Emerging patterns of tuberculosis drug-resistant by data mining with association rules (Apriori): using the R-library tbdr19prediction

A tuberculose (TB) é uma das 10 principais causas de morte no Brasil, aproximadamente 70.000 novos casos são notificados a cada ano e há aproximadamente 4.500 mortes por tuberculose. A resistência a medicamentos em Mycobacterium tuberculosis surge de mutações cromossômicas espontâneas em baixa frequência, a tuberculose droga resistente (TBDR) clínica ocorre em grande parte como resultado da seleção feita pelo individuo durante o tratamento da doença dessas alterações genéticas por meio de fornecimento errático de medicamentos, prescrição médica abaixo do ideal e paciente pobre aderência. Diante disso, tornou-se necessário desenvolver um algoritmo de mineração de dados para produzir modelos preditivos, visando analisar padrões emergentes. Para atingir esse objetivo, a implementação de um algoritmo de regra de associação com a apriori foi a escolha mais adequada, permitindo a identificação de padrões ligados a desfechos desfavoráveis como abandono, falência e morte. Além disso, as regras válidas obtidas do modelo preditivo foram exploradas e analisadas, fornecendo novos conhecimentos para identificar itens significativos de pacientes vulneráveis para cada desfecho desfavorável

Food classification guidelines across Australia - concordance and implications of differences

Background: Each Australian jurisdiction produces separate food and drink classification guidelines for different institutional settings (e.g., schools) to guide food service providers on what constitutes a nutritious offering. Australian food manufacturers, suppliers and retailers frequently report that it is challenging to align their product range with a multitude of different classification systems. This study aimed to investigate the concordance between guidelines from all Australian jurisdictions across various settings, based on their application to a range of packaged food and drink products. Methods: Products from top selling brands in Australian food service settings across 10 product categories (e.g., sweet snacks) were classified according to each of the 20 state and territory food classification guidelines applying to schools, workplaces, and healthcare settings (primarily ‘traffic light’ classification systems). Product nutrition information was retrieved from manufacturer, supplier, or retailer websites. The level of concordance between each combination of two guidelines using a traffic light’ based classification system was determined by the proportion of products rated as ‘amber’ across both guidelines. Results: 747 food and drink products were assessed. 88% products were classified at the same level of healthiness across all ‘traffic light’-based systems. Concordance in ‘amber’ food classifications ranged between 63% and 96% across guidelines for different jurisdictions. For school guidelines, ‘ice creams and frozen desserts’ had the highest concordance across guidelines (97%); ‘meat and seafood products’ had the lowest concordance (80%). Discrepancies mainly arose from differences in food categories included in guidelines, e.g., the ‘ready-to-eat meals’ category was absent from some guidelines. Conclusions: There is a need for national coordination and greater evidence-based consistency in food classification guidelines across Australian jurisdictions. This will help ensure clarity for businesses on how to better support community health, including food manufacturer product development and reformulation, and food outlets offerings

Pareamento de registros das grandes bases do SUS para permitir análises longitudinais de pacientes com câncer

OBJETIVO: gerar uma base de dados de pacientes com câncer construída por meio de pareamento de registros das grandes bases de dados do SUS para permitir análise longitudinal do diagnóstico ao tratamento dos casos mais suscetíveis a tratamento, com ênfase em um conjunto de canceres potencialmente tratáveis e/ou frequentes. MÉTODO: realizamos um estudo descritivo utilizando bases de dados do SUS com dados nominais, que foram disponibilizados pelo DATASUS. A organização da base de dados oncológicos iniciou com os dados da base de Autorização de Procedimentos de Alta Complexidade (SIA/APAC), do período de 2000 a 2012, para quimioterapia e radioterapia. Essas bases de APAC tiveram suas informações combinadas, formando uma única base oncológica. Os pacientes submetidos a tratamento de quimioterapia e/ou radioterapia receberam identificador único derivado da aplicação de pareamento probabilístico de registros. Essa identificação possibilitou a avaliação da trajetória do paciente ao longo do tratamento oncológico do SUS. Utilizamos o pareamento probabilístico de registros em outras duas etapas: 1) vinculação da base de químio-radioterapia com informações de hospitalização oriundas do Sistema de Informações Hospitalares do SUS (SIH/SUS); 2) vinculação de registros da base de oncologia com o Sistema de Informação sobre Mortalidade (SIM) – corrigindo informação sobre óbito, importante para futura análise de sobrevida. A base de dados de oncologia foi desenvolvida e controlada no programa de computador Statistical Analysis SAS®. Realizamos os pareamentos de registros no FRIL versão 2.1.5. Sobre esta base final, computamos estatísticas descritivas para os cânceres passíveis de prevenção, detecção precoce e tratamento definidos por Farmer et al. 2010. Calculamos as tendências das medidas epidemiológicas desses cânceres por meio do programa de computador JoinPoint Regression, versão 4.5.0.0. RESULTADOS: construímos uma base de dados para oncologia, de âmbito nacional, orientada para análise epidemiológica, com informações de pacientes atendidos pelo SUS. Obtivemos estimativas de incidência de tratamentos e exploramos evolução do tempo entre diagnóstico e início de tratamento para o conjunto de canceres potencialmente tratáveis e/ou frequentes, no SUS. A análise epidemiológica do tratamento oncológico público no Brasil mostrou que o SUS ampliou o acesso ao 13 cuidado oncológico no âmbito de quimio e radioterapia nesse período. O tempo de espera entre diagnóstico e início do tratamento é longo e não se atenuou entre 2008 e 2012 consideravelmente. CONCLUSÃO: o pareamento de dados se mostrou um processo efetivo para criação de uma base nacional de pacientes com câncer em tratamento de quimio- e/ou radioterapia no SUS, entre 2000 e 2012. A base de dados APAC oncologia concentra importante informação epidemiológica sobre tratamento do câncer no SUS. Dessa forma, ela apresenta grande potencial para ser usada no sentido de prover informação de serviço e políticas públicas. Além disso, representa uma importante ferramenta para o Ministério da Saúde desenvolver indicadores e monitorar o câncer no País – itens importantes assumidos no Plano de Ações Estratégicas para o Enfrentamento das Doenças Crônicas Não Transmissíveis no Brasil e a definição das metas globais para o enfrentamento dessas doenças até 2025.OBJECTIVE: creation of a national database of cancer patients whose care was financed by the Brazilian national health system (SUS) through record linkage, in order to perform a longitudinal analysis of diagnosis through the treatment of cases most susceptible to treatment, with an emphasis on a set of potentially treatable cancers and / or frequent. METHODS: the data was obtained from SUS databases provided by the Ministry of Health with nominal data permitting linkage. The creation of this cancer database begins with the database of High Complexity Procedures Authorization (SIA / APAC), period from 2000 to 2012, including chemotherapy and radiotherapy. Chemo- and radiotherapy database information has been combined into a single cancer database. A unique identifier derived from the application of probabilistic matching records was set to each patient receiving these therapies. This identification process enabled an evaluation of the patient trajectory through oncological diagnosis and treatment financed by SUS. Probabilistic record linkage was also used in other two instances: 1) linking the APAC chemo-radiotherapy (oncology) database with hospitalization information from the SUS Hospital Information System (SIH / SUS to capture additional treatments; and 2) linking oncology database records with the Mortality Information System (SIM) in order to qualify information concerning patient deaths and well as provide information for survival analyses. The oncology database was developed and controlled by the Statistical Analysis System (SAS® 9.4). Record linkage was performed in FRIL (Fine-grained record linkage software) version 2.1.5. Descriptive statistics for treatment times for cancers considered potentially curable with early detection and treatment, as defined by Farmer et al. 2010(Farmer et al., 2010), were computed. Trend analysis of epidemiological measures for patients with these cancers were performed using Joinpoint Regression, version 4.1.1.3. RESULTS: a Brazilian national oncology database, designed for epidemiological analysis, with information from SUS cancer patients. We obtained estimates of incidence of treatments and described trends of time between diagnosis and treatment initiation of patients with a subset of cancers potentially treatable and/or frequent. CONCLUSION: record linkage showed to be an effective process for the creation of a national database of cancer patients in chemo- and/or radiotherapy treatment in the SUS between 2000 and 2012. APAC Oncology database concentrates important epidemiological information and can be useful to generate evidence to inform policy and services. SUS-APAC oncology database may be an important tool for the Ministry of Health, to construct indicators and monitoring, in accordance with Brazilian Strategic Action Plan to Combat Chronic Non-communicable Diseases and the global targets set to confront these diseases by 2025. Treatment of this group of cancers expanded notably over these 12 years. Time from diagnosis to treatment during this period of wider geographic reach and major expansion of coverage showed stable, emphasizing the necessity of continuous monitoring of this indicator to guide the implementation of public policies aimed at improving care of patients with cancer

TB STIGMA – MEASUREMENT GUIDANCE

TB is the most deadly infectious disease in the world, and stigma continues to play a significant role in worsening the epidemic. Stigma and discrimination not only stop people from seeking care but also make it more difficult for those on treatment to continue, both of which make the disease more difficult to treat in the long-term and mean those infected are more likely to transmit the disease to those around them. TB Stigma – Measurement Guidance is a manual to help generate enough information about stigma issues to design and monitor and evaluate efforts to reduce TB stigma. It can help in planning TB stigma baseline measurements and monitoring trends to capture the outcomes of TB stigma reduction efforts. This manual is designed for health workers, professional or management staff, people who advocate for those with TB, and all who need to understand and respond to TB stigma

Managing Intellectual Property to Foster Agricultural Development

Over the past decades, consideration of IPRs has become increasingly important in many areas of agricultural development, including foreign direct investment, technology transfer, trade, investment in innovation, access to genetic resources, and the protection of traditional knowledge. The widening role of IPRs in governing the ownership of—and access to—innovation, information, and knowledge makes them particularly critical in ensuring that developing countries benefit from the introduction of new technologies that could radically alter the welfare of the poor. Failing to improve IPR policies and practices to support the needs of developing countries will eliminate significant development opportunities. The discussion in this note moves away from policy prescriptions to focus on investments to improve how IPRs are used in practice in agricultural development. These investments must be seen as complementary to other investments in agricultural development. IPRs are woven into the context of innovation and R&D. They can enable entrepreneurship and allow the leveraging of private resources for resolving the problems of poverty. Conversely, IPRs issues can delay important scientific advancements, deter investment in products for the poor, and impose crippling transaction costs on organizations if the wrong tools are used or tools are badly applied. The central benefit of pursuing the investments outlined in this note is to build into the system a more robust capacity for strategic and flexible use of IPRs tailored to development goals

Core evidence elements for generating medicine safety evidence for pregnancy using population-based data: Recommendations from IMI-ConcePTION

Background: The risks and benefits of medicine use during pregnancy are typically established through post-approval population-based observational studies. Currently, there is heterogeneity in the identification, selection and the definitions of key pregnancy and maternal outcomes of interest, exposures, risk factors, and confounders. There is also a large range of different study designs and statistical tools available for these studies. Objectives: IMI-ConcePTION (https://www.imi-conception.eu/) identified the need to create recommendations for standardized key concepts and research methods. Methods: The core evidence elements guide for population-based observational studies was compiled using expertise in pharmacovigilance, pharmacoepidemiology, perinatal epidemiology, statistics, perinatal clinical pharmacology, and health services research, both internal and external to IMI-ConcePTION. It also included reviews of the literature, best practices, and regulatory guidance documents. Results: The recommendations cover core evidence elements including gestational age, exposures (dose/duration of medicine and etiological window); relevant confounders; pregnancy outcomes (live and non-live births), congenital anomalies, infant/childhood outcomes (including long-term outcomes), and maternal outcomes; research design considerations; analytical methods; statistical power/sample size considerations and study limitations. A list of “default” core evidence elements is also proposed as a minimal set of elements that should be considered in all pregnancy medicine safety surveillance studies. The recommendations also include guidance when assessing the quality of data sources. Conclusions: This core evidence elements recommendations will facilitate setting standards with regards to the definitions used in medicine and pregnancy studies, the quality of the data and the suitability of data sources used for this work. It can also be tailored to address studies with specific research questions, particular medicines/disease areas or specific outcomes. It will promote the conduct of more standardized, high quality and clinically meaningful population-based studies among pregnant women. It will also help with alignment across different studies to improve evidence synthesis

Using whole Plasmodium falciparum genomes for monitoring of escape from diagnosis, drug treatment and vaccine-induced immunity in Central-West Africa

As malaria control programs continue to push for local malaria elimination, novel molecular tools embedded into ongoing surveillance systems are needed. Information generated from molecular methods allows for improved monitoring of parasite drug resistance and diagnostic evasion, therefore helping inform and adapt control strategies. The overall aim of this doctoral work is to use molecular monitoring of P. falciparum, the causative parasite of the most pathogenic form of malaria, to identify hidden reservoirs of the parasite, to monitor for rapid diagnostic test evasion, to understand parasite transmission dynamics and to inform on the next generation vaccine development. Whole genome sequencing data was generated from filter paper blood samples collected within the framework of yearly malaria indicator surveys conducted on Bioko Island, Equatorial Guinea to describe the island’s parasite transmission dynamics. The connectiveness of parasite populations within the island and importation from the African continent is delineated for the first time. A novel, portable PCR device together with a ready to use, lyophilized quantitative PCR assay was deployed locally on Bioko Island at larger scale to detect reservoirs of parasite carriers that potentially contribute to transmission, but evade detection by rapid diagnostic tests. Whole genome sequencing was further utilized to conduct the first whole genome sieve analysis with blood samples collected during a field efficacy study evaluating a whole organism malaria vaccine in West Africa. This sieve analysis identified candidate genes that may encode protective immune targets for next generation malaria vaccines. Ultimately, these molecular methods will allow for improved assessment of ongoing control methods and their impact on parasite populations, providing information for enhanced resource allocation, leading to continued progress towards malaria control and potential local elimination