Measurements of neutron emission from a fusion plasma can provide a wealth of information on the underlying temporal, spatial and energy distributions of reacting ions and how they are affected by a wide range of magneto-hydro-dynamic (MHD) instabilities. This thesis focuses on the interpretation of the experimental measurements recorded by neutron flux monitors with and without spectroscopic capabilities installed on the Mega Ampere Spherical Tokamak (MAST). In particular, the temporally and spatially resolved measurements of the neutron rate measured by the neutron camera, which also possesses spectroscopic capabilities, are combined with the temporally resolved measurements of the total neutron rate provided by the absolutely calibrated fission chamber in order to study the properties of the fast ion distributions in different plasma scenarios. The first part of the thesis describes in detail the two forward modelling methods, which employ the set of interconnected codes developed to interpret experimental observations such as neutron count rate profiles and recoil proton pulse height spectra provided by the neutron camera. In the second part of the thesis the developed methods are applied to model the neutron camera observations performed in a variety of plasma scenarios. The first method, which involves only TRANSP/NUBEAM and LINE2 codes, was used to validate the neutron count rate profiles measured by the neutron camera in three different plasma scenarios covering the wide range of total neutron rate typically observed on MAST. In addition, the first framework was applied to model the changes in the total and local neutron rates caused by fishbone instability as well as to estimate the Hydrogen and Deuterium ion ratio. The second modelling method, which involves TRANSP/NUBEAM, LINE2, DRESS and NRESP, was used to validate the measured recoil proton pulse height spectra in a MHD-quiescent plasma scenario.

As the fluidic devices are miniaturized to improve portability, the friction of the microchannel becomes intrinsically high and a high pumping power will be required to drive the fluid. Since the pumping power delivered by portable devices is limited, one method to reduce this is to render the surface to become slippery. This can be achieved by roughening up the microchannel wall and form a bed of air pockets between the roughness elements, which is known as the superhydrophobic Cassie-Baxter state. While the study on superhydrophobic microchannels are focused mainly in maximizing the friction reduction effects and maintaining the stability of the air pockets, less attention has been given to characterizing the microchannel friction under a metastable state, where partial flooding of the micro-textures may be present, and under heated conditions, where the air pockets are trapped between the micro-textures. In order to quantify the frictional characteristics, microchannels with micron-sized trenches on the side walls were fabricated and tested under varying inlet pressures and heating conditions. By measuring the hydrodynamic resistance and comparing with numerical simulations, results suggest that (1) the air-water interface behaves close to a no-slip boundary condition, (2) friction becomes insensitive to the wetting degree once the micro-trenches become highly wetting, (3) the fully wetted micro-trench may be beneficial over the de-wetted ones in order to achieve friction reduction effects and (4) heating the micro-trenches to induce a highly de-wetting state may actually be detrimental to the microchannel flow due the excessive growth of the air layer. As part of the future work to characterize heat transfer in superhydrophobic microchannels, a rectangular microchannel with microheaters embedded close to the side walls was fabricated and the corresponding heat transfer rates were measured through dual fluorescence thermometry. Results suggested that significant heat is lost through the environment despite the high thermal resistance of the microchannel material. An extra insulation is suggested prior to characterizing the convective heat transfer coefficients in the superhydrophobic microchannel flow. / text

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This thesis presents the development and optimization of a high-throughput fluorescence microbead based approach for multiplexed, large scale medical diagnostics of biological fluids. Specifically, different sizes of semiconductor nanocrystals, called quantum dots, are infused into polystyrene microspheres, yielding a set of spectrally unique optical barcodes. The surface of these barcodes are then used for sandwich assays with target molecules and fluorophore-conjugated detection antibodies, changing the optical spectra of beads that have associated with (or captured) biomolecular targets. These assayed microbeads are analyzed at a single bead level in a high-throughput manner using an electrokinetic microfluidic system and laser induced fluorescence. Optical signals collected by solid state photodetectors are then processed using novel signal processing algorithms. This document will discuss developments made in each area of the platform as well as optimization of the platform for improved future performance.

In the field of cancer research and diagnostics it is crucial to have reliable methods for detecting molecules involved in the disease. New and better methods for diagnostics, prognostics and drug delivery therefore remain a permanent aim. In this thesis applications of the in situ proximity ligation assay (in situ PLA) were developed for diagnostics and research. Two new methods were developed, one more cost effective proximity assay without the use of enzymes and one method for loading pharmaceuticals in lipid rafts made from detergent resistant membranes (DRMs) to be used as a drug delivery platform. In Paper I the aim was to develop a flow cytometric detection method of the fusion protein BCR-ABL that is the hallmark of chronic myeloid leukemia (CML). By using in situ PLA the malignant cells carrying the fusion protein could be detected in patients in a convenient workflow. Paper II describes an application of multiplex in situ PLA, where extracellular vesicles (EVs) are detected and identified using flow cytometry. Up to five different antigens are targeted on the EVs, reflected in three different colors during detection in the flow cytometer. By using antibodies targeting proteins specific for prostasomes a population of prostasomes could be identified in human blood plasma. In Paper III a new method is described for using lipid raft for drug delivery. In this method, lipid rafts, derived from prostasomes or erythrocytes, are loaded with pharmaceuticals. The vehicles were loaded with doxorubicin, added to cells and counted. Cells that received the vehicle with doxorubicin stopped proliferating and died, while controls that received the lipid raft vehicle without doxorubicin were not affected, suggesting that the vehicles are effectively loaded with the drug and that they are safe. This lipid raft vehicle could provide a safe drug delivery system.      Paper IV investigates the crosstalk between the two major signal pathways Hippo and Wnt, and how these are affected in gastric cancer. When looking at different colon cancer tumor stages, we found that the cellular localization of TAZ/β-catenin interactions were different. We also found that protein complexes involved in the crosstalk increased in sparsely growing cells compared to more densely growing cells. On the basis of these results the protein E-cadherin, involved in maintenance of the epithelial integrity, was investigated and was found to have a probable role in regulating the crosstalk between Hippo and Wnt.     A new method for localized protein detection is described in paper V. Here a proximity assay, based on the hybridization chain reaction (HCR), was developed. This assay, proxHCR, is more cost effective than in situ PLA because no enzymes are required. ProxHCR successfully detects protein interactions and can be used together with both fluorescence microscopy and flow cytometry.

<p>Despite its ubiquitous abundance, Hsp90 inhibitors have shown promise in anti-cancer clinical trials, suggesting that Hsp90 inhibitors selectively target tumor cells while exhibiting minimal effects in normal cells. Extracellular expression of heat shock protein 90 (eHsp90) by tumor cells is strongly correlated with malignancy. Development of small molecule probes that can specifically detect eHsp90 in vivo may therefore have utility in the early detection of malignancy. We synthesized a fluorescent cell impermeable Hsp90 inhibitor, HS-131, to target eHsp90 in vivo. HS-131 was characterized biochemically to ensure specificity for eHsp90, and an inactive analog was also synthesized to be used as an in vivo control. </p><p>Through confocal microscopy, eHsp90 can be visualized with cell impermeable, fluorophore-tagged Hsp90 inhibitors. High resolution confocal and real time lattice light sheet microscopy showed that probe-bound eHsp90 accumulates in punctate structures on the plasma membrane of breast tumor cells and is subsequently actively internalized. This internalization occurs in the presence and absence of inhibitors. The extent of internalization correlates with tumor cell aggressiveness, and this process can be induced in benign cells by over-expressing p110HER2, leading to malignant transformation of these cells. Internalization of eHsp90 is also increased after inhibition of Hsp70, suggesting that overcompensation of the heat shock response can also upregulate the eHsp90 trafficking mechanism. Whole body 3D cryo fluorescence imaging and histology of flank and spontaneous tumor-bearing mice strongly suggests that eHsp90 expression is a unique phenomenon in vivo. </p><p>Taken together, these results suggest that active and differential internalization of eHsp90 in aggressive cancer cells contributes to the selectivity observed upon Hsp90 inhibitor treatment and may provide a novel metastatic biomarker for solid tumors and may lead to the development of a tumor-specific drug delivery system.</p> / Dissertation

DNA microarrays represent an ultra-high throughput gene expression assay employed to study the transcriptomic profiles of biological tissues. These devices are increasingly being used to study many aspects of gene regulation, and there is growing interest in the biotechnology and pharmaceutical industries for developing such devices in efforts toward rational product/drug design. The DNA microarray also provides a unique and objective means for diagnosis and prognosis of human diseases based on patterns of gene expression. This is especially important in cancer research and the thrust toward personalized medicine. This dissertation details the design and development of oligonucleotide microarrays and the design and execution of a gene expression study conducted using human glioma specimines. Chapter 2 details the design and development a ~10,000 gene human oligonucleotide microarray. This device consisted of a 21,168 features, each composed of a particular human gene-probe and was applied to the challenge of diagnostic and prognostic estimation for human gliomas (chapter 3). Gliomas are the most frequent and deadly neoplasms of the human brain characterized by a high misdiagnosis rate and low survival. The study in chapter 3 demonstrated that the specified design and development parameters were appropriate for conducting gene expression analysis and that this platform can be used successfully to predict malignancy grade and survival for glioma patients.

This Diploma thesis thematizes the problem of students' time perspective and its diagnostics. The whole text is divided into two parts - theoretical and practical with emphasis on the theoretical part. The theoretical part will look upon the conceptions of time perspective. Ideas of time perception, the influence of time on human behavior and a connection of time pespective with an achievement motivation are presented. The personality-motivational concept of time perspective by European expert of motivational psychology Jopeph Nuttin are analyzed. From the domestic authors I describe the concept of perpsective orientation by Isabella Pavelkova. These theories are completed with information gained by Rayner, Gjesme and Fraisse. The important section is a chapter where diagnostics and specifics methods are presented. The empirical section contains the results of research provided by 5 classes of high school students with an eight year (or four year) study plan in April 2012 in Caslav. Using two questionaries (Motivational Induction Method and Perspective Orientation Questionary). Motivational Induction Method investigates objects of students' time perspective and summarized these themes into exact time frames. The Perspective Orientation Questionnaire helps investigate external validity. Key words:...

Master of Science / Department of Biological & Agricultural Engineering / Mei He / Anemia affects about 25% of the world’s population and causes roughly 8% of all disability cases. The development of an affordable point-of-care (POC) device for detecting anemia could be a significant for individuals in underdeveloped countries trying to manage their anemia. The objective of this study was to design and fabricate a 3D printed, low cost microfluidic mixing chip that could be used for the diagnosis of anemia. Microfluidic mixing chips use capillary flow to move fluids without the aid of external power. With new developments in 3D printing technology, microfluidic devices can be fabricated quickly and inexpensively. This study designed and demonstrated a passive microfluidic mixing chip that used capillary force to mix blood and a hemoglobin detecting assay. A 3D computational fluid dynamic simulation model of the chip design showed 96% efficiency when mixing two fluids. The mixing chip was fabricated using a desktop 3D printer in one hour for less than $0.50. Blood samples used for the clinical validation were provided by The University of Kansas Medical Center Biospecimen Repository. During clinical validation, RGB (red, green, blue) values of the hemoglobin detection assay color change within the chip showed consistent and repeatable results, indicating the chip design works efficiently as a passive mixing device. The anemia detection assay tended to overestimate hemoglobin levels at lower values while underestimating them in higher values, showing the assay needs to go through more troubleshooting.

The aim of this thesis is to in various ways explore protein expression in human normal tissue and in cancer and to apply that knowledge in biomarker discovery. In Paper I the prognostic significance of RNA-binding motif protein 3 (RBM3) is explored in malignant melanoma. To further evaluate the prognostic significance of RBM3 expression was assessed in 226 incident cases of malignant melanoma from the prospective populationbased cohort study Malmö Diet and Cancer Study using tissue microarray technique (TMA). RBM3 was shown to be down regulated in metastatic melanoma and high nuclear expression in the primary tumor was an independent marker of prolonged over all survival. As a tool to facilitate clinical biomarker studies the Human Protein Atlas has created a tissue dictionary as an introduction to human histology and histopathology. In Paper II this work is introduced. A cancer diagnosis can be a complex process with difficulties of establishing tumor type in localized disease or organ of origin in generalized disease. Immunohistochemically assisted diagnosis of cancer is common practice among pathologists where its application combined with known protein expression profiles of different cancer types, can strengthen or help dismiss a suspected diagnosis. In Paper III the diagnostic performance of 27 commonly used antibodies are tested in a predominantly metastatic, multicancer cohort using TMA technique. Overall these 27 diagnostic markers showed a low sensitivity and specificity for its intended use, highlighting the need for novel, more specific markers. Breast, ovarian, endometrial and ovarian cancers affect predominantly women. Differential diagnostics between these cancer types can be challenging. In Paper IV an algorithm, based on six different IHC markers, to differentiate between these cancer types is presented. A new diagnostic marker for breast cancer, namely ZAG is also introduced. In Paper V the transcriptomic landscape of the adrenal gland is explored by combining a transcriptomic approach with a immunohistochemistry based proteomic approach. In the adrenal gland we were able to detect 253 genes with an elevated pattern of expression in the adrenal gland, as compared to 31 other normal human tissue types analyzed. This combination of a transcriptomic and immunohistochemical approach provides a foundation for a deeper understanding of the adrenal glands function and physiology.