We study some topological properties of dynamical systems. In particular the rela- tionship between spatio-temporal chaotic and Li-Yorke sensitive dynamical systems establishing that for minimal dynamical systems those properties are equivalent. In the same direction we show that being a Li-Yorke sensitive dynamical system implies that the system is also Li-Yorke chaotic. On the other hand we survey the possibility of lifting some topological properties from a given dynamical system (Y, S) to an- other (X, T). After studying some basic facts about topological dynamical systems, we move to the particular case of interval maps. We know that through the knowl- edge of interval maps, f : I → I, precious information about the chaotic behavior of general nonlinear dynamical systems can be obtained. It is also well known that the analysis of the spectrum of time series encloses important material related to the signal itself. In this work we look for possible connections between chaotic dynamical systems and the behavior of its Fourier coefficients. We have found that a natural bridge between these two concepts is given by the total variation of a function and its connection with the topological entropy associated to the n-th iteration, fn(x), of the map. Working in a natural way using the Sobolev spaces Wp,q(I) we show how the Fourier coefficients are related to the chaoticity of interval maps.

Over the last decade, immobilization of proteins onto inorganic materials is becoming more crucial to extend a deep understanding of interaction between proteins and nanoparticles. With understanding of the real interaction lying under the protein-nanoparticle relations, it is possible to organize the conformation and orientation of surface and framework species of nanoparticles to generate ideal surfaces for potential biotechnological applications. Due to their unique properties such as large clean surface, tunable surface properties, adjustable surface charge, and dispersibility in aqueous solutions, zeolite and zeo-type materials are one of the remarkable classes of inorganic materials that are widely studied in the literature. These properties make zeolites promising alternative candidates for the immobilization of enzymes and incorporation into biosensing devices. In the current study, a new approach was developed for direct determination of urea, glucose, and butyrylcholine where zeolites were incorporated to the electrode surfaces of a conductometric biosensor and Ion Sensitive Field Effect Transistors were used to immobilize the enzymes. Biosensor responses, operational stabilities, and storage stabilities of the new approach were compared with results obtained from the standard membrane methods for the same measurements. For this purpose, different surface modification technique, which are simply named as Zeolite Modified Transducers (ZMTs) were compared with Standard Membrane Transducers (SMTs). During the conductometric measurements ZMT electrodes were used, which allowed the direct evaluation of the effect of zeolite morphology on the biosensor responses for the first time. It was seen that silicalite added electrodes lead to increased performances with respect to SMTs. As a result, the zeolite modified urea and glucose biosensors were successfully applied for detecting urea and glucose, which can offer improved possibilities to design biosensors. The results obtained show that zeolites could be used as alternatives for enzyme immobilization in conductometric biosensors development. Furthermore, the sensitivities of urease and butyrylcholinesterase biosensors, prepared by the incorporation of zeolite Beta crystals with varying acidity on the surface of pH-sensitive

Objective¡G The purpose of this research is (1) to find out the overall trends of the common avoidable hospitalization diseases in Taiwan since the implementation of the National Health Insurance (NHI), (2) to compare the different distributions of the common avoidable hospitalization diseases across age groups, genders, regions, and the hospital¡¦s characters, (3) to make the related useful information and suggestions of improving avoidable hospitalizations to the policy makers, hospitals, and the general public. Method¡G Standardized rates of avoidable hospitalization from 1997 to 2004 were derived from the National Health Insurance database and the Taiwan census data. In this research, we focus on the four main diseases¡GAsthma, Pneumonia, Diabetes, Hypertension as the avoidable hospitalization diseases. Logistic regression and chi-squire tests are used to detect and describes trends in data. Results¡G During the 8-year research period, AHCs (Avoidable Hospitalization Conditions)of Asthma and Hypertension decline overall, conversely, AHCs of Pneumonia and Diabetes show increasing trends overall¡Fin the hospital characters aspects, AHCs are mostly occurred in the local hospitals¡Ffrom the viewpoint of the patients¡¦ characters, AHCs of Asthma and Pneumonia are always occurred in children male, on the other hand, AHCs of Diabetes and Hypertension are always occurred in female and above 65 years old¡Fin the regional aspect, the AHCs of Asthma and Pneumonia are comparatively higher in east Taiwan. Conclusion¡G According to the results of this research, we can find that the avoidable hospitalizations in Taiwan still need to be improved. We suggest the policy makers and the hospitals may use the ¡uavoidable hospitalization¡vas an indicator to monitor the quality of care and the outpatient care quality in Taiwan¡¦s healthcare system. Thus can not only reduce the unnecessary expenditure, but also can offer the general public better quality of healthcare and improve their quality of life.

A few computational models currently exist to predict heat production and dissipation in tissue when a tumor containing optically-tunable gold nanoparticles such as nanoshells or nanorods is illuminated with near infrared (NIR) laser. The validity of any computational model still needs to be established by experiments before its wide use for various future clinical applications. One of the possible ways to validate the model is through the heat measurements within a phantom made with tissue-equivalent heat-sensitive gel. Currently, there are a few recipes available for this type of gel and the majority of them use severely toxic ingredients. However, none of them seems to perfectly serve the current purposes. Therefore, the primary goal of this thesis work was to develop and characterize two new types of heat-sensitive gels, using relatively non-toxic substances for the in-phantom validation of computational models. Specifically, two novel agar based phantoms, TG1 and TG2, were developed and characterized. The basic optical response of these phantoms at 808 nm NIR light was determined to test their equivalency to human tissue. Thermal damage to the phantoms was quantified by heating them to specific temperatures and obtaining calibration curves to relate temperature and R2 relaxation rates. The phantoms were scanned with magnetic resonance imaging (MRI) to obtain T2 values. TG1 gel, agar and bovine serum albumin (BSA) mixture, was found not to be optically tissue-equivalent. However, TG1 gel demonstrated unambiguous digital response capable of distinguishing temperature of at least 70 °C compared to the sample receiving no heat. Additionally, TG1 gel produced high degree of linearity in the thermal therapy temperature regime (60 - 80 °C). TG2 gel containing agar mixed with BSA and Intralipid has exhibited tissue equivalency based on laser transmission measurements. TG2 gel exhibited heat damage based on T2 values, only when the temperature reaches 80 °C. This digital response is considered less sensitive in view of the fact that BSA starts to undergo denaturing and cause optical density change at approximately 70 °C. Both gels, however, have shown to be thermally stable at temperatures up to 80 °C with no evidence of gel melting being observed.

Genomic and proteomic investigations have yielded, and continue to produce, a large amount of information about genes and their protein products. In contrast, the evidence bearing on physiological roles of specific proteins is much more scarce. To address the functional part of biological inquiry, one would like to perturb, at will and selectively, the function of any protein of interest in vivo and to analyze the resulting phenotypic effects, thereby probing the protein’s role in a cell. Ideally, a method for doing so should be applicable both to individual gene products and to a large collection of them. Gene knockouts, a powerful tool to study gene function, have limitations in the study of development when the early phenotypes are cell- or organismal- lethal. Conditional mutants are particularly useful for analysis of genes whose functions are essential for the organism’s viability. A conditional mutant retains the function of a gene under one set of conditions, called permissive, and shows an inactive phenotype under a different set of conditions, called nonpermissive; the latter must be still permissive for the wild type (wt) allele of a gene. Conditional mutants make possible the analysis of physiological changes that follow controlled inactivation of a gene or gene product and can be used to address the function of any gene. Temperature sensitive (ts) mutants are an important class of conditional mutants whose phenotype is similar to that of wt at lower (permissive) temperature, but show low or reduced level of activity above a certain temperature called restrictive temperature, while the wt gene shows a similar phenotype at both the temperatures. Ts mutants provide an extremely powerful tool to study gene expression in vivo and in cell culture. They provide a reversible mechanism to lower the level of a specific gene product simply by changing the temperature of growth of the organism. Ts mutants are typically generated by random mutagenesis; either by ultraviolet light, a chemical mutagen or by error-prone PCR followed by often laborious screening procedures. Therefore, they are cumbersome to make, especially in the case of organisms with long generation times. Keeping in view the importance of ts mutants in biology, Varadarajan et al. 1996, had developed an algorithm to predict ts mutants at predicted, buried sites of a globular protein from its amino acid sequence. Experimental tests of the algorithm were carried out on the CcdB toxin of Escherichia coli to further refine and improve the method (Chakshusmathi et al. 2004). Based on this result simple rules for the design of ts mutants were suggested. This thesis aims at validating and improving on these rules and to find out if ts mutants of a protein can also be generated by perturbing functionally important residues. In addition, it is currently unclear with what frequency ts mutants of a protein isolated in one organism will show a ts phenotype in a completely different organism. This thesis makes preliminary efforts to address this issue. The model system chosen to carry out these studies is a protein called Gal4, which is a yeast transcriptional activator. This protein is biologically relevant as it has been used for ectopic gene expression in diverse organisms including yeast, fruitflies, zebrafish, mice and frogs (Ornitz et al. 1991; Brand and Perrimon 1993; Rahner et al. 1996; Andrulis et al. 1998; Scheer and Camnos-Ortega 1999; Hartley et al. 2002). The introductory chapter (Chapter 1) discusses the importance of ts mutants and our understanding and progress in this field so far, relevant for the work reported in this thesis. Chapter 2 describes generation of ts mutants of Gal4 in yeast. Full length Gal4 (fGal4) is an 881-aa protein. To simplify the construction of ts Gal4, we have designed a functional truncated Gal4 (miniGal4 or mGal4) of 197 residues. Five residues (9, 10, 15, 18 and 23) of the Gal4 DNA binding domain, which are in close contact with the DNA, were randomized in mGal4. Based on average hydrophobicity and hydrophobic moment, 68, 69, 70, 71, and 80 are the only residues in the region 1-150 that are predicted to be buried at the 90% confidence level. Of these five sites, residues 68, 69 and 70 were chosen for mutagenesis. At these three sites, four stereochemically diverse substitutions (Lys, Ser, Ala and Trp) were made. In a separate set of experiments each predicted, buried residues were also individually randomized in both mini and in full length Gal4 (fGal4). In all cases, we have been successful in isolating ts mutants in more than one position. At both permissive and restrictive temperatures, the activity of the Gal4 ts mutants is substantially lower than the wt. However, at the restrictive temperature, the activity of the ts Gal4 is lowered below the threshold required for reporter gene expression. This view of how ts mutants function is quite different from the general notion that the ts and wt behave similarly at permissive temperatures. Chapter 3 deals with transferability of two of the ts constructs mutated at DNA binding residues (R15W and K23P) to Drosophila. Two fGal4 encoding DNA fragments carrying the mutations were cloned into P element vectors under control of Elav and GMR promoters and several transgenic Drosophila lines were generated. These were crossed to various UAS reporter lines and progeny were characterized for reporter gene expression as a function of temperature. We show that both of these yeast ts mutants also show a ts phenotype in Drosophila. We have compared our ts Gal4 system with a popularly used system (TARGET) (McGuire et al. 2003) used for conditional gene expression in Drosophila. Our ts Gal4 mutants appear to provide tighter control at the restrictive temperature and a more uniform and rapid induction of gene expression upon shifting from the restrictive to the permissive temperature than the TARGET system with the promoters and the reporters we have used. Although cold sensitive (cs) mutants are often more useful than ts mutants, for reasons currently unclear, cs mutants are much more difficult to isolate than ts mutants. In Chapter 4, we have attempted to convert the ts phenotypes observed with Gal4 mutants in Drosophila and CcdB mutants in E. coli (Chakshusmathi et al. 2004) to cs phenotypes by increasing the expression level of these mutant proteins selectively at higher temperature. Several ts mutants of CcdB have been previously reported (Chakshusmathi et al. 2004). For converting the ts phenotype observed by E. coli toxin CcdB mutants (Chakshusmathi et al. 2004) to a cs phenotype, the arabinose inducible plasmid pBAD24CcdB and its mutant derivatives were used. By inducing expression of the mutant protein at higher temperature with arabinose, while keeping the basal level of expression without arabinose at lower temperature, we have been able to show cold sensitive behavior by these CcdB ts mutants in E. coli. For producing a cs phenotype with Gal4 mutants in Drosophila, we have used a P element vector where the GMR element is placed in-between hsp70 binding sites. This driver results in enhanced expression of downstream genes at 30 relative to 18°C because of the presence of the hsp elements (Kramer and Staveley 2003). Ts mutants at DNA binding and buried residues of fGal4 were cloned into this vector and several transgenic lines for each construct were obtained. The Gal4 mutants at exposed DNA binding residues but not at buried residues show a cs phonotype when they were crossed to various UAS-reporters lines. The buried residue mutants are likely to be destabilized and their degradation pathway might differ in yeast and in Drosophila. Because of this, these mutants might not be showing the desired cs phenotype in Drosophila. Although mGal4 and fGal4 have very similar activities in yeast, it was necessary to examine if they also had identical activities in Drosophila. Determining their relative activities in Drosophila is the aim of Chapter 5. To this end, mGal4 was cloned into P element vectors under control of hsp70 or GMRhs promoters and transgenic flies were generated. The transgenic lines were crossed to various UAS-reporters and reporter gene activities in the progeny were characterized. Although mGal4 and fGal4 showed similar activity in yeast, in Drosophila for reasons that are currently unclear, mGal4 was considerably less active than fGal4. As some of the fGal4 mutants showed a cs phenotype under GMRhs driver as shown in the earlier chapter (Chapter 4), several ts mutants of mGal4 in yeast in buried and as well as at the DNA binding residues were transferred to Drosophila under hs and GMRhs promoter. The transgenic lines obtained were tested for cold sensitivity by crossing with various UAS-reporter lines. However, in all cases mutant mGal4 showed an inactive phenotype in Drosophila. We suggest that this is because the intrinsic activity of these mGal4 mutants is substantially weaker than wt mGal4 even at permissive temperature in yeast. The further lowering of activity in Drosophila pushes the activity below the threshold required for reporter gene expression resulting in an inactive phenotype. The concluding chapter (Chapter 6) summarizes the conclusions drawn from this entire study and provides insights into possible mechanisms responsible for ts and cs phenotypes. The mutant phenotypes of Gal4 in yeast and in Drosophila suggest that ts phenotypes appear to result from a threshold effect. Such mutations lower the activity and/or level of the protein relative to the wt at all temperatures. Since maximal stability temperatures are rarely in excess of room temperature, with an increase in temperature, the activity of an already marginally active mutant can fall below the threshold required for function resulting in a temperature sensitive phenotype. The strategies we used for producing ts mutants have several advantages over standard approaches of generating ts alleles by random mutagenesis. We anticipate that conclusions of this study would be useful for generation of ts mutants of other globular proteins in diverse organisms. We also show that exposed, functional residues involved in protein: ligand or protein: protein interactions appear to be attractive candidate sites for generating ts mutants that are transferable between organisms. In addition, the active site mutants of fGal4 in Drosophila, which show ts and cs phenotypes depending on the Drosophila promoter chosen for expression, can be used for conditional and reversible expression of a number of other genes using the Gal4-UAS system (Brand and Perrimon 1993).

<p>Multifunctional drug delivery systems incorporated with stimuli-sensitive drug release, magnetic nanoparticles and magnetic resonance (MR) <em>T</em>₂ contrast agents is attracting increasing attention recently. In this thesis, works on polymer nanospheres response to temperature change, superparamagnetic iron oxide nanoparticles (SPION)/polymeric composite materials for MR imaging contrast agents are summarized.</p><p>A “shell-in-shell” polymeric structure has been constructed through a “modified double-emulsion method”. Thermosensitive inner shell is comprised of poly(<em>N</em>-isopropylacrylamide) which undergoes phase transition at body temperature. Such a feature could facilitate drug release at an elevated temperature upon administration. Furthermore, the dual-shell structure is covered by a layer of gold nanoparticles. According to the cytotoxicity tests, the biocompatibility is shown to be enhanced due to the layer of gold.</p><p>SPION have been prepared using a high temperature decomposition method. Particle growth of SPION is monitored by transmission electron microscope and synchrotron X-ray diffraction. Poly(L,L-lactide)@SPION (PLLA@SPION) composite particles have been prepared through surface-initiated ring-opening polymerization which has been developed in our lab. For biomedical applications, it is essential to transfer the particles to physiological solutions from organic solutions. Phase transfer of SPION has been carried out by utilizing small molecules. Stability at the neutral pH is of large concern for such transfer systems. A novel phase transfer agent, Pluronic F127 (PF127), a triblock copolymer has been applied and the stability of the aqueous PF127@oleic acid (OA)@SPION solution has been greatly enhanced over a broad pH range. Most interestingly, PF127@OA@SPION show remarkable efficacy as T2 contrast agents as indicated by relaxometric measurements compared with commercially available products.</p>

<p>The application of pulse shape analysis (PSA) and γ-ray tracking techniques has attracted a great deal of interest in the recent years in fields ranging from nuclear structure studies to medical imaging. These new data analysis methods add position sensitivity as well as directional information for the detected γ-rays to the excellent energy resolution of germanium detectors. This thesis focuses on the application of PSA on planar segmented germanium detectors, divided into three separate studies. The pulse shape analysis technique known as the matrix method was chosen due to its ability to treat events with arbitrary number and combinations of interactions within a single detector. It has been applied in two experiments with the 25-fold segmented planar pixel detector -- imaging and polarization measurements -- as well as in a simulation of upcoming detectors for DESPEC at NuSTAR/FAIR.</p><p>In the first experiment, a point source of ¹³⁷Cs was imaged. Events where the 662 keV γ-rays scattered once and were then absorbed in a different segment were treated by the PSA algorithm in order to find the locations of these interactions. The Compton scattering formula was then used to determine the direction to the source. The experiment has provided a robust test of the performance of the PSA algorithm on multiple interaction events, in particular those with interactions in adjacent segments, as well as allowed to estimate the realistically attainable position resolution. In the second experiment, the response of the detector to polarized photons of 288 keV was studied. The polarization of photons can be measured through the observation of the angular distribution of Compton-scattered photons, Hence the ability to resolve the interaction locations had once again proven useful.</p><p>The third study is focused on the performance of the proposed planar germanium detectors for the DESPEC array. As these detectors have not yet been manufactured at the time of this writing, a set of data simulated in GEANT4 was used. The detector response was calculated for two of the possible segmentation patterns -- that with a single pixelated contact and one where both contacts are segmented into mutually orthogonal strips. In both cases, PSA was applied in order to reconstruct the interaction locations from this response. It was found that the double-sided strip detector can achieve an over-all better position resolution with a given number of readout channels. However, this comes at the expense of a small number of complex events where the reconstruction fails. These results have also been compared to the performance of the 25-fold pixelated detector.</p>

A principal goal of neural engineering is to control the activation of neural circuits across space and time. The ability to control neural circuits with surrogate inputs is needed for the development of clinical neural prostheses and the experimental interrogation of connectivity between brain regions. Electrical stimulation provides a clinically viable method for activating neural tissue and the emergence of optogenetic stimulation has redefined the limitations on stimulating neural tissue experimentally. However, it remains poorly understood how these tools activate complex neural circuits. The goal of this proposed project was to gain a greater understanding of how to control the activity of neural circuits in-vivo using a combination of experimental and computational approaches. Voltage sensitive dye imaging was used to observe the spatiotemporal activity within the rodent somatosensory cortex in response to systematically varied patterns of sensory, electrical, and optogenetic stimulation. First, the cortical response to simple patterns of sensory and artificial stimuli was characterized and modeled, revealing distinct neural response properties due to the differing synchrony with which the neural circuit was engaged. Then, we specifically designed artificial stimuli to improve the functional relevance of the resulting downstream neural responses. Finally, through direct optogenetic modulation of thalamic state, we demonstrate control of the nonlinear propagation of neural activity within the thalamocortical circuit. The combined experimental and computational approach described in this thesis provides a comprehensive description of the nonlinear dynamics of the thalamocortical circuit to surrogate stimuli. Together, the characterization, modeling, and overall control of downstream neural activity stands to inform the development of central nervous system sensory prostheses, and more generally provides the initial tools and framework for the control of neural activity in-vivo.

Understanding the effects of aged microstructures on the thermomechanical fatigue (TMF) properties of nickel-base (Ni-base) superalloys remains unclear. Few experimental results are currently available in this area, and of the limited results available, some promote aged microstructures as beneficial, while others as detri- mental. The importance of these aged structures arises from the fact that when components used in the hot sections of gas turbine engines remain in service for ex- tended periods of time, the local temperature and stress provides the catalyst for the evolution of the microstructure. An experimental assessment of a negative misfit directionally solidified (DS) Ni- base superalloy was undertaken to characterize the aging kinetics and understand the influence of the TMF cycle temperature extremum, temperature-load phasing, mean strain, creep-fatigue, orientation effects, and microstructure on TMF fatigue crack initiation. To determine the effects of aging on the TMF response, the as-heat- treated alloy was artificially aged to three unique microstructures identified in the aging kinetics study. The experiments revealed that not all aged microstructures are detrimental to the fatigue life behavior. Specifically, when the γ′ precipitates age in a manner to align themselves parallel to the axis of the applied stress, an increase in the fatigue life over that of the as-heat-treated microstructure is observed for out-of-phase TMF with dwells. To extend the experimental understanding of the aged microstructures into ser- vice component design and life analysis, a temperature-dependent crystal viscoplas- ticity (CVP) constitutive model is developed to capture the sensitivity of the aged microstructure through embedding additional variables associated with the current state of the γ′ particles. As a result of the adaptations, the CVP model has the ability to describe the long-term aging effects of directional coarsening relevant to the analysis industrial gas turbine hot section components.

Cancer can develop through a series of genetic events in combination with external influential factors that alter the progression of the disease. Gene expression studies are designed to provide an enhanced understanding of the progression of cancer and to develop clinically relevant biomarkers of disease, prognosis and response to treatment. One of the main aims of microarray gene expression analyses is to develop signatures that are highly predictive of specific biological states, such as the molecular stage of cancer. This dissertation analyzes the classification complexity inherent in gene expression studies, proposing both techniques for measuring complexity and algorithms for reducing this complexity. Classifier algorithms that generate predictive signatures of cancer models must generalize to independent datasets for successful translation to clinical practice. The predictive performance of classifier models is shown to be dependent on the inherent complexity of the gene expression data. Three specific quantitative measures of classification complexity are proposed and one measure ( f) is shown to correlate highly (R 2=0.82) with classifier accuracy in experimental data. Three quantization methods are proposed to enhance contrast in gene expression data and reduce classification complexity. The accuracy for cancer prognosis prediction is shown to improve using quantization in two datasets studied: from 67% to 90% in lung cancer and from 56% to 68% in colorectal cancer. A corresponding reduction in classification complexity is also observed. A random subspace based multivariable feature selection approach using costsensitive analysis is proposed to model the underlying heterogeneous cancer biology and address complexity due to multiple molecular pathways and unbalanced distribution of samples into classes. The technique is shown to be more accurate than the univariate ttest method. The classifier accuracy improves from 56% to 68% for colorectal cancer prognosis prediction.  A published gene expression signature to predict radiosensitivity of tumor cells is augmented with clinical indicators to enhance modeling of the data and represent the underlying biology more closely. Statistical tests and experiments indicate that the improvement in the model fit is a result of modeling the underlying biology rather than statistical over-fitting of the data, thereby accommodating classification complexity through the use of additional variables.