VictorJuiz/thesis huggingface dataset:
Solution-processed Hybrid Materials for Light Detection

Inorganic semiconductors form the foundation of modern electronics and optoelectronics. These materials benefit from excellent optoelectronic properties, but applications are generally limited due to high cost of fabrication. More recently, organic semiconductors have emerged as a low-cost alternative for light emitting devices. Organic materials benefit from facile, low temperature fabrication and offer attractive features such as flexibility and transparency. However, these materials are inherently limited by poor electronic transport. In recent years, new materials have been developed to overcome the di- chotomy between performance and the cost. Hybrid organic–inorganic semiconductors combine the superior electronic properties of inorganic materials with the facile assembly of organic systems to yield high-performance, low- cost electronics. This dissertation focuses on the development of solution-processed light detectors using hybrid material systems, particularly colloidal quantum dots (CQDs) and hybrid perovskites. First, advanced architectures for colloidal quantum dot light detectors are presented. These devices overcome the responsivity–speed–dark current trade-off that has limited past reports of CQD-based devices. The photo-junction field effect transistors presented in this work decrease the dark current of CQD detectors by two orders of magnitude, ultimately reducing power consumption (100×) and noise current (10×). The detector simultaneously benefits from high gain (∼10 electrons/photon) and fast time response (∼10 μs). This represents the first CQD-based three-terminal-junction device reported in the literature. Building on this success, hybrid perovskite devices are then presented. This material system has become a focal point of the semiconductor research community due to its relatively unexplored nature and attractive optoelectronic properties. Herein we present the first extensive electronic characterization of single crystal organolead hybrid perovskites for the first time. High mobility and long diffusion length (μ > 100 cm2 /V s, D > 10 μm), supported by an exceptionally low density of trap states in the bandgap (ntrap ∼ 10^10 cm−3 ), were found. This material was then implemented to produce a high-performance visible-light detector with high gain (> 10^4 electrons/photon superior to previously reported perovskite detectors) and high gain–bandwidth product (> 10^8 Hz).

Keywords: Colloidal quantum dots
Infrared
Perovskites
Photodetectors
Advisor: Sargent, Edward H
Reasoning about Change with Domain-specific Process Ontologies

The expanding use of information systems in industrial and commercial settings has increased the need for interoperation between software systems. This is, however, inhibited because different systems may use distinct terminologies or assume different meanings for the same terms. A common solution to this problem is to develop ontologies which act as an intermediate language between different parties. For systems which communicate process information within a specific domain, the semantic integration requires an intermediate language between theories which axiomatize possible processes within the domain. In this thesis, we take the first steps toward integrating dynamic information systems. We present a methodology for design and verification of process ontologies which are specific to a particular domain, such as biology, or manufacturing. Furthermore, we show how ontology modularization techniques can be exploited as a means of reusing existing domain-specific process ontologies in developing new domain-specific process ontologies. We also discuss the applications of domain-specific process ontologies in axiomatizing qualitative spatial change. We then describe cases in which domain-specific process ontologies are not sufficient for semantic integration, and characterize a class of theories of actions, called canonical action theories, which can act as intermediate languages between different parties in those cases. In particular, we show that for each domain with finite number of elements there exists a canonical action theory such that all correct plans and process descriptions of the domain can be described in terms of activities axiomatized by the canonical action theory. Both in designing domain-specific process ontologies and characterizing canonical action theories we use an algebraic structure for representing change which enables us to abstract away domain-dependent properties of processes and activities, and demonstrate general properties of formalisms required for semantic integration of dynamic information systems.

Advisor: Grüninger, Michael
Translocation of Virus-derived Nucleic Acids to Chloroplasts and Mitochondria in Plants

In this study, I demonstrated that a non-coding RNA sequence from potato virus X as small as 127 nucleotides (located near the 3´end of 8 kDa and the start of CP genes as well as the non-coding intergenic region) is capable of translocating not only its own sequence but also a reporter gene, fluorescent green protein mRNA into chloroplasts of the transgenic tobacco plants. This is the first evidence showing that a small viral RNA sequence (designated “RNA tractor”) is capable of translocating RNA sequences to the chloroplast. The chloroplast translocation efficiency of the PVX RNA tractor was determined to be 120 X lower than that of Eggplant latent viroid, a member of the Avsunviroidae family that replicates and accumulates in the chloroplast. Furthermore, I investigated two begomoviruses on various Nicotiana species to assess the effects of their ploidy level on infectivity and symptomatology. For this purpose, infectious clones of Ageratum enation virus (AEV), a monopartite (DNA-A with Beta-satellite DNA particle) and Tomato leaf curl New Delhi virus (ToLCNDV), a bipartite (DNA-A and DNA-B), begomoviruses were used. All plants inoculated with ToLCNDV were systemically infected and showed characteristic symptoms. However, in the case of AEV, all plants except N. tabacum cv. Xanthi were infected by the virus but remained symptomless. Taken together, these results indicate that there is no clear relationship between infectivity and ploidy levels; furthermore, symptomatology depends on the type of virus and/or plant species. Another key question to answer was whether or not the genomes of the begomoviruses could be isolated from chloroplasts of the infected tobacco and tomato plants. PCR results confirmed the presence of only DNA-A of the AEV in the chloroplasts. Preliminary studies clearly show that the “RNA tractor” sequence and AEV genome are incapable of targeting the mitochondria. These findings suggest that members from different viral families may be associated with the same organelle, but that members do not necessarily target the different organelles. Thus, the present study could be important for understanding the evolutionary importance of the interactions of viral genomes with different organelles of plant cells and their consequential pathological effects.

Keywords: Agrobacterium
Begomoviruses
Chloroplasts
Mitochontria
PVX
Translocation
Advisor: AbouHaidar, Mounir G.
Automatic Detection of Mild Cognitive Impairment in Older Adults Using Unobtrusive Sensing Technologies

The public health implications of growing numbers of older adults at risk for dementia place pressure on identifying dementia at its earliest stages so as to develop proactive management plans. However, this capability of early detection is very challenging with the contemporary detection process in the form of conventional clinician visits, which are typically not sensitive to detecting mild cognitive or functional decline. Fortunately, some studies have documented that changes in motor capabilities precede and may be indicative of cognitive impairment. A major motivation for this thesis was: can we utilize changes in motor capabilities and activity patterns to automatically predict the onset of dementia in older adults through continuous monitoring using unobtrusive sensors? Many studies have demonstrated that the prodromal dementia phase commonly identified as mild cognitive impairment is an important target for this early detection of impending dementia amenable to treatment. Consequently, in this thesis we explored different approaches for the automatic detection of mild cognitive impairment using unobtrusive sensing technologies. We started off by exploring the feasibility of detecting mild cognitive impairment in older adults using a number of predefined measures associated with their in-home walking speed. We were able to achieve this goal with an area under the ROC curve and an area under the precision-recall curve of 0.97 and 0.93, respectively, using a time frame of 24 weeks. We were also very interested in exploring the feasibility of detecting mild cognitive impairment in older adults using changes in their activity patterns. We used inhomogeneous Poisson processes to build generalized linear models of older adults' activity that would model their presence in different rooms throughout the day. Using these models, we extracted very interesting insights and visualized significant changes in older adults' activity patterns as they started experiencing cognitive impairment. Finally, we devised a method for automatic detection of mild cognitive impairment using changes in older adults' activity models, and we achieved this goal with an F0.5 score of 85.6 percent. We also investigated the two subtypes of mild cognitive impairment, namely the amnestic and the non-amnestic subtypes, and made very interesting observations.

Keywords: Generalized Linear Models
Home Activity
Machine Learning
Mild Cognitive Impairment
Older Adults
Unobtrusive Sensing Technologies
Advisor: Mihailidis, Alex
Prostitution, Community, and Civic Regulation in Early Modern Bologna

While during the late Middle Ages most major European cities legalized and regulated prostitution, historians have argued that in the sixteenth and seventeenth centuries religious reform and shifting ideas about acceptable sexual and gendered behaviour resulted in the criminalization and repression of prostitution. Scholars have also demonstrated that early modern cultural depictions and social attitudes increasingly cast prostitutes and their clients as greedy and immoral, as socially and publically disruptive, and as sinners in need of reform. This dissertation argues, however, that in the northern-Italian city of Bologna secular and religious civic authorities, magistrates, law enforcement, and the general populace approached prostitution primarily as an issue of economics and public order, and secondarily as an issue of morality and public decorum. Due to the city's economic reliance on university students who sought sex and companionship, since the late Middle Ages civic authorities regulated prostitution as a civic, commercial issue and prostitutes as fee- and fine-paying workers governed by their own civic magistracy, the Ufficio delle Bollette. This approach developed further in the early modern period due to Bologna's continuing economic reliance on students, the demands and needs of workers (both male and female) in its growing, seasonal silk industry, its particular political traditions, and its local social customs. As a result, late sixteenth- and early seventeenth century Bolognese civic authorities neither criminalized prostitution nor attempted to repress it, but instead issued comparatively relaxed, moderately restrictive legislation. Likewise, the Bollette's officials and functionaries negotiated between legislation, their own desires, and the needs of individual prostitutes when enforcing regulation. Finally, the hundreds of women who registered annually as prostitutes were more-or-less integrated into local communities through residence and through familial, work, and affective relationships and had greater opportunities for agency than broader cultural, religious, and social ideals would lead us to expect.

Keywords: Bologna
Early Modern
History of Sex
Prostitution
Renaissance
Women's History
Advisor: Terpstra, Nicholas
Educating in a Multispecies World

The widespread deterioration of our planet's life support system is a global challenge facing humanity. This dissertation is based on the premise that changing course requires fundamentally reconstructing how we think about humans and the rest of nature. If a sustainable course requires that we see ourselves as members of an ever-evolving biotic community, then we will have to abandon ways of thinking and acting that distort a sense of continuity between our species and others, replacing kinship with radical separation. Insofar as education is concerned with human learning processes while considering learning in other species as irrelevant or nonexistent, it institutionalizes and perpetuates attitudes that prevent us from reintegrating back into our web of relations. These attitudes are no longer biologically, philosophically, or ethically warranted. They do not keep up with the extent of our empirical and theoretical progress beyond thinking in terms of metaphysical dualisms. To evolve a better discipline, I claim that we must ecologize education; we must dare to imagine and enact an interspecies pedagogy. In the seven papers that follow, I draw from various philosophical, scientific and pedagogical sources to trace pathways into interspecies pedagogy and I try to overcome some of the ways my culturally-informed biases have blocked me from taking the concept seriously. The papers are diverse but they also overlap, showing the process by which I have worked to develop a theoretical alternative that erases the line between education and biology. As such, this publication fits within the larger "posthumanist" shift occurring variously throughout the university. My partial solutions and explorations are admittedly situated and contextual. However, I hope that they can help those who suffer similar blockages as I do to feel more viscerally that the world around them is responsive, attentive, and worthy of pedagogical consideration, and that the range of human affairs treating the biological world as but scenery set behind the great human story is as miseducative for other species as it is for us, and in need of a swift dismantling.

Keywords: biosemiotics
cybernetics
eve devo
interspecies interaction
relational pedagogy
transactionalism
Advisor: Bredo, Eric
Fast CAD for FPGAs

As field-programmable gate array (FPGA) capacities continue to increase in lockstep with semiconductor process shrinking, they are being used for increasingly complex applications. However, because FPGAs are bit-level programmable, the task of generating an FPGA implementation from a user's application description is quite complicated. The CAD tools responsible for this are long-running, taking up to a day to generate an FPGA implementation for the largest applications. This thesis presents several approaches to speed-up FPGA CAD tools.The first proposed approach is to parallelize routing, one of the longest running FPGA CAD steps. The second approach is to modify the FPGA architecture such that a coarsened graph representation can be used during the routing stage, which reduces run-time. This approach involves both architectural and algorithmic changes.Next, a fast analytical technique is proposed for the placement stage, another of the longest-running CAD phases. Following that, this thesis proposes that a library of pre-compiled solutions to commonly occurring application fragments be maintained and re-used when possible. Re-using these application fragments leads to a reduction in CAD run-time, since the entire FPGA implementation need not be generated from scratch. Lastly, this thesis presents an approach that can be used to reduce bitwidths, leading to smaller circuits, which reduces CAD complexity and run-time.

Keywords: CAD
FPGA
parallel
placement
routing
run-time
Advisor: Anderson, Jason H
MCL-1 - Guardian of the Ovarian Reserve: Characterization of the Contribution of MCL-1 to Oocyte Survival

Oocyte quality and the maintenance of the ovarian reserve are essential factors in reproductive competence and fertility. The predominant portion of ovarian follicles are lost to natural death and the disruption of factors involved in conservation of the oocyte pool result in an untimely follicle exhaustion known as premature ovarian failure. Additionally, advancing maternal age is accompanied by accelerated follicle loss and the production of oocytes with poor developmental competence. Thus, identification of factors regulating oocyte quality and survival are essential in management and preservation of fertility. The anti-apoptotic Bcl-2 family member MCL-1 plays a pro-survival role in various cell types; however, its contribution to oocyte survival is unknown. In this thesis we characterized the phenotype caused by oocyte-specific Mcl-1-deficiency, and determined its role in the maintenance of the primordial follicle pool, growing oocyte survival and oocyte quality. Disruption of Mcl-1 resulted in a premature exhaustion of the ovarian reserve, characterized by early primordial follicle loss. The increasingly diminished surviving cohort of growing oocytes possessed elevated markers of autophagy and mitochondrial dysfunction. Ovulated Mcl-1 deficient oocytes displayed an increased susceptibility to cellular fragmentation with elevated activation of the apoptotic cascade. Concomitant deletion of the pro-apoptotic Bax rescued the primordial follicle phenotype and ovulated oocyte death, but did not impact mitochondrial dysfunction associated with Mcl-1-deficiency.Furthermore, we assessed the impact of the cytokine Kit ligand and metabolic supplementation, both associated with increased oocyte survival, on MCL-1 expression. We identified MCL-1 as a pro-survival target of these pathways in oocytes. Diminished Mcl-1-levels, both induced as well as physiologically driven, coincide with impaired mitochondrial output; resulting in starvation-induced autophagy and poor ovarian reserve. We classify MCL-1 as the essential survival factor required for maintenance of the primordial follicle pool, growing follicle survival and effective oocyte mitochondrial bioenergetics.

Keywords: Bcl-2
Mcl-1
Mitochondria
Oocyte
Ovary
Advisor: Jurisicova, Andrea
Planar Resonant Structures for Biosensing Applications

This thesis presents theoretical studies of spontaneous Raman scattering and coherent anti-Stokes Raman scattering (CARS) from molecules on resonant multilayer structures. A simple isotropic model is exploited to describe the Raman polarizability of molecules, and a Green function method is used to calculate the scattering fields from molecules. The response of the multilayer structures to incident fields is characterized through a transfer matrix method that allows derivation of semi-analytic expressions for Raman cross sections and CARS powers in terms of Fresnel coefficients of the structures. The main focus in this thesis is on purely dielectric structures, especially truncated periodic multilayers that support Bloch surface waves (BSW). The dispersion relation of these resonances can be engineered to allow resonant coupling of all incoming and outgoing fields in spontaneous Raman scattering and CARS. As a result, the spontaneous Raman cross section is enhanced up to 10^6 in particular directions and the CARS power from monolayers is significant for millimeter wide incident beams. I compare the spontaneous Raman and CARS powers from thin layers of molecules on multilayer structures supporting BSWs and show how these ratios scale when the molecules form lipid bilayers. I present experimental realizations of surface enhanced Raman scattering from acetone and sulphur molecules on BSW structures and show that the excitation of BSWs results in observation of Raman lines that are not observable on a bare prism. I use a Fresnel coefficient pole analysis to develop a systematic strategy for designing multilayer structures that support long range surface plasmons (LRSPs) and design a periodic multilayer structure that supports a LRSP with propagation length about 2 mm. With a view toward biosensing applications, I derive semi-analytic expressions for a standard surface sensing parameter in arbitrary planar resonant structures and compare the exact and approximate calculations for the designed LRSP structure.

Keywords: biosensing
plasmonics
Advisor: Sipe, John E.
Parenting and Pedagogical Practices: The Racial Socialization and Racial Identity of Pre-school Trinidadian Children

Much scholarly attention has been devoted to Caribbean family dynamics. Researchers have examined family structure, parenting practices, and, to a lesser extent, child outcomes. Indeed, empirical studies have identified a range of child-rearing strategies adopted by Caribbean parents. However, while research has shown that issues of race and racism remain pertinent in the Caribbean context, there is scarce empirical literature on the race-related messages that parents and educators transmit to pre-school children about the meaning and social significance of race. Similarly, a paucity of research exists on Caribbean children's awareness of race and their self-identification in racial terms. This study attends to the critical gap in the literature by examining components of children's racial identity, and the roles of parents, educators, and curricula in racial socialization in Trinidad. More specifically, it examines two dimensions of racial socialization practices: messages about racial identity and messages that promote positive cross-ethnic interactions. This qualitative study is based on interviews with 20 parents, 18 four-and-a-half-year-olds, and 4 teachers who self-identified as Indian, African Trinidadian, or Mixed, and observations of classroom materials and activities. The data revealed a low prevalence of explicit racial socialization. In fact, most of the parents and teachers did not communicate any direct messages to the children about racial identity. Further, it appeared that the nationalist ideology, in particular its emphasis on silence on matters of race, has fostered a conceptualization of race and racism in the adult participants that contributes to their reticence to engage in explicit racial socialization.Lastly, while the children were found to be basing their racial identification on hair and skin colour, an analysis of the children's, parents', and educators' data indicated that children's developing cognitions, along with environmental factors such as racial socialization by parents and teachers--as well as the context-specific race relations of Trinidadian society--influence how children understand racial terms, how they perceive and assign value to racial criteria, and how they identify with their respective racial group(s).

Keywords: caribbean
children and race
family processes
racial identity
racial socialization
Advisor: Escayg, Kerry-Ann