VictorJuiz/thesis huggingface dataset:
Localization of general transcription factors and RNA polymerase II on Drosophila polytene chromosomes

The regulation of gene transcription involves many components. I have focused on the General Transcription Factors (GTFs), required for RNA Polymerase II (Pol II) gene transcription, tracking the distribution of Heat Shock Factor, Pol IIo and several GTFs on Drosophila polytene chromosomes before and after heat shock induced gene transcription. I looked at whether their re-distribution better supports the stepwise or holoenzyme models of Pol II transcription initiation, and examined how they behave following promoter clearance. My results suggest that TFIID (TBP and TAFII230) and TFIIB arrive at active gene promoters independently of Pol II, while TFIIA and TFIIH arrive with Pol II supporting a model that is intermediate between the stepwise and holoenzyme model. Following promoter clearance, TFIID remains at the promoter, TFIIB likely falls off and must then reassociate with the promoter, and TFIIA and TFIIH appear to remain associated with Pol II throughout transcription.
Effects of developmental plasticity and antagonistic selection on phenotypic variation in spiders

In this dissertation, I ask whether developmental plasticity can explain the variation of phenotypic distributions as an adaptive response to variation in population demography and changes in the strength and direction of selection. I use three spider species to examine this question. Using a combination of field attraction and mark-recapture experiments, I first ask how male spiders locate females and the choices they make while mate searching. I demonstrate that males can distinguish between females of different species, populations and ages using long-distance pheromones, and that males increase mate searching risks because they are searching for specific females. As these long-distance pheromones can provide cues of female density, I next examine whether juvenile males alter their development when reared in the presence or absence of female's pheromones (cues of high and low female density, respectively). My results demonstrate that males alter their ontogeny to mature the phenotype that is most beneficial in the competitive context they are likely to experience at maturity. Males develop significantly faster when females are present, and are significantly larger and in better condition when females are absent. Since small size is apparently the result of a decision that is independent of resource availability, I next examine whether male fitness is phenotype specific. By testing small and large males in the competitive environments in which they mature, I show that although larger males are superior in direct competitions, smaller males have higher fitness when tested in the context that leads to their more rapid development. These results challenge the concept of male quality as a fixed trait value, demonstrating the necessity of taking life-history traits into consideration. I next use field populations to demonstrate that demographic variables fluctuate within a season, and depend on the scale of the examination. The strength of selection pressures also varied significantly throughout the breeding season. As a result, males are likely to experience different competitive challenges and selection pressures at different spatial and temporal scales, making a single phenotypic optimum unlikely. I end with a discussion regarding the adaptive nature of developmental plasticity, and when it is likely to evolve.
Microencapsulation: Implications for cell based gene therapy to the lung

Cell therapy has been utilized for the potential treatment of a number of pulmonary pathological conditions. The efficacy of cell therapy, however, is limited by a massive loss of both somatic and regenerative cells after implantation. In cases where genetically modified cells are used the efficiency of the gene therapy is dependent on the level and duration of secretion of an active gene product. To increase the efficacy of cell therapy, single-cell microencapsulation in agarose matrices was used to (1) assess the protein secretion distribution of plasmid transfected rat fibroblasts used in cell-based gene delivery studies; (2) provide an engineered agarose capsule to enhance the viability of both somatic and regenerative cells in suspension culture and (3) enhance the engraftment of cells in the pulmonary microvasculature of rats. Plasmid transfection resulted in marked variability with cells producing 5.7+/-1.3 to 35+/-4 fnof;g of VEGF/cell/h. The majority of protein secretion resulted from a relatively small proportion of the transfected population, 19.5+/-6.22% (3.1% of the total population). Analysis of sorted populations showed a range of 9,500 to 168,000 with a significant correlation between VEGF secretion and plasmid copy number (R2=0.62; slope=0.00013; p=0.012; n=3). Microencapsulation of cells in an adhesion molecule optimized matrix resulted in a 44.7%+/-12.3 (p
Methodologies for access control and fingerprinting of multimedia

This thesis deals with design strategies for access control and traitor tracing. Inspired by the chameleon cipher, a joint fingerprinting and decryption (JFD) architecture is proposed as a computational and bandwidth efficient solution for securing multicast content and tracing pirates. In JFD, slightly different decryption keys are derived from a single encryption key and this structural difference is responsible for casting a fingerprint at the receiver. Based on this methodology a DCT sign bit encryption and fingerprinting algorithm is proposed for protecting and tracking JPEG compressed images in a multicast environment. One powerful attack within the JFD framework is collusion, in which a group of pirates collude their decryption keys or their fingerprinted copies to remove traces of the fingerprint. Such attacks can be deterred by integrating anti-collusion codes (ACCs) into the decryption key design. The size and effectiveness of an ACC codebook depends on the watermark modulation strategy used and the collusion attack model. In this thesis, we construct an ACC tailored specifically to resist linear collusion attacks, but can also be used against other forms of non-linear collusion such as median, min and max functions. The proposed codebook requires O(n) basis vectors for tracking any K < n colluders in a group of n users. All the codewords within this codebook are maximally equidistant with constant weight and can be built using (v, [special characters omitted])-BIBDs derived from Hadamard matrices. Finally we explore the problem of traitor tracing within a n -out-of-n joint access framework, where every subset of n users is treated as a traitor set and must be tracked. As a first step in the investigation we propose a non-perfect secret sharing algorithm called MIX-SPLIT for both access control and tracking. In MIX-SPLIT, every share of the secret has a unique signature which can be used to identify the owner. There is also a unique association between any two shares, which facilitates tracking. One application for MIX-SPLIT is joint access and tracking of highly sensitive data such as medical images. This algorithm can also be engineered to create mixed shares of two different information pieces such as different biometric PINS in applications which require secure PIN storage.
Dismissal and indeterminacy in environmental and other large scale issues

The thesis examines the efficiency of human perception in the process of understanding large scale issues. The cognitive mechanisms that allow the emergence of dismissal are analyzed. Special emphasis is given to the conflict between intuition and reasoning, judgment under uncertainty, judgmental heuristics and associated biases as well as choice subject to "decision frames". The concepts of dismissal and indeterminacy are first defined and examined on a practical level from the perspective of mathematics. The cases of zero and infinity are discussed. Then, emphasis is given to natural large scale phenomena. The slow understanding of the continental drift is presented as well as the difficulties humans faced in their efforts to grasp the main idea of the hydrologic cycle. Finally, there is a reflection on these ideas and connections are identified with contemporary global environmental problems.
The effects of platelet releasate on the migration and proliferation of bone marrow-derived cells cultured under osteogenic conditions

Concentrated platelets and their products are currently being used as a clinical tool to accelerate endosseous wound healing. However, there is a lack of understanding regarding the actions of platelets and platelet released products on osteogenic cells. In the current study, we show that releasate from thrombin activated platelets increases the migration and proliferation of osteogenic cultures of bone marrow cells by a dose-dependent mechanism. Using a scratch wound assay, we demonstrated that platelet releasate (PR) stimulated up to a 2.40 +/- 0.50-fold increase in scratch closure in serum-free medium, relative to a control containing thrombin. In the presence of serum, the addition of PR resulted in a 1.45 +/- 0.13-fold increase in scratch closure. To isolate migration from proliferation, cell monolayers were pre-incubated with 5, 10 and 20 mug/ml of Mitomycin C (MMC), which inhibits cell division. This resulted in a large overall decrease in the leading front of scratch closure, which indicated that PR stimulated cell mitogenesis. However, irrespective of MMC pre-treatment, PR stimulated a motogenic response. These results provide a possible mechanism whereby platelets may influence bone regeneration.
A place on its own: Re-imagining "home" in late-Victorian slum fiction

The powerful influence which the slum exerted on the Victorian imagination is evident in the enormous body of fictional and non-fictional accounts of urban poverty produced during the nineteenth century. During the 1880s and '90s in particular, the slum became a familiar site for literary representation. The many novels written about slum life during this period provide an opportunity to examine antithetical versions of Victorian domesticity. Unlike Ruskin's celebrated domestic model, outlined in Sesame and Lilies (1865), slum domiciles did not exclude injury, terror, doubt and division; rather they incorporated these very elements, producing homes in which more familiar domestic scenes are reproduced in inverted, distorted or parodic form. In the fictional slum, normative domestic ideology is interrogated, and new social possibilities are rehearsed. The fictional slum's seclusion from the surrounding city makes it particularly eligible as site for a re-writing of the domestic narrative. There are four defining tropes which are repeatedly used in slum fiction: the labyrinth, the stage, the prison and the sanctuary. These contradictory images serve to underscore the slum's identity as an anti-domestic locus by violating and/or parodying more standard images of home. These tropes work together to produce a locus where matters which are only subliminally present in more familiar domestic surroundings may be fully articulated. As in Freud's model of psychological repression, culturally unheimlich ("uncanny/unhomelike") material which cannot be fully recognised in the heimlich realm of everyday domestic life finds expression in the shadowy underworld of the slums. Characters who visit the fictional slum frequently discover fulfillment there; almost invariably, this involves the recuperation of missing, suppressed or occluded aspects of their own former lives. Their adventures mirror the complex reconfiguration of Victorian domestic ideology which was taking place not only in contemporary slum fiction but on many other fronts as well.
Multiuser linear precoding for the downlink of MIMO-OFDM systems

Multi-tone transmission using orthogonal frequency division multiplexing and multiple antennas has the potential of drastically improving the capacity and the performance of next generation multiuser communications. However, such systems are inherently complex and require a cumbersome computational load. This thesis investigates the efficient extension of linear processing techniques to multi-carrier transmission from a base station to multiple users using multiple antennas at the transmitter and/or the receiver. Previous work in this area focused on the single carrier case. We propose a technique based on interpolation across frequencies to reduce the computational load involved in deriving the linear filters for each frequency. We also consider the problem of user selection to carriers and develop a sum mean squared error based, computationally efficient algorithm to select the best set of users onto each frequency in order to optimize the system's performance.
Simmel's stranger: in theory and in practice

Georg Simmel's excursus, “The Stranger,” is one of the most widely read texts of the sociological literature; however, neither the links between this text and Simmel's sociology, nor its significance for sociological theory and research have been investigated extensively. This study aims to fill that gap. “The Stranger” delineates a unique form of social distinction (where a person is objectified on the basis of his/her origins) and a unique form of social interaction (where “distance,” both in a symbolic and spatial sense, overshadows but does not preclude “nearness”). Simmel focuses not on abstract cultural differences but on the interplay of distance and nearness through which these differences are lived and sustained. The distance of strangers is not a purely negative condition, but it endows them with distinct capacities. Strangers are often assigned to special (mostly “undesirable”) tasks, and group members can form various relationships with them that they cannot form with each other. Thus, certain hidden potentials/tendencies in the group can become activated in stranger-relations. In this sense, strangeness is a “positive” relation. Yet because of their intimate relation to the hidden potentials and “internal otherness” of the group, and because of the undesirable nature of the tasks they carry out, strangers are often feared or despised, ending up as “scapegoats.” In shifting the focus from abstract differences to socio-spatial interaction, from the negative effects of distance to its positive potentials, and from the otherness of the stranger to the otherness of the group, Simmel's exposition might allow us to challenge the widespread conception of the stranger as a mere outsider and a marginal topic of inquiry. Indeed, for Simmel, the category of the stranger is central to social theory since stranger-relations epitomize the processes of objectification that permeate all social relations. Simmel's conception, however, also has its limitations. First, the “stranger” is an analytical tool and not a substitute for historical-empirical research. Secondly, some crucial sociological variables, particularly gender, are left untouched by Simmel. Finally, we need to question the applicability of Simmel's conception to stranger-relations in contemporary contexts.
Islanding detection and control of an islanded electronically-coupled distributed generation unit

This thesis presents a control strategy for islanded (autonomous) operation of an electronically-coupled Distributed Generation (DG) unit and its local load. In a grid-connected mode of operation, the grid dominantly dictates frequency and voltage at the Point of Common Coupling (PCC) and the DG unit controls its exchanged real and reactive power components with the grid, using the conventional control strategy based on dq-current components. Subsequent to an islanding detection and confirmation, the dq-current controller is disabled and the proposed robust controller is activated. The proposed controller utilizes (i) an internal oscillator for frequency control and (ii) a feedback control system to regulate the island voltage. Despite load parameters uncertainties and unbalanced load conditions, the proposed controller guarantees robust stability and pre-specified performance criteria, e.g. fast transient response and zero steady-state error. To provide smooth transition from a grid-connected mode to an autonomous (islanded) mode, a fast and accurate islanding detection method is also proposed and investigated in this thesis. The islanding detection method is based on injecting a negative-sequence current through the Voltage Sourced Converter (VSC) controller of a DG unit and detecting and quantifying the corresponding negative-sequence voltage at the PCC, as the islanding indicator, by means of a Unified Three-phase Signal Processor (UTSP). Performances of the islanding detection method and the proposed robust controller are demonstrated based on digital time-domain simulation studies in the PSCAD/EMTDC software, and validated based on a laboratory scale experimental setup.
Influence of dietary protein, carbohydrate, and fat on cognitive performance and appetite in healthy elderly persons

The primary hypothesis of this thesis was that energy ingestion from carbohydrates (glucose, potato, and barley), protein (whey), and fat (safflower oil) enhances cognitive performance compared with a placebo in healthy elderly persons. The secondary hypothesis was that carbohydrates influence satiety differently from each other, and protein (whey) induces higher satiety than carbohydrate (glucose) or fat (safflower oil) in this population. Experiment 1 examined the effects of 50g of carbohydrate as glucose, potatoes or barley, compared with a non-energy placebo on cognition, subjective appetite, and food intake over 120min in healthy subjects (aged 60–82y) after an overnight fast. Experiment 2 examined the effects of isoenergetic, equal volume drinks of pure whey protein, glucose, and safflower oil compared with a placebo on the same variables and age group as experiment 1, over 90min. The relationship between glucose regulation and these variables was determined. Experiment 1 showed that poor baseline memory was associated with poor glucose regulation, but this was not reproduced in experiment 2. All carbohydrates improved memory in subjects with poorer glucose regulation and baseline memories independently of plasma glucose concentration in experiment 1. Glucose, whey protein, and safflower oil improved memory in experiment 2 independently of plasma glucose concentration, however, the effects were not related to glucose regulation. Each macronutrient also had unique effects on cognition. In both experiments, the strongest effects occurred 15min after ingestion and on declarative memory. The appetite measures showed that carbohydrates had different effects on subjective appetite and food intake but glycaemic index (GI) did not predict these effects (experiment 1). Experiment 2 showed that whey protein and safflower oil induced higher subjective satiety than placebo, but only whey protein decreased food intake. These findings showed that glucose regulation may be associated with cognition in healthy elderly subjects, that energy ingestion can improve memory independently of plasma glucose concentration, and that each macronutrient exerts unique effects on cognition. These findings also showed that the elderly respond to physiologic appetite signals, that GI does not predict satiety, and that protein (whey) decreases food intake more than carbohydrate (glucose) or fat (safflower oil) in this population.
A rule mechanism for peer-to-peer data management

We are interested in the creation of Peer-to-Peer systems that consist of autonomous databases coordinated by event-condition-action rules. Such systems could be used for the exchange of information among peers who do not desire wholesale integration of their respective databases. For example, a patient's history could be automatically updated in the database of her family doctor whenever she is admitted in a hospital. Conversely, the hospital database may automatically get medical data on patients. The thesis presents a rule language and a rule execution model designed for the creation and the distributed evaluation of rules in a P2P multi-database system. A primary objective in the design of the rule mechanism has been the minimization of communication load among peers. It is assumed that all peer databases are relational. The thesis reports on a prototype implementation of the basic features of the proposed rule mechanism and illustrates its applications with examples.
Studies on the effect of PSC 833, a potent inhibitor of P-glycoprotein function on the development of cancer

P-glycoprotein (Pgp, product of MDR1 gene) is portrayed as the hallmark of multidrug resistance (MDR) in cancer. However, high expression of Pgp is seen in several untreated human as well as experimental cancers. In recent years, we and others have implicated a role for Pgp in promoting tumor cell proliferation while resisting cell death and differentiation and in tumor versus host immune responses. Based on these observations, we hypothesized that over-expression of Pgp is intimately associated with the development of cancer and inhibition of Pgp should inhibit the carcinogenic process. To test this hypothesis, we examined the effect of PSC 833 (PSC, Novartis), a potent inhibitor of Pgp function, on the growth of several human cancer cell lines in vitro as well as development of experimental cancers in vivo. Using several human cancer cell lines including liver, breast, colorectal, melanoma and astrocytoma, we demonstrate that PSC inhibits the growth by activation of cell cycle arrest and/or apoptosis. Extending these studies to in vivo experimental rat model systems, we show that PSC inhibits the growth and progression of chemically induced liver, colorectal and mammary carcinogenesis. To determine the mechanism of PSC action, we examined alterations in ceramide and p21 signaling in a human hepatocellular carcinoma cell line (HepG2) and in two human breast cancer cell lines (MDA-MB-231 and MCF-7). The results indicate that PSC induced intracellular ceramide levels by several fold, and reversal of this induction partially rescued the cells from apoptosis. Changes in PSC-induced p21 levels were directly correlated to activation of cell cycle arrest and inversely correlated to apoptosis. Based on these results, we tentatively conclude that PSC inhibits the development of cancer by selectively targeting tumor cells to undergo cell cycle arrest and/or apoptosis mediated via Pgp, ceramide and p21 signaling.
Bayesian semi-parametric logistic and Poisson regression

The exciting feature of our proposed method is that it is also applicable to survival analysis to estimate hazard functions which should be studied further. Non-parametric and semi-parametric extensions of logistic and Poisson regression have been studied by different approaches from Bayesian and non-Bayesian perspectives. In this thesis, we propose the semi-parametric Bayesian way of estimating the regression curve for binary and count data based on density estimation. We jointly model the response variable y and covariate x, and the regression function is obtained from the expected conditional predictive distribution. The fitted regression curve is estimated as the k number of distinct mixtures of logistic functions, or exponential functions for Possion regression, weighted by functions of marginal distribution of covariates. Our method provides a regression curve which is similar to kernel regression for binary and count data. The parameters related to the amount of smoothing are also studied in the thesis. This Bayesian model provides an easy-to-implement simulation environment and also formal assessment of uncertainties about the estimated regression functions. The Dirichlet process mixture model is used to develop an appropriately flexible class of mixture distributions, and a Gibbs sampling is used for the computations. The performance of this method is illustrated by using both simulated and real datasets.