In recent years, digitalization and computer-based technologies have greatly revolutionized the field of bioinformatics. Advance research and development of computer-based programs have enhanced various DNA sequencing technologies. This advancement has significantly broadened our understanding of genomic evolution and has widely contributed to the application of clinical genomics. Cancer has been one of the major causes of death across the world. Cancer is mainly caused due to the damage or changes in DNA that affect the function of genes which contain a set of instructions that control various functions of cells. This damage in genes that maintain DNA repair mechanism may lead towards genome instability allowing rapid growth of cancer.   Microsatellite instability (MSI) is one such condition characterized due to genomic alteration leading towards the failure of DNA repair mechanism in cancerous cells. MSI is found in various types of cancer but is most often found in colorectal cancer, gastric cancer, and endometrial cancer. Hence, detection of this MSI can greatly contribute towards cancer therapies and enable to plan for the best treatment. This study mainly focuses on evaluating the performance of MSI calling algorithms using targeted sequencing methods.   The literature provides a detailed outline of various topics related to MSI detection. Moreover, different computational methods like MSIsensor, MSIsensor-ct, MSIsensor-pro, MSings, MiMSI, and MSIsensor2 were used in this study for the detection of MSI in selected samples are thoroughly discussed in the methodology section. Finally, the findings of this study conclude that the MSI calling algorithms mentioned above provide accurate detection of MSI in the chosen samples. Also, these algorithms enable us to determine the MSI status of the chosen samples more precisely

Dissertation submitted in partial compliance with the requirements of the Master's Degree in Technology: Homoeopathy, Durban Institute of Technology, 2006. / The aim of the study was to evaluate the efficacy of a Nutritional Supplement (Advanced Brain Food®) and a homoeopathic complex (Quietude®) in the management of Attention Deficit Hyperactivity Disorder (ADHD). ADHD is primarily a childhood disorder affecting ten to twenty percent of school going children. The three main presenting features of ADHD are inattention, impulsivity, and hyperactivity. This triad often results in numerous adjustment difficulties for the child in the social and academic sectors (NIH Consensus Statement, 1998). / M

Made available in DSpace on 2015-03-26T13:39:32Z (GMT). No. of bitstreams: 1 texto completo.pdf: 858033 bytes, checksum: 47ecfa99d4daebf535cd0232206fe4c2 (MD5) Previous issue date: 2009-07-24 / This study aimed to evaluate the effects of homeopathic preparations of Conyza bonariensis in twelve dinamizations of two dilution’s proximate scales, centezimal and decimal. The plant Conyza bonariensis, agronomically considered na invader, mainly of soybean crops, in the south of Brazil. It has resistant biotypes to agrochemicals and it’s allelopathic activity was observed in laboratory experiments. Lettuce seeds of Regina variety, without chemicals, were used in allelopathic tests of germination and growth. The experiment followed a completely randomized design with 4 replicates, distilled water as treatment of control and 7 treatments: 10, 30, 50, 70, 90 and 100% of the aqueous extract of C. bonariensis. The plots were conditioned in BOD in the period of seven days under the conditions prescribed in the Rule Analysis Seeds (RAS). After the trial period, it was found by variance analysis, followed by a regression that high concentrations of aqueous extract of C. bonariensis interfered in germination and seedlings’s growth. The preliminary phytochemical screening of crude compound of C. bonariensis indicated the presence of organic acids and alkaloids. These secondary metabolites may be involved in the allelopathic activity observed in the plant. In order to analyze the presence of the same behavior of the plant, with ultra high dilutions it was obtained to the mother-tincture and the homeopathic preparations of C. bonariensis, according to the Homeopathic Brazilian Pharmacopoeia in the Homeopathy Laboratory of UFV. The experiments studied the effects of homeopathy in the proximate and decimal scales. Lettuce Plants of "Regina" were used as the test-plant, being parts of the plants from seeds treated with the crude extract of C. bonariensis in the pre-germination of 3 hours and part of plants from seeds weren’t treated. Both experiments followed the design in randomized blocks with 28 treatments and 4 replicates. The homeopaths were applied daily, 10 drops/100mL of deionized water in each plot/pot. Data were analyzed through variance analysis and compared averages, using the using the criterion of Scott-Knott, taking up the level of 5% probability. Considering the lettuce plants healthy bodies, it can be inferred that the quantified data characterize the pathogenesis of homeopathic preparations’s dinamizations. Each preparation served according to the principle of similarity. / O presente trabalho teve como objetivo avaliar os efeitos dos preparados homeopáticos de Conyza bonariensis em doze dinamizações nas duas escalas de diluição, centesimal e decimal. A planta Conyza bonariensis, considerada agronomicamente invasora de cultivos principalmente de soja no interior do sul do Brasil, tem biótipos resistentes aos defensivos agrícolas e foi verificada a atividade alelopática em experimentos laboratoriais. Sementes de alface da variedade Regina, sem defensivos, foram utilizadas nos testes alelopáticos de germinação e crescimento. O experimento seguiu o delineamento inteiramente casualizado com 4 repetições, água destilada como tratamento controle e 7 tratamentos: 10, 30, 50, 70, 90 e 100% do extrato aquoso de C. bonariensis. As parcelas foram condicionadas em BOD no período de sete dias, nas condições prescritas na Regra de Análise de Sementes (RAS). Após o período experimental, verificou-se pela análise de variância seguida de regressão que as altas concentrações do extrato aquoso de C. bonariensis interferiram na germinação e no crescimento das plântulas. A triagem fitoquímica preliminar do composto bruto de C. bonariensis indicou a presença de ácidos orgânicos e alcalóides. Esses metabólitos secundários podem estar envolvidos na atividade alelopática verificada na planta. A fim de analisar a presença do mesmo comportamento da planta, com ultradiluições foi obtida a tintura-mãe e os respectivos preparados homeopáticos de C. bonariensis de acordo com a Farmacopéia Brasileira Homeopática no Laboratório de Homeopatia da UFV. Em experimentos foram estudados os efeitos das homeopatias nas escalas centesimal e decimal. Plantas de alface “Regina” foram utilizadas como plantateste, sendo parte das plantas provenientes de sementes tratadas com o extrato bruto de C. bonariensis no período de pré-germinação de 3 horas e parte das plantas provenientes de sementes não tratadas. Os dois experimentos seguiram o delineamento em blocos ao acaso com 28 tratamentos e 4 repetições. As homeopatias foram aplicadas diariamente, 10 gotas/100mL de água deionizada em cada parcela/vaso. Os dados foram analisados por meio de análise de variância e as médias comparadas utilizando o critério de Scott-Knott adotando-se o nível de 5% de probabilidade. Considerando as plantas de alface organismos sadios, pode ser inferido que os dados quantificados caracterizam a patogenesia das dinamizações dos preparados homeopáticos. Cada preparado atuou conforme o princípio da similitude.

Thesis (M.Tech.: Homoeopathy)-Dept. of Homoeopathy, Durban Institute of Technology, 2006 xxv, 261 leaves / The aim of the study was to evaluate the efficacy of a Nutritional Supplement (Advanced Brain Food®) and a homoeopathic complex (Quietude®) in the management of Attention Deficit Hyperactivity Disorder (ADHD). ADHD is primarily a childhood disorder affecting ten to twenty percent of school going children. The three main presenting features of ADHD are inattention, impulsivity, and hyperactivity. This triad often results in numerous adjustment difficulties for the child in the social and academic sectors (NIH Consensus Statement, 1998).

Um sistema de análises em fluxo com multicomutação foi desenvolvido para a mecanização do bioensaio de toxicidade aguda com a bactéria Vibrio fischeri, o qual é baseado na diminuição da luminescência bacteriana causada por espécies tóxicas.Microbombas solenoide foram utilizadas para melhorar as condições de mistura, permitindo também que diluições fossem realizadas em linha com a alteração do volume de amostra e a sobreposição parcial entre a zona da amostra e a suspensão bacteriana. Uma cela de fluxo em espiral, posicionada na janela de emissão de um espectrofluorímetro, foi empregada para as medidas de luminescência e um banho de água construído em laboratório, baseado no efeito Peltier, foi utilizado para manter a temperatura do bioensaio em (13,0±0,1) °C. Um pequeno volume da suspensão bacteriana (120 ?L) foi selecionado visando minimizar o consumo e, consequentemente, os custos do ensaio. O tempo de contato entre a suspensão bacteriana e a amostra foi reduzido para 5 min para aumentar a frequência de amostragem e evitar a atenuação da luminescência devido ao tempo de vida curto das bactérias. Os valores de CE50 para os controles positivos foram estimados em 2,5 ± 0,7, 2,0 ± 0,5 e 10 ± 4 mg L-1 para o Zn(II), Cu(II), e Cr(VI), respectivamente, sendo concordantes com os valores da literatura. Os valores de CE50 para alguns poluentes emergentes (parabenos, cafeína, acetaminofeno, diclofenaco e ácido salicílico) concordaram com os obtidos utilizando o kit comercial BioTox(TM), realizado em micro placa, a nível de confiança de 95 %. Os coeficientes de variação foram estimados em 2,4 e 2 % (n = 10), na ausência e na presença de 0,6 mg L-1 de Zn(II), respectivamente. O sistema de análises em fluxo proposto é, então, uma alternativa simples, rápida, robusta e precisa para a determinação da toxicidade aguda utilizando pequenos volumes de amostra e suspensão bacteriana. Além disso, o sistema apresenta vantagens em comparação com os bioensaios em batelada e em fluxo, tais como ajuste de salinidade e diluições das amostras em linha e a determinação da cinética de toxicidade das espécies químicas / A multicommuted flow system was developed for automation of the acute toxicity bioassay using Vibrio fischeri bacteria, which exploits the decrease of the bacterial luminescence caused by toxic species. Solenoid micro-pumps were employed to improve mixing conditions and to perform on-line dilutions of the tested compounds by changing the sample volume and exploiting the partial overlap between sample zone and the bacterial suspension. A spiral flow cell, placed at the emission window of a spectrofluorimeter, was employed for signal measurement and a lab-made water bath based on the Peltier effect was used for maintain the temperature of the bioassay at (13.0±0.1) oC. A low volume of the bacterial suspension (120 ?L) was selected in order to minimize its consumption and, consequently, the costs of the assay. The contact time between bacterial suspension and sample was reduced to 5 min to increase the sampling rate and to avoid luminescence fading due to the bacteria short lifetime. EC50 values for positive controls were estimated as 2.5 ± 0.7, 2.0 ± 0.5 and 10 ± 4 for Zn(II), Cu(II), and Cr(VI), respectively, being in agreement with literature values. The EC50 values for some emerging pollutants (parabens, caffeine, acetaminophen, diclofenac and salicylic acid) agreed with those obtained from commercial BioTox(TM) kit performed in micro plate at the 95% confidence level. The coefficients of variation were estimated as 2.4 and 2 % (n=10), in the absence and presence of 0.6 mg L-1 Zn(II), respectively. The proposed flow system is then a simple, fast, robust and accurate alternative for acute toxicity determination, using low sample and bacterial suspension volumes. Furthermore, the system presents advantages in comparison to batch and previous flow-based bioassays, such as the achievement of in-line salinity adjustment and sample dilutions, and the determination of toxicity kinetic for every assayed chemical species

Um sistema de análises em fluxo com multicomutação foi desenvolvido para a mecanização do bioensaio de toxicidade aguda com a bactéria Vibrio fischeri, o qual é baseado na diminuição da luminescência bacteriana causada por espécies tóxicas.Microbombas solenoide foram utilizadas para melhorar as condições de mistura, permitindo também que diluições fossem realizadas em linha com a alteração do volume de amostra e a sobreposição parcial entre a zona da amostra e a suspensão bacteriana. Uma cela de fluxo em espiral, posicionada na janela de emissão de um espectrofluorímetro, foi empregada para as medidas de luminescência e um banho de água construído em laboratório, baseado no efeito Peltier, foi utilizado para manter a temperatura do bioensaio em (13,0±0,1) °C. Um pequeno volume da suspensão bacteriana (120 ?L) foi selecionado visando minimizar o consumo e, consequentemente, os custos do ensaio. O tempo de contato entre a suspensão bacteriana e a amostra foi reduzido para 5 min para aumentar a frequência de amostragem e evitar a atenuação da luminescência devido ao tempo de vida curto das bactérias. Os valores de CE50 para os controles positivos foram estimados em 2,5 ± 0,7, 2,0 ± 0,5 e 10 ± 4 mg L-1 para o Zn(II), Cu(II), e Cr(VI), respectivamente, sendo concordantes com os valores da literatura. Os valores de CE50 para alguns poluentes emergentes (parabenos, cafeína, acetaminofeno, diclofenaco e ácido salicílico) concordaram com os obtidos utilizando o kit comercial BioTox(TM), realizado em micro placa, a nível de confiança de 95 %. Os coeficientes de variação foram estimados em 2,4 e 2 % (n = 10), na ausência e na presença de 0,6 mg L-1 de Zn(II), respectivamente. O sistema de análises em fluxo proposto é, então, uma alternativa simples, rápida, robusta e precisa para a determinação da toxicidade aguda utilizando pequenos volumes de amostra e suspensão bacteriana. Além disso, o sistema apresenta vantagens em comparação com os bioensaios em batelada e em fluxo, tais como ajuste de salinidade e diluições das amostras em linha e a determinação da cinética de toxicidade das espécies químicas / A multicommuted flow system was developed for automation of the acute toxicity bioassay using Vibrio fischeri bacteria, which exploits the decrease of the bacterial luminescence caused by toxic species. Solenoid micro-pumps were employed to improve mixing conditions and to perform on-line dilutions of the tested compounds by changing the sample volume and exploiting the partial overlap between sample zone and the bacterial suspension. A spiral flow cell, placed at the emission window of a spectrofluorimeter, was employed for signal measurement and a lab-made water bath based on the Peltier effect was used for maintain the temperature of the bioassay at (13.0±0.1) oC. A low volume of the bacterial suspension (120 ?L) was selected in order to minimize its consumption and, consequently, the costs of the assay. The contact time between bacterial suspension and sample was reduced to 5 min to increase the sampling rate and to avoid luminescence fading due to the bacteria short lifetime. EC50 values for positive controls were estimated as 2.5 ± 0.7, 2.0 ± 0.5 and 10 ± 4 for Zn(II), Cu(II), and Cr(VI), respectively, being in agreement with literature values. The EC50 values for some emerging pollutants (parabens, caffeine, acetaminophen, diclofenac and salicylic acid) agreed with those obtained from commercial BioTox(TM) kit performed in micro plate at the 95% confidence level. The coefficients of variation were estimated as 2.4 and 2 % (n=10), in the absence and presence of 0.6 mg L-1 Zn(II), respectively. The proposed flow system is then a simple, fast, robust and accurate alternative for acute toxicity determination, using low sample and bacterial suspension volumes. Furthermore, the system presents advantages in comparison to batch and previous flow-based bioassays, such as the achievement of in-line salinity adjustment and sample dilutions, and the determination of toxicity kinetic for every assayed chemical species