VictorJuiz/thesis huggingface dataset:
Hardware Accelerated protein identification

The proteins in living organisms perform almost every significant function that governs life. A protein's functionality depends upon its physical structure, which in turn depends on its constituent sequence of amino acids as specified by its gene of origin. While many protein sequences are known, many remain to be discovered. Recent advances in mass spectrometry are capable of determining unknown protein sequences but the process is very slow. We review a new method of de-novo protein sequencing that requires a fast search of the genome. In this thesis, we present the design of FPGA-based hardware that can perform this search in a very fast and cost-effective manner. This hardware solution is between 3 to 60 times more cost effective than an equivalent software platform. In addition, we provide a framework to estimate the cost of the hardware at a desired level of performance.
Errorless embedding in the classroom: increasing the on-task behaviour of children with behaviour difficulties

Children with behaviour difficulties often display high levels of off-task behaviour that interferes with the completion of academic tasks. Errorless embedding was developed to increase on-task behaviour without the use of punishment. In the present study, errorless embedding was used to improve the on-task behaviour of three children referred to a clinical classroom. Pre-treatment observations revealed high levels of off-task behaviour for all children when they were asked to work independently. During the initial stages of the intervention, brief durations of independent work were embedded into longer durations of adult-supported work. Gradually, the proportion of time the child was engaged in independent work was increased according to a predetermined schedule. Toward the end of treatment the duration of adult-supported work was faded back to baseline levels. Results demonstrated that by treatment completion, off-task behaviour for all the children had significantly decreased while their independent on-task behaviour was substantially improved.

Keywords: Behavior disorders in children
Behavior modification
Motivation in education
Ontogeny of ifosfamide nephrotoxicity

Drug-induced nephrotoxicity may adversely affect the health and well-being of children, especially when the developing kidney is exposed to toxic agents that may lead to acute glomerular, tubular or combined toxicity. Repeated administration of such agents (e.g., cancer chemotherapy) may lead to acute or chronic renal damage often associated with devastating effects on long-term child health. Loebstein et al. has shown that the cancer chemotherapeutic ifosfamide (IF) causes serious renal damage substantially more in younger children (less than 3 years of age) than among older children. The mechanism of the age-related IF-induced renal damage is not known. This thesis demonstrates that the localized metabolism of IF in the kidney and the ensuing production of nephrotoxic chloroacetaldehyde results in oxidative stress. The major hypothesis underlying this work is that there is renal ontogeny in the expression and activity of CYP enzymes responsible for IF metabolism and resultant nephrotoxicity. The presence of CYP3A4, 3A5 and 2136 was confirmed in human fetal, pediatric and adult kidney as was the metabolism of IF (both R-IF and S-IF) by renal microsomes to 2-dechloroethylifosfamide (2-DCEIF) and 3-dechloroethylifosfamide (3-DCEIF). There was a correlation between the S-IF metabolite R-3-DCEIF and CYP3A4/5 and between S-2-DCEIF with CYP2136 enzyme levels. Ontogeny in CYP3A expression and 2B22 activity was assessed in piglets ranging in age from 1 day to adult. Kidney CYP3A expression peaked in age consistent with toddlerhood as did the metabolic activity, corroborating the clinical experience in children. This is the first documentation of renal CYP ontogeny and of renal drug metabolism, leading to age-dependent nephrotoxicity.
Investigation of some methodological factors in determining the glycemic index

This thesis addresses recently suggested technical changes to the glycemic index (GI) methodology. The first objective was to determine the effect of providing subjects with coffee/tea compared to water during GI testing. Coffee/tea did not affect mean GI but tended to reduce the variation by about 30%. The second objective was to investigate the effect of using two fasting blood samples compared to duplicate glucose measurement in a single sample. There were no significant differences between methods on mean GI, however using duplicate measures in single blood sample tended to reduce the variation slightly. The third objective was to determine the effect of analyzing all blood samples in duplicate compared to single analysis. There was no significant effect of duplicate analysis on mean GI or variation. Therefore, the results do not support adoption of the suggested changes in GI methodology.
The linguistic trivialization of human rights across legal and political spheres

The static language of human rights is replete within the discourse of legal academia and political activism. The paper suggests that this conceptual revolution suffers a discursive trivialization and rhetorical misplacement within international human rights treaties themselves---a linguistic fallacy that essentially precipitates a decline in legal compliance. The inadequacy bolsters esoteric whims whilst fundamentally jeopardizing the legal agenda of international human rights. An analysis of contemporary debate will be sought to assess the language of the law as it stands today, as well as the opportunities presented in adopting this linguistic lense. The purpose is to offer reflections on the linguistic structure and interpretation of human rights norms, which is philosophical in the sense that it is not restricted to the conclusions of any one academic sphere, but rests on a general survey of all the relevant and available data.

Keywords: Law, Language
Human rights
Cognitive, linguistic and affective aspects of learning to read in Spanish by English speaking adults with and without reading disability

The inquiry reported here describes cognitive, linguistic and affective aspects of reading in Spanish by English speaking adults with and without reading disabilities. Seven detailed case studies describe the different aspects that were involved in the process of learning and teaching to read in a second language. The author of this thesis, who was the teacher of the course, used a longitudinal approach in this research to study the way 4 normal readers (NR) and 3 disabled readers (DR) learn to read in Spanish. The 2 hour sessions were held in the teacher's home 2 times a week for a period of 6 months. The students voluntarily enrolled in the Spanish course because they were interested in Spanish culture. The goal was to determine to what extent problems faced by adults with and without reading disability in English, a language with a "deep" orthography, were transferred to Spanish, a language with a "shallow" orthography, and to identify through direct observation, periodic testing and individual and collective interviews those aspects that might facilitate or interfere with reading in Spanish. The results of working with DR and NR adults suggest that both the central processing hypothesis and the idea that a shallow orthography is easier to decode are important in understanding reading acquisition of a second language. In the present study, DR students experienced problems in developing reading skills in Spanish in spite of the less complex nature of the Spanish orthography. They also had more difficulty in developing vocabulary and grammar skills. NR did not experience similar problems and could acquire with ease the rudiments of Spanish vocabulary, syntax and reading. To measure the linguistic and cognitive aspects, periodic tests were given which included decoding, spelling, word recognition, pseudowords, comprehension and memory components. Affective aspects, which played an important role among the DR especially, were measured using individual and collective interviews as recorded on audio-tape. Throughout the instructional period, the role of the students changed in that they became participants, and as they wrote their stories with myself as a partner, they became co-researchers. Through this research there was an opportunity for getting insights into whether a reading disability is as much of a limitation in one language (Spanish) as it is in another (English) and to develop principles and implications of teaching adults to read a second language. In spite of the fact that the DR showed extreme difficulty in understanding grammar because of their lack of learning strategies, it was a positive experience for them since they had the opportunity to deal with their limitations in learning. (PsycINFO Database Record (c) 2016 APA, all rights reserved)

Keywords: Affective education
Cognitive learning
Reading (Adult education)
Reading disability
Second language acquisition
Spanish language, Study and teaching (Higher)
Mothers of the nation, guardians of the hearth: women, family and nationalism in 20th century Europe

Theories of nationalism can be grouped into two camps: those that argue that nationalism is modern/modernizing (Gellner, 1983; Greenfeld, 1992; Kohn, 1969) and those that argue that it is a traditionalist reaction to modernity (Kedourie, 1998; Lipset, 1983). This work tests the validity of these perspectives by assessing how nationalist regimes treat half their population: women. This is done by assessing nationalist government policies that apply to women and families. The goal is to answer the question: Do policies of nationalist governments modernize gender relations or do they represent a traditionalist aim to preserve, or reestablish where shaken, unequal and "pre-modern" gender relations, in effect archaizing gender relations? What makes this work unique is its use of four cases: Italy, Germany, USSR/Russia and Yugoslavia/Croatia, compared at two points in time. The two cases that were ruled by nationalist regimes in the first period (the inter-war period): Italy and Germany, are analyzed again in the second period (post-1989), this time, as non-nationalist cases. Coetaneously, revolutionary Russia and the Kingdom of Yugoslavia begin as non-nationalist or multinational polities but are governed by nationalists regimes in the second period of study. This comparison was intended to establish to what degree nationalist regimes differ from non-nationalist regimes in their policies on the position of women and families; second, to what degree nationalists succeed in either modernizing or archaizing gender and family relations. This work demonstrates that the nationalist regimes under scrutiny intended to return women to their "traditional" place in the home, as housewives and mothers, regardless of the time period studied. At both points in time, this was done by proposing and/or implementing policies aimed at removing women from the public sphere and "encouraging" them to magnanimously fulfill their reproductive duty for the future glory of the nation. Despite attempts to archaize gender relations and re-patriarchalize families, the nationalist regimes examined did not succeed in their aim of relegating women to traditional roles of mothers of the nation and keepers of the hearth. An analysis of aggregate data reveals that policy changes had relatively little effect on overall demographic trends. Nonetheless, given that these nationalist regimes attempted to archaize gender relations and repatriarchalize families, they clearly cannot be classified as modern/modernizing.
Expression of modulators of collagen and elastin remodelling in the vaginal wall of premenopausal women with severe pelvic organ prolapse

Pelvic floor dysfunction, including pelvic organ prolapse (POP) and urinary incontinence, are major health issues for women in the reproductive and menopausal years. Although the prevalence is as high as 50% in some reports, the underlying mechanism and basic pathophysiology remain poorly understood. This study tested the hypothesis that the expression of modulators of elastin and collagen differ in women affected by pelvic organ prolapse compared to asymptomatic controls. We studied the differential expression of proteins participating in (1) collagen and elastin biogenesis and (2) the major proteolytic enzymes and their inhibitors, in vaginal skin of patients with advanced POP and controls using Real-Time PCR method, immunoblot and immunohistochemical analysis. We found a reduction at the gene and protein expression level of enzymes crucial for collagen and elastin synthesis; furthermore, there was an increase in the proteolytic enzymes involved in collagen and elastin degradation, coupled with a reduction of their specific tissue inhibitors. These alterations in the ECM proteins may play a specific biochemical role in the etiology of POP in women.
Development of a vignette-based scale for measuring empathy in teaching

A new approach for developing a vignette-based measurement of empathy in teaching has been proposed in this paper. This new approach addresses many of the limitations of the tests that have been used for measuring teacher empathy to date. This paper presents and discusses the results of the initial stages of the development procedure. The first part of the development involved a focus group session with five experienced teachers. The focus group determined, by consensus, the definition of empathy to be used in developing the new scale. The focus group then developed some vignettes based on their experiences. These vignettes were presented with open-response questions to a separate group of teachers. Responses to the vignettes were analyzed, and used to develop a selected-response empathy scale. Some preliminary work was done in assigning ratings to each of the response options in the new selected-response scale.
Conjugation of proteins to hemoglobin

There is a considerable interest in developing hemoglobin bioconjugates for therapeutic applications. For example, conjugates of hemoglobin and the enzyme superoxide dismutase might be useful as red cell substitutes with antioxidant properties, while conjugates of hemoglobin and insulin might serve as hepatoselective and long-acting insulin analogues. Currently, conjugation of proteins to hemoglobin relies on gene fusion using a recombinant DNA technology or on oligomerization using polymerizing agents. We developed an alternative approach, which relies on chemical modification and conjugation of proteins in a site-specific manner. Two novel reagents for chemical modification of proteins were synthesized and used to generate hemoglobin-superoxide dismutase and hemoglobin-insulin conjugates. The tetrafunctional reagent N, N'-Bis[bis(sodium methyl phosphate)-5-aminoisophthalyl)]-4,4'-disulfanlydibenzamide, (1) reacts with human hemoglobin A in a site-specific manner at the Val-1 and Lys-82 of the beta globin chain. The reagent simultaneously cross-links hemoglobin tetramers intramolecularly and bridges them with a disulfide bond. The reduction of the disulfide bond generates cross-linked hemoglobins that have an exogenous thiol group, which is available for conjugate formation. The chemoselective reaction of the thiol group of hemoglobin with the maleimide group on the cross-link of a second protein produces conjugates in a controlled manner. Evaluation of the properties of the resulting hemoglobin-superoxide dismutase and hemoglobin-insulin conjugates showed that the conjugated proteins retain their function. This establishes that designed conjugates of hemoglobin can be produced and are functional. These should be useful for applications requiring enhanced stability and circulation time. Superoxide dismutase is chemically modified at the interface of two subunits using the reagent N, N'-[N-(4-maleimidobenzoyl)-5-aminoisophthalyl]-5-aminoisophthalyl bis(sodium methyl phosphate) (2). This cross-links two sub-units of the enzyme by modifying the epsilon-amino groups of the Lys3 and Lys151 on one subunit and the c-amino groups of the Lys68' and Lys134' on the other subunit. Modification with 2 also introduces a maleimide group. Maleimidobenzoyl-N-hydroxy succinimide was used to incorporate a maleimide group into insulin at the alpha-amino group of the Phe1 residue of B chain.
The role of HGF and met in Wilms tumour

The pathobiological mechanism of Wilms tumour invasiveness and metastasis is unknown. Autocrine/paracrine regulation of hepatocyte growth factor (HGF) and its tyrosine kinase receptor met have been shown in many adult cancers to play a key role in tumour invasion and metastasis. HGF/met were studied in a series of homotypic and heterotypic Wilms tumours and showed high levels of expression in both phenotypes with higher levels in metastatic tumours as compared to normal kidney. Investigation of a number of intrinsic target proteins of met, important in cell-cell adhesion such as E-cadherin, beta-catenin, gamma-catenin and ezrin, revealed aberrant expression with significantly lower levels of E-cadherin and gamma-catenin with nuclear localization of beta-catenin in metastatic tumours compared to cytoplasmic localization in primary tumours. These results suggested that aberrant expression of adhesion proteins correlated with acquisition of an invasive and metastatic phenotype in Wilms tumour. The isolation of a novel Wilms tumour cell line, WiT49, from a Wilms tumour lung metastasis allowed us to investigate the role of HGF/met in Wilms tumour cells. WiT49 showed expression of an intact WT1, overexpression of IGF2 and harbored a common p53 missense mutation, 248Arg, previously documented in metastatic Wilms tumours. Importantly, WiT49 expressed high levels of HGF and met, with co-localization of met and beta-catenin at the cell membrane and showed a notable loss of E-cadherin protein, similar to that found in the parent tumour. The MAPK and PKB mediated signaling pathways, associated with growth and motility and activated through HGF binding to met, were expressed in WiT 49. Addition of recombinant HGF to WiT9 cultures induced an increase in met expression, recruitment of adapter protein Gab-1, and release of beta-catenin bound to met. Analysis of matrix metalloproteinases MMP9 and MMP2, indicated constitutive expression in WiT49 supporting the notion of possible beta-catenin mediated transcriptional activation. The studies presented here have identified new players in the pathobiology of Wilms tumour, supporting a role for HGF/met in regulation of the invasive and metastatic phenotype in Wilms tumour.
Content delivery networks: competition, request routing and server placement

The role of competition and monetary benefits in the design of Content Delivery Networks (CDNs) is largely an unexplored area. In this thesis, we investigate the effect of competition among the Web based CDNs and show that little difference in their performance may cause significant financial gain/loss. It turns out that the economy of scale effect is very significant and CDN peering might be a lucrative option. Since performance and conforming to the service level agreement (SLA) with content providers is very important, we then focus on designing CDN from this perspective. We provide an asymptotically optimal static request routing policy under a model where the CDN company guarantees a certain level of user latency to the content providers in the SLA. We also look at the monetary benefit issues for monopolistic enterprise CDN and give a solution for surrogate server allocation and placement problem from that perspective.
Developing a study to evaluate the impact of a goal-oriented, protocol-driven program with home telemonitoring on the blood pressure of type 2 diabetic patients with uncontrolled hypertension

The objective for this study is to compare self-measurement of blood pressure (BP) at home and office BP measurements in hypertensive patients with type (II) diabetes mellitus to determine whether home readings can be used by health care providers to make treatment decisions. Over a period of 2 to 3 weeks, 21 patients attending the hypertension clinic at Mount Sinai Hospital had 3 clinic, 20 or more home and one ambulatory BP measurements. The mean systolic BP at home was 1.2 mm Hg lower than that at the office, although the difference was not significant (F = 1.09, P = 0.35). On the other hand, the mean home diastolic BP was 7 mm Hg higher, and the difference was highly significant (F = 9.6, P = 0.0004). It was concluded that self-measurement of BP at home is feasible and acceptable and provides valuable information that may be used in making treatment decisions.
Modulation of gene expression in osteosarcoma by demethylation

Osteosarcoma (OS) is an aggressive tumor where a significant subset of patients responds poorly to the current treatments. Methylation-silencing of gene expression is a feature of many tumors and is reversible by demethylation drugs, such as decitabine. Demethylation reactivates methylation-silenced genes and leads to induction of differentiation, growth arrest, and apoptosis. Since genes associated with tumor progression and aggressive disease may be repressed by hypermethylation, it follows that decitabine treatment may influence tumor growth, and can be used to identify gene targets for novel epigenetic therapies in OS. In the first part of this thesis, microarray expression profiling was used to identify decitabine-dependent changes in gene expression in U2OS cells. In parallel U2OS xenografts were used to study the effect of decitabine on tumor growth and differentiation. Microarray expression profiling of U2OS cultured cells showed that decitabine treatment caused a significant induction of more than 50 genes. Six of these genes were shown to be involved in apoptosis, and were induced in U2OS xenografts when mice were treated with decitabine. Importantly, drug-treatment of U2OS xenografts significantly reduced tumor size, decreased mitotic activity, increased bone matrix production, and increased the number of apoptotic cells. Promoter regions of these genes were demethylated in response to decitabine treatment and they were re-expressed. In the second part of my thesis I present an analysis of therapeutic modulation of Gadd45a using decitabine. Nuclei from the decitabine-treated U2OS xenografts exhibited increased amounts of Gadd45a proteins. GADD45A was also found demethylated in response to decitabine treatment in the OS cell line MG63. This demethylation was associated with elevated expression of GADD45A and induction of apoptosis. To show the specificity of this gene for decitabine-induced apoptosis in OS, GADD45A mRNAs were disrupted using siRNA and the ability of the drug to induce apoptosis was found to be reduced. Collectively, these data provide novel insights regarding the use of epigenetic modifiers in OS treatment. Understanding the role of demethylation of GADD45A in re-expression of this pathway and restoration of apoptotic control have important implications for understanding OS oncogenesis and for development of new targeted therapeutic approaches involving demethylation drugs.