VictorJuiz/thesis huggingface dataset:
Identification and characterization of Zfp206, a transcription factor active in ES cells

Embryonic stem (ES) cells are derived from inner cell mass (ICM) of early development embryos. They are pluripotent cells with the capacity to give rise to all cell types of the adult organism. Understanding the mechanisms that underline ES cell pluripotency is fundamental to realizing its potential applications and to understanding early mammalian development. The objective of the project presented in this thesis is to study these mechanisms, particularly, to explore transcriptional regulation in ES cells and early development. Initially, I studied mouse gene expression in order to identify ES cell specific genes. I surveyed 55 mouse tissues including R1 embryonic stem (ES) cells using two custom Agilent microarrays containing sim;40,000 known and predicted mouse transcripts. I identified 43 ES cell specific genes. Among these genes was the putative Scan-Zinc finger transcription factor Zfp206. I confirmed this observation and showed that the expression of Zfp206 was down-regulated rapidly upon differentiation of cultured mouse ES cells, and during early development of mouse embryos. I characterized the Zfp206 cDNA and found that there are at least six isoforms of the Zfp206 transcript, the longest being predominant. Then, I functionally characterized Zfp206. I demonstrated that Zfp206 promoted formation of undifferentiated ES cell clones, and positively regulated abundance of a very small set of transcripts, whose expression is also specific to ES cells and the two- to four-cell stages of preimplantation embryos. This set includes members of the Zscan4, Thoc4, Tcstv1 and elF-lA gene families, none of which have been functionally characterized in vivo but whose members include apparent transcription factors, RNA-binding proteins and translation factors. Moreover, I demonstrated that Zfp206 was located in the nuclei of cultured ES cells and bound to the promoter regions of its three targets Zscan4, Thoc4 and elF-1A. Together, these data suggest that Zfp206 is a transcription factor that has a role in maintaining ES cell pluripotency and controls a set of genes expressed in ES cells and very early development. The studies presented here have expanded upon our understanding of the transcriptional regulation governing the ES cell differentiation and early development.
Network synchrony of GABAergic interneurons in the intact hippocampus: role of electrotonic coupling

Rhythmic population neuronal activities of various frequencies have been observed in the hipocampus in vivo. Hippocampal interneurons play a crucial role in these neuronal population oscillations. This work investigates the properties of O/A interneurons and their interaction with emphasis on the synchronizing role of gap junctions. All experiments were performed in the isolated whole hippocampus preparation in which local neuronal circuits are intact and spontaneously rhythmic activities with peak frequencies ranging from 0.3 to 4 Hz are apparent. O/A interneurons manifested spontaneous polyphasic EPSPs which were highly synchronized between O/A interneurons and closely phase-related to the spontaneous rhythmic field potentials recorded in the nearby pyramidal CA1 region. Although common glutamatergic drive and mutual inhibition played a critical role in maintaining the spontaneous synchronized polyphasic EPSPs in O/A interneurons, gap junctional communication was also essential. Indeed, 10.6% of dual whole cell recordings in O/A interneurons in the present study showed direct electrotonic coupling. This coupling might mostly occur in distal dendrites because of the generally small coupling coefficient (6.9 ± 4.7%, range: 1.3 to 17.6%) and was intermittent. However, spikes in one of the coupled neurons were associated with small electrotonic EPSPs (spikelets) in those neuron pairs with coupling coefficients greater than 10%. Although the coupling rate estimated from dual whole cell recording was less than 10%, electrotonic coupling between O/A interneurons was much more extensive when scrutinizing individual whole cell recordings. In about 60% of recorded O/A interneurons, spontaneous postsynaptic potentials (PSPs) were apparent, and 20–30% of these PSPs were sensitive to gap junctional blockers. Moreover, the slow (<12 Hz) baseline membrane potential oscillations of O/A interneurons were also markedly significantly affected by gap junctional blockers. These experimental results indicate that gap junctions link O/A interneurons extensively and play a vigorous and significant role in conducting and synchronizing electric signals between them.
Software landscape prototype and evaluation

Graphical views of software system architecture are helpful in that they facilitate the understanding of complicated structures. Among such proposals, Penny proposes a formally defined abstraction for programming-in-the-large: the Software Landscape. The key concept is “Structure Views” versus “Interface Views” for graphical locality of reference. It allows the re-drawing of “Interface Views” of imported subsystems in the “Structure Views” of importing subsystems. However, this abstraction has never been fully implemented or validated. In this thesis, we implement a version of the Software Landscape, and test it on several software systems. We conclude that the prototype implementation is practical when a software system has been architected with its landscape representation in mind, but less practical for pre-existing systems. In either case, the structure view of each subsystem can be understood in isolation, and the use of structure and interface views effectively solves the problem of remote usage in graphical system views.
Portable and scalable FPGA-based acceleration of a direct linear system solver

FPGAs are becoming an attractive platform for accelerating many computations including scientific applications. However, their adoption has been limited by the large development cost and short life span of FPGA designs. We believe that FPGA-based scientific computation would become far more practical if there were hardware libraries that were portable to any FPGA with performance that could scale with the resources of the FPGA. To illustrate this idea we have implemented one common supercomputing function: the LU factorization method for solving linear systems. This dissertation discusses issues in making the design both portable and scalable. The design is automatically generated to match the FPGA's capabilities and external memory through the use of parameters. We compared the performance of the design on the FPGA to a single processor core and found that it performs 2.2 times faster, and that the energy dissipated per computation is 5 times less.
Searching for missing baryons

More than 90% baryons are likely in the form of intergalactic medium (IGM) and have been difficult to detect directly. To understand the IGM state, such as density, temperature, peculiar velocity and metalicity, stands as a major challenge to both observation and theory, and is crucial to understand the thermal history of the universe and galaxy formation. In this thesis, I investigate various observable IGM tracers such as the thermal and kinetic Sunyaev Zel'dovich effect and the soft X-ray background. I build analytical models to calculate their statistics and their dependence on cosmological parameters, the IGM state and the thermal history of the universe. I then run and analyze hydro simulations to understand more detailed physics, test the analytical models and fix some free parameters in the analytical models. I then simulate upcoming observations using simulation data to suggest the optimal survey strategies and data analysis methods and forecast the sensitivity and accuracy of these observations. Applying these understandings to observation data, the IGM state and the thermal history of the universe is very likely to be extracted.
DTDMatch: dynamically matching streaming documents to DTDs

In this paper, we present the DTDMatch system, which solves this problem by dynamically maintaining a set of sub-structures that are common to DTDs and documents. By using a sequence of filters that combine positive and negative information (which sub-structures in a newly arriving document can or cannot be instantiated by a DTD), the DTDMatch system quickly reduces the number of DTDs relevant to each incoming document, while guaranteeing no false negatives in the resulting set of candidates DTDs. XML is now widely accepted as a markup standard for data exchange. Given a large collection of closely related DTDs, and an XML document which doesn't specify which DTD it conforms to, a basic problem is to identify the DTD against which the document can be validated. This problem is challenging when the DTD identification needs to performed over a high-volume stream of XML documents.
Two essays on the impact of goals on consumer behavior

This dissertation includes two essays on the impact of goals on consumer behavior. The first essay investigates the moderating role of regulatory focus in resolving product choice involving conflicting goals. Specifically, the results of four experiments demonstrate that when both a high-level and a low-level consumer goal are active, but cannot be satisfied by a single product, consumers with a promotion focus are more likely to choose a product that satisfies the high-level goal whereas consumers with a prevention focus are more likely to choose a product that satisfies the low-level goal. These experiments also find that these effects occur because the promotion focus and the prevention focus has different effects on the accessibility of the high-level and low-level goals, and the accessibility of goals, in turn mediates the effects on conflicting product choice. The results of five experiments show that (1) the brand-as-means is different from other brands that are perceived to be equally capable of satisfying this goal. Specifically, when the goal is activated, both its cognitive properties (e.g., activation) and its motivational properties (e.g., wanting and specific affective experience) get transferred to the brand-as-means, but not to other brands (experiment 1 to 3), and (2) when the goal is activated, the brand-as-means is more likely to be selected over other brands (experiment 4 and 5). The second essay examines situations in which there are multiple brands in a product category that consumers perceive as equally capable of satisfying an active goal. Based on the recent goal system theory in social psychology (Kruglanski et al. 2002), we propose the concept of brand-as-means and demonstrate how it differs from other brands. We conceptualize brand-as-means as a consumer's idiosyncratic way to achieve their personal goal. Others may use other brands to achieve the same goal, but these brands could vary by consumer. We further propose that the brand-as-means is a part of a consumer's goal system, whereas other brands are exclusively represented in the consumer' knowledge structure.

Keywords: Marketing
Dissertations, Academic, Canada
Transformation of redology at the turn of the twentieth century

In the Movement of “reorganization of the national heritage” of the May Fourth period, many cultural heritages experienced a process of reevaluation and reformation; the study of Hongloumeng was one of the most extraordinary issues at the time and a great transformation had proceeded in the field of redology. This paper discusses the passage of the history from two aspects: practical base and theoretical backing and introspects the transformation from historiographic and aesthetic perspectives.
Studies on mechanisms involved in hypoxia-increased metastatic efficiency

Hypoxia exists in many solid tumors due to the structural and functional abnormality of tumor vasculature. Both clinical and experimental studies have indicated tumor hypoxia as a negative prognostic factor associated with increased metastasis and failure of local control. The purpose of this project is to understand the mechanisms involved in the effect of hypoxia on metastasis. Our hypothesis is that hypoxia can modify the sensitivity of tumor cells to apoptosis through epigenetic changes; the altered apoptotic potential contributes to hypoxia-mediated metastatic efficiency. To test the hypothesis, experiments were performed to investigate the role of apoptosis in hypoxia-enhanced metastases and the molecular mechanisms involved. The studies in this project provide better understanding of hypoxia-promoted tumor progression by revealing that increased metastasis can be due to increased tumor cell survival, which may also contribute to the resistance of some tumors to certain therapies. Although the importance of these mechanisms in hypoxia-enhanced metastatic efficiency need to be further investigated in different tumor types and at different organs, studies in this project underscore the importance of targeting hypoxia-increased tumor cell survival in the treatment for patients with hypoxic tumors. Our initial studies using KHT-C cells identified apoptosis to be a mechanism responsible for the death of tumor cells in lungs, and hypoxia pretreatment increased the survival of lung arrested tumor cells. Additional studies indicated that hypoxia could decrease tumor cell apoptotic potential by suppressing p53 activity through a p53-independent upregulation of Mdm2, thereby increasing tumor cell metastatic efficiency. The role of hypoxia-suppressed p53 in increased tumor cell survival was further investigated using ionizing radiation and/or hyperthermia. The suppression of p53 activity and increased resistance to radiation and/or hyperthermia was observed in KHT-C and SCC VII cells after chronic or cyclic hypoxia pretreatment, but not in HT 1080-GFP cells, in which hypoxia induced, rather than suppressed, p53 activity. Although hypoxia did not suppress p53 activity in HT1080-GFP cells, hypoxia pretreatment still increased their metastatic efficiency. Increased survival of lung arrested cells was again identified to be the responsible mechanism. However, the molecular mechanisms are different from previously identified in KHT-C cells.
Analyzing high-dimensional microarray data using Variational-SOM

This thesis focuses on analyzing high-dimensional microarray data using the proposed algorithm, Variational-SOM. The original Self-Organizing Map (SOM) algorithm is an unsupervised neural network method and can be used to reduce the dimensionality of microarray data. The main disadvantage of SOM is that the topology of the map must be fixed from the beginning. In order to solve the problem, the Variational-SOM, of which the map's topology is determined dynamically, is proposed. The DNA microarray technology makes it possible to monitor expression levels of thousands of genes simultaneously. However, these data are of little use unless we are able to analyze them. Experimental results show that the Variational-SOM can reduce the dimensionality of data according to the information that the data contains and help to extract biological significance from the data. The analysis using Variational-SOM can produce more well-separated clusters with respect to clinical information than using the original SOM.
Bi-quartic spline collocation methods for fourth-order boundary value problems with an application to the biharmonic Dirichlet problem

We present optimal bi-quartic spline collocation methods for the numerical solution of fourth-order boundary value problems on rectangular domains, and apply a particular instance of these methods to the biharmonic Dirichlet problem. The methods are based on quartic splines and the collocation discretization methodology with midpoints of a uniform partition as the collocation points. While the standard quartic spline method usually provides second-order approximations, the two bi-quartic spline collocation methods developed in this thesis are observed to produce approximations which are of sixth order at grid points and midpoints, and of fifth order at other points. Both are based on high order perturbations of the differential and boundary conditions operators. The one-step (extrapolated) method forces the approximations to satisfy a perturbed problem, while the three-step (deferred-correction) method proceeds in three steps and perturbs the right sides of the linear equations appropriately. The three-step bi-quartic spline collocation method is then applied to the biharmonic Dirichlet problem and a fast solver for the resulting linear systems is developed. The fast solver consists of solving an auxiliary biharmonic problem with Dirichlet and second derivative boundary conditions along the two opposite boundaries, and a one-dimensional problem related to the two opposite boundaries. The linear system arising from the bi-quartic spline collocation discretization of the auxiliary problem is solvable by fast Fourier transforms. The problem related to the two opposite boundaries is solved by preconditioned GMRES (PGMRES). We present a detailed analysis of the performance of PGMRES by studying bounds for the eigenvalues of the preconditioned matrix. We show that the number of PGMRES iterations is independent of the grid size n. As a result, the complexity of the fast solver is O(n 2log(n)). Numerical experiments from a variety of problems, including practical applications and problems more general than the analysis assumes, verify the accuracy of the discretization scheme and the effectiveness of the fast solver.
Sustainable development of groundwater resources in urban areas

Determining the sustainable yield of groundwater resources is a key issue for sustainable groundwater development. However, urbanization has made the hydrological process more complex in a city, thus resulting in more difficulties to estimate sustainable yield. A water budget equation in an urban context is developed in this thesis, taking into consideration man-made sources of groundwater recharge, such as the leakage from water mains and sewage pipelines, seepage through sewer systems such as septic tanks and cesspools, and artificial recharge. Besides the change in natural recharge and discharge, the change in groundwater fluxes is also incorporated into this equation. The water budget equation is applied to the urban Beijing and the sustainable yield of the groundwater system is determined. There are uncertainties in this analysis, therefore, Monte Carlo simulation is used to analyze the probability distribution of the result and provides a likely range of sustainable yield.
A semantic environment for documenting lessons learned in the building industry

This research thesis presents a taxonomy (BCTAXO) used to support a semantic environment in the building and construction industry. BCTAXO is an extension of e-COGNOS core taxonomy and has inherited its skeleton. This research employed IDEF0 and UML methods to analyze processes and develop object models for different systems, by which relevant concepts and their semantic relationships are captured. BCTAXO took into account some existing classification systems in this industry and absorbed concepts from an extensive range as a supplement. All these concepts are categorized into nine superclasses and their subclasses, according to an object-oriented process-centered approach. To validate the BCTAXO project, a well-designed survey was conducted and eight experienced industry experts with different backgrounds and areas of expertise were interviewed. The research objectives are acknowledged by the survey result.
Early reading and writing development among Chinese kindergarten children in Montessori and traditional Chinese schools

This study was conducted to discover whether Chinese children would go through a similar process of building their theories of print as their English-speaking peers, and whether different schooling (traditional Chinese schooling and Montessori schooling) in the same cultural context affect children's literacy development in different ways. 79 children of age four and age five respectively from one traditional school and one Montessori school were participated in the study. This study found that there were similarities in the early phases of reading and writing development between two languages, Chinese and English. Children from different schooling systems in the same cultural context showed different developmental performance in these tasks indicating that different schooling may have different impacts on children's development of reading and writing. Children from traditional Chinese kindergarten performed better than those from Montessori school in both tasks.

Keywords: Language acquisition
Montessori method of education, China
Kindergarten, China
Reading (Early childhood), China
Thermal poling of twin-hole fibers

We developed a poling system that allows simultaneous inducing and characterizing second-order nonlinearity (SON) in fibers. The SON in fibers is induced via heating the fiber to an elevated temperature while applying an external voltage across the core of the fiber. The induced SON in fibers is characterized by measuring the electro-optical coefficient of the fiber using a fiber Mach-Zehnder Interferometer (MZI). Using this poling system, we characterized in real time the evolution of the SON induced in a twin-hole fiber during thermal poling and thermal erasure. A SON of 0.1pm/V was recorded in the fiber. We developed a charge dynamics model, involving a fast charge carrier Na+ and a slow charge carrier H+, to simulate the mechanism of fiber thermal poling. Good agreement between the simulated results using the model and our experimental observation in poling a twin-hole fiber was achieved.
Accelerated weathering performance of natural fiber plastic composites and its effect on the efficacy of the maleated anhydride coupling agents

One of the issues affecting market expansion of wood/natural fiber plastic composites is related to the performance degradation under weathering conditions. In this study, the effect of accelerated weathering conditions on the composites' performance was examined. Weathering degradation of the bonding strength and the role of coupling agents were also studied. The results showed that exposing the coupling agent for 250 hours alone under UV and UV with water spray did not change the coupling efficiency. The composites with coupling agents had a lower percentage loss in performance after accelerated weathering for 1650 hours. The coupling agents improve the bonding strength, reduce water absorption, and give a higher degree of retention of bonding strength after weathering for 1650 hours. The use of the coupling agents delayed the occurrence of the significant reduction in property and had a lower percentage loss in the bonding strength after 4 weeks of water soaking.
Finite element modeling of mass transport to endothelial cells

The progression of atherosclerosis involves transport of blood-borne atherogenic molecules into the arterial wall. Understanding these mass transport phenomena may advance atherogenesis research. Endothelial cells serve as the interface between lumenal blood and the vessel wall, playing an important role in mass transport. The objectives of this study were to investigate the local mass transport patterns on endothelial cells, and specifically, the effect of endothelial cell surface configuration on transport patterns. A semi-Lagrangian finite element solver for the advection-diffusion equation was developed based on an existing code so as to improve accuracy and efficiency. Flow and mass transport simulations were performed on two endothelial monolayer surfaces (aligned and non-aligned cells), which were constructed from the topography measurements by atomic force microscopy. The results showed a highly heterogeneous distribution of mass flux at the cell surface. We conclude that cell surface configuration greatly affects the intracellular mass transport.