VictorJuiz/thesis huggingface dataset:
Intrinsic Organization and Function of Human Brain Networks Supporting the Spontaneous Dynamics of Attention and 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.

Keywords: attention
brain dynamics
connectome
functional connectivity
mind wandering
pain
Advisor: Karen, D Davis
Antifouling and Antithrombogenic Ultrathin Surface Chemistry for Bioanalytical and Biomedical Applications

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 (

Keywords: Antifouling
Antithrombogenicity
Bioanalytical
Biomedical
Surface Chemistry
Advisor: Michael, Thompson
The Role of the RING Finger Protein Makorin-1 in the Embryonic Stem Cell Gene Regulatory Network

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.

Keywords: apoptosis
genomics
RNA biology
stem cells
stress granules
systems biology
Advisor: William, L Stanford
From Protest to Party: The Transformation of Anti-Communist Opposition Movements in East-Central Europe

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.

Keywords: coalitions
Hungary
party switching
Poland
political parties
post-communism
Advisor: Jeffrey, Kopstein
Patient Education in Cardiac Rehabilitation: The Role of Knowledge on Behavior Change and its Mediators

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.

Keywords: behavior change
cardiac rehabilitation
HAPA model
knowledge
needs assessment
patient education
Advisor: Scott, Thomas
Uterine Stem Cells and Cardiac Regeneration

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.

Keywords: Canopy 2
cardiovascular health
cell therapy
stem cells
telocytes
uterus
Advisor: Ren-Ke, Li
Molten Salt Electrodeposition of Silicon in Cu-Si

Widespread use of solar energy has not been realized to date because its cost is not competitive with conventional energy sources. The high price of solar grade silicon has been one of the barriers against photovoltaic industry achieving its much anticipated growth. Therefore, developing a method, which is energy efficient and will deliver inexpensive silicon feedstock material is essential. The electrodeposition of Si from a cryolite-based melt was investigated in the present work as a possible solution. This study proposed electrowinning of Si in molten Cu-Si alloy, to decrease the working temperature and increase the efficiency. Solvent refining can be used to recover Si from Cu-Si and also as a second purification method. The physicochemical properties of the potential electrolyte, cryolite-SiO2 melts, were studied in the first step of this work. The deposition potential of Si on a graphite cathode was measured to determine the working potential and the effect of SiO2 concentration on it. In the next step, the deposition potential of Si from cryolite-SiO2 melt on Cu and Cu-Si cathodes was determined using cyclic voltammetry. Next, the cathodic and the anodic current inefficiencies of the process were measured. Continuous analysis of the evolved gas enabled the instantaneous measurement of the current efficiency and the kinetics of the deposition. Finally, the effectiveness of the process in delivering high purity Si was investigated. Si dendrites were precipitated out of the Cu-Si cathode and recovered to determine the purity of the final product as the final step of this study. The produced Si was separated from the alloy matrix by crushing and acid leaching and the purity was reported. The findings of this research show that the proposed method has the potential to produce high purity silicon with low B content. Further development is required to remove some metallic impurities that are remained in Si.

Keywords: Electrowinning
Molten salt
Solar grade silicon
Solvent refining
Advisor: Mansoor, Barati
Inelastic Neutron Scattering Studies of Novel Quantum Magnets

Inelastic neutron scattering was used to study the magnetic excitation spectrum of three quantum magnets: (i) the double perovskite Ba2FeReO6; (ii) the two-dimensional square lattice Heisenberg antiferromagnet Sr2CuO2Cl2; and (iii) the quasi-two-dimensional frustrated two-leg ladder BiCu2PO6.We have conducted inelastic neutron scattering measurements on powder samples of the double perovskite compound Ba2FeReO6. The measurements revealed two well defined dispersing spin wave modes. No excitation gap was observable and the spectrum can be explained with a local moment model incorporating the interactions of Fe spins with spin-orbital locked degrees of freedom on the Re site. The results reveal that both significant electronic correlations and spin-orbit coupling on the Re site play a significant role in the spin dynamics of Ba2FeReO6.High resolution neutron scattering measurements of magnetic excitations in the parent cuprate Sr2CuO2Cl2 reveal a significant dispersion and momentum dependent damping of the zone boundary magnons. We directly compare our measurements with previous resonant inelastic x-ray scattering measurements and find a ~25 meV discrepancy between the two techniques for the measured zone boundary energy at (1/2, 0). The deviations are greatest precisely in the region of phase space where the magnon damping is strongest. This comparison shows that the inelastic x-ray spectrum must contain significant contributions from higher energy excitations not previously considered. Our measurements demonstrate that the high energy continuum of magnetic fluctuations is a ubiquitous feature of the magnetic spectrum among insulating monolayer cuprates, and that these excitations couple to both inelastic neutron and light scattering.A comprehensive series of inelastic neutron scattering measurements was used to investigate spin excitations in the frustrated two-leg ladder compound BiCu2PO6. The measurements revealed six branches of steeply dispersing triplon excitations. Dynamic spin correlations in BiCu2PO6 are the quantum analog of the incommensurate spiral order that appears in classical frustrated magnets and the dispersion minimum occurs at an incommensurate wavevector with a gap of 1.67(2) meV. Neutron scattering measurements in applied magnetic field show that the triplon degeneracy in zero field is completely broken by anisotropic magnetic interactions and each branch was observed to exhibit an anomalous Zeeman behavior. The lowest energy excitation spectrum and anomalous Zeeman splitting is captured by a bond-operator theory, incorporating very significant anisotropic magnetic exchange interactions. At high energies, we have also observed a continuum of two-triplon scattering and a unique two-triplon bound state excitation. Anharmonic terms in the magnetic Hamiltonian of BiCu2PO6 result in a spectacular spontaneous decay of the triplon quasiparticles.

Advisor: Young-June, Kim
Problems in Service Operations with Heterogeneous Customers

We study three problems in service operations with heterogeneous customers. In Chapter 2, we consider the problem of locating facilities of two types at nodes of a tree network, where each facility incurs a fixed cost. Customers may need just one type of service, or both types. It is required to minimize the sum of the total transportation and fixed costs. For the problem with a single facility of each type, we present an O(n) exact algorithm, and for the problem with multiple facilities of each type, we present an O(n^5) algorithm.In Chapter 3, we study the problem of maximizing profits for an inbound call center with abandonment by controlling customer acquisition, retention, and service quality via promotions, priorities, and staffing. This chapter makes four contributions. First, we develop a novel marketing-operations model of a call center that captures the evolution of the customer base as a function of past demand and queueing-related service quality. Second, we characterize the optimal controls analytically based on a deterministic fluid approximation and show via simulation that these prescriptions yield near-optimal performance for the underlying stochastic model. Third, we derive three metrics which play a key role in call center decisions and link customer and financial parameters with operational service quality, reflecting the system load and the priority policy. Fourth, we generate novel guidelines on managing a call center based on these metrics, the cost of promotions, and the capacity cost per call.In Chapter 4, we extend our call center model by considering a firm that follows a periodic advertising policy and receives time-varying demand response. The objective function is to maximize profit by controlling the advertisement policy and service levels for new and base customers. We show that the optimal service level allocation to new and base customers takes the form of a bang-bang policy. That is, at each moment during the advertisement period, the call center should serve all or none of the calls from each type of customers, and the policy transitions between these two extremes at most once during the advertisement period.

Keywords: Call center
Facility location
Heterogeneous Customers
Marketing-Operations Interface
Service Operations
Advisor: Opher, Baron
Representations of Gender and Embodiment in Children's Picture Books

This study examined representations of embodiment among male and female characters in a sample of children's picture books. The data was comprised of four book samples: best-selling books featuring female protagonists, best-selling books featuring male protagonists, multicultural books featuring female protagonists, and multicultural books featuring male protagonists. A total of 112 books were qualitatively analyzed via conventional content analysis and multimodal discourse analysis to investigate how the book narratives and illustrations depicted embodied experiences for male and female characters. Two core-categories emerged. The first identified Observed Norms and Ideals of Gender throughout the analyzed books, specifically within the domains of Behaviour, Appearance, and Ability. The second core-category delineated discourses that pertained to Family Relational Processes. Quantitative content analysis was then used to assess for significant differences in thematic occurrences across the four samples. Overall, quantitative results demonstrated that appearance-based norms occurred most frequently in best-selling books featuring females, that stereotypes related to socioeconomic status were most prevalent in multicultural picture books featuring males, and that the role of the family was highlighted more often in multicultural books than it was in best-selling books. This research expanded on other assessments of gender depictions in children's literature by delineating the complex range of embodied experiences that are depicted for male and female picture book characters.

Keywords: Children
Embodiment
Gender
Media
Picture Books
Stereotypes
Advisor: Joan, Peskin