Infusões prolongadas de 5-fluorouracil são mais seguras e potencialmente mais efetivas no tratamento do câncer de cólon metastático do que infusões rápidas da mesma medicação. No entanto, infusões prolongadas requerem a disponibilidade de um acesso venoso central, bem como de bombas de infusão dispendiosas. O desenvolvimento de fluoropirimidinas orais permitiu que pacientes fossem expostos ao 5-fluorouracil por longo tempo, com maior conveniência. UFT e leucovorin administrados três vezes ao dia demonstraram previamente uma eficácia equivalente, com menor toxicidade, quando comparados a um regime convencional de infusão rápida de 5- fluorouracil e leucovorin. Este estudo com 98 pacientes foi desenhado e conduzido com objetivo de demonstrar equivalência no tempo de progressão com o uso de UFT e leucovorin administrados duas vezes ao dia, com o uso da mesma combinação administrada três vezes ao dia. Objetivos secundários incluíram análise de toxicidade, resposta objetiva e sobrevida global. O tempo mediano de progressão foi de 3,8 meses, comparado com 3,5 meses observados com o uso da medicação três vezes ao dia e a taxa de resposta foi de 11%, com uma sobrevida mediana de 12,8 meses, sendo comparável aos resultados de 12% e 12,4 meses obtidas com o uso da combinação três vezes ao dia. A incidência de diarréia com graus 3 e 4 foi de 30% no regime de administração duas vezes ao dia, e 21% no de três vezes ao dia. Esses resultados sugerem que o uso de UFT e leucovorin duas vezes ao dia tem eficácia e toxicidade similares àquelas obtidas com o uso da mesma medicação três vezes ao dia. / Prolonged infusions have been shown to be safer and potentially more effective than bolus regimens of 5- fluorouracil as treatment for advanced colorectal cancer. However, infusional 5- fluorouracil requires central venous access and costly infusion pumps. Development of oral fluoropyrimidines has allowed longer exposures to 5-fluorouracil with increased convenience. UFT and leucovorin given thrice daily showed improved safety and no significant difference in survival or response rate compared with bolus 5- fluorouracil and leucovorin. This study with 98 patients was conducted to evaluate whether UFT and leucovorin given twice daily provided comparable time to progression (TTP) to the same combination administered three times a day. Secondary objectives included evaluation of toxicity, overall tumor response rate, and survival. Median time to progression was 3.8 months, compared with 3.5 months observed with the thrice-daily regimen. The twice-daily regimen had a response rate of 11% and median survival of 12.8 months, comparable to the 12% and 12.4 months seen with the thrice-daily regimen. The incidence of grade 3-4 drug-related diarrhea was 30% on the twice-daily and 21% on the thrice-daily schedule. Results suggest that the twice-daily schedule has similar safety and efficacy to the thrice-daily schedule.

Infusões prolongadas de 5-fluorouracil são mais seguras e potencialmente mais efetivas no tratamento do câncer de cólon metastático do que infusões rápidas da mesma medicação. No entanto, infusões prolongadas requerem a disponibilidade de um acesso venoso central, bem como de bombas de infusão dispendiosas. O desenvolvimento de fluoropirimidinas orais permitiu que pacientes fossem expostos ao 5-fluorouracil por longo tempo, com maior conveniência. UFT e leucovorin administrados três vezes ao dia demonstraram previamente uma eficácia equivalente, com menor toxicidade, quando comparados a um regime convencional de infusão rápida de 5- fluorouracil e leucovorin. Este estudo com 98 pacientes foi desenhado e conduzido com objetivo de demonstrar equivalência no tempo de progressão com o uso de UFT e leucovorin administrados duas vezes ao dia, com o uso da mesma combinação administrada três vezes ao dia. Objetivos secundários incluíram análise de toxicidade, resposta objetiva e sobrevida global. O tempo mediano de progressão foi de 3,8 meses, comparado com 3,5 meses observados com o uso da medicação três vezes ao dia e a taxa de resposta foi de 11%, com uma sobrevida mediana de 12,8 meses, sendo comparável aos resultados de 12% e 12,4 meses obtidas com o uso da combinação três vezes ao dia. A incidência de diarréia com graus 3 e 4 foi de 30% no regime de administração duas vezes ao dia, e 21% no de três vezes ao dia. Esses resultados sugerem que o uso de UFT e leucovorin duas vezes ao dia tem eficácia e toxicidade similares àquelas obtidas com o uso da mesma medicação três vezes ao dia. / Prolonged infusions have been shown to be safer and potentially more effective than bolus regimens of 5- fluorouracil as treatment for advanced colorectal cancer. However, infusional 5- fluorouracil requires central venous access and costly infusion pumps. Development of oral fluoropyrimidines has allowed longer exposures to 5-fluorouracil with increased convenience. UFT and leucovorin given thrice daily showed improved safety and no significant difference in survival or response rate compared with bolus 5- fluorouracil and leucovorin. This study with 98 patients was conducted to evaluate whether UFT and leucovorin given twice daily provided comparable time to progression (TTP) to the same combination administered three times a day. Secondary objectives included evaluation of toxicity, overall tumor response rate, and survival. Median time to progression was 3.8 months, compared with 3.5 months observed with the thrice-daily regimen. The twice-daily regimen had a response rate of 11% and median survival of 12.8 months, comparable to the 12% and 12.4 months seen with the thrice-daily regimen. The incidence of grade 3-4 drug-related diarrhea was 30% on the twice-daily and 21% on the thrice-daily schedule. Results suggest that the twice-daily schedule has similar safety and efficacy to the thrice-daily schedule.

Malgré leur importance dans le déterminisme du sexe chez de nombreux organismes, les chromosomes sexuels ont été étudiés chez quelques espèces seulement du fait du manque de séquences disponibles. En effet, le séquençage et l'assemblage des chromosomes sexuels est rendu très difficile par leurs abondantes séquences répétées. Durant cette thèse, une méthode probabiliste a été développée pour inférer les gènes liés au sexe à partir de données RNA-seq chez une famille. Des tests de cette méthode appelée SEX-DETector sur des données réelles et simulées suggèrent qu'elle fonctionnera sur une grande variété de systèmes. La méthode a inféré ∼1300 gènes liés au sexe chez Silene latifolia, une plante dioïque qui possède des chromosomes sexuels XY pour lesquels quelques données de séquence sont disponibles (dont certaines obtenues lors de cette thèse par séquençage de BACs). Les gènes du Y sont moins exprimés que ceux du X chez S. latifolia, mais le statut de la compensation de dosage (un mécanisme qui corrige la sous-expression des gènes liés au sexe chez les males) est encore controversé. L'analyse des nouveaux gènes liés au sexe inférés par SEX-DETector a permis de confirmer la compensation de dosage chez S. latifolia, qui est effectuée par la surexpression du X maternel, possiblement via un mécanisme epigénétique d'empreinte. Les données ont également été utilisées pour étudier l'évolution de l'expression biaisée pour le sexe chez S. latifolia et ont révélé que la majorité des changements de niveaux d'expression ont eu lieu chez les femelles. Les implications de nos résultats concernant l'évolution de la dioécie et des chromosomes sexuels sont discutés / In many organisms, sexes are determined by sex chromosomes. However, studies have been greatly limited by the paucity of sex chromosome sequences. Indeed, sequencing and assembling sex chromosomes are very challenging due to the large quantity of repetitive DNA that these chromosomes comprise. In this PhD, a probabilistic method was developed to infer sex-linked genes from RNA-seq data of a family (parents and progeny of each sex). The method, called SEX-DETector, was tested on simulated and real data and should performwell on a wide variety of sex chomosome systems. This new method was applied to Silene latifolia, a dioecious plant with XY system, for which partial sequence data on sex chromosomes are available (some of which obtained during this PhD by BAC sequencing), SEX-DETector returned ∼1300 sex-linked genes. In S. latifolia, Y genes are less expressed than their X counterparts. Dosage compensation (a mechanism that corrects for reduced dosage due to Y degeneration in males) was previously tested in S. latifolia, but different studies returned conflicting results. The analysis of the new set of sex-linked genes confirmed the existence of dosage compensation in S. latifolia, which seems to be achieved by the hyperexpression of the maternal X chromosome in males. An imprinting mechanism might underlie dosage compensation in that species. The RNAseq datawere also used to study the evolution of differential expression among sexes in S. latifolia, and revealed that in this species most changes have affected the female sex. The implications of our results for the evolution of dioecy and sex chromosomes in plants are discussed

Over the last decade, development and application of a set of molecular genomic approaches based on the chromosome conformation capture method (3C), combined with increasingly powerful imaging approaches have enabled high resolution and genome-wide analysis of the spatial organization of chromosomes. The aim of this thesis is two-fold; 1), to provide guidelines for analyzing and interpreting data obtained from genome-wide 3C methods such as Hi-C and 3C-seq and 2), to leverage the 3C technology to solve genome function, structure, assembly, development and dosage problems across a broad range of organisms and disease models. First, through the introduction of cWorld, a toolkit for manipulating genome structure data, I accelerate the pace at which *C experiments can be performed, analyzed and biological insights inferred. Next I discuss a set of practical guidelines one should consider while planning an experiment to study the structure of the genome, a simple workflow for data processing unique to *C data and a set of considerations one should be aware of while attempting to gain insights from the data. Next, I apply these guidelines and leverage the cWorld toolkit in the context of two dosage compensation systems. The first is a worm condensin mutant which shows a reduction in dosage compensation in the hermaphrodite X chromosomes. The second is an allele-specific study consisting of genome wide Hi-C, RNA-Seq and ATAC-Seq which can measure the state of the active (Xa) and inactive (Xi) X chromosome. Finally I turn to studying specific gene – enhancer looping interactions across a panel of ENCODE cell-lines. These studies, when taken together, further our understanding of how genome structure relates to genome function.

Indiana University-Purdue University Indianapolis (IUPUI) / Introduction: Regenerative endodontic therapy in immature teeth promotes continuation of root development and likely increases the prognosis of these teeth. The use of double antibiotic paste (DAP), equal parts of ciprofloxacin and metronidazole, followed by the dentin conditioner, ethylenediaminetetraacetic acid (EDTA), has been suggested for canal disinfection and facilitation of stem cell attachment/proliferation, respectively. However, the effect is unknown when all these agents are used on on radicular dentin surfaces to facilitate the level of stem cell proliferation. Objectives: The aim of this in-vitro study is to compare the proliferation of human dental pulp stem cells (hDPSCs) on human radicular dentin treated with two different concentrations of DAP followed by EDTA. Materials and Methods: Human premolars and incisors were prepared into standardized polished 4 mm x4 mm radicular dentin specimens. Groups of specimens were treated with DAP 500 mg/mL, DAP 1 mg/mL, DAP 500 mg/mL followed by 17-percent EDTA, DAP 1 mg/mL followed by 17-percent EDTA; 17% EDTA, or no treatment. All groups treated with antibiotics were incubated with DAP at 37°C for one week. All specimens were washed with distilled water. The hDPSCs were seeded across all specimens and unattached cells were collected after 24 hours. LDH assay was completed on unattached cells for quantification. Three days after attachment, WST viability and LDH cytotoxicity assays were performed. Hypothesis: There is no significant difference in hDPSC viability, unattachment, and cytotoxicity on dentin specimens treated with DAP and 17-percent EDTA. Clinical Significance: These results can be used to help identify the best treatment concentrations when using DAP and/or EDTA to promote endodontic regeneration. Results: The results demonstrated significantly less viability of hDPSCs on specimens treated with 500 mg/mL DAP with and without 17-percent EDTA. Groups treated with 1 mg/mL DAP, 1 mg/mL DAP and 17-percent EDTA, and 17-percent EDTA alone had no statistically significant difference in viability compared with control untreated dentin. The results of the unattached cells from the LDH demonstrated that cells from the specimens treated with solely 500 mg/mL and 1 mg/mL DAP had significantly higher levels of unattached cells when compared with all other groups. The LDH assays in summation with the WST assays showed a trend of a lack of proliferation on groups treated with 500 mg/mL DAP with and without 17-percent EDTA. Conclusions: Paste-like concentrations (500 mg/mL) of DAP are detrimental to hDPSC viability, whereas the present study supports the use of low-concentration antibiotics consistent with current recommendations for intracanal medicaments used during endodontic regenerative procedures.

Indiana University-Purdue University Indianapolis (IUPUI) / The purpose of this study was to investigate the antibacterial efficacy of 0.12-percent and 2.0-percent chlorhexidine gluconate (CHX) on eliminating Enterococcus faecalis from dentinal tubules, and whether this antibacterial effect was enhanced by heat. To date there have been no published articles that describe the heating of 2.0-percent CHX and its antimicrobial efficacy and clinical relevance towards E. faecalis within dentinal tubules in root canal systems. Ninety-five human extracted, single rooted, maxillary, anterior teeth were used to prepare dentin disk specimens. After proper sterilization, a 2.5-mm ISO-sized diameter lumen was prepared, and then the canals were filled with brain-heart infusion (BHI) broth infected with E. faecalis. The BHI was removed and the specimens in equally divided groups were rinsed with sterile saline and filled with saline, or 0.12 percent CHX or 2.0 percent CHX at ambient temperature (24°C) or experimental temperature (46°C) and incubated at oral temperature (37°C) or the experimental temperature (46°C), respectively. The specimens were frozen to -70˚C and pulverized in liquid nitrogen. Serial dilutions were prepared of 1:100 and 1:1000 and spiral plated on BHI agar plates in duplicate. They were incubated, and the number of bacterial colonies was recorded 24 hours later for data analysis. A two-way analysis of variance (ANOVA), with factors for solution, solution temperature, and the solution-by-temperature interaction was used to determine antibacterial efficacy. Pair-wise comparisons between groups were examined for significance using the Fisher’s Protected Least Significant Differences Method. The E. faecalis CFU were log-transformed to satisfy the assumptions required for the ANOVA. The results of this investigation demonstrated no statistically significant difference with the addition of heat to either test irrigation solution regarding the elimination of E. faecalis from dentinal tubules within the root canal system. There was a statistically significant difference in the antibacterial efficacy of CHX against E. faecalis in comparison with the concentration tested. A higher concentration of 2.0-percent CHX demonstrated a significantly higher antibacterial efficacy against E. faecalis compared with 0.12-percent CHX, and likewise with the saline control. It can be concluded that the use of a higher concentration of 2.0-percent CHX is advantageous as a final irrigation solution after copious amounts of NaOCl and EDTA have been utilized for effective antimicrobial efficacy and substantivity.

The efficacy and safety of oral nadolol in supraventricular tachycardia were evaluated prospectively in 27 children (median age 5.5 years). Fifteen patients had an unsuccessful trial of digoxin therapy. Intravenous nadolol was given to seven patients during electrophysiologic study; five of these had an excellent response and two had a partial response (25% decrease in tachycardia rate). Six of these patients had a similar response to oral nadolol. Twelve patients received both propranolol and nadolol. Among six patients, intravenous propranolol was successful in four and unsuccessful in two; all six had a similar response to oral nadolol. With oral propranolol, tachycardia was well controlled in four patients and persistent in two; five of five patients had a similar response to oral nadolol. Twenty-six patients were treated with oral nadolol; the arrhythmia was well controlled in 23, 2 had recurrent tachycardia and 1 patient had tachycardia at a 25% slower rate. The effective dose of nadolol ranged between 0.5 and 2.5 mg/kg body weight once daily (median dose 1 mg/kg per day). During follow-up (3 to 36 months), compliance and tolerance were excellent; excluding 2 patients with reactive airway disease who developed wheezing, only 3 (12%) of 24 had side effects necessitating a change in drug therapy. Once a day nadolol is a safe and effective agent in the management of supraventricular tachycardia in children. Its long-term efficacy can be predicted by the short-term response to intravenous nadolol or propranolol during programmed electrophysiologic study.

BACKGROUND AND PURPOSE: Pharmacokinetic assessment of drug tissue permeation following iontophoresis is limited. The depth of ketoprofen tissue permeation following cathodic iontophoresis (4 mA, 40 minutes) and the stereoselectivity of drug delivery were examined in this study. SUBJECTS: Ketoprofen (750 mg) was iontophoresed onto one porcine medial thigh, with passive drug permeation conducted on the other thigh. METHODS: Skin, subcutaneous fascia, and muscle biopsies from the drug delivery sites were harvested and stored separately, and the "R" and "S" ketoprofen enantiomers were determined. Results. Iontophoretic and passive applications yielded equivalent total ketoprofen concentrations in the skin and fascia. In contrast, multivariate analysis demonstrated that the ketoprofen concentration in the first centimeter of muscle following iontophoresis was greater than the drug concentration in the deeper underlying muscle layers and greater than that delivered to any muscle layer following passive delivery. No transcutaneous stereoselective delivery) of ketoprofen was detected. CONCLUSION AND DISCUSSION: Compared with passive delivery, iontophoresis enhances nonstereoselective ketoprofen permeation into the fascia-muscle interface. With delivery to deeper tissue sites, however, there is no apparent enhancement over passive application.

Bien que la majeure partie du génome humain soit présente en deux copies (une copie héritée de chaque parent), certains segments peuvent être délétés (une copie) ou dupliqués (trois copies). La recherche a montré que plusieurs variations du nombre de copies (CNVs) augmentent le risque de troubles neurodéveloppementaux (e.g. autisme, TDAH, schizophrénie). Or, on connait peu les effets des CNVs sur le développement et le fonctionnement cérébral. L’électroencéphalographie (EEG) au repos s’avère être une méthode adaptée pour étudier les perturbations de l’activité neuronale chez les porteurs de CNVs. L’objectif de ce projet était de déterminer s’il existe des signatures EEG à l’état de repos qui sont caractéristiques des enfants porteurs de CNVs pathogéniques. L’activité cérébrale au repos de 109 porteurs de CNVs (66 délétions, 43 duplications) âgés de 3 à 17 ans a été enregistrée en EEG durant 4 minutes. Pour mieux prendre en compte les variations développementales, les indices EEG (puissance spectrale et connectivité fonctionnelle) ont été corrigés avec un modèle normatif estimé à partir de 256 contrôles du Heatlhy Brain Network. Les résultats ont montré une puissance bêta et gamma accrue dans les régions postérieures ainsi qu’une sous-connectivité globale à des échelles temporelles distinctes chez les porteurs de CNVs. Les porteurs d’une délétion et d’une duplication pouvaient être différenciés par leur connectivité dans les fréquences bas-alpha: la connectivité des porteurs d’une duplication était plus perturbée que celle des porteurs d’une délétion. Les perturbations distinctives en connectivité se sont avérées plus proéminentes à l’adolescence. Les résultats suggèrent que les porteurs de CNVs présentent des altérations électrophysiologiques par rapport aux témoins neurotypiques, indépendamment de la région génomique affectée. / Although most of the human genome is present in two copies (one copy inherited from each parent), some segments can be deleted (one copy) or duplicated (three copies). Research has shown that many copy number variations (CNVs) increase the risk of neurodevelopmental disorders (e.g. autism, ADHD, schizophrenia). However, little is known about the effects of CNVs on brain development and function. Resting-state electroencephalography (EEG) is a suitable method to study the disturbances of neuronal functioning in CNVs. We aimed to determine whether there are resting-state EEG signatures that are characteristic of children with pathogenic CNVs. Resting-state brain activity of 109 CNVs carriers (66 deletions, 43 duplications) aged 3 to 17 years was recorded in EEG for 4 minutes. To better account for developmental variations, EEG indices (power spectral density and functional connectivity) were corrected with a normative model estimated from 256 Heatlhy Brain Network controls. Results showed increased beta and gamma power in posterior regions as well as a global under-connectivity at distinct frequency bands in CNVs carriers. Deletion and duplication carriers can be differentiated by their connectivity in low alpha frequencies: the connectivity of the duplication carriers was more disrupted than that of the deletion carriers. The distinctive connectivity perturbations were found to be most prominent during adolescence. The results suggest that CNVs carriers show electrophysiological alterations compared to neurotypical controls, regardless of the gene dosage effect and of their affected genomic region. Moreover, a specific signature of the molecular alterations associated with deletions was found.

Thesis (M. Tech. (Diagnostic Radiography)) Central University of Technology, Free State, 2014 / Over the past two decades, interventional radiology has been a fast developing field with great advances in technology in the diagnosing and treatment of patients. Interventional radiology procedures are minimally invasive and require little to no hospitalisation time. These procedures are fluoroscopically guided and serial runs are used for documentation, so they have the potential to deliver high doses to patients. Reports about deterministic skin reactions resulting from interventional radiology have become more and more prevalent from the early 1990s. Worldwide concern thus led to legislation for the limitation, justification and optimisation of these doses. Setting of diagnostic reference levels (DRLs) for these procedures is difficult, as they can be complex in nature and are often clinically open-ended. In the case where DRLs were used, they needed to be for a specific locality and had to be refined for the specific circumstances. Patients must be informed of the doses they will be receiving during diagnostic or interventional procedures before consent can be obtained from them. Little information on dose audits was available for South Africa at the time of the study, and it was decided to determine dose ranges at a local level. The research question of this study was: “What radiation doses do patients receive when undergoing vascular, diagnostic and interventional procedures in the interventional suites at a tertiary training hospital in the Free State?” The primary objective was to determine the doses and dose ranges to patients. A secondary objective was to identify specific high dose procedures to individual patients and to the population. A third objective was to investigate the factors influencing these doses. The data of patients who received procedures in two fluoroscopic rooms at the research site were documented over a three-year period. The dose area product (DAP) values were used to calculate skin dose. With the information gathered, dose ranges for frequently performed procedures were determined and specific high dose procedures to individuals and the population identified. Factors influencing the dose were also investigated. This included the relationship of the level of technology, a VI patient’s BMI and practitioners’ level of experience on dose as the research site was a training facility. The results indicated that both diagnostic and interventional procedures have the potential to deliver high doses, as was evident with the isolated occurrences where the response threshold for deterministic effects was exceeded. Most of the locally performed procedures delivered lower or on par radiation dose, compared to values in the literature. Increased BMI values of patients can negatively influence doses received. The level of a practitioner’s experience also plays a vital role in the dose that the patient will receive. Specific recommendations and the implementing of a dose optimisation protocol are proposed to reduce and optimise doses at the research site. This dose optimisation programme will create greater awareness about radiation dose and effects, follow-up procedures and dose reduction methods amongst role-payers. Key words: interventional radiology; limitation, justification and optimisation of radiation dose; deterministic effects; radiation dose awareness