VictorJuiz/thesis huggingface dataset:
Chemical-assisted Femtosecond Laser Writing of Lab-in-fiber Sensors
Keywords: Chemical Etching
Femtosecond Laser Processing
Lab in Fiber
Lab-on-Chip
Optical Fiber
Optofluidics

Three-dimensional (3D) patterning inside optical fiber was shown to be a powerful tool for embedding refractive index and microfluidic structures inside the flexible glass fiber for enabling novel sensing opportunities with lab-in-fibers (LIFs). A femtosecond laser was tightly focused into optical fibers using an oil-immersion lens to eliminate extreme optical aberrations from the cladding-air interface. The laser interactions were then optimized to bring ~12 nm rms surfaces for the first time inside the fiber cladding by precisely conforming planar nanograting structures when assembled by the writing laser. Further, the unprecedented integration of cladding waveguides, X-couplers, fiber Bragg gratings (FBGs), microholes, mirrors, optofluidic resonators, and microfluidic reservoirs defined the building blocks for facile interconnection of inline core-waveguide devices with fiber cladding optofluidics. Laser templating was restricted to the single mode fiber (SMF) cladding or formed inside all-fused silica coreless optical fibers to meet with buried laser-formed waveguides that were fused to SMFs for novel seamless inline probing while avoiding undesired concave surface profiles and negative lensing losses associated with writing optofluidic templates across the germanium-doped SMF core waveguide.With these components, more advanced, integrated, and multiplexed fiber microsystems were demonstrated for fluorescence detection, Fabry Perot interferometer (FPI) refractometry, and simultaneous sensing of refractive index, temperature, and bending strain. Tapered access ports were found to minimize fiber mechanical weakening and thereby avoid fiber breakage during optofluidic sensing. Optical resonator arrays (ORAs) were then explored to deepen fringe contrasts beyond that available with a single FPI for opening new prospects for fiber inline pass-band optical filters and broadband reflectors. Finally, wavefront splitting interferometers (WSIs) were targeted to improve fringe contrast and peak resolution beyond that available with FPIs and offer a significant theoretical improvement in refractometer sensitivity.The advanced laser processes optimized here may provide a new base for photonics, microfluidics, and optofluidics fabrication in a LIF platform with multiplexed functionality and rapid prototyping capabilities of fully integrable 3D optofluidic systems. The proposed LIF devices define new micro-systems for temperature, strain, pressure, refractive index, and bend strain sensing that may find application in the acoustic, aerospace, automotive, biological, chemical, civil, or medical fields.
The Pharmacology of Periconceptional Folic Acid Supplementation
Keywords: folic acid
fortification
periconceptional period
pharmacokinetics
pharmacology
pregnancy

Periconceptional folic acid supplementation is associated with a reduction in the risk of neural tube defects, other birth defects, as well as positive maternal outcomes during pregnancy. Current healthcare recommendations regarding the timing and dosage of prenatal supplementation are based on studies in non-pregnant women of childbearing age. The overall objective of this thesis is to characterize risk factors associated with the periconceptional period, validate the effectiveness of folic acid supplementation based on pregnancy-related pharmacokinetics, analyze the current folate status of women in Toronto, as well as explore recruitment strategies for clinical trials in pregnant women. The first study was a two-arm, randomized, clinical trial assessing the long-term folate kinetics in pregnant women supplementing with either 1.1mg (regular dose) or 5mg (high dose) of folic acid. This study evaluated dose-dependent and gestational age-dependent changes in the pharmacokinetics among pregnant women, which have not been previously studied at these doses of supplementation. We found non-linear folate pharmacokinetics in the 5mg group, as well as altered pharmacokinetics in both dose-groups due to pregnancy-related changes. The second study was based on secondary analysis emerging from the randomized clinical trial, where we tackled the challenges associated with recruitment of pregnant women (a vulnerable population) into a study on folic acid supplementation at a time when a high degree of supplementation awareness already exists among women in Toronto. We used social media as a novel tool for recruitment, and found a 12-fold increase in recruitment rate. The third study was a systematic review and meta-analysis investigating the effect of oral contraceptive use on blood folate concentrations among women. We found that oral contraceptives had a folate-lowering effect and recommended continued folate supplementation among oral contraceptive users. Finally, in our fourth population-based cohort study, we evaluated blood folate concentrations among women in Toronto and found that 93% of women of childbearing age had optimally protective blood folate concentrations against neural tube defects.Recommendations for periconceptional folic acid supplementation should be re-evaluated based on population-level data, and be tailored to individual risk factors such oral contraceptive use or altered folate demands during pregnancy.
Shaping the World in One's Image: An Essay on the Nature and Value of Achievements
Keywords: achievement
value theory

This project is a philosophical exploration of the common sense notion that achievements are among the things that make a life go well. Parts I and II develop an account of achievements as competently reached goals and discuss in virtue of what some such goals are more of an achievement than others. Part III argues that, given the account of achievements developed in parts I and II, we have good reason to think that the common sense idea is true: achievements are intrinsically valuable. We can see that this is so by reflecting on the fact that achieving our goals realizes certain valuable relations of harmony between mind and world.
The Response of Particles in Periodic Potentials to External Forces: New Perspectives
Keywords: Anomalous velocity
Effective mass
Electroabsorption
Franz-Keldysh effect
Optical lattices
Wave packet dynamics

We study the effects of an external constant and uniform force on particles in periodic potentials in the context of transport and optical phenomena. We consider two types of systems: charged carriers in a crystal subject to a constant (dc) electric field and ultracold atoms in optical lattices subject to external forces of various origins. Both systems are described by a Hamiltonian where the force is coupled to the position operator. In the context of transport phenomena, we study the motion of a wave packet prepared in one band of a periodic potential when a uniform force is suddenly applied and left constant afterwards. The semiclassical description of wave packet dynamics in periodic potentials with applied forces, slowly varying in time and space, relies on the concepts of effective mass, group velocity, and anomalous velocity. If the force is suddenly applied, these quantities do not correctly describe the dynamics, since the wave packet cannot respond instantaneously according to the properties of the lattice. We show that dynamical generalizations of the group and anomalous velocities, and of the inverse effective mass tensor, provide an appropriate description. Our approach is based on modified Bloch states that include the interband mixing due to the force; we compare our results with full numerical calculations, showing excellent agreement when Zener tunneling is negligible. We illustrate our results with one- and two-dimensional optical lattices, where the experimental detection of these dynamics is more accessible than in typical solid-state systems.In the context of optical phenomena, we consider the absorption of light by bulk semiconductors in the presence of a dc electric field including excitonic and interband coupling effects. The absorption coefficient is calculated from the time evolution of the interband polarization excited by an optical pulse. We illustrate the formalism with a numerical calculation for bulk GaAs using a 14-band k.p model, and we study the dependence of the excitonic enhancement of the absorption coefficient on the strength of the dc field and the optical polarization. We find that the polarization anisotropy described by the independent particle approximation can be modified significantly by the Coulomb interaction.
State-sanctioned Violence and Mental Health: Implications for Learning and Treatment
Keywords: Democratic Republic of the Congo
Mental health education
Public health
Refugee war trauma

This qualitative study examines how Canadian mental health systems may better accommodate people from the Democratic Republic of the Congo (DRC) who are living now in Canada and who may be suffering psychosocial consequences of political violence. Using an anti-racist-feminist lens, analysis of seven interviews highlights the significance of socio-political histories and conceptualisations of trauma in mental health education. Discussions focus on mental health dimensions of war and aspects of resilience in complex life-experiences which are only recently gaining representation (and transformation) in medical discourse. By correlating social and political forces with particular mental health outcomes, I focus on treatment-areas that may be discriminatory for a subset of refugees.As immigrant and refugee experiences may lack reference within traditional treatment paradigms, it becomes essential to understand specificities within which healing and social change for refugees may be relevant. A first objective looks at processes of resilience where recovery may be more meaningful, countering notions of illness as pathology within systems of deficit. Similarly, greater considerations of state-sanctioned violence, its nature and intentions, are needed to plan comprehensive mental health supports. A second objective is then to identify social indicators which may more fully articulate, express, or enable change at group and family levels. Finally, as interventions are most effective when informed by group realities, a third objective brings forward cultural, political, and social forces currently underrepresented in what we know about `treating war trauma'. In sum, this study highlights that greater attention to structural violence in mental health education may lead to better treatment outcomes. Treatments may be more effective by offering alternate pathways to care, considering broader conceptualisations of trauma, and encouraging notions of participatory, group-level initiatives. Findings critically suggest that present mental health systems may unintentionally (re)produce victims, more than enable survivors to rebuild lives after fleeing the complexity and brutality of war-affected circumstances.
Intrinsic Organization and Function of Human Brain Networks Supporting the Spontaneous Dynamics of Attention and Pain
Keywords: attention
brain dynamics
connectome
functional connectivity
mind wandering
pain

The intrinsic dynamics of human brain activity enable us to flexibly shift our attention between the external environment and cognition unrelated to immediate sensation. The interplay of stimulus-dependent and stimulus-independent experience characterizes the nature of our personal interactions with the world and differences among individuals. Brain networks involved in attention, sensory modulation, and stimulus-independent cognition have been described. The present work was designed to disentangle how these networks are intrinsically organized and how fluctuating activity in these networks relates to cognition and a basic perception that is fundamental for survival, pain. The salience/ventral attention network, implicated in stimulus-driven attention, was shown to exhibit right hemisphere-lateralized intrinsic organization, both in structural and functional connectivity. The default mode network (DMN), implicated in attention away from the external environment, was shown to have dynamic fluctuations in the functional organization of its subnetworks that relate to ongoing, freely flowing thoughts (mind-wandering). In the context of pain, activity in multiple networks was associated with spontaneous attentional fluctuations. Attention toward pain was represented as increased salience/ventral network activation. Attention away from pain occurred during increased DMN activation and enhanced functional connectivity between the DMN and periaqueductal gray (PAG), a key node of the descending pain modulatory system. Furthermore, individuals with higher tendency to mind-wander away from pain exhibited stronger PAG-DMN structural connectivity and more dynamic PAG-DMN spontaneous functional connectivity. These findings underscore the behavioural significance of activity fluctuations within attention and sensory modulation networks. While activity in these networks is constrained by structural and functional properties that underlie inter-individual differences, it is also highly flexible and tracks attentional fluctuations toward and away from the present sensory environment. This work has implications for understanding of pathological states such as chronic pain, where altered activity dynamics in attention/antinociceptive networks may determine disease prognosis and therapeutic outcomes.
Antifouling and Antithrombogenic Ultrathin Surface Chemistry for Bioanalytical and Biomedical Applications
Keywords: Antifouling
Antithrombogenicity
Bioanalytical
Biomedical
Surface Chemistry

Whether the aim is to merely prevent the adsorption and accumulation of biological species, or to inhibit the surface-mediated activation of potentially harmful biological processes, biomaterial research invariably faces the need for man-made, foreign surfaces intimately contacting bodily fluids/tissues to be `bioinert'. A popular strategy to address this technological constraint consists in passivating substrate materials with an antifouling (respectively a biocompatible) organic coating. Yet, despite tremendous research activity and progress in recent times, efficient adlayers are scarce, and endowing artificial surfaces with such properties remains, in essence, a difficult task. This PhD Thesis describes recent research contributions in the development of original and versatile stealth coatings, based on novel oligoethylene glycol trichlorosilane surface chemistry, for bioanalytical and biomedical healthcare applications. Surface modification also has the advantage of being straightforward, rapid and inexpensive.One primary objective was to engineer biosensors capable of selectively and sensitively detecting target analytes in real-world biofluids - exploiting the transducing technology of the ultra-high frequency electromagnetic piezoelectric acoustic sensor (EMPAS) system - as potential clinical assay alternatives to current screening/diagnostic tests. Biosensing platforms featured dual-functional, binary organosilane surface chemistry on quartz combining high analyte binding capability (for biorecognition) with pronounced antifouling properties (to minimize the otherwise overwhelming interference signal from the biological matrix). Clinical testing performance was successfully demonstrated through the detection of bacterial endotoxin - a potent pathogen associated with the highly-incident, deadly condition of sepsis. EMPAS measurements performed in full human blood plasma (and in a real-time and label-free advanced fashion compared to modern clinical assays that rely on chromogenic reporter molecules) showed that samples at abnormally high concentration (1000 pg/mL) can be readily differentiated from those presenting basal endotoxin level (
The Role of the RING Finger Protein Makorin-1 in the Embryonic Stem Cell Gene Regulatory Network
Keywords: apoptosis
genomics
RNA biology
stem cells
stress granules
systems biology

Stem cell behaviour is orchestrated as a balance of molecular events that ultimately activate and repress gene expression. These molecular events are collectively referred to as the gene regulatory network (GRN). In embryonic stem cells (ESCs), GRNs coordinate gene expression to maintain ESC identity; however, the complete repertoire of factors that regulate these processes is not fully understood. Our previous temporal microarray analysis of undifferentiated and early committed mouse ESCs identified Mkrn1 as a gene that is preferentially expressed in undifferentiated ESCs and concomitantly down-regulated early upon commitment. Using multilayered systems-level analysis we explored the molecular and cellular functions for the RING Finger Protein Makorin-1 (MKRN1) in undifferentiated ESC populations. Specifically, using a FLAG:MKRN1 ESC clone we compiled an MKRN1-centered `interactome' from undifferentiated ESC populations at the proteomic and ribonomic level. We find that in undifferentiated ESC populations, MKRN1 is predominantly associated with proteins involved in mRNA metabolism including regulators of mRNA turnover, transport and/or translation. At the RNA level, FLAG:MKRN1 associates with a varied set of transcripts encoding for functionally related regulatory proteins involved in processes such as cell differentiation, apoptosis, and/or mRNAs encoding proteins that are destined for translation through the secretory pathway. Informed by our integrated network analysis, we found that MKRN1 is a novel stress granule resident protein, which prompted us to explore MKRN1 function in ESC populations downstream from the oxidative and genotoxic stress responses. Manipulation of MKRN1 expression in ESC populations undergoing cellular stress resulted in modest increases in early apoptotic markers depending on the type of stress response evoked, but manipulation of MKRN1 was not found to promote or impair the extent of nuclear fragmentation (a hallmark of apoptosis) in ESC populations responding to oxidative or genotoxic stress. Our unbiased systems level analysis of MKRN1 function in undifferentiated ESC populations supports a role for MKRN1 as a messenger ribonucleoprotein in ESCs and a potential gene regulatory protein within the ESC GRN.Supplementary Tables:Table S4: Summary of FLAG:MKRN1 AP-MS results.Table S5: Summary of the FLAG:MKRN1 RIP-chip data set.Table S6: Summary of enriched GO Biological Process terms in the unfiltered RIP-chip data set.Table S7: List of 224 genes with established function in the maintenance of mESC self-renewal and/or pluripotency.Table S8: BLASTn results for alignments of shMKRN1 sequences.Table S9: List of 411 differentially expressed transcripts in MKRN1 knockdown ESC population with associated GO terms.Table S10: List of transcripts comprising gene sets in sub-groups of the MKRN1-mRNA network.
From Protest to Party: The Transformation of Anti-Communist Opposition Movements in East-Central Europe
Keywords: coalitions
Hungary
party switching
Poland
political parties
post-communism

AbstractViable and stable political parties are a key element for the establishment of healthy democracies in post-authoritarian countries. In that sense, the study of why some countries have greater difficulties than others in this regard is an important gauge of the quality of democracy in various polities. My paper is based on a comparison of these issues in Poland and Hungary. Why did some of the anti-communist opposition movements spend years going through repeated rounds of fragmentation producing weak parties, while others were able to produce relatively stable parties early on in the transition to party-based competition? While the literature tends to attribute such differences to electoral systems or social cleavages, this paper argues that the historical regime divide between the former communist party and the former anti-communist opposition as well as the extent to which the ex-communist party was able to compete in the new system had a crucial impact on this question. The deeper the regime divide, the more difficult it proved for the anti-communist opposition movements to produce stable parties if the communist party was able to become an effective player in the new democratic system. The effect of the regime divide is also dependent to a certain extent on the competitive dynamics of the post-communist party systems. The impact of the regime divide on party stability is reduced if the former communists are unable to become major challengers for power in the new system.
Patient Education in Cardiac Rehabilitation: The Role of Knowledge on Behavior Change and its Mediators
Keywords: behavior change
cardiac rehabilitation
HAPA model
knowledge
needs assessment
patient education

The purpose of this series of studies was to investigate the relationship between patient education and behavior change in CR and the role of knowledge on behavior change and its mediators in the context of the Health Action Process Approach (HAPA). The first study was a systematic review aimed to investigate the impact of education on patients' knowledge and health behavior change in cardiac patients. Findings from this review support the benefits of educational interventions in CAD, through increase in patients' knowledge and behavior change. The second study aimed to develop and psychometrically-validate a tool to assess information needs in CR patients. After a review by an expert panel, a pilot test, and a psychometric test in 203 CR patients, the tool - called INCR - demonstrated to have good reliability and validity. The INCR was completed by 306 CR patients and 28 CR providers in the third study. Results showed that CR patients desire information in many areas and that providers were highly cognizant of those needs. The forth study aimed to develop and psychometrically-validate the second version of the CADE-Q (Coronary Artery Disease Education Questionnaire), a tool to assess CR patients' knowledge. After a strict process, including a psychometric test in 307 CR patients, the CADE-Q II was considered valid and reliable. Finally, the fifth study investigated: (1) changes in knowledge and HAPA constructs among CR patients following participation in educational programs; and, (2) the theoretical correlates of exercise behavior change among CR patients receiving educational interventions. There was a significant improvement in patients' overall knowledge, some HAPA constructs, and exercise from pre- to post-CR regardless of curriculum. Path analysis revealed that knowledge was a significant motivational construct leading to intention formation, and intentions to engage in physical activity were not directly related to behavior, needing especially action planning, which was related to self-efficacy. Overall, results from all five studies were valuable in the area of patient education in CR and showed the importance of assessing patients' information needs and knowledge as well as to identify behavior determinants related to educational interventions.
Uterine Stem Cells and Cardiac Regeneration
Keywords: Canopy 2
cardiovascular health
cell therapy
stem cells
telocytes
uterus

The uterus is a unique organ equipped with unique cells that allow the tissue to undergo cyclical regeneration of decidua during the menstrual cycle and pregnancies. The regeneration of epithelial and stromal tissue is accompanied by angiogenesis. The remarkable regenerative potential of the cells that populate this tissue was studied on the postulate that cells from this milieu can perform reparative functions when transplanted to sites of injury. Uterine cells were isolated, studied and transplanted into a rodent model of myocardial infarction. Results demonstrated uterine cell transplantation leads to detectable improvement in heart function. Additionally, during the course of identifying uterine cell candidates for transplantation, unique cells were identified, including endometrial telocytes, Canopy 2 detectable cells and rounding macrophages.