VictorJuiz/thesis huggingface dataset:
Anillin Stabilizes Membrane-cytoskeleton Interactions During Drosophila Male Germ Cell Cytokinesis

The scaffolding protein anillin plays a crucial role during cytokinesis – the physical separation of daughter cells following chromosome segregation. Anillin binds filamentous F-actin, non-muscle myosin II and septins, and in cell culture models has been shown to restrict actomyosin contractility to the cleavage furrow. Whether anillin also serves this function during the incomplete cytokinesis that occurs in developing germ cells has remained unclear. Localization of anillin to several actin-rich structures in developing male germ cells also suggests potential roles for anillin outside of cytokinesis. In this study, I demonstrate that anillin is required for cytokinesis in dividing Drosophila spermatocytes. In addition, spermatid individualization is defective in anillin-depleted cells, although similarities to another cytokinesis mutant, four wheel drive, suggest this may be a secondary effect of failed cytokinesis. Anillin, septins and myosin II stably associate with the cleavage furrow in wild-type dividing spermatocytes. Anillin is necessary for recruitment of septins to the cleavage furrow, and for maintenance of Rho, F-actin and myosin II at the equator in late stages of cytokinesis. Membrane trafficking appears unaffected in anillin-depleted cells, although, unexpectedly, ectopic expression of one membrane trafficking marker, DE-cadherin-GFP, suppresses the cytokinesis defect. DE-cadherin-GFP recruits β-catenin (armadillo) and α-catenin to the cleavage furrow and stabilizes F-actin at the equator. Taken together, my results suggest that the anillin-septin and cadherin-catenin complexes can serve as alternative means to promote tight physical coupling of F-actin and myosin II to the cleavage furrow and successful completion of cytokinesis.

Keywords: cell division
cytokinesis
Drosophila
Advisor: Brill, Julie
Development of Novel Methodologies for the Evaluation of Fetal and Pediatric Drug Exposure

Passive exposure of children to drugs is common, but difficult to ascertain as direct studies are in many cases not possible, and currently available indirect measures of drug exposure, such as maternal reports, are likely to be inaccurate. Novel, indirect methods to evaluate drug exposure in the uterus and early life are needed, and may provide risk estimates that can be later correlated with clinical outcomes. In the studies presented here, I have applied novel methods such as measurement of hair drug concentrations and population pharmacokinetics modeling and simulation to evaluate fetal and infant exposure to drugs and potential associated risks. Testing for methamphetamine allowed demonstration, for the first time, that it freely crosses the human placenta. In contrast, analysis of paired maternal–infant hair showed limited cocaine placental transfer, in agreement with animal models. Results of hair tests from children found in marihuana grow houses and other drug operations showed that passive exposure tends to be higher in infants, likely due to higher dependence on, and proximity to care givers. We also demonstrated the importance of measuring drug metabolites to distinguish between systemic exposure to MDMA and simple external hair contamination secondary to drug present in the home environment. Finally, we developed a population pharmacokinetics and simulation approach to accurately estimate drug excretion into breast milk. This novel technique was applied to fluoxetine and to nifurtimox. Use of our approach allowed us to define, for the first time, the limited extent to which fluoxetine and nifurtimox would be expected to cross into breast milk and estimate potential degree of exposure of breastfed infants. In summary, results presented here support the value of these novel methods for the evaluation of fetal and infant drug exposure and suggest a promising value in estimating risks to children passively exposed to drugs.

Keywords: pediatric clinical pharmacology
hair testing
placental drug transfer
population pharmacokinetics
breast milk
infant drug exposure
methamphetamine
cocaine
fluoxetine
nifurtimox
Chagas disease
Advisor: Koren, Gideon
The Cooperative Classroom: Scaffolding EFL Elementary Learners' English Literacies Through the Picture Word Inductive Model -- The Journey of Three Teachers in Taiwan

Children in Taiwan start their English classes in grade three. As they progress through the grades, they generally do not demonstrate high English proficiency. In addition, they also gradually lose their interest in learning English (“Education Minister,” 2009). To respond to the problem of achievement and motivation related to learning English, the Picture Word Inductive Model and Cooperative Learning were integrated as an alternative approach to the current instructional method in order to more effectively improve the Taiwanese elementary learners’ English literacy and highly motivate their interest in acquiring a foreign language. The focus of this study was to discover the participating teachers’ and students’ perspectives toward this new teaching approach and to understand the difficulties they encounter during the process of initiating and implementing an educational change. This eleven-month qualitative study involved three elementary English teachers and their 71 students from grades 4, 5 and 6 as participants. The data were collected through field notes from onsite classroom observations, teachers’ weekly reflective journals, in-class video recordings, and transcripts of teachers’ monthly meetings and personal interviews with the participants. Although one teacher and her students had to withdraw from the study because of intense pressure from school authorities and parents, the results of this study indicate that the remaining teachers and students highly recommended implementing this alternative approach in English classes and believed that this new way of teaching not only helped students become more autonomous and responsible for their own learning, but also provided them with more opportunities to interact with their peers. Although having doubts about this new approach at the beginning of the study and encountering difficulties during the process of implementation, the two teachers reported that their students’ English vocabulary had increased and they were able to compose meaningful English paragraphs as a result of this non-traditional strategy. The students also revealed that their motivation toward learning English had improved. Furthermore, the results show that support from school authorities and parents is essential to the initiation and maintenance of a change in education settings.

Keywords: Cooperative Learning
Literacy
The Picture Word Inductive Model
Change
English as a Foreign Language
Advisor: Bennett, Barrie
Biogeochemical Defluoridation

Fluoride in drinking water can lead to a crippling disease called fluorosis. As there is no cure for fluorosis, prevention is the only means of controlling the disease and research into fluoride remediation is critical. This work begins by providing a new approach to assessing fluoride remediation strategies using a combination of groundwater chemistry, saturation indices, and multivariate statistics based on the results of a large groundwater survey performed in a fluoride-contaminated region of India. From the Indian groundwater study, it was noted that one technique recommended for defluoridation involved using hydrous ferric oxide (HFO) as a solid phase sorbent for fluoride. This prompted investigation of bacteriogenic iron oxides (BIOS), a biogenic form of HFO, as a means of approaching bioremediation of fluoride. Batch sorption experiments at ionic strengths ranging from 0.001 to 0.1 M KNO3 and time course kinetic studies with BIOS and synthetic HFO were conducted to ascertain total sorption capacities (ST), sorption constants (Ks), and orders of reaction (n), as well as forward (kf) and reverse (kr) rate constants. Microcosm titration experiments were also conducted with BIOS and HFO in natural spring water from a groundwater discharge zone to evaluate fluoride sorption under field conditions. This thesis contributes significant, new information regarding the interaction between fluoride and BIOS, advancing knowledge of fluoride remediation and covering new ground in the uncharted field of fluoride bioremediation.

Keywords: fluoride
bacteriogenic iron oxides
BIOS
hydrous ferric oxide
HFO
fluorosis
defluoridation
Talcher
Angul
Orissa
saturation indices
SI values
principal component analysis
PCA
geochemical modeling
sorption
Fractal Langmuir isotherm
bioremediation
India
groundwater
Advisor: Ferris, F. Grant
Errorless Academic Compliance Training for Children with Autism Spectrum Disorders: Effects on Compliance and Social Communicative Responses

Children with autism often display oppositionality and severe disruptive behaviour in relation to academic tasks and other parental requests. Social deficits also represent a core symptom of this disorder. As a means of treating the challenging behaviours of these children, Ducharme and Drain (2004) evaluated a proactive, non-aversive intervention, errorless academic compliance training that was focused on building child tolerance to challenging demands. In this study, the four children demonstrated impressive improvements in child compliance to academic requests throughout and following treatment. Substantial generalization to untrained academic and non-academic requests also occurred. The current study replicated the intervention used in Ducharme and Drain (2004) with a larger sample of children with autism (eight) to further substantiate the efficacy of the approach and to examine potential covariant change in child social behaviours as a result of the intervention. In a multiple baseline across subjects design, parents implemented errorless academic compliance training with their children. During baseline, they delivered various academic and household requests to determine the probability of compliance for each request. We then developed a hierarchy of academic requests ranging from high probability (i.e., Level 1) to low probability (i.e., Level 4). At the beginning of treatment, parents delivered academic requests from Level 1 and provided praise and reinforcement for compliant child responses. Children were gradually introduced to increasingly more challenging requests from subsequent probability levels and rewarded for compliance to these requests. During both baseline and treatment, we also measured aspects of child social behaviour during sessions in which parents engaged in activities with their children. Participant children demonstrated high levels of compliance throughout and following treatment, as well as generalized cooperation to untrained academic and general household requests that were not the focus of treatment. Parents reported covariant behavioural improvements (i.e., reduced problematic behaviour and positive social gains), particularly for children exhibiting more core deficits of autism. Treatment gains were maintained up to 6 months following treatment. Errorless academic compliance training appears to hold considerable potential for improving the learning and social opportunities of children with autism.

Keywords: autism
intervention
behavior
Advisor: Ducharme, Joseph
Urban Cartographies: The Spanish Baroque City and the Contemporary Latin American City

“Urban Cartographies: The Spanish Baroque City and the Contemporary Latin American City” examines baroque and postmodern narratives through the representation of urban life. This study argues that the baroque reflects the crisis posed by the encounter with the other in the new continent of America, while the postmodern is related to a crisis of knowledge. Selected narrative texts illustrate the main literary tendencies of these two periods and demonstrate similarities in the responses of literary characters to their urban settings. The sense of crisis is both a central literary theme and a response to the historical conditions of urban life during the two periods. Even though the concept of crisis appears to involve a unique experience, the parallels between the two periods suggest that the postmodern crisis is not unique. The social and cultural responses of literary characters to the sense of crisis are similar in both periods. Postmodern social conditions of urban existence are seen as repetitions of the patterns of the baroque. This observation emphasizes literary traditions; parallels and differences between baroque and postmodern texts attest to the idea that all literature revisits previous literary forms through the dynamics of intertextuality. Another focus is the value of the concept of mapping, as a literary theme and a personal practice. As a means for discovering of urban spaces and of defining the human subject mapping suggests that in times of crisis subjects produce parallel systems to control their circumstances. Lastly, this work discusses an experimental literature generated in response to urban disorder, in which disruption and chaos lead to new narrative forms. Ultimately, picaresque and postmodern narratives both respond to complex urban spaces through forms that innovate and integrate new cultural and literary elements.

Keywords: Baroque, Urban, City, Crisis,
Cartography, Postmodern, Latin American
Advisor: Rupp, Stephen
Compact Dynamical Foliations

According to the work of Dennis Sullivan, there exists a smooth flow on the 5-sphere all of whose orbits are periodic although there is no uniform bound on their periods. The question addressed in this thesis is whether such an example can occur in the partially hyperbolic context. That is, does there exist a partially hyperbolic diffeomorphism of a compact manifold such that all the leaves of its center foliation are compact although there is no uniform bound for their volumes. We will show that the answer to the previous question under the very mild hypothesis of dynamical coherence is no. The thesis is organized as follows. In the first chapter we give the necessary background and results in partially hyperbolic dynamics needed for the rest of the work, studying in particular the geometry of the center foliation. Chapter two is devoted to a general discussion of compact foliations. We give proof or sketches of all the relevant results used. Chapter three is the core of the thesis, where we establish the non existence of Sullivan's type of examples in the partially hyperbolic domain, and generalize to diffeomorphisms whose center foliation has arbitrary dimension. The last chapter is devoted to applications of the results of chapter three, where in particular it is proved that if the center foliation of a dynamically coherent partially hyperbolic diffeomorphism is compact and without holonomy, then it is plaque expansive.

Keywords: Compact Foliations
Partially Hyperbolic
Dynamical Systems
Advisor: Pugh, Charles Chapman
Shub, Michael
Interprocedural Static Single Assignment Form

Static Single Assignment (SSA) is an Intermediate Representation (IR) that simplifies the design and implementation of analyses and optimizations. While intraprocedural SSA is ubiquitous in modern compilers, the use of interprocedural SSA (ISSA), although seemingly a natural extension, is limited. In this dissertation, we propose new techniques to construct and integrate ISSA into modern compilers and evaluate the benefit of using ISSA form. First, we present an algorithm that converts the IR into ISSA form by introducing new instructions. To our knowledge, this is the first IR-based ISSA proposed in the literature. Moreover, in comparison to previous work we increase the number of SSA variables, extend the scope of definitions to the whole program, and perform interprocedural copy propagation. Next, we propose an out-of-ISSA translation that simplifies the integration of ISSA form into a compiler. Our out-of-ISSA translation algorithm enables us to leverage ISSA to improve performance without having to update every compiler pass. Moreover, we demonstrate the benefit of ISSA for a number of compiler optimizations. Finally, we present an ISSA-based interprocedural induction variable analysis. Our implementation introduces only a few changes to the SSA-based implementation while enabling us to identify considerably more induction variables and compute more loop trip counts.

Keywords: compiler
analysis
Advisor: Zhu, Jianwen
GISTMARG: GPS and GIS for Traffic Monitoring and Route Guidance

Cell phone providers have started fitting assisted global positioning system (AGPS) chips in new cell phones. The phone users travel on the roads voluntarily and if the phones can be queried anonymously at a reasonable cost, the phones can replace costly dedicated probe vehicles. The major challenge in using AGPS chips is that the phones may not always be on the roads. Even if they were on the roads, they could be in different modes of transportation. Since traffic conditions are usually monitored in terms of private automobiles, the modes of transportation the phones are in first needs to be determined in order for them to be used as traffic probes. Once the traffic data is correctly identified as coming from the private automobile mode, it is another challenge to combine the information with different information sources. This thesis develops a method to fuse the multiple sources of traffic data for more reliable estimation of traffic conditions. Traditionally, route guidance systems generally have focused on the shortest or the fastest route for a particular pair of origin and destination. However, by utilizing available three dimensional (3-D) and geospatial data, it is possible to aid route guidance systems that are optimizing for other objectives such as finding the most scenic, the most level or the safest route. The objective of this thesis is to develop a framework of traffic monitoring and route guidance system named GISTMARG (GPS and GIS for Traffic Monitoring and Route Guidance) that deals with incorporating cell phones or mobile GPS devices as probes, fusing the traffic data from multiple sources and incorporating 3-D and geospatial data into route guidance methods.

Keywords: Civil Engineering
Advisor: Abdulhai, Baher
Shalaby, Amer Saïd
Semantic Feature Type Constrains the Organization and Computation of Concrete Conceptual Knowledge

This thesis addresses the computation and organization of conceptual knowledge. Specifically, it focuses on the recruitment of concrete knowledge during single word reading using behavioural and electrophysiological methodologies. Chapters 1 and 2 assess how number of visual semantic features listed by participants as being part of a given concept influence the speed of word meaning computation, and its neural underpinnings, providing evidence for modality-specific neural organization. Chapter 3 assesses the flexibility of knowledge activation as a function of specific task constraints, suggesting a multi-faceted approach to semantic richness is needed. Chapter 4 describes a novel application of recent statistical advances to the analysis of real-time electrophysiological data, and highlights some limitations of standard analytical approaches. Chapter 5 assesses the real-time influence of several types of knowledge on the neuroelectric activity underlying concrete word meaning computation. A timecourse of sensory-based knowledge type activation is outlined. Finally, Chapter 6 describes a novel approach whereby real-time electrophysiological brain activity is used to predict the speed of semantic decision making, providing further evidence of a highly flexible, but finely structured, human semantic memory system.

Keywords: conceptual knowledge
semantic memory
language comprehension
word recognition
mixed-effects
ERP
Advisor: Cree, George
MADD-2, a Homolog of the Opitz Syndrome Protein MID1, Regulates Guidance to the Midline in Caenorhabditis elegans

Cell migration and extension is essential for development. The ability of a cell or cell extension to reach its target is dependent on spatial cues and receptors that translate positional information into directed plasma membrane extension. For example, the UNC-40/DCC receptor is required to direct circumferential migrations towards the source of the ligand, UNC-6/Netrin, expressed at the ventral midline. To better understand the process of cell extension, I used a specialized process called muscle arms as a model system. In C. elegans, body wall muscles (BWMs) extend membrane projections called muscle arms to the nearest nerve cord at the midline. These muscle arms harbor the postsynaptic element of the neuromuscular junction and extend in a stereotypical and regulated manner. In a screen for muscle arm development defective (Madd) mutants, I isolated madd-2, a novel component of the UNC-40 pathway. MADD-2 is a C-1 TRIM protein and functions cell-autonomously to direct numerous muscle and axon extensions to the ventral midline of worms. In a striking analogy, mutations in a human homologue of MADD-2, MID1, cause numerous ventral midline defects that culminate as Opitz Syndrome. How MID1 regulates midline development is unclear. MADD-2 enhances UNC-40 pathway activity by facilitating the physical interaction between UNC-40 and the downstream Rho-GEF, UNC-73. It is possible that MID1 may mediate the function of a DCC-like pathway at the ventral midline of humans. This work provides the first indication that C1-TRIM proteins may have a conserved biological role of regulating midline-oriented development events and may provide key insights into the role of MID1 in the pathogenesis of Opitz syndrome.

Keywords: Caenorhabditis elegans
guidance
Advisor: Roy, Peter John
Harsh State Repression and Suicide Bombing: The Second Palestinian Intifada (Uprising), 2000-05

This dissertation draws attention to the interaction between insurgents and the target state as the appropriate context for explaining the motivations of suicide bombers, the rationales of the organizations that support them, and the popularity in certain societies of suicide bombing. Based mainly on data collected from 88 interviews conducted in 2006 with senior leaders of six Palestinian political organizations and close relatives and friends of a 25 percent representative sample of Palestinian suicide bombers during the second intifada, it demonstrates the following: (1) During the second intifada, changes in the political opportunity structure, especially extreme state repression, were chiefly responsible for growing public support for suicide bombing, the development of organizational rationales justifying suicide bombing, and the crystallization of suicide bombers’ motivation to act. State repression produced a widespread desire for revenge at all levels of Palestinian society. (2) Cultural forces, notably the growing popularity of fundamentalist Islam and its embodiment in the political culture of certain militant organizations, were of secondary importance in causing the spread of suicide bombing. (3) Strategic calculations (“rational choice”) aimed at speeding the liberation of occupied territory were of tertiary importance in motivating suicide bombers but they figured more prominently at the level of organizational rationales. (4) While the literature often invokes creative agency, psychopathology, and material deprivation to explain the rise of suicide bombing, little or no effect was discovered for these variables.

Keywords: state repression
suicide bombing
Advisor: Brym, Robert