VictorJuiz/thesis huggingface dataset:
Exploring the Extent of Interactions in Activity-Based Models: A Critical Examination of Intra-Household and Spatial Interactions Through Choice Modelling
Keywords: Choice Modelling
Intrahousehold Interactions
Spatial Interactions
Travel Behaviour
Travel Demand

This research increases the overall understanding of a subset of interactions that influence patterns of behaviour: intra-household interactions and spatial interactions. Understanding these interactions and their influence on travel behaviour is essential to developing policy sensitive models. These models provide much of the prerequisite information for evidence based planning. This understanding is framed through a review of existing best practices in travel demand modelling and a discussion of how independent models can be integrated within a larger framework. The thesis presents four empirical models that incorporate either one or both interactions. A model of joint household mode choice which incorporates decisions regarding joint travel and vehicle allocation is estimated. To accomplish this, the model uses a novel choice set formation technique. This is the first modelling to accomplish these tasks simultaneously. Models of transit station location choice are estimated using a newly proposed model structure, the spatially weighted error correlation model. These spatial models are used to compare the difference between independent (transit accessed by driving alone) and joint (transit accessed by being dropped off) spatial choices. The presented model outperforms existing models used to capture the same trend and provides new behavioural insights. A model of chauffeur allocation and location choice for daycare trips is estimated. This model incorporates spatial constraints in this decision through the application of a stochastic frontier model to generate task allocation specific spatial choice sets. This allows for a reduction in the sampling frame for spatial choices. Finally, a model of high school escort and household mode choice is estimated using a parallel constrained choice logit formulation. This empirical investigation generalizes the parallel constrained choice logit to allow for any number of household members to be considered. Concurrently, this empirical analysis highlights a flaw within an existing “best practice” modelling framework.
Effects of Cranial Irradiation on Adult Hippocampal Neuronal Development and the Role of p53
Keywords: aging
cranial radiation
neurogenesis
neuroinflammation
p53
senescence

Cranial radiotherapy is a standard treatment for brain tumours, but is associated with late side effects including compromised cognitive functions that can significantly impair patients’ quality of life. Cognitive impairment is a major dose-limiting factor for cranial radiotherapy, and has therefore been an important subject of study. A large body of preclinical studies suggest that injury to the hippocampus, a key structure for learning and memory, contributes to radiation-induced cognitive impairment. Hippocampus houses the life-long generation of new neurons, a process termed neurogenesis. Neurogenesis inhibition is considered to be one of the most important mechanisms leading to post-irradiation cognitive impairment. Mechanistic insights into how radiation affects neurogenesis could therefore help to alleviate the undesirable effects from cranial radiotherapy. I postulate that p53, an extensively studied tumor suppressor known to play an important role in both radiation biology and stem cell biology, regulates post-irradiation neurogenesis. The role of p53 in post-irradiation hippocampal neurogenesis was examined using transgenic mice with different copy numbers of the p53 gene. We also examined the effects of aging on post-irradiation hippocampal neurogenesis because of the reported age-dependent increase of p53 in the hippocampus. The impact of cranial irradiation on hippocampus was further evaluated using a set of endpoints characterizing cellular senescence to complement limitations associated with neurogenesis endpoints. We showed for the first time that p53 deficiency exacerbated the disruption of hippocampal neuronal development after irradiation in adult mouse brain (Chapter 3). This profound post-irradiation neurogenesis inhibition was associated with increased neural stem cell activation and the depletion of neuronal stem cell pool. Although p53 has been shown to increase with aging in the hippocampus, cranial irradiation was found to further inhibit the age-dependent decrease in hippocampal neurogenesis (Chapter 4). Cranial irradiation resulted in increased expression of senescence markers in mouse dentate gyrus (Chapter 5). Ablation of p53 may alter radiation-induced cellular senescence in the hippocampus, although further investigations are needed to determine the functional significance of this finding. These investigations provide mechanistic insight into the effects of cranial irradiation on hippocampal neuronal development and the pathophysiology of cognitive impairment after cranial irradiation.
Low power high speed optical links in CMOS
Keywords: CMOS
equalizer
Optical
receiver
transmitter
VCSEL

This thesis presents dierent methods for power ecient implementation of optical receivers in CMOS. The major sources of power consumption in short reach optical links are the transimpedance amplier, and the gain stages in the receiver and the laser biasing and equalization in the transmitter. To reduce the power in the receiver this thesis proposes methods that utilize the fast switching properties of Advanced CMOS technologies and avoid the power hungry gain ampliers less suited to CMOS. It has been shown that the proposed methods can also improve the sensitivity of the receiver which in turn reduces the demand on the very strong drive of the laser in the transmitter. On the transmitter side a new type of the equalizer is proposed which allows for lowering the laser bias and compensating for resulting poor transient response in the electrical domain. The low power implementation of the equalizer also helped to reduce the link lower further more.
Characterizing the Nuclear Function of the Cell Adhesion Molecule Fat and Chromatin Regulation by the Inner Nuclear Membrane Protein Speg
Keywords: DamID
Fat
nuclear envelope
nucleus
Speg (CG9723)
the Hippo pathway

Tissue growth, pattern formation and cell metabolism are fundamental to animal development. Coordination of these aspects requires elegant signal transduction systems. In Drosophila, fat (ft) encodes an enormous atypical cadherin that is important for such coordination. Ft functions at the cell surface, regulating tissue growth through the Hippo pathway and Planar Cell Polarity (PCP) tissue patterning. Ft also enters mitochondria to regulate mitochondrial function and metabolic state. However, the coordination of Ft’s functions remains largely unknown. In the first part of my thesis, I present surprising results suggesting that Ft can be cleaved to release an intracellular fragment, which translocates into the nucleus. In the nucleus, Ft is associated with chromatin. Using DamID-microarray, a DNA binding site mapping technique, I showed that Ft binds to specific genomic loci in vivo. Through ChIP-seq, I characterized the genome-wide DNA binding profile of Ft in vivo. ChIP-seq results suggested that nuclear Ft binds mostly open chromatin. Interestingly, the ChIP-seq profile of Ft is highly correlated with that of the Hippo pathway transcription cofactor Yki. Overall, I propose that nuclear translocation of Ft is a novel mechanism by which Ft exerts function. In the second part of my thesis, I focused on Speg, an inner nuclear membrane protein essential for germ cell development. Although the nuclear envelope and lamina have been implicated in chromosome organization and gene regulation, the role of Speg is unknown. Using DamID, I found that Speg is specifically associated with repressive chromatin in vitro and the Speg-associated genes are clustered. Using ATAC-seq chromatin accessibility assay and mRNA-seq in vivo, I found that chromatin accessibility is affected and some affected regions correlate with gene expression changes in speg mutants. Overall, I propose that speg is important for the regulation of chromosome organization and gene transcription.
The Role of Visual Representations in a Knowledge Community and Inquiry Curriculum
Keywords: Curriculum design
Educational technology
Elementary science
Knowledge building
Visual representations

This design-based research study describes the design, implementation, and evaluation of a suite of technology applications, curriculum materials, and activities, created to support a learning community to collectively investigate a digital ecosystem simulation called WallCology. The specific research goal is to understand the role of visual representations within student and teacher practices, including their use of digital technologies and paper-based activities. Curriculum designs were intended to support small groups of students in their progression through an inquiry script, within the broader context of the whole community. The theoretical construct that guided the creation of this script, and all associated tools and materials, was the Knowledge Community and Inquiry model, in which a collective inquiry curriculum is indexed to specific learning goals, to ensure that the learning community makes directed progress towards these goals. The analysis of this Wallcology community has two parts. The first analysis uses an innovative visual timeline methodology to understand the participant structures, activity types, and roles associated with activities involving visual representations. Findings show that visual representations were used in several distinct participant structures: individual, small group, whole-class discussion, and teacher-guided construction. Visual representations played a role in four distinct activity types: foundational work, contributing to the digital knowledge base, problem solving, and verbal knowledge sharing. Finally, visual representations played a wide range of logistical, pedagogical and conceptual roles within the curriculum, serving as attentional beacons, facilitating connections, providing exemplars and templates, organizing group knowledge, and scaffolding activities. The second analysis evaluates how students engaged in scientific explanations within presentations that were made during the Investigation phase of the unit, with a focus on the role of visual representations during each component of their explanation. Students used visual representations fluently within their scientific discourse. This thesis closes with recommendations for future designers of classroom inquiry experiences.
The Psychology of Ritual: An Empirical Investigation of Ritual’s Regulatory Functions and Psychological Processes
Keywords: emotions
group bias
group processes
joint coordination
performance
ritual

Traditionally, ritual has been studied from broad sociocultural perspectives. Recently, however, psychologists have begun turning their attention to the study of ritual, uncovering the causal properties driving this puzzling yet universal aspect of human behavior. With growing interest in the psychology of ritual, the aim of this dissertation was twofold: First, I propose an integrative theoretical framework of ritual that organIntroizes recent empirical work from psychology and the cognitive and neuroscience fields. In this framework I propose that all ritual serves three regulatory functions. Namely, rituals regulate (1) social behaviors, (2) goal states, and (3) emotions. I explain each function by drawing on bottom-up and top-down processes, and suggest that all forms of ritual are a result of some combination of these two levels of psychological processing. Second, I use the framework to generate testable predictions and outline seven experiments as part of this research program. In Studies 1 and 2, I found evidence that novel rituals strengthen ingroup ties but at the expense of outgroup distrust (Study 1), a bias response that is amplified as a ritual becomes more effortful (Study 2). In Study 3, I found that minor variations in the amount of (mis)matching in a ritual sequence predicts differences in group functioning. In Studies 4 and 5, I found evidence to suggest that how a ritual is created, in terms of its physical features, depends on the underlying motivational context (Study 4). As a built-in regulatory mechanism, the embodiment of ritual allows a group to anticipate future goal states, with physical styles of ritual either helping or hindering collective performance (Study 5). The last two studies examined the role that personal ritual plays in mitigating anxiety. In Study 6, I found that ritual is capable of muting the neuroaffective response to failure. Finally, the findings from Study 7 suggest that ritualized movements minimize anxiety by blocking out surrounding emotional stimuli. The current research contributes to the growing interest in the psychology of ritual. Together, by appreciating the value of psychological theory and experimental methods, the current dissertation broadens our understanding of ritual and human behavior more generally.
Monitoring Depth of Anaesthesia through 40-Hz ASSR
Keywords: 40-Hz ASSR
Depth of anaesthesia
Fuzzy C-means
Wavelet denoising

Awareness during general anaesthesia is a devastating experience that frequently leads to post traumatic stress disorder for years after the incident. The rate of intra-operative awareness with memory formation is estimated between 1 to 2 per thousand operations, the rate increases in patients with less healthy physical status. The thesis proposes an anaesthesia monitoring system, that accurately measures depth of anaesthesia (DoA) through 40-Hz auditory steady state response (ASSR). With accurate and fast DoA measuring the monitor can reduce the incidence of awareness during surgical operation. On a preliminary stage to anaesthesia monitoring 40-Hz ASSR is recorded from 26 subjects while awake and asleep. The signals variation are studied during wakefulness and N3 stage of sleep. The cycles at the two stages are classiﬁed with as low as 0.5% error rate. On the anaesthesia monitoring stage data is recorded from 32 human subjects before, during and after induction of anaesthesia, while anaesthesia is being maintained, and during emergence from anaesthesia. The buried under electroencephalogram (EEG) 40-Hz ASSR cycles are extracted with a novel adaptive multi-level denoising algorithm. The proposed algorithm enabled the system to extract ASSR cycles over short periods of time which is of crucial importance in monitoring anaesthesia, increase accuracy and signal to noise ratio (SNR) of the extracted cycles. The modiﬁed fuzzy c-means clustering scheme, proposed to improve clustering performance in noisy data bases where no prior information about the level of noise and signal energy is available, is used for clustering the ASSR cycles. The DoA index is deﬁned and determined at each cycle based on the clustering information of the cycle and the previous ones. The accuracy of DoA index is validated through the subjects’ medical markers, clinical parameters and the recorded Bispectral index (BIS). DoA index is veriﬁed to be accurate; and able to detect fast transitions between diﬀerent levels of anaesthesia. The computed DoA indices detected the induction of anaesthesia on average 55 seconds faster than BIS; were able to detect small changes in DoA during maintenance and were robust to tracheal intubation which has a negative eﬀect on EEG and BIS.
MAST CELLS IMPROVE CARDIAC FUNCTION TRANSIENTLY AFTER AN MI AND MODULATE DIFFERENTIATION/PROLIFERATION STAGE OF MESENCHYMAL STEM CELLS THROUGH PDGF
Keywords: Cell therapy
Heart failure
Mast cell
Mesenchymal stem cells
Myocardial infarction
Tissue repair

Mast cells (MCs) were originally considered as just multifunctional effectors of allergy. However, recent studies have indicated their involvement in other physiological and pathological processes. The existence of MCs in the myocardium has been recognized. However, the exact function of these cells in cardiac pathology remains undefined. Aside from their remarkable potential to produce and release of a wide array of bio-active mediators, a dramatic increase in MC numbers following myocardial infarction suggests their importance in the cardiac wound healing process. I hypothesized that MCs can perform reparative functions when implanted to the site of cardiac injury. MCs were prepared from bone marrow, studied, and implanted into the myocardium of a mouse model of myocardial infarction. The results indicated MC implantation transiently improved cardiac function. Further investigation demonstrated that the beneficial impacts of MC implantation were associated with greater angiogenesis and myofibroblastic responses, which countered the augmented inflammatory response. Additionally, studies of MC-mesenchymal stem cell (MSC) interactions demonstrated that MSCs oscillate between proliferative and more-differentiated states and that MCs promote proliferation and suppress myogenic differentiation in MSCs through platelet derived growth factor and its downstream mediators miR-143/145. The pro-proliferative actions of MCs enlarge the MSC pool prior to differentiation, thereby ultimately facilitating elevated MSC-origin myofibroblast numbers. These new insights unveil beneficial MC involvement in cardiac repair and regeneration beyond their role in post-MI early inflammation.
Building on Borrowed Time: The Temporal Horizons of Infrastructural Breakdown in the Delta of Semarang
Keywords: Disaster
Java
Temporality
Tidal Flooding
Urban Transformation

Based on 12 months of ethnographic fieldwork and one month of archival research, this doctoral thesis describes the predicament of residents of a coastal sub-district in the city Semarang, Indonesia. They must constantly adapt to the sinking foundations of their houses as well as dysfunctional drainage infrastructure. As neighbourhoods threaten to sink below sea level, daily incidents of tidal flooding demand timely adaptation and constant repair of houses and river banks. “Building on Borrowed Time” portrays the multiple ways of enduring this situation, exploring the divergent and often contradictory temporalities that congregate around water. It argues that residents endure a situation of chronic breakdown. It is through the logic of chronic breakdown that ecological transformations as well as political shifts are analyzed in this thesis. While it describes the temporal horizons of breakdown from the perspective of riverside residents, it also offers a historical account of the emergence of coastal settlements in late colonial times. Here, state interventions force indigenous coastal dwellers into a marginal position regarding the city’s spatial and political configuration. Today, in view of the region’s advanced disconnect from the ‘modern’ spaces of the city, the post-colonial state’s concern with sanitation, crime, and ecological degradation explains the emergence of a specific governance of local time. This governance reproduces a present in which ecological disaster in the lives of coastal dwellers is recursive and requires constant managing. Drawing on Cazdyn’s notion of the ‘chronic’ and Povinelli’s concept of ‘quasi-events,’ I show that state agencies, through neighbourhood-level organs of power and bottom-up development schemes, cultivate a ‘meantime’ that does not produce lasting relief, but further “colonizes” the future. An ethnography of the present reveals the temporal practices of this meantime, such as repair and maintenance of infrastructure. These practices effectively replace development (“pembangunan”) projected in plans with continuous but desultory stacking-up (“peninggian”) and fixing of infrastructure. While a spirit of ‘real’ development converges upon the area, driven by crisis scenarios of Dutch and Indonesian water experts, these plans are characteristic of a neoliberal remaking of lifeworlds that ultimately reinforces the chronic.
Illness- and Gender- Related Identity Processes and Psychosocial Well-being among Young Breast Cancer Survivors: A Mixed Method Study
Keywords: breast cancer survivors
embodied identity
embodiment
mixed method
quality of life

The purpose of the current investigation was to explore Identity Integration, defined as the reformation of post-illness identities, and its impact on psychosocial well-being among young breast cancer survivors. Two key aspects of identity were assessed: a) illness-related identity—women’s experience of themselves in relation to developing breast cancer and b) gender-related identity—women’s experience of themselves in relation to stereotypic and hegemonic gender constructions. A triangulation mixed method design was utilized to collect data on identity processes and related shifts among young breast cancer survivors. In the quantitative inquiry, 113 young women breast cancer survivors, diagnosed at age 36.25 (SD=5.89), mostly between stages I-III (93.9%) completed a measure of illness-related identity: the Impact on Self-Concept Scale (ISCS), four measures of gender-related identity: Gender Role Socialization Scale (GRSS), Objectify Body Consciousness Scale (OBCS), Mental Freedom Scale (MF), and Silencing the Self Scale (SS), as well as two measures of well-being: the Functional Assessment of Cancer Therapy-Breast (FACT-B), and the Experience of Embodiment Scale (EES). As predicted, the illness- and gender-related identity subscales were significantly correlated with both measures of well-being. In the multiple regression models, GRSS and MF significantly predicted FACT-B scores, R2=40.0%. In contrast, OBCS and MF predicted EES scores, R2=61%. In the qualitative inquiry, 12 women between the ages of 24 and 44 at diagnosis participated in one interview about identity processes and related shifts before, during, and after their breast cancer experience. Six core dimensions of women’s identity emerged in the Constructivist Grounded Theory analysis: 1) Loss and Adversity, 2) Connection to the Physical Body, 3) Social Power Related to Bodily Experiences, 4) Internalization Versus Rejection of Gender- and Illness-Related Discourses, 5) Relational Connections, and 6) Meaning and Life Goals. Related to the centrality of body experiences in these emergent themes, the results suggested that identity was intertwined with bodily experiences and was therefore referred to as ‘embodied identity’. Taken together, findings from the study highlighted a critical relationship between young women’s altered bodies, illness- and gender-related identities, and their psychosocial well-being after a breast cancer experience. Unlike previous research in psychosocial oncology, which considered identity as disconnected from the body, this study underscored the importance of examining identity through an embodied lens. Theoretical innovation and clinical implications for psychological intervention are discussed.