VictorJuiz/thesis huggingface dataset:
A Theoretical Roadmap for Optical Lithography of Photonic Band Gap Microchips
Keywords: optics
photonic band gap
photonic crystals

This thesis presents designs and fabrication algorithms for 3D photonic band gap (PBG) material synthesis and embedded optical waveguide networks. These designs are suitable for large scale micro-fabrication using optical lithography methods. The first of these is a criss-crossing pore structure based on fabrication by direct photo-electrochemical etching in single-crystal silicon. We demonstrate that a modulation of the pore radius between pore crossing points leads to a moderately large PBG. We delineate a variety of PBG architectures amenable to fabrication by holographic lithography. In this technique, an optical interference pattern exposes a photo-sensitive material, leading to a template structure in the photoresist whose dielectric-air interface corresponds to an iso-intensity surface in the exposing interference pattern. We demonstrate PBG architectures obtainable from the interference patterns from four independent beams. The PBG materials may be fabricated by replicating the developed photoresist with established silicon replication methods. We identify optical beam configurations that optimize the intensity contrast in the photoresist. We describe the invention of a new approach to holographic lithography of PBG materials using the diffraction of light through a three-layer optical phase mask (OPM). We show how the diffraction-interference pattern resulting from single beam illumination of our OPM closely resembles a diamondlike architecture for suitable designs of the phase mask. It is suggested that OPML may both simplify and supercede all previous optical lithography approaches to PBG material synthesis. Finally, we demonstrate theoretically the creation of three-dimensional optical waveguide networks in holographically defined PBG materials. This requires the combination of direct laser writing (DLW) of lines of defects within the holographically-defined photoresist and the replication of the microchip template with a high refractive index semiconductor such as silicon. We demonstrate broad-band (100-200~nm), single-mode waveguiding in air, based on the light localization mechanism of the PBG as well as sharp waveguide bends in three-dimensions with minimal backscattering. This provides a basis for broadband 3D integrated optics in holographically defined optical microchips.
Modeling Uncertainty with Evolutionary Improved Fuzzy Functions
Keywords: 0800

Fuzzy system modeling (FSM)– meaning the construction of a representation of fuzzy systems models–is a difficult task. It demands an identification of many parameters. This thesis analyses fuzzy-modeling problems and different approaches to cope with it. It focuses on a novel evolutionary FSM approach–the design of “Improved Fuzzy Functions” system models with the use of evolutionary algorithms. In order to promote this analysis, local structures are identified with a new improved fuzzy clustering method and represented with novel “fuzzy functions”. The central contribution of this work is the use of evolutionary algorithms – in particular, genetic algorithms– to find uncertainty interval of parameters to improve “Fuzzy Function” models. To replace the standard fuzzy rule bases (FRBs) with the new “Improved Fuzzy Functions” succeeds in capturing essential relationships in structure identification processes and overcomes limitations exhibited by earlier FRB methods because there are abundance of fuzzy operations and hence the difficulty of the choice of amongst the t-norms and co-norms. Designing an autonomous and robust FSM and reasoning with it is the prime goal of this approach. This new FSM approach implements higher-level fuzzy sets to identify the uncertainties in: (1) the system parameters, and (2) the structure of “Fuzzy Functions”. With the identification of these parameters, an interval valued fuzzy sets and “Fuzzy Functions” are identified. Finally, an evolutionary computing approach with the proposed uncertainty identification strategy is combined to build FSMs that can automatically identify these uncertainty intervals. After testing proposed FSM tool on various benchmark problems, the algorithms are successfully applied to model decision processes in two real problem domains: desulphurization process in steel making and stock price prediction activities. For both problems, the proposed methods produce robust and high performance models, which are comparable (if not better) than the best system modeling approaches known in current literature. Several aspects of the proposed methodologies are thoroughly analyzed to provide a deeper understanding. These analyses show consistency of the results.
IgG-mediated Immune Suppression: the Effect on the Host Immune System
Keywords: Hemolytic Disease of the Newborn
Immunotherapy
Antibody-mediated immune suppression
Immune regulation

One of the most effective immunological interventions for human disease prevention is the administration of anti-red blood cell (RBC) IgG, more specifically, anti-D IgG, for prevention of hemolytic disease of the fetus and newborn (HDN), a serious and potentially fatal condition caused by the maternal immune response against the Rhesus (Rh) blood group system D antigen on fetal RBC. Despite its widespread clinical use, the mechanism of the suppressive anti-RBC IgG effect is not fully understood. In a murine model of immunity to foreign RBCs, transfusion of mice with IgG-opsonized RBCs strongly attenuated the antibody response compared to transfusion of untreated RBCs. This model was used to study the anti-RBC IgG effect on the host immune response. Contrary to the predominant theories of the anti-D effect, here it is shown that IgG-mediated RBC clearance is not sufficient for the attenuation of antibody responses. IgG-opsonized RBCs internalized by the mononuclear phagocytic cells could stimulate T and B cell responses against RBC antigens. This thesis also shows that the adaptive tolerance at the T or B cell level is not the reason for the attenuation of the antibody response. Instead, IgG selectively prevented the appearance of antigen-primed RBC-specific B cells and, surprisingly, induced the host B cell response against the IgG in complex with RBCs. These results suggest that the inability of RBC-specific B cells to recognize and present RBC-specific epitopes may explain the inhibitory IgG effect.
A Randomized Double-blind Placebo-controlled Clinical Study Investigating Clinical Outcome and Gene Expression Responses to Insulin-enhanced Cardioplegia during Cardiac Surgery in Infants with Tetralogy of Fallot
Keywords: insulin
cardiac surgery
pediatric
gene expression
tetralogy of Fallot

Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart defect and infants with TOF incur significant right ventricular(RV) dysfunction due to perioperative injury. Insulin has been shown to reduce perioperative myocardial injury and significantly improve postoperative cardiac function. However, studies are limited to the adult population and the effects in a pediatric heart with a CHD are unknown. To the best of our knowledge, this is the first randomized, double blind, placebo-controlled clinical study designed to investigate insulin’s potential cardioprotective effects postoperatively and mechanisms of action during pediatric cardiac surgery. Thirty infants with TOF were equally randomly allocated to receive either standard cardioplegia (SC) or 10UI insulin-enhanced (IC). Expression profiles of surgery were generated from biopsies extracted from the right ventricular outflow tract (end ischemia and five minutes of reperfusion) and hybridized to Affymetrix HG-U133A GeneChips. Gene expression profiles were generated using two softwares, ArrayAssist V2.6 (paired t-test) and affylmGUI (ANOVA). Survival rate was 100%. Compared to patients in the SC group, patients in the IC group demonstrated a trend toward a 1.8 fold decrease (p = .06) in reperfusion duration (61.93 ± 61.12 vs. 35.20 ± 23.16 hrs., respectively), a significant 2-fold decrease in the length of ICU stay (p = .04) (4.2 ± 3.9 vs. 2.3 ± 1.1 days, respectively) and a trend toward a 2.5 fold decrease in intubation duration (p= .06) (2.5± 12.2 vs. 55.0 ± 67 hrs., respectively). Patients in the IC group also demonstrated significantly lower inotropic scores, calculated at 12-hour intervals across a 48-hour ICU period, (ANOVA p = .01) and significantly greater urine volume, by 71%, (p = .02). IC evoked a cardioprotective gene expression profile aimed at mitigating perioperative myocardial injury, specifically; apoptosis, inflammation, cardiac hypertrophy, arrythmias and fibrosis. The improved postoperative outcome and cardioprotective gene expression signature with IC suggests that, administration of insulin during cardiac surgery in infants with TOF may prevent cardiac dysfunction as a result of mitigating perioperative myocardial injury. Overall, this exploratory study demonstrated insulin-enhanced cardioplegia to be a potential cardioprotective agent during pediatric heart surgery.
Valuing and Evaluating Evidence in Medicine
Keywords: Philosophy
Philosophy of Medicine
Social Epistemology
Evidence-based Medicine

Medical decisions should be based on good evidence. But this does not mean that health care professionals should practice evidence-based medicine. This dissertation explores how these two positions come apart, why they come apart, and what we should do about it. I begin by answering the descriptive question, what are current standards of evidence in medicine? I then provide a detailed critique of these standards. Finally, I address the more difficult normative question, how should we determine standards of evidence in medicine? In medicine, standards of evidence have been established by the pervasive evidence-based medicine (EBM) movement. Until now, these standards have not been subjected to comprehensive philosophical scrutiny. I outline and defend a theory of knowledge – a version of Helen Longino’s Critical Contextual Empiricism (CCE) – which enables me to critically evaluate EBM. My version of CCE emphasizes the critical evaluation of background assumptions. In accordance with this, I identify and critically evaluate the three substantive assumptions underlying EBM. First, I argue that medicine should not be held to the restrictive definition of science assumed by proponents of EBM. Second, I argue that epidemiological evidence should not be the only “base” of medical decisions. Third, I argue that not only is the particular hierarchy of evidence assumed by EBM unjustified, but that any attempt to hierarchically rank research methods is incoherent and unjustifiably restricts medical knowledge. Current standards of evidence divert attention from many legitimate sources of evidence. This distorts medical research and practice. In the remainder of the dissertation I propose means for improving not only current standards of medical evidence but also the process of producing and defending future standards. On the basis of four CCE norms, I argue that we have reason to protect and promote those features of the medical community that facilitate diversity, transparency, and critical interaction. Only then can we ensure that the medical community retains its ability to produce evidence that is both rigorous and relevant to practice.
Hybrid Mobile Robot System: Interchanging Locomotion and Manipulation
Keywords: Mobile Robots
Teleoperation
Mechatronic Systems
Control System Design
Autonomous Navigation
Simulations & Animations
Prototype Development

This thesis presents a novel design paradigm of mobile robots: the Hybrid Mobile Robot system. It consists of a combination of parallel and serially connected links resulting in a hybrid mechanism that includes a mobile robot platform for locomotion and a manipulator arm for manipulation, both interchangeable functionally. All state-of-the-art mobile robots have a separate manipulator arm module attached on top of the mobile platform. The platform provides mobility and the arm provides manipulation. Unlike them, the new design has the ability to interchangeably provide locomotion and manipulation capability, both simultaneously. This was accomplished by integrating the locomotion platform and the manipulator arm as one entity rather than two separate and attached modules. The manipulator arm can be used as part of the locomotion platform and vice versa. This paradigm significantly enhances functionality. The new mechanical design was analyzed with a virtual prototype that was developed with MSC Adams Software. Simulations were used to study the robot’s enhanced mobility through animations of challenging tasks. Moreover, the simulations were used to select nominal robot parameters that would maximize the arm’s payload capacity, and provide for locomotion over unstructured terrains and obstacles, such as stairs, ditches and ramps. The hybrid mobile robot also includes a new control architecture based on embedded on-board wireless communication network between the robot’s links and modules such as the actuators and sensors. This results in a modular control architecture since no cable connections are used between the actuators and sensors in each of the robot links. This approach increases the functionality of the mobile robot also by providing continuous rotation of each link constituting the robot. The hybrid mobile robot’s novel locomotion and manipulation capabilities were successfully experimented using a complete physical prototype. The experiments provided test results that support the hypothesis on the qualitative and quantitative performance of the mobile robot in terms of its superior mobility, manipulation, dexterity, and ability to perform very challenging tasks. The robot was tested on an obstacle course consisting of various test rigs including man–made and natural obstructions that represent the natural environments the robot is expected to operate on.
Analytic Modeling of Four-wave-mixing with Inter-channel Walk-off in Wavelength-division-multiplexed Optical Links
Keywords: WDM
FWM

Fiber nonlinearity can cause interactions and crosstalk between co-propagating dense wavelength division multiplexed channels in high capacity optical fiber communication systems. The crosstalk between channels leads to degradation of the bit error performance of the system. One of the mechanisms of this crosstalk is Four-Wave-Mixing (FWM) caused by the fiber nonlinearity. It is important to have an analytic model for the FWM to estimate and minimize the impact of FWM for a given transmission system design. Conventional analytic models for FWM ignore the inter-channel walk-off effect. In this thesis a model for FWM is developed which rigorously accounts for the walk-off effect. The model is derived for degenerate and non-degenerate FWM. This model is derived for conventional RZ-OOK and the emerging RZ-DPSK modulation formats. A detailed physical understanding of the walk-off contribution to the FWM noise is developed. The first direct comparison, between an analytic model for FWM and split-step Fourier (SSF) simulations for the general case of random modulated channels is presented, for a single span 10-Gb/s link. It is shown that for both RZ-OOK and RZ-DPSK modulation formats the walk-off effect significantly increases the FWM noise variance for all FWM types before any filtering at the end of fiber. When a multiplexer/de-multiplexer is used the walk-off effect is significant and observable for the degenerate FWM case but is no longer significant for the non-degenerate FWM case. In the typical situation when a sub-bit-rate electrical low pass filter is also used, the walk-off effect is effectively removed for all three types of FWM. Comparing the models for the two modulation formats it is found that the FWM noise standard deviation and related BER penalty are much smaller for RZ-DPSK as compared to that for RZ-OOK at the same average launch power.
Human Brain Responses to Speech Sounds
Keywords: Evoked responses
Speech
Steady-state responses
Brainstem
Auditory cortex

Electrophysiologic responses are used to estimate hearing thresholds and fit hearing aids in young infants, but these estimates are not exact. An objective test of speech encoding could be used to validate infant fittings by showing that speech has been registered in the central auditory system. Such a test could also show the effects of auditory processing problems on the neural representation of speech. This thesis describes techniques for recording electrophysiologic responses to natural speech stimuli from the brainstem and auditory cortex. The first technique uses a Fourier analyzer to measure steady-state brainstem responses to periodicities and envelope changes in vowels, and the second uses a windowed cross-correlation procedure to measure cortical responses to the envelopes of sentences. Two studies were conducted with the Fourier analyzer. The first measured responses to natural vowels with steady and changing fundamentals, and changing formants. Significant responses to the fundamental were detected for all of the vowels, in all of the subjects, in 19 – 73 s (on average). The second study recorded responses to a vowel fundamental and harmonics. Vowels were presented in opposite polarities to distinguish envelope responses from responses to the spectrum. Significant envelope responses were detected in all subjects at the fundamental. Significant spectral responses were detected in most subjects at harmonics near formant peaks. The third study used cross-correlation to measure cortical responses to sentences. Significant envelope responses were detected to all sentences, at delays of roughly 180 ms. Responses were localized to the posterior auditory cortices. A model based on a series of overlapping transient responses to envelope changes could also account for the results, suggesting that the cortex either directly follows the speech envelope or consistently reacts to changes in this envelope. The strengths and weaknesses of both techniques are discussed in relation to their potential clinical applications.
The L2 Acquisition and L1 Attrition of the Interpretation and Use of Aspectual Properties in Spanish among English-speaking L2 Learners and Long-term Spanish Immigrants
Keywords: Second Language Acquisition/L1 Attrition
Spanish-English bilinguals, Tense and Aspect

This thesis examines the L2 acquisition and L1 attrition of aspectual properties in Spanish. Specifically, it investigates preterite versus imperfect distinctions and the ongoing value of the Spanish present tense among English-speaking L2 learners and long-term Spanish immigrants. In contrast to previous research which explains L2 learners’ difficulties as a result of either maturational constraints or morphosyntactic development, this study provides a supplementary explanation focusing on L1 transfer of the semantic patterns of tense morphemes. The study proceeds by comparing data from L2 learners with that of long-term Spanish immigrants. Unlike what is argued for L2 acquisition difficulties, the difficulties immigrants may have with tense and aspect cannot stem solely from impairment reasons. These immigrants acquired the L2 as adults. Therefore, to the extent that L2 learners share similar patterns of errors with adult immigrants, L2 speakers’ difficulties cannot be unequivocally linked to causes related to impairment. Instead, following a selectional approach to aspectual variation (De Swart, 1998), it is argued that transfer of the selectional patterns of tense morphemes offers a more encompassing explanation of the difficulties L2 speakers face with tense and aspect. Data collection involved two truth-value judgment tasks, two acceptability judgment tasks and two elicited production tasks. Twenty long-term immigrants, twenty English-speaking L2 learners of Spanish, and twenty native speakers of Spanish serving as control participants took part in the study. Results show incorrect activation of aspectual patterns by both experimental groups and similar patterns of difficulties in some of the conditions under investigation. I conclude that transfer from the other language offers a more adequate explanation of the difficulties L2 learners face
Davidson on Conceptual Schemes
Keywords: Davidson
conceptual schemes
relativism
interpretation

In his influential essay “On the Very Idea of a Conceptual Scheme”, Donald Davidson argues that we cannot make sense of conceptual relativism, the doctrine that there could be incommensurably different systems of concepts applicable to a single world. According to Davidson, there is no criterion of identity for language that does not imply or presuppose the possibility that we interpret that language by means of our own language. Given some plausible assumptions, this implies that there is at most one conceptual scheme, one way of interpreting or representing the world. But then the very idea of a conceptual scheme is empty. The dissertation is an examination of Davidson’s reasoning, and a defence of a different position regarding conceptual relativism. I reject much of Davidson’s argumentation, and his radical (subordinate) conclusion that we would be able, at least in principle, to make sense of any language. Languages that we would be unable to translate or interpret, even in principle, are at least logically possible, in my view. However, this possibility should not be thought to imply or encourage conceptual relativism. In this respect, I think that Davidson and many of his critics have conflated the notion of a difference in conceptual scheme, which requires incommensurability between languages or systems of concepts, and mere conceptual difference. I argue that a genuinely alternative conceptual scheme would be associated with language unintelligible to us because of its relation to our language. For what is at issue, supposedly, is a conceptual relation: a relation between languages, not a relation between speakers, or their capacities, on the one hand, and languages, on the other. I try to show how some of Davidson’s arguments, suitably modified, can be deployed against the possibility of an alternative scheme, so understood, and provide some additional arguments of my own. My position is thus significantly weaker than Davidson’s: there could not be languages that we would be unable to interpret because they are incommensurable with our own.