solutions as memory and the other deriving from a surrogate model trained on earlier solutions, were established to be worthwhile for integration into quality-based search. The resulting schemes were applied to a real-world airfoil optimization task, showing both to perform better than the baseline method of multiple standard optimization runs. The model-based approach delivers the best results, in the sense that it finds more solutions, more diverse solutions, and better-quality solutions than the baseline method. Show less
Population growth and the drop in the returns from the major cash crop (coffee) for small farmers are the main drivers that have influenced the farming systems and mobility of farmers in the... Show morePopulation growth and the drop in the returns from the major cash crop (coffee) for small farmers are the main drivers that have influenced the farming systems and mobility of farmers in the Western Highlands of Cameroon (WHC). The main objective of this research activity was to determine the interactions between farming systems and human mobility in the WHC. A comparative study was conducted through household and field surveys in three villages and conceptualized based on the systems approach. The different types of mobility were influenced by household social factors, the quest for ‘high valued' farm plots and hired labour. Urban-rural migration contributed to occupation diversification and social mobility. The sustainability factor was a function of land use intensity, intensity of off-farm inputs, the household adjustment factor and mobility of the household. The sacred groves were rich in plant diversity of varied ecological and economic importance. Nitrogen mining was common at all levels of the farming system. These determinants and types of mobility claims are pertinent to the research area; the sustainability results of the farming systems reflect the reality on the ground; the nutrient flux evaluated at the crop and farm levels constitute a valuable database for future research. Show less
This thesis involves excitonic physics in bilayers of strongly correlated electron materials. The fermionic bilayer extended Hubbard model is studied by means of mean field theory and Determinant... Show moreThis thesis involves excitonic physics in bilayers of strongly correlated electron materials. The fermionic bilayer extended Hubbard model is studied by means of mean field theory and Determinant Quantum Monte Carlo simulations. A bosonic low-energy effective theory is developed, called the exciton t-J model. The phase diagram and the elementary excitations of this model are investigated. Surprisingly, the excitons are predicted to exhibit Ising confinement physics in the antiferromagnetic phase. In the exciton superfluid phase the magnetic triplon modes borrow kinetic energy from the excitons. Show less
When soft, repulsive particles, like foam bubbles or emulsion droplets, are sheared, they show interesting scaling behaviour. We develop a simple scaling model that captures the rheological... Show moreWhen soft, repulsive particles, like foam bubbles or emulsion droplets, are sheared, they show interesting scaling behaviour. We develop a simple scaling model that captures the rheological behavior starting from three assumptions that explicitly depend on the microscopic interactions. This model starts from three ingredients: energy conservation, the concept of an effective steady state strain in our flowing system and a constitutive elasticity equation linking the effective strain to the shear stress. Our model allows for non-linear microscopic particle interactions and it predicts that the global rheological behaviour depends on the details of the microscopic interactions between the particles - in contrast to standard critical scaling theory. We test our model in computer simulations of soft, massless particles under steady shear and find that the numerics are broadly consistent with our model. jamming, rheology, foam, critical scaling Show less
This thesis focuses on the development of image analysis methods for ultra-high content analysis of high-throughput screens where cellular phenotype responses to various genetic or chemical... Show moreThis thesis focuses on the development of image analysis methods for ultra-high content analysis of high-throughput screens where cellular phenotype responses to various genetic or chemical perturbations that are under investigation. Our primary goal is to deliver efficient and robust image analysis platforms which can 1) automatically detect cellular structures of interest from florescence microscope images and 2) quantify dynamics and organization of multi-cellular systems with phenotypic features. To recover heterogeneity of cellular behavior, we aim to develop single-cell-based image analysis methods so that cell subpopulations can be distinguished and investigated. Furthermore, we intend to develop methods to extract an ultra-high level of phenotypic details from images. This would enable system-level studies of phenotype characterization. Show less
In this thesis the behavior and functionality of peptide amphiphiles at the surface of bilayer vesicles is examined. By controlling the behavior of the surface bound peptides, I was able to... Show moreIn this thesis the behavior and functionality of peptide amphiphiles at the surface of bilayer vesicles is examined. By controlling the behavior of the surface bound peptides, I was able to construct assemblies which could: 1) release their content (triggered by pH), 2) fuse in a targeted and controlled manner or 3) dock to cells and zebrafish embryos Show less
CRANK is a suite that links different macromolecular X-ray crystallographic programs to solve macromolecular crystal structures automatically from experimental phasing data. In chapter 2, several... Show moreCRANK is a suite that links different macromolecular X-ray crystallographic programs to solve macromolecular crystal structures automatically from experimental phasing data. In chapter 2, several new algorithms implemented within CRANK increase the robustness and speed of the structure solution process. The new MULTICOMB program, discussed in chapter 3, provides a new phase combination algorithm for the density modification step of the structure solution process. MULTICOMB implements a novel advanced multivariate function that considers the single-wavelength anomalous diffraction (SAD) data directly, accounts for the correlation between the initial and density-modified maps and refines errors that can occur in a SAD experiment. Testing of these new algorithms with over 100 real data sets showed a dramatic improvement over state-of-the-art methods. These novel methods were also applied in solving the new structure of the DNA-binding protein Sso10a2 from Sulfolobus solfataricus reported in chapter 4. This structure provides insight to the observed differences in behaviour between Sso10a2 and its close homolog Sso10a. The last chapter of this work describes the crystallization conditions for a recombinant, fully glycosylated form of the human C1 inhibitor protein, which is involved in hereditary angioedema, a potentially life threatening condition. Show less
Most scientific literature on hyena-human interrelationships in Africa sug-gests conflict situations, often resulting in the killing of hyenas. Hyenas survive with difficulty in human-altered... Show moreMost scientific literature on hyena-human interrelationships in Africa sug-gests conflict situations, often resulting in the killing of hyenas. Hyenas survive with difficulty in human-altered habitats and coexistence between hyenas and local communities is problematic. This is because hyenas need extensive areas, usually with few people and sufficient prey. In contrast to this, the present dissertation presents an exceptional case of peaceful co-existence between hyenas and humans. Based on regular observations of hyenas and anecdotal reports, I hypothesized that hyenas in the Tigray re-gion, northern Ethiopia, survive in human-dominated landscapes because of a unique combination of adaptation to anthropogenic food and cultural tolerance towards hyenas. My research aimed to investigate hyena ecology and behavior in human-dominated and prey-depleted landscapes in Tigray. Hyenas are common in many parts of Ethiopia, and in most of those areas, prey populations have been depleted. In northern Ethiopia, the natural prey base is depleted due to agricultural expansion, deforestation, human settle-ment, and habitat fragmentation and degradation Show less
This thesis describes the application of a variety of different classical and paramagnetic NMR to different protein system. To this end cytochrome P450cam was assigned using classical techniques... Show moreThis thesis describes the application of a variety of different classical and paramagnetic NMR to different protein system. To this end cytochrome P450cam was assigned using classical techniques and paramagnetic NMR was used to investigate the solution state of this enzyme in complex with its binding partner, putidaredoxin. The solution structure of Avr2 was also solved using classical NMR spectroscopy techniques. Additionally, an algorithm for the assignment of protein nuclei on the basis pseudocontact shifts, PARAssign, is presented. An investigation of the dynamic behaviour of a paramagnetic tag attached to T4 lysozyme using relaxation dispersion is described. Show less
Photosynthesis in plants, algae and cyanobacteria releases oxygen and is referred to as oxygenic photosynthesis. Among all the photosynthetic reaction centers only PSII provides a redox potential... Show morePhotosynthesis in plants, algae and cyanobacteria releases oxygen and is referred to as oxygenic photosynthesis. Among all the photosynthetic reaction centers only PSII provides a redox potential sufficiently strong for water oxidation. While the electron flow in PSII is strictly asymmetric, in PSI different levels of bidirectionality indicate functional flexibility of this complex. Photo-CIDNP is non-Boltzmann nuclear magnetization caused by photochemical reactions and can be observed by NMR spectroscopy as strongly enhanced absorptive or emissive signals. In this thesis photo-CIDNP solid state NMR with selective isotope labeling is applied to get direct access to the heart of large PSII and PSI photosynthetic complexes in intact and isolated systems of Spirodela oligorrhiza and Synechocyctis. For the first time the direct observation of selective atoms within the heart of the PSII and PSI complexes by experiment s on entire plants and whole cells is reported. In this way the conservation of the electronic structure of the PSII electron donor at various levels of biological preparations have been addressed and the electron spin density (ρi) in the active cofactors of PSI has been constructed. In addition the functional heterogeneity of the PSI electron donor among different plant species was probed. Show less
While aging remains one of the most significant risk factors for development of Alzheimer disease (AD), increasing evidence strongly points to the potential roles of cerebrovascular and white... Show moreWhile aging remains one of the most significant risk factors for development of Alzheimer disease (AD), increasing evidence strongly points to the potential roles of cerebrovascular and white matter abnormalities in the disease development. A better understanding of the manner in which these abnormalities contribute to disease progression can be achieved by in vivo characterization of AD related pathologies. To this end, MR based techniques serve as effective non-invasive tools to longitudinally monitor changes in AD brain. In this thesis, a variety of MR based techniques were optimized and employed to longitudinally monitor the AD progression in transgenic mouse models of the disease at 9.4T and 17.6T. In Chapter 2, age-dependent blood flow alterations were examined in a Tg2576 mouse model of Alzheimer's disease using MR angiography at 17.6T. AD is linked to abnormalities in the vascular system. In Chapter 3, in vivo T2 changes were longitudinally monitored in the corpus callosum, of the Tg2576 mice. In Chapter 4, age-dependent regional brain T1 and T2 changes in healty mice were established at 17.6T. In vivo imaging of these mouse models at ultra-high magnetic field strengths can permit a better understanding of the underlying cellular mechanism of AD. Show less
The work described in this thesis focuses on the application of various NMR techniques to the study of interactions between proteind and small molecules and proteins and peptides, incluiding the... Show moreThe work described in this thesis focuses on the application of various NMR techniques to the study of interactions between proteind and small molecules and proteins and peptides, incluiding the well-established classical NMR approaches, and the precently developed paramagnetic NMR methods. computational tools have been used to complement and visualized the experimental data. Show less
This thesis is dedicated to the empirical study of image analysis in HT/HC screen study. Often a HT/HC screening produces extensive amounts that cannot be manually analyzed. Thus, an automated... Show moreThis thesis is dedicated to the empirical study of image analysis in HT/HC screen study. Often a HT/HC screening produces extensive amounts that cannot be manually analyzed. Thus, an automated image analysis solution is prior to an objective understanding of the raw image data. Compared to general application domain, the efficiency of HT/HC image analysis is highly subjected to image quantity and quality. Accordingly, this thesis will address two major procedures, namely image segmentation and object tracking, in the image analysis step of HT/HC screen study. Moreover, this thesis focuses on expending generic computer science and machine learning theorems into the design of dedicated algorithms for HT/HC image analysis. Additionally, this thesis exemplifies a practical implementation of image analysis and data analysis workflow via empirical case studies with different image modalities and experiment settings. However, the data analysis theorem will be generally illustrated without further expansions. Finally, the thesis will briefly address supplementary infrastructures for end-user interaction and data visualization. Show less
