VictorJuiz/thesis huggingface dataset:
Nutrigenomics, inflammation and biomarkers of cardiovascular disease

Chronic inflammation is a common feature of obesity, type 2 diabetes and cardiovascular disease. Nuclear factor kappa B (NF-kappaB) is a transcription factor that plays a central role in inflammation by regulating the expression of a number of important genes, such as the major pro-inflammatory cytokine tumor necrosis factor (TNF)-alpha. Both NF-kappaB and TNF-alpha have been implicated in the pathogenesis of insulin resistance and the development of a pro-atherogenic lipid profile. Their production can be modulated by dietary polyunsaturated fatty acids (PUFAs), from both the n-3 and n-6 series, as well as by genetic variations that alter transcriptional activity. The objective of this thesis was to determine whether common variations in major genes regulating inflammation (NF-kappaB and TNF-alpha) modify the association between dietary PUFAs intake and biomarkers of cardiovascular disease in two different populations. In summary, the NF-kappaB -49Ins/Del ATTG and TNF-alpha -238G>A and -308 G>A polymorphisms modify the association between dietary PUFAs intake and plasma HDL-cholesterol in two different populations. Taken together, these findings suggest that inflammation may mediate the effect of dietary PUFAs on the reverse cholesterol transport and impact the risk of cardiovascular disease. The first population involved overweight or obese men and women (n=109) aged 42--75 years with type 2 diabetes. The second population involved mostly lean and healthy men and women (n=595) aged 20--29 years. Subjects were genotyped for the NF-kappaB -49Ins/Del ATTG and for the TNF-alpha -238G>A and -308G>A polymorphisms. Dietary intake was assessed using either a 3-day food record or a food frequency questionnaire. Among individuals with type 2 diabetes, the association between dietary PUFAs intake and plasma HDL-cholesterol concentrations was modified by variations in both the NF-kappaB and TNF-alpha genes. The association between PUFAs intake and HDL-cholesterol was either positive, inverse or null, depending on the particular NF-kappaB and TNF-alpha genotype. In the population of young adults, genetic variations in both the NF-kappaB and TNF-alpha genes also modified the association between dietary PUFAs intake and plasma HDL-cholesterol. NF-kappaB and TNF-alpha genotypes did not modify the association between other dietary fatty acids and other plasma lipids in either population.
Analysis of particulate matter using time-of-flight secondary ion mass spectrometry (TOF-SIMS)

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) was used to study particulate matter of environmental relevance. Aerosols with known chemical composition were produced using a vibrating orifice aerosol generator (VOAG). The characteristic patterns of the particles were obtained through the use of mass-resolved secondary ion images and mass spectra. The evaluation of several filters was conducted and mixed cellulose filters were selected as the appropriate substrate to sample aerosols. The size and morphology of particles was determined by scanning electron microscopy (SEM). Principal component analysis (PCA) was applied to differentiate chemically distinct areas produced by the aerosol particles and the background and found to improve the extraction of the essential chemical information from the enormous amount of data generated by ToF-SIMS imaging.
Learning dynamics and social interaction among knowledge workers in the electronics industry: evidence from Canada and Mexico

This thesis explores and integrates the social, economic and cognitive factors of knowledge transfer using a theory that is grounded in the nature and dynamics of interactions among knowledge workers. At the individual level, learning must be accessible and collaborative in order to facilitate the production and transfer of new knowledge. At the macro level, organizations are required to provide access to information and knowledge sharing, and to be open to collaboration across their own boundaries. An important theoretical contribution of this study is the recognition of the interrelationships among factors that expand learning capabilities and perceptions of professional and personal development in the context of work. The model developed in this thesis represents an attempt to test an integrated theory of learning dynamics and social capital. Results suggest that social interaction in the workplace plays a key role in enhancing learning by creating opportunities for a wider range of activities through which knowledge is shared and implicit implications for personal development are expected. A web-based survey of employees in selected firms in the electronics sector in Canada and Mexico is used to test the model of learning and social interaction. There are two reasons for selecting the electronics industry: continuous learning has been a significant feature of this industry in which rapid technological changes are demanding constant skill upgrades and knowledge transfer, and the role of information technology in learning dynamics, and more specifically in social interaction, is broadly recognized in technology-driven firms as a factor for success, but how access to information can affect personal quality of life is unclear.
The synergy of daidzein and high calcium on bone mass and biomechanical bone strength in ovariectomized mice

The combination of a mixture of isoflavones and high calcium (Ca) protects against bone loss in ovariectomized rodents. The objective of this study was to determine if the combination of daidzein, at two different doses, and high Ca was more effective at preserving bone mineral density (BMD) and biomechanical bone strength in ovariectomized mice compared to either treatment alone, and whether mice metabolize daidzein to its more estrogenic metabolite, equol. The combination of high daidzein and Ca preserved BMD and bone strength of the femur and vertebrae but not to a significantly greater extent than high Ca alone, except for femur yield load. High daidzein preserved femur but not vertebrae BMD despite the fact that all mice produced equol. These results suggest that the dose of daidzein and Ca is an important consideration when developing a dietary strategy to preserve BMD and decrease the risk of fragility fracture.
Structuring and supporting persistent chat conversations

Recent trends indicate that there is great potential for the medium of online chat to take an integral role in a variety of collaborative tasks. In this thesis, we add persistence to chat in order to increase its efficacy for collaboration. Persistence in chat refers to the availability of old conversational content, and has been found to be valuable, but cumbersome to use without appropriate tools. We present the design goals for a novel persistent chat system, which are based on three broad objectives: support review and reuse of chat content, support polysynchronous interaction, and support discussion over shared artifacts. We then present the design and implementation of two persistent chat prototypes based on these goals. Finally, we present the results of several informal evaluations, a laboratory evaluation, and a longitudinal evaluation of our prototypes. Results were encouraging, showing that our system has quantitative and qualitative advantages over basic chat.
Probabilistic fault diagnosis

All systems are susceptible to failures. Fault diagnosis is a methodology that determines the continuing viability of an existing system. This thesis focuses on discrete-event systems with permanent single-fault scenario which can be represented by hidden Markov models. A real-time passive probabilistic diagnoser is proposed, which uses the output sequence of the system as input to identify progressively the condition of the system. This alleviates the problem of undiagnosable failure modes and insufficient observed outputs. Prognostic analysis is then integrated with the diagnostic system to estimate the remaining life and conditions of the system for both homogeneous and nonhomogeneous Markov chains. Additional algorithms are developed to refine the prognostic results as more outputs are observed. The feasibility of the developed algorithms are demonstrated by two implementation examples.
Chronic depolarization upregulates mitochondrial protein import in differentiated PC12 cells

99% of mitochondrial proteins are nuclear-encoded and must be imported into mitochondria. Little is known about how protein import is regulated in neurons. Hypothesis. Depolarization (50mM KCl) will modulate mitochondrial protein import in differentiated PC12 cells. 50mM KCl significantly increased mtGFP (a nuclear-encoded matrix protein) import at 12hrs to 5days. KCl treatment increased mtGFP expression but mitochondrial number was unaffected. Intramitochondrial degradation was unchanged for up to 24hrs but thereafter showed a small decline. KCl treatment increased Ca i2+ levels. BayK (+/-KCl) enhanced mtGFP import but nimodipine (+/-KCI) had no effect. Calcineurin expression and activity were unchanged with KCl treatment but treatment with forskolin increased mtGFP import. KCl increased the import of two physiological, mitochondrial proteins; mtHsp70 and mtTFA, but did not increase Tom20 levels. These findings suggest that mitochondrial protein import in neurons can be modulated by depolarization and can be regulated by Ca2+ influx and cAMP signaling.
Transcriptional regulation of the human recombination activating gene 2

The assembly of antigen receptors from multiple gene segments constitutes a significant contribution in the generation of a diverse immune repertoire. This assembly process is termed V(D)J recombination. The products of the recombination activating genes 1 (RAG1) and 2 (RAG2) are essential to V(D)J recombination and are exquisitely regulated during lymphocyte development. The goal of my studies is to understand the transcriptional regulation of RAG2. In the past six years, a great deal of knowledge has been gained into the transcriptional regulation of RAG1 and RAG2 expression. Here, I discuss my contributions to these studies through my work on the human RAG2 promoter. First, I have defined the transcription initiation site for RAG2 and have since characterized the RAG2 promoter. Second, I have assessed the negative regulation of RAG transcription by the Egr proteins. And third, I have analyzed the human and mouse RAG intergenic regions for transcription silencing activity. Currently a great deal of controversy surrounds the question of RAG re-expression in mature lymphocytes. If RAG re-expression does exist, what is its purpose? I have used a microarray approach to determine whether RAG re-expression in a mature B cell-line influences the expression of other genes. These studies and those assessing factors that modulate RAG2 promoter activity have contributed novel insights into our understanding of RAG regulation.
Monastic devotion in Ireland: The Céli Dé movement in the eighth and ninth centuries

Received wisdom has long held that the Céli Dé (‘servants/clients of God’), a group of religious who first appeared in Ireland in the latter half of the eighth century, were the promulgators of a monastic reform. Following a period of general decline in monastic discipline and devotion brought on by increasing secularity in the Irish Church, the Céli Dé are commonly believed to have scorned the older churches in Ireland and advocated a return to stricter standards of asceticism. Yet an examination of the primary sources for monasticism in Ireland from the fifth into the eighth century reveals no conclusive evidence for an ascetic decline among Irish religious prior to the appearance of the Céli Dé; on the contrary, there are strong signs of continuity of expectations, if not actual practice, throughout this period. A fresh understanding of the Céli Dé is needed, one that takes into account all the extant writings associated with the movement. Turning to the considerable corpus of texts that various scholars have ascribed to the Céli Dé, however, we find that close consideration of the manuscript histories of these texts and the internal evidence that purportedly links them to the Céli Dé does not admit nearly so many of them as has been supposed to be likely products of the movement. Those texts which we can assign to the Céli Dé with a degree of confidence indicate that they were indeed deeply intent upon asceticism, but not in a manner which contrasts noticeably with prior ascetical practice in Ireland. Nor were they primarily concerned with asceticism; matters such as liturgy, personal devotion, pastoral care, and Sunday observance receive at least as much attention in their writings. Taken together, the evidence offers considerable support to the theory that the Céli Dé are best understood not as a reformist movement with an agenda, but rather as élite religious. Accordingly they distinguished themselves from other monks and monastic communities in their personal devotion and other matters, not out of a desire to bring about universal change, but in an effort to demonstrate or perhaps validate their status as belonging to the personal retinue of God, just as their name implies.
The errorless classroom: a success-focused, non-intrusive approach to intervention for severe behaviour

Errorless acquiescence training (EAT) was used to improve the social skills of 8 children referred to a clinical classroom due to severe antisocial and oppositional behaviors. Prior to treatment, all 8 children evinced low levels of cooperation and high levels of antisocial behaviors. An errorless paradigm was used to teach children to tolerate and yield to the will and provocations of their peers without retaliation (i.e., acquiescence). Consistent with all errorless paradigms, key intervention components (i.e., instructions, prompts, reinforcements, and performance feedback) were systematically faded at a slow enough rate during treatment to ensure successful social interactions among peers. Throughout and following treatment, all 8 children demonstrated an increase in acquiescent responding, significant reductions in antisocial behaviors, and substantial improvements in prosocial verbal responding. The effects of EAT extended to improvements in prosocial physical responding and clean-up behaviors.

Keywords: Conduct disorders in children, Treatment
Behavior disorders in children, Treatment
Problem children
Social skills in children
Social skills, Study and teaching
Development of a scalable bioprocess for the culture of undifferentiated murine embryonic stem cells

A reliable source of qualified ES cells would enable the development of protocols to test their potential in regenerative medicine models and the design of robust assays to study stem cell differentiation and signaling. Unfortunately, conventional ES cell culture methods are impractical for large-scale cell production under controlled conditions. Two stirred-suspension undifferentiated ES cell culture systems were developed and compared with tissue culture flask and Petri dish controls. Fifteen-day ES cell microcarrier cultures expanded 192 +/- 11.3-fold, with a doubling time of 13.9 +/- 0.7 hrs. (versus 14.8 +/- 1.3 hrs. for tissue flask controls). Cells cultured as aggregates, with agglomeration inhibited by shear, expanded 53.4 +/- 9.6-fold and had a doubling time of 23.5 +/- 5.8 hrs. (versus 20.1 +/- 4.5 hrs. for Petri dish controls). ES cells remained undifferentiated in both systems (i.e., predominantly SSEA-1+, E-cadherin +, Oct-4+). Expected differentiation kinetics and markers were demonstrated upon EB formation. Results suggest that with optimization these systems can support large-scale ES cell production.
Design of a tissue-engineered adipose substitute

A tissue-engineered adipose substitute would have numerous applications in plastic and reconstructive surgery. This thesis involved the investigation of naturally-derived placental decellular matrix (PDM) and cross-linked hyaluronan (XLHA) scaffolds for soft tissue augmentation. The initial work focused on developing a protocol to decellularize an intact, large segment of the human placenta. To facilitate decellularization, a perfusion system was designed to deliver the required chemicals via the placental vasculature. Following processing, the extracellular matrix architecture was preserved, including an intact vascular network. Histology, immunohistochemistry, and electron microscopy confirmed cellular removal and characterized the PDM composition and structure. Preliminary in vitro cell culture experimentation showed that the PDM could facilitate the adhesion of primary human adipose-derived stem cells (ASC). Following the finalization of the decellularization protocol, the in vitro cellular response of primary human ASC to several different PDM and XLHA scaffolds was studied. Cellular organization, viability, proliferation, and glucose consumption were assessed during the proliferative phase prior to the induction of differentiation. The ASC differentiation response was characterized in terms of glycerol-3-phosphate dehydrogenase (GPDH) activity, intracellular lipid accumulation, and adipogenic gene expression. The cellular response was impacted by the scaffold environment and cell donor source. The cell-adhesive PDM scaffolds promoted ASC attachment, spreading, and proliferation. In contrast, while all of the scaffolds could support the adipogenic differentiation of the ASC to some extent, differentiation was augmented when the cells were encapsulated in the non-cell-adhesive XLHA gels. The PDM and PDM with XLHA scaffolds, seeded with primary human ASC, were investigated in a subcutaneous athymic mouse model. The in vivo response at 3 and 8 weeks was characterized using histological and immunohistochemical staining. Fibrous capsule formation was scored and the relative number of adipocytes in each scaffold was quantified. Undifferentiated ASC were localized using immunostaining for human vimentin. Unilocular and multilocular adipocytes were identified by intracellular lipid accumulation. Staining for murine CD31 assessed implant vascularization. Both scaffolds macroscopically maintained their three-dimensional volume and could support mature adipocyte populations in vivo. The results suggested that incorporating the XLHA had a positive effect in terms of angiogenesis and adipogenesis.
Resonant atomic switching near a photonic band-gap: towards an all-optical micro-transistor

In this thesis we demonstrate that the photonic band edge facilitates fundamental switching effects for resonant two-level atomic systems. In a photonic crystal, a coherent laser beam can drive a two-level atom to inverted atomic states, a phenomenon forbidden in ordinary vacuum. In this process, the atomic system switches from a passive medium to a gain medium as a function of the driving field intensity. We show that the large differential gain exhibited by the atomic medium is robust against non-radiative relaxation and dephasing mechanisms. This switching effect exhibits collective enhancement for a large number of two-level atoms within a cubic wavelength. In this case, the ensemble of atoms sharply switches to a highly inverted state at a very well defined threshold value of the laser field intensity. We next demonstrate that a probe laser field of prescribed wavelength experiences a substantial differential gain by slight modulations in the control laser field. We suggest that a doped photonic band gap material may, in this sense, be used as an all-optical micro-transistor. We analyze the effects of inhomogeneous line broadening on the probe beam spectrum and demonstrate that further electromagnetic density of states engineering combined with photo-bleaching techniques can be used to both offset the deleterious effects of inhomogeneous broadening and to enlarge the switching bandwidth. We investigate the prospects and challenges in designing microstructures with characteristics required by our proposal. We further show that the switching power and the response time of an all-optical transistor can be dramatically reduced by including collective effects, which also provide a natural mechanism of broadening of the gain spectrum. Finally, we develop an exact multi-photon scattering theory of resonance fluorescence in frequency-dependent photonic reservoirs. We show that, in the limit of weak driving field, the scattering cross section becomes strongly non-Lorentzian, reflecting the non exponential character of the atomic decay. As the driving field intensity increases, the scattered field acquires new features, consistent with predictions of a dynamical decoupling of the atomic system from the photonic reservoir.
Lasing in strongly scattering dielectric microstructures

In the first part of this thesis, a detailed analysis of lasing in random multiple-light-scattering media with gain is presented. Random laser emission is analyzed using a time-dependent diffusion model for light propagating in the medium containing active atoms. We demonstrate the effects of scatterers to narrow the emission spectral linewidth and to shorten the emitted pulse duration at a specific threshold pump intensity. This threshold pump intensity decreases with scatterer density and excitation spot diameter, in excellent agreement with experimental results. The coherence properties of the random laser are studied using a generalized master equation. The random laser medium is treated as a collection of low quality-factor cavities, coupled by random photon diffusion. Laser-like coherence, on average, is demonstrated above a specific pumping threshold. We demonstrate that with stronger scattering, the pumping threshold for the transition from chaotic to isotropic coherent light emission decreases and enhanced optical coherence for the emitted light is achieved above threshold. The second part of this thesis presents a study of lasing in photonic crystals (PCs). The emission from an incoherently pumped atomic system in interaction with the electro-magnetic reservoir of a PC is analyzed using a set of generalized semiclassical Maxwell-Bloch equations. We demonstrate that the photonic band edge facilitates the enhancement of stimulated emission and the reduction of internal losses, leading to an important lowering of the laser threshold. In addition, an increase of the laser output at a photonic band edge is demonstrated. We next develop a detailed quantum theory of a coherently pumped two-level atom in a photonic band gap material, coupled to both a multi-mode wave-guide channel and a high-quality micro-cavity embedded within the PC. The cavity field characteristics are highly distinct from that of a corresponding high-Q cavity in ordinary vacuum. We demonstrate enhanced, inversionless, and nearly coherent light generation when the photon density of states (DOS) jump between the Mollow spectral components of atomic resonance fluorescence is large. In the case of a vanishing photon DOS on the lower Mollow sideband and no dipolar dephasing, the emitted photon statistics is Poissonian and the cavity field exhibits quadrature coherence.