BACKGROUND: Prevalence of HIV, smoking, and pulmonary infections in South Africa are high. OBJECTIVES: We investigated the role of smoking and HIV status on lung function. METHODS: This is a secondary analysis of a cross-sectional study conducted in South Africa. Data included demographics, pulmonary risk factors and a spirometry test to obtain the forced expiratory volume in one second (FEV1) and the ratio of FEV1/forced vital capacity (FVC). In the initial multivariable regression analysis, the effect of smoking on pulmonary function in HIV-positive adults was assessed. The analysis was repeated, assessing the influence of HIV status on lung function in both HIV-negative and HIV-positive smokers. The models were adjusted for age, sex, body mass index (BMI), time since HIV diagnosis, antiretroviral treatment (ART) use, occupational hazards, history of tuberculosis or pneumonia, indoor smoking and the presence of an indoor fireplace during childhood. RESULTS: This study included 524 people living with HIV (PLWH, 66.7% female, mean age 40.9 years [s.d.; 9.4]) and 79 HIV-negative smokers (77.2% male, mean age 34.4 years [s.d.: 12.1]). Of the PLWH, 118 (22.5%) were past or current smokers and 406 (77.5%) were non-smokers. Smoking was not associated with changes in the FEV1 or FEV1/FVC ratio in multivariable regression analysis. In the second analysis, HIV status was also not associated with reduced pulmonary function following adjustment for confounders. CONCLUSION: Neither smoking nor being HIV-positive was associated with decreased pulmonary function in this relatively young population. These findings should be confirmed in a longitudinal study, including an older population.

Resumo Mensurações de indicadores de saúde raramente estão disponíveis para todas as populações e períodos de interesse, e os dados disponíveis podem não ser comparáveis. As Diretrizes para o Relato Transparente e Preciso de Estimativas de Saúde (Declaração GATHER) definem as melhores práticas para redação de estudos que calculam estimativas de saúde para várias populações, no tempo ou espaço, usando múltiplas fontes de informação. As estimativas de saúde que se enquadram no escopo da Declaração GATHER incluem todas as estimativas quantitativas de indicadores de saúde em nível populacional (estimativas globais, regionais, nacionais ou subnacionais), abrangendo indicadores da situação de saúde, da incidência e prevalência de doenças, lesões e incapacidades, e funcionalidades; e indicadores de determinantes da saúde, incluindo comportamentos e exposições de saúde. A Declaração GATHER compreende uma lista de 18 itens que são essenciais para as melhores práticas de redação. Um documento mais detalhado sobre a explicação e elaboração das diretrizes, que descreve a interpretação e a base lógica de cada item a ser relatado, juntamente com exemplos de boas redações, está disponível no site da Declaração GATHER (http://gather-statement.org).

Abstract Measurements of health indicators are rarely available for every population and period of interest, and available data may not be comparable. The Guidelines for Accurate and Transparent Health Estimates Reporting (GATHER) define best reporting practices for studies that calculate health estimates for multiple populations (in time or space) using multiple information sources. Health estimates that fall within the scope of GATHER include all quantitative population-level estimates (including global, regional, national, or subnational estimates) of health indicators, including indicators of health status, incidence and prevalence of diseases, injuries, and disability and functioning; and indicators of health determinants, including health behaviours and health exposures. GATHER comprises a checklist of 18 items that are essential for best reporting practice. A more detailed explanation and elaboration document, describing the interpretation and rationale of each reporting item along with examples of good reporting, is available on the GATHER website (http://gather-statement.org).

Resumo Mensurações de indicadores de saúde raramente estão disponíveis para todas as populações e períodos de interesse, e os dados disponíveis podem não ser comparáveis. As Diretrizes para o Relato Transparente e Preciso de Estimativas de Saúde (Declaração GATHER) definem as melhores práticas para redação de estudos que calculam estimativas de saúde para várias populações, no tempo ou espaço, usando múltiplas fontes de informação. As estimativas de saúde que se enquadram no escopo da Declaração GATHER incluem todas as estimativas quantitativas de indicadores de saúde em nível populacional (estimativas globais, regionais, nacionais ou subnacionais), abrangendo indicadores da situação de saúde, da incidência e prevalência de doenças, lesões e incapacidades, e funcionalidades; e indicadores de determinantes da saúde, incluindo comportamentos e exposições de saúde. A Declaração GATHER compreende uma lista de 18 itens que são essenciais para as melhores práticas de redação. Um documento mais detalhado sobre a explicação e elaboração das diretrizes, que descreve a interpretação e a base lógica de cada item a ser relatado, juntamente com exemplos de boas redações, está disponível no site da Declaração GATHER (http://gather-statement.org).

Abstract Measurements of health indicators are rarely available for every population and period of interest, and available data may not be comparable. The Guidelines for Accurate and Transparent Health Estimates Reporting (GATHER) define best reporting practices for studies that calculate health estimates for multiple populations (in time or space) using multiple information sources. Health estimates that fall within the scope of GATHER include all quantitative population-level estimates (including global, regional, national, or subnational estimates) of health indicators, including indicators of health status, incidence and prevalence of diseases, injuries, and disability and functioning; and indicators of health determinants, including health behaviours and health exposures. GATHER comprises a checklist of 18 items that are essential for best reporting practice. A more detailed explanation and elaboration document, describing the interpretation and rationale of each reporting item along with examples of good reporting, is available on the GATHER website (http://gather-statement.org).

Some of the most significant breakthroughs in the biological sciences this century will emerge from the development of next generation sequencing technologies. The ease of availability of DNA sequence made possible through these new technologies has given researchers opportunities to study organisms in a manner that was not possible with Sanger sequencing. Scientists will, therefore, need to embrace genomics, as well as develop and nurture the human capacity to sequence genomes and utilise the 'tsunami' of data that emerge from genome sequencing. In response to these challenges, we sequenced the genome of Fusarium circinatum, a fungal pathogen of pine that causes pitch canker, a disease of great concern to the South African forestry industry. The sequencing work was conducted in South Africa, making F. circinatum the first eukaryotic organism for which the complete genome has been sequenced locally. Here we report on the process that was followed to sequence, assemble and perform a preliminary characterisation of the genome. Furthermore, details of the computer annotation and manual curation of this genome are presented. The F. circinatum genome was found to be nearly 44 million bases in size, which is similar to that of four other Fusarium genomes that have been sequenced elsewhere. The genome contains just over 15 000 open reading frames, which is less than that of the related species, Fusarium oxysporum, but more than that for Fusarium verticillioides. Amongst the various putative gene clusters identified in F. circinatum, those encoding the secondary metabolites fumosin and fusarin appeared to harbour evidence of gene translocation. It is anticipated that similar comparisons of other loci will provide insights into the genetic basis for pathogenicity of the pitch canker pathogen. Perhaps more importantly, this project has engaged a relatively large group of scientists including students in a significant genome project that is certain to provide a platform for growth in this important area of research in the future.

The national and Victorian burden of disease studies in Australia set out to examine critically the methods used in the Global Burden of Disease study to estimate the burden of mental disorders. The main differences include the use of a different set of disability weights allowing estimates in greater detail by level of severity, adjustments for comorbidity between mental disorders, a greater number of mental disorders measured, and modelling of substance use disorders, anxiety disorders and bipolar disorder as chronic conditions. Uniform age-weighting in the Australian studies produces considerably lower estimates of the burden due to mental disorders in comparison with age-weighted disability-adjusted life years. A lack of follow-up data on people with mental disorders who are identified in cross-sectional surveys poses the greatest challenge in determining the burden of mental disorders more accurately.

Se estudió la carga de morbilidad en el conjunto de Australia y en el Estado de Victoria de ese país al objeto de analizar críticamente los métodos empleados en el estudio sobre la Carga Mundial de Morbilidad (CMM) para estimar la carga de trastornos mentales. En los estudios de Australia se utilizó un sistema de ponderación de la discapacidad que, a diferencia del empleado en el estudio CMM, permitía hacer estimaciones más detalladas en función del nivel de gravedad. Además, se hicieron ajustes para la comorbilidad entre trastornos mentales, se midió un mayor número de trastornos mentales, y se modelizaron como enfermedades crónicas el abuso de sustancias, los trastornos de ansiedad y el trastorno bipolar. En consecuencia, las estimaciones australianas difirieron notablemente de las del estudio CMM. Así, en Australia, en lo que concierne a la dependencia del alcohol en los hombres, el hallazgo de unas tasas de AVAD inferiores en un 48% podía explicarse en parte por las diferencias en la prevalencia observada de la afección y en parte por los ajustes para la comorbilidad por otros trastornos mentales y la menor ponderación de la gravedad. Las ponderaciones más bajas de la discapacidad consideradas para la depresión grave en Australia se tradujeron en una carga de depresión grave inferior en un 36% entre los hombres y en un 45% entre las mujeres, pero la inclusión de la distimia redujo esas diferencias en más de la mitad. Pese a que ponderamos más la discapacidad correspondiente, nuestras estimaciones para los trastornos obsesivo-compulsivos fueron inferiores a la cuarta parte de las realizadas en el estudio CMM, debido a que se usaron estimaciones mucho más bajas de la prevalencia. Las muy inferiores cifras calculadas para la carga de trastorno de pánico, y las superiores para el trastorno de estrés postraumático, se obtuvieron a partir de modelos de las enfermedades que introducían una mayor ponderación de la discapacidad, estimaciones mayores de la prevalencia, y ajustes para los periodos asintomáticos registrados durante la evolución crónica de la enfermedad. Las estimaciones de la carga total de trastornos de ansiedad fueron casi del doble debido a que en los estudios australianos se incluyeron otras cuatro dolencias. La ponderación uniforme por edades utilizada en los estudios australianos arrojó estimaciones considerablemente inferiores de la carga de trastornos mentales en comparación con los AVAD ponderados en función de la edad. Con la ponderación según la edad, la cifra de trastornos mentales en Victoria aumentó en un 57% como proporción de los AVAD globales, superando a las enfermedades cardiovasculares y al cáncer en orden de importancia. La falta de datos de seguimiento sobre las personas con trastornos mentales identificadas en las encuestas transversales constituye el mayor obstáculo para poder determinar más exactamente la carga de trastornos mentales. Si bien las mejoras de los métodos presentados en este artículo son un paso importante para calcular con más exactitud la carga de trastornos mentales, queda todavía amplio margen para perfeccionar esas estimaciones.

Les études sur la charge de morbidité effectuées pour l’ensemble de l’Australie et l’Etat de Victoria visent à examiner d’un œil critique les méthodes utilisées dans l’étude sur la charge de morbidité dans le monde pour estimer la charge représentée par les troubles mentaux. Les études australiennes se servent d’une série de coefficients de pondération des incapacités différents de ceux employés dans l’étude précitée, permettant des estimations plus détaillées selon le degré de gravité. En outre, on a effectué des ajustements pour tenir compte de la comorbidité entre les troubles mentaux et on a mesuré un plus grand nombre de ces derniers ; par ailleurs, on a rassemblé les troubles liés à la consommation de substances, les troubles anxieux et les troubles bipolaires en un modèle d’affections chroniques. En conséquence, les estimations australiennes ont montré des différences marquées par rapport à celles de l’étude sur la charge de morbidité dans le monde. En Australie, le nombre d’années de vie ajustées sur l’incapacité (DALY) inférieur de 48 % ainsi obtenu pour la dépendance alcoolique chez l’homme a été en partie attribué à des différences dans la prévalence de cette affection et en partie aux ajustements effectués pour tenir compte d’une comorbidité avec d’autres troubles mentaux, et à une pondération moins importante en fonction de la gravité. En Australie, les estimations plus basses qui ont été faites du coefficient de pondération de l’incapacité en cas de dépression majeure ont fait que cette dernière représente une charge inférieure de 36% chez les hommes et de 45% chez les femmes, mais l’inclusion de la dysthymie a diminué de moitié au moins les écarts observés. Bien que nous ayons utilisé un coefficient de pondération de l’incapacité plus élevé, nos estimations relatives aux troubles obsessionnels compulsifs ont représenté moins du quart de celles de l’étude précitée du fait d’estimations de la prévalence bien inférieures. Des estimations bien plus faibles de la charge de morbidité des troubles paniques et bien plus élevées de celle de l’état de stress post-traumatique ont été tirées de modèles de morbidité dans lesquels le coefficient de pondération de l’incapacité et les estimations de la prévalence étaient plus élevés et qui comportaient des ajustements tenant compte des périodes asymptomatiques survenues au cours de la maladie chronique. Les estimations relatives à la charge de morbidité totale attribuable aux troubles anxieux ont été presque deux fois plus élevées du fait que quatre autres pathologies ont été incluses dans les études australiennes. L’absence de pondération en fonction de l’âge dans les études australiennes a donné des estimations considérablement plus faibles de la charge de morbidité imputable aux troubles mentaux, par comparaison avec les DALY pondérés en fonction de l’âge. Avec une telle pondération, la part représentée par les troubles mentaux dans l’ensemble des DALY a progressé de 57% dans l’Etat de Victoria et a dépassé en importance les maladies cardio-vasculaires et le cancer. L’absence de données relatives au suivi des patients présentant un trouble mental identifiés lors d’enquêtes transversales constitue le problème le plus important pour déterminer plus précisément la charge de morbidité des troubles mentaux. Si les améliorations apportées dans les méthodes présentées dans cet article constituent un progrès important vers plus de précision dans le calcul de la charge de morbidité des troubles mentaux, les perspectives de développement ultérieur restent importantes.