VictorJuiz/thesis huggingface dataset:
Design and Analysis of Coded Cooperation in Relay Networks

This dissertation deals with wireless communications using cooperating relay nodes. Specifically, this dissertation relaxes two restrictive conditions ubiquitous in the current literature. First, the assumption that relay nodes can perform complex calculations is lifted. Demodulate-encode-forward (DEF) is a low-complexity relaying scheme where the relay is asked only to demodulate, not decode, a source transmission. The implementation of DEF and various methods that can be used with DEF to improve the performance while satisfying the hardware complexity limitations are detailed here. Second, we remove the assumption that the relays either transmit the complete source codeword or not transmit at all. When relays have limited resources, each relay may only be able to transmit part of the source codeword. Fractional cooperation, which allows nodes to transmit a fraction of the source codeword, is proposed and analyzed. Fractional cooperation is also very flexible because coordination between relaying nodes is not required. A third contribution of this dissertation is the use of the union-Bhattacharyya bound (UBB) to analyze relay networks. The bound has the significant advantage of accounting for the specifics of the system parameters and coding scheme used. The UBB is shown here to provide an effective and efficient scheme for relay selection, performance prediction, and system design. It can also be used to distribute relay resources in order to optimize the total energy consumed and error rate performance. A sub-optimal distributed algorithm that can be used to solve the optimization problems is introduced.

Keywords: Communications Engineering
Relay Networks
Coded Cooperation
Advisor: Adve, Raviraj
Children's Understanding of Intentional Causation in Moral Reasoning About Harmful Behaviour

When evaluating a situation that results in harm, it is critical to consider how a person’s prior intention may have been causally responsible for the action that resulted in the harmful outcome. This thesis examined children’s developing understanding of intentional causation in reasoning about harmful outcomes, and the relation between this understanding and mental-state reasoning. Four-, 6-, and 8-year-old children, and adults, were told eight stories in which characters’ actions resulted in harmful outcomes. Story types differed in how the actions that resulted in harm were causally linked to their prior intentions such that: (1) characters wanted to, intended to, and did perform a harmful act; (2) they wanted and intended to perform a harmful act, but instead, accidentally brought about the harmful outcome; (3) they wanted and intended to perform a harmful act, then changed their mind, but accidentally brought about the harmful outcome; (4) they did not want or intend to harm, but accidentally brought about a harmful outcome. Participants were asked to judge the characters’ intentions, make punishment judgments, and justify their responses. Additionally, children were given first- and second-order false-belief tasks, commonly used to assess mental-state reasoning. The results indicated that intention judgment accuracy improved with age. However, all age groups had difficulty evaluating the intention in the deviant causal chain scenario (Searle, 1983), in which the causal link between intention and action was broken but a harmful intention was maintained. Further, the results showed a developmental pattern in children’s punishment judgments based on their understanding of intentional causation, although the adults’ performance did not follow the same pattern. Also, younger children referred to the characters’ intentions less frequently in their justifications of their punishment judgments. The results also revealed a relation between belief-state reasoning and intentional-causation reasoning in scenarios that did not involve, or no longer involved, an intention to harm. Further, reasoning about intentional causation was related to higher-level understanding of mental states. The implications of these findings in clarifying and adding to previous research on the development of understanding of intentional causation and intentions in moral reasoning are discussed.

Keywords: theory of mind
moral reasoning
intention understanding
developmental differences
Advisor: Astington, Janet
Quantifying Effects of Oppositely and Similarly Related Semantic Stimuli on Design Concept Creativity

Creativity is important in the design and manufacture of successful products, yet neither creativity nor the early stages of design are well understood. This lack of understanding limits the tools that can be developed to support the crucial earlier stages of design that ultimately determine product success. My research aims to better understand creativity by studying and quantifying the potential of semantic stimuli (words) presented during concept generation. Natural language was chosen as design stimuli because language provides a systematic framework for stimuli generation. Furthermore, natural language is ubiquitous and intimately related to cognitive functions required in design such as reasoning and memory. Ultimately, the results of this research will assist in the development of early-design support tools. In a series of four experiments, the effects of semantic stimuli oppositely and similarly related to the experiment problem were examined with respect to creativity and designers’ language patterns. Results show that opposite-stimulus concepts were significantly more creative than similar-stimulus concepts. It also was observed that opposite stimuli elicited designer behaviours that may encourage creative concepts. These results suggest that the use of oppositely related stimulus words is a practical method for encouraging creative design.

Keywords: Engineering Design
Concept Generation
Design Stimuli
Language
Creativity
Advisor: Shu, Lily H.
Evolutionary Ecology of Social Interactions among Plants

Neighbouring plants can interact strongly, competing for resources including light, water, animal mutualists, and local germination sites. From an evolutionary perspective, this implies that a plant’s best resource acquisition strategy will usually depend on the traits of its neighbours, and for plants in particular, neighbours are often genealogical relatives. Here, I use a combination of theory and experiments to expose some important consequences of social interactions among plants. The first model analyzes selection on traits used to attract pollinators, showing that competitive interactions (in the absence of local relatedness) can select for exaggerated secondary sexual characters. To complement this model, I performed experiments that confirm the mechanisms by which adaptive pollinator foraging naturally leads to interactions among plants. The observed foraging behaviour (of bumble bees) also provides unique evidence for ‘Bayesian foraging’, a sophisticated type of resource assessment that depends on prior experience in a particular environment. A second model considers how selection on the sex allocation of cosexual, animal-dispersed plants leads to competition and cooperation over local germination sites, sometimes leading to the origin of gender dimorphism. The model reveals novel ecological contexts in which disruptive selection on sex allocation can arise, and in general, illustrates how selection for cooperation can facilitate or inhibit evolutionary diversification. In the models considered here, cooperation is indiscriminant, but plants might also assess the relatedness of neighbours and cooperate with kin over non-kin. In the final chapter, I present experimental evidence that is consistent with preferential cooperation over soil resources among sibling plants. This study is the first to link a potentially cooperative resource allocation strategy with an increase in the mean fitness of related plants.

Keywords: social evolution
sex allocation
animal foraging
mathematical model
competition
cooperation
Advisor: Abrams, Peter
Adaptive Optimal-control Algorithms for Brainlike Networks

Many neural control systems are at least roughly optimized, but how is optimal control learned in the brain? There are algorithms for this purpose, but in their present forms they aren’t suited for biological neural networks because they rely on a type of communication that isn’t available in the brain, namely weight transport — transmitting the strengths, or “weights”, of individual synapses to other synapses and neurons. Here I show how optimal control can be learned without weight transport. I explore three complementary approaches. In the first, I show that the control-theory concept of feedback linearization can form the basis for a simple mechanism that learns roughly optimal control, at least in some sensorimotor tasks. Second, I describe a method based on Pontryagin’s Minimum Principle of optimal control, by which a network without weight transport might achieve optimal open-loop control. Third, I describe a mechanism for building optimal feedback controllers, without weight transport, by a method based on generalized Hamilton-Jacobi-Bellman equations. Finally, I argue that the issues raised in these three projects apply quite broadly, i.e. most control algorithms rely on weight transport in many different ways, but it may be possible to recast them into forms that are free of such transport by the mechanisms I propose.

Advisor: Tweed, Douglas
Identification and Characterization of Potential Modulators of TEK/TIE-2 Signaling

The development of a functional vascular system is impinged upon the restructuring of a primitive vasculature into a more complex and mature vessel network via a process known as angiogenesis. Of particular importance to this vascular remodeling process is the function of the Tek/Tie-2 receptor tyrosine kinase. Mouse gene-targeting studies have shown that Tie-2 deficient embryos succumb to embryonic death at embryonic day 9.5 due to insufficient sprouting and remodeling of the primary capillary plexus. Over the years, the functions and the signaling pathways downstream of Tie-2 receptor have been elucidated; however, the repertoire of genes controlled by Tie-2 signaling leading to angiogenesis had not been studied. To identify the underlying genetic mechanisms, transcriptomes from Tie-2 wild-type (WT) and knockout (KO) embryonic day 8.5 yolk sac tissues were quantitatively analyzed using a gene expression profiling technique called Serial Analysis of Gene Expression (SAGE). Tie-2 WT and KO SAGE libraries were constructed, sequenced and compared to identify genes that were differentially expressed. A list of candidate genes was selected for further validation using semi-quantitative PCR that included 4933402E13Rik, a novel transcript encoding a protein product containing the melanoma-associated antigen (MAGE) domain. Initial characterization of 4933402E13Rik suggested a murine-specific expression profile restricted to the yolk sac, embryo, placenta, testis, endothelial and embryonic stem cells. The expression of 4933402E13Rik in mouse endothelial cells was found to be regulated by Tie-2 signaling since down-regulation of Tie-2 level via siRNA knockdown resulted in decreased 4933402E13Rik mRNA expression. In contrast, stimulation of Tie-2 in mouse endothelial cells using its ligand, Angiopoietin-1, increased 4933402E13Rik mRNA levels. Additionally, 4933402E13Rik expression was found to be modulated through epigenetics especially by histone deacetylation. Mouse endothelial cells treated with Trichostatin A, a potent inhibitor of histone deacetylase, led to an increase in the expression of 4933402E13Rik. Taken together, the results of this study shed new insight on the repertoire of genes implicated in Tie-2 signaling. The identification of 4933402E13Rik as a novel gene modulated by Tie-2 provides a new avenue of research on Tie-2 signaling that may contribute further to our understanding of vascular development.

Keywords: Tek/Tie-2
SAGE
MAGE
Angiogenesis
Advisor: Dumont, Daniel Joseph
Verdazyl Radicals as Mediators in Living Radical Polymerizations and as Novel Substrates for Heterocyclic Syntheses

Verdazyl radicals are a family of multicoloured stable free radicals. Aside from the defining backbone of four nitrogen atoms, these radicals contain multiple highly modifiable sites that grant them a high degree of derivatization. Despite having been discovered more than half a century ago, limited applications have been found for the verdazyl radicals and little is known about their chemistry. This thesis begins with an investigation to determine whether verdazyl radicals have a future as mediating agents in living radical polymerizations and progresses to their application as substrates for organic synthesis, an application that to date has not been pursued either with verdazyl or nitroxide stable radicals. The first part of this thesis describes the successful use of the 1,5-dimethyl-3-phenyl-6-oxoverdazyl radical as a mediating agent for styrene and n-butyl acrylate stable free radical polymerizations. The study of other verdazyl derivatives demonstrated the impact of steric and electronic properties of the verdazyl radicals on their ability to mediate polymerizations. The second part of this thesis outlines the initial discovery and the mechanistic elucidation of the transformation of the 1,5-dimethyl-3-phenyl-6-oxoverdazyl radical into an azomethine imine, which in the presence of dipolarophiles, undergoes a [3+2] 1,3-dipolar cycloaddition reaction to yield unique pyrazolotetrazinone structures. The reactivity of the azomethine imine and the scope of the reaction were also examined. The third part of this thesis describes the discovery and mechanistic determination of a base-induced rearrangement reaction that transforms the verdazyl-derived pyrazolotetrazinone cycloadducts into corresponding pyrazolotriazinones or triazole structures. The nucleophilicity, or the lack thereof, of the base employed leading to various rearrangement products was examined in detail. The final part of this thesis demonstrates the compatibility of the verdazyl-initiated cycloaddition and rearrangement reactions with the philosophy of diversity-oriented synthesis in generating libraries of heterocycles. A library of verdazyl-derived heterocycles was generated in a short amount of time and was tested non-specifically for biological activity against acute myeloid leukemia and multiple myeloma cell lines. One particular compound showed cell-killing activity at the 250 mM range, indicating future potential for this chemistry in the field of drug discovery.

Keywords: stable free radical
living radical polymerization
verdazyl
cycloaddition
rearrangement
diversity-oriented synthesis
azomethine imine
Advisor: Georges, Michael
Structure-function Relationships in the Inositol 1,4,5-Trisphosphate Receptor

The divalent Ca2+ metal ion acts as a universal second messenger in virtually all eukaryotic cells from fungi to plants to mammals. In mammals, Ca2+ signaling is vital to a variety of physiological processes including fertilization, cell proliferation, secretion, and muscular contraction. In electrochemically non-excitable tissues, the release of Ca2+ from intracellular stores such as the endoplasmic reticulum is tightly regulated by the inositol 1,4,5-trisphosphate receptor (IP3R). The IP3R Ca2+ release channel is activated by the binding of the small molecule inositol 1,4,5-trisphosphate (IP3) in response to extracellular stimuli such as hormones, growth factors, and neurotransmitters. The conformational changes accompanying IP3 binding were investigated using a biophysical approach. A specific focus of this work is to decipher how signals of ligand binding are transmitted from the N-terminal IP3-binding core to the C-terminal channel domain. To such end, biophysical studies of the ligand-induced conformational changes within the N-terminal domain of IP3R (a.a. 1 – 604) were performed. The results implicated the presence of two flexible linkers which join stably folded domains. This prompted the proposal of a model in which an equilibrium mixture of conformational substrates containing compact and more extended structures co-exist. Determinants within the N- and C-terminal regions of IP3R have previously been reported to be critical to channel function. Employing nuclear magnetic resonance (NMR) as well as biochemical methods, an intermolecular interaction between the S4-S5 linker, the cytoplasmic loop between the fourth and fifth transmembrane helices of IP3R, and the suppressor domain was identified. The determination of the crystal structure of the suppressor domain from isoform type 3 IP3R (IP3R3SUP) allowed us to map the residues involved in this interaction to one face of the molecule. The characterization of this interaction provides insight into the N- and C-terminal determinants essential to the IP3R channel gating mechanism.

Keywords: calcium
ion channel
Advisor: Ikura, Mitsuhiko
A Longitudinal Investigation into the Association of Smoking and Depression among Adolescents: Exposures, Outcomes, and Auxiliary Hypotheses

Introduction: The association between smoking and depression has been well established, but the nature of the relationship has not been determined. A synthesis of longitudinal studies examining the onset of smoking and depression among adolescents demonstrated consistent evidence of both smoking predicting depression and depression predicting smoking in multiple populations; however, more work is needed to develop and test the mechanisms associated with the onset of the co-occurrence of smoking and depression. This thesis examines the role of a broad range of potential confounders on the relationship between smoking and depression, and investigates a potential mechanism of effect. Method: Analyses were conducted using the Nicotine Dependence in Teens (NDIT) cohort which included 1293 students initially aged 12-13 years recruited from all grade seven classes in a convenience sample of ten secondary schools in Montreal, Canada surveyed twenty times over five years. Multiple regressions were performed to examine the temporal relationship of potential confounders on the relationship between smoking and depression and to empirically observe variables that could be intermediate on pathways between smoking and depression. A growth curve model was developed to test the effect of perceived self medication on changes in depression scores over time. Results: A concept map of the smoking and depression relationship in the NDIT cohort was developed according to the results of proportional hazard and fixed effect regressions in which friend smoking, stress, and anxiety-associated variables were identified as intermediate variables. Perceived self-medication was associated with decelerated rates of change of depressive symptoms over times, suggesting that smoking may increase mean levels of stress and depressive symptoms, but may offer the perception of control. Conclusion: In concert, this thesis suggests a model in which stress and the perceived control of psychobiological function using cigarettes lead to the development of increased depressive symptoms and increased cigarette use.

Keywords: Depression
Smoking
Advisor: Cohen, Joanna
Understanding the Complexities of Trichotillomania: Women's Recollections of the Road to Discovering Trichotillomania and the Journey that Followed

This study examines the childhood and social experiences of 10 women with trichotillomania (compulsive hair pulling) and the various pathways that led them to the discovery of trichotillomania. Trichotillomania is a chronic and devastating condition that affects a significant number of women, which has long-term consequences that can be debilitating and psychologically and emotionally scarring. The 10 women participated in semi-structured interviews during which they were asked to describe their childhood and social experiences. This is the first study that has attempted to understand childhood and social experiences from the perspective of women living with trichotillomania. Utilizing a grounded theory approach (Strauss & Corbin, 1998), the interviews were transcribed, coded, and analyzed. A model, based on the core category, The Road to Discovering Trichotillomania: The Issue of Control, was developed to reflect the experiences of these women. The model is constructed on five major themes: Looking Back: How It All Began; Childhood Environment; Relationship Between Specific Experiences and the Discovery of Hair Pulling; The Role of Hair Pulling; and The Journey of Hair Pulling. The women identified the events (both internal and external) that precipitated the first episode of hair pulling. The underlying theme of these events was the perception that things were out of their control. The discovery of trichotillomania came about as a result of the women’s attempts to regain control of their experiences and environment. The findings of this study make an important contribution to the current literature on trichotillomania by attempting to understand the complexities of the factors involved in the discovery of this condition. In presenting the lived experiences of these 10 women, this study moves the discussion beyond the pathology and towards a richer understanding of trichotillomania. The study’s limitations, implications for future research, and final thoughts are also discussed.

Keywords: trichotillomania
qualitative study
Advisor: Guttman, Mary Alice
Evolution of Duplications Within Mammalian Genomes

Genomic evolution is a continuous process that involves the accumulation of neutral and adaptive variation within DNA sequences. Duplication, a mechanism that introduces new genetic material into a genome, is thought to be the primary source of new genes that have arisen during vertebrate evolution. This hypothesis, popularized by Susumu Ohno in 1970, has transformed the field of evolutionary biology. Consequently, many evolutionary studies have concentrated on identifying examples of gene duplication and assessing their impact on the evolution of genomes. This thesis presents the identification and analysis of three examples of gene duplication involved in shaping mammalian genomes. Through these analyses, I investigate the fate of duplicated genes and discuss the potential impact of duplication on genomic evolution. The fates depicted within these studies range from the pseudogenization of recent gene duplications to the preservation of ancient duplications for over 100 million years in multiple mammalian genomes. The consequences of these fates include neofunctionalization, subfunctionalization, and gene relocation. In additional, the analyses in this thesis demonstrate different rates and directions of evolution following gene duplication. Some duplicated genes are shown to diverge gradually over time throughout mammalian evolution, while others exhibit an accelerated evolutionary rate within a specific lineage. In other rare cases, divergence is impeded such that duplicated genes evolve in synchronization, under a process known as concerted evolution. This can lead to examples showing mosaic evolution, where both divergent and concerted evolutionary signatures are observed within a single duplicated gene. Through the analyses presented in this thesis, I illustrate some of the different evolutionary histories that result from gene duplication and examine the variety of forces that influence the evolution of duplicated genes. These studies examine the role of duplication in mammalian evolution and represent a significant contribution to the growing body of knowledge in the field of evolutionary biology.

Keywords: Genetics
Evolution
Advisor: Scherer, Stephen W.