On Using Machine Learning to Identify Knowledge in API Reference Documentation

Using API reference documentation like JavaDoc is an integral part of software development. Previous research introduced a grounded taxonomy that organizes API documentation knowledge in 12 types, including knowledge about the Functionality, Structure, and Quality of an API. We study how well modern text classification approaches can automatically identify documentation containing specific knowledge types. We compared conventional machine learning (k-NN and SVM) and deep learning approaches trained on manually annotated Java and .NET API documentation (n = 5,574). When classifying the knowledge types individually (i.e., multiple binary classifiers) the best AUPRC was up to 87%. The deep learning and SVM classifiers seem complementary. For four knowledge types (Concept, Control, Pattern, and Non-Information), SVM clearly outperforms deep learning which, on the other hand, is more accurate for identifying the remaining types. When considering multiple knowledge types at once (i.e., multi-label classification) deep learning outperforms na\"ive baselines and traditional machine learning achieving a MacroAUC up to 79%. We also compared classifiers using embeddings pre-trained on generic text corpora and StackOverflow but did not observe significant improvements. Finally, to assess the generalizability of the classifiers, we re-tested them on a different, unseen Python documentation dataset. Classifiers for Functionality, Concept, Purpose, Pattern, and Directive seem to generalize from Java and .NET to Python documentation. The accuracy related to the remaining types seems API-specific. We discuss our results and how they inform the development of tools for supporting developers sharing and accessing API knowledge. Published article: https://doi.org/10.1145/3338906.333894

Self-reported side effects and adherence to antiretroviral therapy in HIV-infected pregnant women under option B+: a prospective study

BACKGROUND: Antiretroviral therapy (ART) regimens containing efavirenz (EFV) are recommended as part of universal ART for pregnant and breastfeeding women. EFV may have appreciable side effects (SE), and ART adherence in pregnancy is a major concern, but little is known about ART SE and associations with adherence in pregnancy. METHODS: We investigated the distribution of patient-reported SE (based on Division of AIDS categories) and the association of SE with missed ART doses in a cohort of 517 women starting EFV+3TC/FTC+TDF during pregnancy. In analysis, SE were considered in terms of their overall frequency, by systems category, and by latent classes. RESULTS: Overall 97% of women reported experiencing at least one SE after ART initiation, with 48% experiencing more than five SE. Gastrointestinal, central nervous system, systemic and skin SE were reported by 81%, 85%, 79% and 31% of women, respectively, with considerable overlap across groups. At least one missed dose was reported by 32% of women. In multivariable models, ART non-adherence was associated with systemic SE compared to other systems categories, and measures of the overall burden of SE experienced were most strongly associated with missed ART doses. CONCLUSION: These data demonstrate very high levels of SE in pregnant women initiating EFV-based ART and a strong association between SE burden and ART adherence. ART regimens with reduced SE profiles may enhance adherence, and as countries expand universal ART for all adult patients, counseling must include preparation for ART SE

Inequity in the distribution of non-communicable disease multimorbidity in adults in South Africa: An analysis of prevalence and patterns

The present study examined the prevalence and patterns of noncommunicable disease multimorbidity by wealth quintile among adults in South Africa. The South African National Income Dynamics Study Wave 5 was conducted in 2017 to examine the livelihoods of individuals and households. We analysed data in people aged 15 years and older (N = 27,042), including self-reported diagnosis of diabetes, stroke, heart disease and anthropometric measurements. Logistic regression and latent class analysis were used to analyse factors associated with multimorbidity and common disease patterns

Efficient Parallel Statistical Model Checking of Biochemical Networks

We consider the problem of verifying stochastic models of biochemical networks against behavioral properties expressed in temporal logic terms. Exact probabilistic verification approaches such as, for example, CSL/PCTL model checking, are undermined by a huge computational demand which rule them out for most real case studies. Less demanding approaches, such as statistical model checking, estimate the likelihood that a property is satisfied by sampling executions out of the stochastic model. We propose a methodology for efficiently estimating the likelihood that a LTL property P holds of a stochastic model of a biochemical network. As with other statistical verification techniques, the methodology we propose uses a stochastic simulation algorithm for generating execution samples, however there are three key aspects that improve the efficiency: first, the sample generation is driven by on-the-fly verification of P which results in optimal overall simulation time. Second, the confidence interval estimation for the probability of P to hold is based on an efficient variant of the Wilson method which ensures a faster convergence. Third, the whole methodology is designed according to a parallel fashion and a prototype software tool has been implemented that performs the sampling/verification process in parallel over an HPC architecture

Estimating the changing disease burden attributable to raised low-density lipoprotein cholesterol in South Africa for 2000, 2006 and 2012

Background. Low-density lipoprotein cholesterol (LDL-C) is the most important contributor to atherosclerosis, a causal factor for ischaemic heart disease (IHD) and ischaemic stroke. Although raised LDL-C is a key contributor to cardiovascular disease (CVD), the exact attributable disease risk in South Africa (SA) is unknown. The the first SA comparative risk assessment (SACRA1) study assessed the attributable burden of raised total cholesterol, and not specifically LDL-C. Objectives. To estimate the national mean serum LDL-C by age, year and sex and to quantify the burden of disease attributable to LDL-C in SA for 2000, 2006 and 2012. Methods. The comparative risk assessment (CRA) method was used. Estimates of the national mean of LDL-C, representing the 3 different years, were derived from 14 small observational studies using a meta-regression model. A theoretical minimum risk exposure level (TMREL) of 0.7 - 1.3 mmol/L was used. LDL-C estimates together with the relative risks from the Global Burden of Disease Study 2017 were used to calculate a potential impact fraction (PIF). This was applied to IHD and ischaemic stroke estimates sourced from the Second National Burden of Disease Study. Attributable deaths, years of life lost, years lived with disability and disability-adjusted life years (DALYs) were calculated. Uncertainty analysis was performed using Monte Carlo simulation. Results. LDL-C declined from 2.74 mmol/L in 2000 to 2.58 mmol/L in 2012 for males, while in females it declined from 3.05 mmol/L in 2000 to 2.91 mmol/L in 2012. The PIFs for LDL-C showed a slight decline over time, owing to the slight decrease in LDL-C levels. Attributable DALYs increased between 2000 (n=286 712) and 2006 (n=315 125), but decreased thereafter in 2012 (n=270 829). Attributable age-standardised death rates declined between 2000 and 2012 in both sexes: in males from 98 per 100 000 members of the population in 2000 to 78 per 100 000 in 2012, and in females from 81 per 100 000 in 2000 to 58 per 100 000 in 2012. Conclusions. Mean LDL-C levels were close to 3 mmol/L, which is the recommended level at which cholesterol-lowering treatment should be initiated for people at low and moderate risk for cardiovascular outcomes. The decreasing trend in the age-standardised attributable burden due to LDL-C is encouraging, but it can be lowered further with the introduction of additional population-based CVD prevention strategies. This study highlights the fact that high LDL-C concentration in relation to the TMREL in SA is responsible for a large proportion of the emerging CVD, and should be targeted by health planners to reduce disease burden

Estimating the changing burden of disease attributable to unsafe water and lack of sanitation and hygiene in South Africa for 2000, 2006 and 2012

Background. The incidence of diarrhoeal disease is closely linked to socioeconomic and environmental factors, household practices and access to health services. South African (SA) district health information and national survey data report wide variation in the incidence and prevalence of diarrhoeal episodes in children under 5 years of age. These differentials indicate potential for reducing the disease burden through improvements in provision of water and sanitation services and changes in hygiene behaviour. Objectives. To estimate the burden of disease attributed to unsafe water, sanitation and hygiene (WASH) by province, sex and age group for SA in 2000, 2006 and 2012. Methods. Comparative risk assessment methodology was used to estimate the disease burden attributable to an exposure by comparing the observed risk factor distribution with a theoretical lowest possible population distribution. The study adapts the original World Health Organization scenario-based approach for estimating diarrhoeal disease burden from unsafe WASH, by assigning different standards of household water and sanitation-specific geographical classification to capture SA living conditions in rural, urban and informal settlements. Results. SA experienced an improvement in water and sanitation supply in eight of the nine provinces between 2001 and 2011, with the exception of Northern Cape Province. In 2011, 41% of South Africans lived with poor water and sanitation conditions; however, wide provincial inequalities exist. In 2012, it was estimated that 84.1% of all deaths due to diarrhoeal disease were attributable to unsafe WASH; this equates to 13 757 deaths (95% uncertainty interval (UI) 13 015 - 14 300). Of these diarrhoeal disease deaths, 48.2% occurred in children under 5 years of age, accounting for 13.9% of all deaths in this age group (95% UI 13.1 - 14.4). Between 2000 and 2012, the proportion of deaths attributable to diarrhoea reduced from 3.6% to 2.6%. Gauteng and Western Cape provinces experienced much lower WASHattributable death rates than the more rural, poorer provinces. Conclusion. Unsafe WASH remains an important risk factor for disease in SA, especially in children. High priority needs to be given to the provision of safe and sustainable sanitation and water facilities and promoting safe hygiene behaviours. The COVID-19 pandemic has reinforced the critical importance of clean water for preventing and containing disease

The strategic relevance of manufacturing technology : an overall quality concept to promote innovation preventing drug shortage

Manufacturing is the bridge between research and patient: without product, there is no clinical outcome. Shortage has a variety of causes, in this paper we analyse only causes related to manufacturing technology and we use shortage as a paradigm highliting the relevance of Pharmaceutical Technology. Product and process complexity and capacity issues are the main challenge for the Pharmaceutical Industry Supply chain. Manufacturing Technology should be acknowledged as a R&D step and as a very important matter during University degree in Pharmacy and related disciplines, promoting collaboration between Academia and Industry, measured during HTA step and rewarded in terms of price and reimbursement. The above elements are not yet properly recognised, and manufacturing technology is taken in to consideration only when a shortage is in place. In a previous work, Panzitta et al. proposed to perform a full technology assessment at the Health Technological Assessment stage, evaluating three main technical aspects of a medicine: manufacturing process, physicochemical properties, and formulation characteristics. In this paper, we develop the concept of manufacturing appraisal, providing a technical overview of upcoming challenges, a risk based approach and an economic picture of shortage costs. We develop also an overall quality concept, not limited to GMP factors but broaden to all elements leading to a robust supply and promoting technical innovation

Estimating the changing burden of disease attributable to low levels of physical activity in South Africa for 2000, 2006 and 2012

Background. Physical activity is associated with a lower risk of cardiovascular outcomes, certain cancers and diabetes. The previous South African Comparative Risk Assessment (SACRA1) study assessed the attributable burden of low physical activity for 2000, but updated estimates are required, as well as an assessment of trends over time. Objective. To estimate the national prevalence of physical activity by age, year and sex and to quantify the burden of disease attributable to low physical activity in South Africa (SA) for 2000, 2006 and 2012. Methods. Comparative risk assessment methodology was used. Physical activity was treated as a categorical variable with four categories, i.e. inactive, active, very active and highly active. Prevalence estimates of physical activity levels, representing the three different years, were derived from two national surveys. Physical activity estimates together with the relative risks from the Global Burden of Disease, Injuries, and Risk Factors (GBD) 2016 study were used to calculate population attributable fractions due to inactive, active and very active levels of physical activity relative to highly active levels considered to be the theoretical minimum risk exposure (>8 000 metabolic equivalent of time (MET)-min/wk), in accordance with the GBD 2016 study. These were applied to relevant disease outcomes sourced from the Second National Burden of Disease Study to calculate attributable deaths, years of life lost, years lived with disability and disability adjusted life years (DALYs). Uncertainty analysis was performed using Monte Carlo simulation. Results. The prevalence of physical inactivity (<600 METS) decreased by 16% and 8% between 2000 and 2012 for females and males, respectively. Attributable DALYs due to low physical activity increased between 2000 (n=194 284) and 2006 (n=238 475), but decreased thereafter in 2012 (n=219 851). The attributable death age-standardised rates (ASRs) declined between 2000 and 2012 from 60/100 000 population in 2000 to 54/100 000 population in 2012. Diabetes mellitus type 2 displaced ischaemic heart disease as the largest contributor to attributable deaths, increasing from 31% in 2000 to 42% in 2012. Conclusions. Low physical activity is responsible for a large portion of disease burden in SA. While the decreased attributable death ASR due to low physical activity is encouraging, this burden may be lowered further with an additional reduction in the overall prevalence of physical inactivity, in particular. It is concerning that the attributable burden for diabetes mellitus is growing, which suggests that existing non-communicable disease policies need better implementation, with ongoing surveillance of physical activity, and population- and community-based interventions are required in order to reach set targets

Estimating the changing disease burden attributable to high body mass index for South Africa for 2000, 2006 and 2012

Background. A high body mass index (BMI) is associated with several cardiovascular diseases, diabetes and chronic kidney disease, cancers, and other selected health conditions. Objectives. To quantify the deaths and disability-adjusted life years (DALYs) attributed to high BMI in persons aged ≥20 years in South Africa (SA) for 2000, 2006 and 2012. Methods. The comparative risk assessment (CRA) methodology was followed. Meta-regressions of the BMI mean and standard deviation from nine national surveys spanning 1998 - 2017 were conducted to provide estimates by age and sex for adults aged ≥20 years. Population attributable fractions were calculated for selected health outcomes using relative risks identified by the Global Burden of Disease Study (2017), and applied to deaths and DALY estimates from the second South African National Burden of Disease Study to estimate the burden attributed to high BMI in a customised Microsoft Excel workbook. Monte Carlo simulation-modelling techniques were used for the uncertainty analysis. BMI was assumed to follow a log-normal distribution, and the theoretical minimum value of BMI below which no risk was estimated was assumed to follow a uniform distribution from 20 kg/m2 to 25 kg/m2. Results. Between 2000 and 2012, mean BMI increased by 6% from 27.7 kg/m2 (95% confidence interval (CI) 27.6 - 27.9) to 29.4 kg/m2 (95% CI 29.3 - 29.5) for females, and by 3% from 23.9 kg/m2 (95% CI 23.7 - 24.1) to 24.6 kg/m2 (95% CI 24.5 - 24.8) for males. In 2012, high BMI caused 58 757 deaths (95% uncertainty interval (UI) 46 740 - 67 590) or 11.1% (95% UI 8.8 - 12.8) of all deaths, and 1.42 million DALYs (95% UI 1.15 - 1.61) or 6.9% (95% UI 5.6 - 7.8) of all DALYs. Over the study period, the burden in females was ~1.5 - 1.8 times higher than that in males. Type 2 diabetes mellitus became the leading cause of death attributable to high BMI in 2012 (n=12 382 deaths), followed by hypertensive heart disease (n=12 146), haemorrhagic stroke (n=9 141), ischaemic heart disease (n=7 499) and ischaemic stroke (n=4 044). The age-standardised attributable DALY rate per 100 000 population for males increased by 6.6% from 3 777 (95% UI 2 639 - 4 869) in 2000 to 4 026 (95% UI 2 831 - 5 115) in 2012, while it increased by 7.8% for females from 6 042 (95% UI 5 064 - 6 702) to 6 513 (95% UI 5 597 - 7 033). Conclusion. Average BMI increased between 2000 and 2012 and accounted for a growing proportion of total deaths and DALYs. There is a need to develop, implement and evaluate comprehensive interventions to achieve lasting change in the determinants and impact of overweight and obesity, particularly among women

Estimating the burden of disease attributable to a diet low in fruit and vegetables in South Africa for 2000, 2006 and 2012

Background. Low intake of fruit and vegetables is associated with an increased risk of various non-communicable diseases, including major causes of death and disability such as cardiovascular disease, diabetes mellitus and cancers. Diets low in fruit and vegetables are prevalent in the South African (SA) population, and average intake is well below the internationally recommended threshold. Objectives. To estimate the burden of disease attributable to a diet low in fruit and vegetables by sex and age group in SA for the years 2000, 2006 and 2012. Methods. We followed World Health Organization and Global Burden of Disease Study comparative risk assessment methodology. Population attributable fractions – calculated from fruit and vegetable intake estimated from national and local surveys and relative risks for health outcomes based on the current literature – were applied to the burden estimates from the second South African National Burden of Disease Study (SANBD2). Outcome measures included deaths and disability-adjusted life years (DALYs) lost from ischaemic heart disease, stroke, type 2 diabetes, and five categories of cancers. Results. Between 2000 and 2012, the average intake of fruit of the SA adult population (≥25 years) declined by 7%, from 48.5 g/d (95% uncertainty interval (UI) 46.6 - 50.5) to 45.2 g/d (95% UI 42.7 - 47.6). Vegetable intake declined by 25%, from 146.9 g/d (95% UI 142.3 - 151.8) to 110.5 g/d (95% UI 105.9 - 115.0). In 2012, these consumption patterns are estimated to have caused 26 423 deaths (95% UI 24 368 - 28 006), amounting to 5.0% (95% UI 4.6 - 5.3%) of all deaths in SA, and the loss of 514 823 (95% UI 473 508 - 544 803) healthy life years or 2.5% (95% UI 2.3 - 2.6%) of all DALYs. Cardiovascular disease comprised the largest proportion of the attributable burden, with 83% of deaths and 84% of DALYs. Age-standardised death rates were higher for males (145.1 deaths per 100 000; 95% UI 127.9 - 156.2) than for females (108.0 deaths per 100 000; 95% UI 96.2 - 118.1); in both sexes, rates were lower than those observed in 2000 (–9% and –12%, respectively). Conclusion. Despite the overall reduction in standardised death rates observed since 2000, the absolute burden of disease attributable to inadequate intake of fruit and vegetables in SA remains of significant concern. Effective interventions supported by legislation and policy are needed to reverse the declining trends in consumption observed in most age categories and to curb the associated burden