D. Tech. Biomedical Sciences. / Discusses despite significant advances in andrological techniques, the execution of semen analysis is currently not performed in a sequential manner. As such, it is important that reproductive biology laboratories establish an optimal diagnostic scheme that will assist reproductive health workers to direct patients to a specific therapeutic intervention and procedure.

Thesis (MTech (Biomedical Technology))--Cape Peninsula University of Technology, 2009. / Bibliography: leaves 73-78. Also available online.

Thesis (MTech (Biomedical Technology))--Cape Peninsula University of Technology, 2009. / The role of the mycobacteriology laboratory in the diagnosis of childhood tuberculosis has become increasingly important in the human-immunodeficiency virus era. Due to the paucibacillary nature of childhood mycobacterial disease, laboratory optimisation of mycobacterial cultivation is necessary for paediatric clinical management and epidemiological surveillance. Previous studies have shown that growth supplements markedly improve the recovery rate and time-to-detection in mycobacterial cultures. In this study, we hypothesised that specialised culture media and meat-based growth supplements would improve the recovery rate and time-to-detection in clinical samples from paediatric patients. Pulmonary sputa and gastric aspirates and extra pulmonary fine needle aspiration biopsies were processed from children less than 15 years of age routinely investigated for mycobacterial disease. The processed clinical samples were split into a control aliquot that was cultured in liquid and solid media without growth supplement, and an intervention aliquot cultured on supplemented media. The effect of enrichment of the culture media was then calculated by comparison to the control. These results indicated a significant reduction in the time-to-detection, 18.5 to 12.4 days, and an improved primary recovery rate of 14% in paediatric samples when cultured in liquid media enriched with a nutrient meat broth growth supplement. The findings of this study confirm the value of optimising mycobacterial cultivation with the use of growth supplements to enhance the detection of childhood mycobacterial disease.

Doctorat en kinésithérapie et réadaptation / info:eu-repo/semantics/nonPublished

Thesis (M. Sc. (Medical Sciences)) -- University of Limpopo, 2021 / Background: This study was designed to determine the relationship of immunohistochemical subtypes of breast cancer and clinicopathological features and demographic information in Limpopo since there has been no data published on the association of immunohistochemical subtypes, clinicopathological features and demographic characteristics in recent years. Methods: Data was obtained from records of patients diagnosed with breast cancer between 2015 and 2020. Chi-Square and ANOVA tests were performed, and results considered significant at p ≤ 0.05. Results: The mean age was 50.32 ± 11.40, estrogen receptor positive(ER+), progesterone receptor positive(PR+) and human epidermal growth receptor 2 positive(HER2+) prevalence were 73.5%, 62.3% and 26.5% respectively. More than half of the patients (54.3%) had a Ki-67 level >15%. Grade II tumors were the predominant type of tumors in this study (51.7%). 43.7% of the cases showed lymph node involvement. Luminal B subtype was the most predominant immunohistochemical subtype in the study (46.4%), followed by Luminal A (24.5 %), TNBC (19.9%) and HER2- enriched (6.6%). 2.6 % of the cases were classified as undetermined. Conclusion: A significant association was observed between immunohistochemical subtypes and tumor grade

The genus Enterococcus comprises of a group of commensal organisms of the human gut which has been associated with cases of endocarditis and urinary tract infections. In the present study, 12 Enterococcus isolates were obtained from clinical specimens and characterized using genotyping techniques that have become an integral part of clinical research. There were three different genotyping methods used to identify the enterococci to species level and to determine the level of genetic diversity among the selected strains. These techniques were, randomly amplified polymorphic DNA-PCR (RAPD-PCR), 16S rDNA ribotyping analysis and pulse field gel electrophoresis (PFGE) respectively. The minimum inhibitory concentration (MIC) to penicillin and vancomycin were also determined using a disc diffusion assay and a microtitre plate dilution assay. All twelve strains were found to be vancomycin resistant enterococci (VRE) at a MIC value greater than 100μg/ml. Penicillin growth inhibition based on MIC values were categorized into three groups, susceptible (< 0.25 μg/ml), intermediate (≤ 3μg/ml) and resistant (≥ 4μg/ml) respectively. RAPD-PCR was performed using four random primers. Primers yielding the highest discriminative power were used for phylogenetic analysis. The phylogenetic analysis indicated that all 12 strains yielded clonal dissemination, therefore a low genetic diversity between them. The 16S rDNA of all strains were used to identify the enterococci at species level. The rDNA were sequenced and analysed using the NCBI BLAST algorithm and found to belong to three species of Enterococcus. These were E.faecalis, E.faecium and E.durans. PFGE analysis was performed by restriction of all 12 strain’s genomic DNA with the restriction enzyme SmaI. The PFGE patterns were divided into two groups with low genetic diversity. Compared with the RAPD PCR patterns PFGE gives a higher discriminatory power as a higher dissimilarity between the strains was observed. Similar penicillin MICs for each of the strains in the three categories are grouped together in the phylogenetic trees for both PFGE and RAPD-PCR. RAPDPCR is a sensitive, faster, specific and cost effective technique, PFGE analysis has given a higher discriminatory power, higher reproducibility of the results and the polymorphism seen in the patterns suggest that PFGE has a potential of being an essential tool in clinical diagnostics. / Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2007.

Capes / A respectiva pesquisa encontra-se no contexto de um ciclo produtivo de um laboratório de análises clínicas da área genômica. Esse trabalho propôs um método de redução de dimensionalidade que auxilia o diagnóstico para a medicina laboratorial genômica. O novo método de redução de dimensão de dados é chamado de DRM-F e é capaz de identificar em bases deste domínio os atributos (gene) mais relevantes, por meio de conceitos de equivalência e generalização. Foi efetuada a comparação do Método DRM-F com o Método de Seleção de Atributos. Essa comparação objetivou a avaliação do método proposto com o método já existente na mineração de dados, Seleção de Atributos. O Método DRM-F fundamentado em Framework usou conceitos de equivalência e generalização. Esses dois métodos foram aplicados no domínio de expressão de genes usando três bases, denominadas DLBCL, DLBCL Tumor sobre leucemia e ALL/AML contendo dados do linfoma. Analisando os resultados obtidos, utilizando como critérios de avaliação a Validação Cruzada, verificou-se que o uso dos métodos resultou em uma melhora nos valores de taxa de acerto quando comparados com as bases, possuindo todos os atributos no domínio de expressão gênica. Nesse domínio, o melhor método de redução foi com o uso da Abordagem Wrapper nas três bases. Não obstante, ressalta-se que o método proposto apresentou um resultado superior a 80% de taxa de acerto, não podendo ser considerado um método de redução com desempenho ruim. O Método DRM-F, embora tenha apresentado resultados inferiores ao método de Seleção de Atributos, na média geral não apresentou taxa de acerto inferior a 80% na geração de modelos preditivos. O Método DRM-F busca extrair os atributos (gene) comuns e específicos do domínio de estudo, expressão gênica, porém não somente de uma única base, mas, entre todas as bases que pertencem ao domínio. Assim, podem-se obter os atributos (gene) comuns entre as várias doenças analisadas entre as bases. No presente experimento, foi possível extrair os atributos (gene) comuns e específicos entre as doenças analisadas. Com os atributos (gene) comuns e específicos de cada doença, podem-se submeter esses subconjuntos a uma análise biológica, a fim de verificar o significado biológico dos atributos objetivando uma contribuição na área biomédica e direcionamento de diagnósticos. / The following research is in the context of a production cycle of a clinical laboratory in the genomic area. This work proposed a dimensionality reduction method that helps the diagnosis for the genomic laboratory medicine. The new method of data size reduction is called DRM-F and it is able to identify on bases of this domain the most relevant (gene) attributes, by means of equivalence and generalization concepts. The DRM-F Method was compared to the Attributes Selection Method. This comparison aimed to assess the proposed method with the existing method for data mining, Attributes Selection. In the DRM-F Method based on Framework used equivalence and generalization concepts. These two methods have been applied in the domain of gene expression using three bases, named DLBCL, DLBCL tumor regarding leukemia and ALL/AML containing lymphoma data. Analyzing the results, using as assessment criteria the Cross Validation, it was found that the use of the methods resulted in an improvement in the hit ratio values as compared with bases having all the attributes in the domain of gene expression. In this area the best reduction method was achieved by using the wrapper approach in the three bases. Nevertheless, it is noteworthy that the proposed method showed a result of over 80% in accuracy rate, which cannot be considered a reduction method with poor performance. Although the DRM-F Method presented results below the attributes selection method, in general it showed no average hit rate lower than 80% in the generation of predictive models. The DRM-F Method, aims to extract common and specific (gene) attributes from the field of study, gene expression, but not only from a single base, but among all the bases belonging to the domain. Thus, one can obtain the (gene) attributes common among the various diseases analyzed between the bases. In the present experiment, it was possible to extract the common and specific (gene) attributes among the analyzed diseases. With the (gene) attributes common and specific to each disease it is possible to submit these subsets to biological analysis in order to verify the biological significance of the attributes with the objective of contributing to the area of biomedical diagnostics and routing.

Thesis (Ph. D.)--University of Texas Health Science Center at Houston, School of Public Health, 2008. / Source: Dissertation Abstracts International, Volume: 69-02, Section: B, page: 0769. Advisers: Claudia Pedroza; Asha S. Kapadia. Includes bibliographical references.

Dentre os países da América Latina, o Brasil é o país que mais recebe doações de sangue em volume, alcançando mais de 3,5 milhões de bolsas anualmente só na hemorrede pública. Para que possam ocorrer as transfusões e processamento de hemoderivados é mandatória a realização de testes para detecção de agentes patológicos. Neste cenário está inserido o Instituto de Biologia Molecular do Paraná (IBMP) que, em parceria com a FIOCRUZ, é responsável pelo fornecimento do kit NAT destinado a detecção dos vírus da imunodeficiência humana (HIV), hepatite C (HCV) e hepatite B (HVB) à hemorrede pública brasileira. Visando implementar melhorias e novas tecnologias aos processos existentes, o Instituto adquiriu a licença para utilização da técnica de gelificação na produção de kits para diagnóstico. Esta técnica propõe a estabilização de biomoléculas sem afetar sua funcionalidade, proporcionando a redução de custos de produção, além de possibilitar que os kits sejam armazenados e transportados à temperatura ambiente, aspecto fundamental para simplificar sua cadeia logística e viabilizar a distribuição destes produtos em áreas remotas do Brasil e do mundo. No entanto, ainda há escassez de trabalhos que avaliem aspectos financeiros da implementação desta técnica na indústria. Cabe salientar ainda que a realização de testes em campo seria complexa e demandaria um alto investimento. Uma alternativa para realizar este tipo de avaliação é pelo uso de simulação computadorizada do processo. As ferramentas de simulação possibilitam avaliar diferentes cenários, obtendo dessa forma informações imprescindíveis para melhoria operacional e para tomada de decisões. Neste trabalho, são avaliados os impactos da implementação da técnica de gelificação no custo direto de produção de insumos para diagnóstico por meio de simulação discreta usando o software FlexSim®. Dados obtidos a partir de dezesseis cenários simulados usando a nova tecnologia foram comparados com registros históricos do IBMP na produção de insumos para diagnóstico pelo processo convencional. Dentre os cenários avaliados, seis atenderam às restrições impostas pelo processo e em todos foi possível verificar a redução nos custos diretos, que variou de 3,73% até 5,41% em relação às condições atuais. As reduções de custo ocorreram principalmente devido a reduções nos custos com matéria-prima, que alcançaram economia de 4,1% e nos custos com mão de obra, dada redução do número de operadores no processo. Ademais, os resultados indicam que a implementação da tecnologia propicia melhor aproveitamento da estrutura física da planta sem que ocorra saturação de linhas de processamento. Portanto, baseado em modelos de simulação, este trabalho demonstra a viabilidade do emprego da tecnologia de gelificação no IBMP em termos de custo direto de produção de insumos para diagnóstico. / Among Latin American countries, Brazil is the one that receives more blood donations in volume, reaching up to 3.5 million blood bags in the public blood donation network annually. In order to enable transfusions and processing of blood-derived products, it is mandatory to test the blood against pathologic agents. In association with the Oswaldo Cruz Foundation (FIOCRUZ), the Molecular Biology Institute of Paraná (IBMP) supplies the kit NAT for the detection of the human immunodeficiency, hepatitis B and C viruses (HIV, HBV and HCV) to the Brazilian public blood donation network. Aiming at the implementation of improvements and the introduction of new technologies to its processes, the Institute acquired a license to use the gelification technique in the production of diagnostic kits. The gelification technique proposes the stabilization of biomolecules without harming their functionality, while reducing production costs and allowing the products to be stored and transported at room temperature. It is a key aspect to simplify the logistics chain used to distribute the kit, allowing it to reach World`s remote areas. However, there is still a lack of published studies evaluating financial aspects of the implementation of this technique in the industry. It is worth emphasizing the cost to conduct field experiments of this kind of implementation. One alternative for such an evaluation is by the use of process computer simulation. Simulation tools could be used to analyze different scenarios, providing valuable information for process improvement and decision-making. In this work, the impacts of the gelification technique implementation in the direct production cost of reagents for diagnostic were evaluated using discrete simulation with FlexSim®. Data obtained from sixteen simulated scenarios deploying gelification were compared with historic records of the production of reagents for diagnosis using the conventional process at IBMP. Six of the sixteen evaluated scenarios satisfied the restrictions imposed by the process and all of them indicated a reduction of direct production costs, varying from 3.73% to 5.41% when compared to current conditions. The cost reduction is mainly associated to lower expenses with raw materials, representing savings of up to 4.1% and to the reduction in the number of operators needed. Additionally, results indicate that the implementation of the new technology leads to a better use of the physical structure of the production facility without saturating processing lines. Therefore, based on simulation models, this work shows that the employment of the gelification technology in the manufacturing process of diagnostic reagents at IBMP is viable in terms of direct production costs.

Over the past decade, and accelerated due to the COVID-19 pandemic, there has been increasing adoption of decentralized diagnostic testing, where the testing is brought closer to the patient. This trend has largely been fueled by the development of more accurate diagnostic tools and faster and more reliable data connectivity. Decentralized testing has been shown to greatly reduce turnaround times while increasing accessibility to users in remote regions. However, there are challenges that limit its widespread adoption. In this dissertation, we detail the development of tools and technologies to overcome these barriers and expedite the shift towards decentralized diagnostic testing. First, we demonstrate the ability to develop point-of-care (POC) diagnostic tests with performance that rivals that of traditional lab-based methods. We developed a rapid, multiplexed, microfluidic serological test for Lyme disease, a tick-borne disease caused by the Borrelia burgdorferi bacterium. The recommended testing, the standard 2-tiered (STT) approach, is not sensitive for early-stage infections, is labor-intensive, has long turnaround times, and requires the use of two immunoassays (enzyme-linked immunosorbent assay (ELISA) and the Western Blot). We developed a standalone multiplexed sandwich ELISA assay and adapted it to the mChip microfluidic platform. We validated the assay on a rigorously characterized panel of human serum samples and demonstrated that our approach outperforms the STT algorithm on sensitivity while matching its specificity. The form factor of this technology is amenable to use in physician’s offices and urgent care clinics. We also showed exploratory work towards adapting the mChip platform for diagnosis of Zika disease, a mosquito-borne disease caused by the Zika virus, and acute kidney injury, a syndrome characterized by loss of kidney excretory function. Next, we worked on increasing the adoption of rapid diagnostic tests for self- and partner-testing designed to be used in at-home settings. We developed a smartphone application to be used alongside the INSTI Multiplex test for detecting HIV and syphilis infections. The application was designed to provide users with i) instructions on running the test, ii) an automated deep-learning-based image interpretation algorithm to interpret the rapid test results from a smartphone image, iii) a way to save test results and display/share them, and iv) resources for follow-up care. We adopted a user-centered, iterative design process where we worked with a cohort of study participants composed of men who have sex with men and transgender women at high risk for contracting sexually transmitted infections. We then field tested the application with 48 participants over a duration of three months and found high acceptability for the application, both in terms of functionality and helpfulness. Finally, we sought to address a key limitation with deep-learning-based image classification techniques, specifically, the requirement for large numbers of annotated images for training. We developed a deep-learning image interpretation algorithm that could be quickly adapted to new rapid test kits using only a fraction of the images that would otherwise be needed for training the model. The interpretation algorithm followed a three-step, modular process. First, the rapid test kit and the membrane were extracted from the smartphone image. Second, the constituent zones were cropped from the extracted membrane. Finally, a classifier detected the presence or absence of a line in the individual zones. Fast adaptation was demonstrated by adapting a base model, trained using images of a single COVID-19 rapid test kit, to four different rapid test kits, each with different form factors, using few-shot domain adaptation. After training with 20 or fewer images, the classification accuracies of all the adapted models were > 95%. This approach can provide a digital health platform for improved pandemic preparedness and enable quality assurance and linkage to care for consumers operating new LFAs in widespread decentralized settings. Together, these methods provide a suite of tools that could expedite the shift towards decentralized, POC testing.