Java unit testing tool competition

We report on the results of the eighth edition of the Java unit testing tool competition. This year, two tools, EvoSuite and Randoop, were executed on a benchmark with (i) new classes under test, selected from open-source software projects, and (ii) the set of classes from one project considered in the previous edition. We relied on an updated infrastructure for the execution of the different tools and the subsequent coverage and mutation analysis based on Docker containers. We considered two different time budgets for test case generation: one an three minutes. This paper describes our methodology and statistical analysis of the results, presents the results achieved by the contestant tools and highlights the challenges we faced during the competition

Submicroscopic carriage of Plasmodium falciparum and Plasmodium vivax in a low endemic area in Ethiopia where no parasitaemia was detected by microscopy or rapid diagnostic test.

BACKGROUND: Motivated by the success in malaria control that was documented over the last decade Ethiopia is aiming at malaria elimination by 2020 in selected districts. It is currently unknown if asymptomatic, submicroscopic malaria parasite carriage may form a hurdle to achieve elimination. The elimination effort may further be complicated by possible glucose-6 phosphate dehydrogenase (G6PD) deficiency which would hinder the use of 8-aminoquinolines in the elimination efforts. METHOD: In February 2014 a community-based cross-sectional survey was conducted in Malo, southwest Ethiopia. Finger-prick blood samples (n = 555) were tested for presence of Plasmodium falciparum and Plasmodium vivax with microscopy, rapid diagnostic test (RDT), and nested polymerase chain reaction (nPCR). Multiplicity of P. falciparum infections was determined based on genotyping the polymorphic merozoite surface protein-2 (MSP-2) gene. Individuals were also genotyped for mutations in the gene that produces G6PD. RESULTS: All study participants were malaria infection negative by microscopy and RDT. Nested PCR revealed P. falciparum mono-infection in 5.2% (29/555), P. vivax mono-infection in 4.3% (24/555) and mixed infection in 0.2% (1/555) of individuals. All parasitemic individuals were afebrile (axillary temperature <37.5°C). None of the study participants carried mutations for the G6PD African A-(202GA) and Mediterranean (563CT) variants. All infections, except one, were single-clone infection by MSP-2 genotyping. CONCLUSION: The detection of a substantial number of subpatent malaria infections in an apparently asymptomatic population without evidence for malaria transmission by conventional diagnostics raises questions about the path to malaria elimination. It is currently unknown how important these infections are for sustaining malaria transmission in the study sites. The absence of G6PD deficiency indicates that 8-aminoquinolines may be safely deployed to accelerate elimination initiatives

Comprehensive vs. Assisted Management of Mood and Pain Symptoms (CAMMPS) trial: Study design and sample characteristics

Background Pain is the most common presenting somatic symptom in medical outpatients, and depression and anxiety are the two most common mental disorders. They frequently co-occur, are under-treated, and result in substantial disability and reduced health-related quality of life. Objectives The Comprehensive vs. Assisted Management of Mood and Pain Symptoms (CAMMPS) study is a randomized comparative effectiveness trial designed to test the relative effectiveness of a lower-resource vs. a higher-resource technology-assisted intervention for the management of patients suffering from pain plus anxiety and/or depression. Methods/design CAMMPS has enrolled 294 primary care patients with chronic pain plus comorbid anxiety and/or depression and randomized them to either: 1) Assisted Symptom Management (ASM) consisting of automated symptom monitoring by interactive voice recording or Internet and prompted pain and mood self-management; or 2) Comprehensive Symptom Management (CSM) which combines ASM with optimized medication management delivered by a nurse-physician specialist team and facilitated mental health care. Outcomes are assessed at baseline, 1, 3, 6, and 12 months. The primary outcome is a composite pain-anxiety-depression (PAD) severity score. Secondary outcomes include individual pain, anxiety, and depression scores, health-related quality of life, disability, healthcare utilization, and treatment satisfaction. Discussion CAMMPS provides an integrated approach to PAD symptoms rather than fragmented care of single symptoms; coordinated symptom management in partnership with primary care clinicians and psychologists embedded in primary care; efficient use of health information technology; attention to physical and psychological symptom comorbidity; and the coupling of self-management with optimized medication management and facilitated mental health care

Molecular Markers for Sensitive Detection of Plasmodium falciparum Asexual Stage Parasites and their Application in a Malaria Clinical Trial.

Plasmodium falciparum parasite life stages respond differently to antimalarial drugs. Sensitive stage-specific molecular assays may help to examine parasite dynamics at microscopically detectable and submicroscopic parasite densities in epidemiological and clinical studies. In this study, we compared the performance of skeleton-binding protein 1 (SBP1), ring-infected erythrocyte surface antigen, Hyp8, ring-exported protein 1 (REX1), and PHISTb mRNA for detecting ring-stage trophozoite-specific transcripts using quantitative reverse transcriptase polymerase chain reaction. Markers were tested on tightly synchronized in vitro parasites and clinical trial samples alongside established markers of parasite density (18S DNA and rRNA) and gametocyte density (Pfs25 mRNA). SBP1 was the most sensitive marker but showed low-level expression in mature gametocytes. Novel markers REX1 and PHISTb showed lower sensitivity but higher specificity for ring-stage trophozoites. Using in vivo clinical trial samples from gametocyte-negative patients, we observed evidence of persisting trophozoite transcripts for at least 14 days postinitiation of treatment. It is currently not clear if these transcripts represent viable parasites that may have implications for clinical treatment outcome or transmission potential

The shape of the iceberg: quantification of submicroscopic Plasmodium falciparum and Plasmodium vivax parasitaemia and gametocytaemia in five low endemic settings in Ethiopia.

BACKGROUND: The widespread presence of low-density asymptomatic infections with concurrent gametocytes may be a stumbling block for malaria elimination. This study investigated the asymptomatic reservoir of Plasmodium falciparum and Plasmodium vivax infections in schoolchildren from five settings in northwest Ethiopia. METHODS: Two cross-sectional surveys were conducted in June and November 2015, enrolling 551 students from five schools and 294 students from three schools, respectively. Finger prick whole blood and plasma samples were collected. The prevalence and density of P. falciparum and P. vivax parasitaemia and gametocytaemia were determined by 18S rRNA quantitative PCR (qPCR) and pfs25 and pvs25 reverse transcriptase qPCR. Antibodies against blood stage antigens apical membrane antigen-1 (AMA-1) and merozoite surface protein-1 (MSP-119) were measured for both species. RESULTS: Whilst only 6 infections were detected by microscopy in 881 slides (0.7%), 107 of 845 blood samples (12.7%) were parasite positive by (DNA-based) qPCR. qPCR parasite prevalence between sites and surveys ranged from 3.8 to 19.0% for P. falciparum and 0.0 to 9.0% for P. vivax. The median density of P. falciparum infections (n = 85) was 24.4 parasites/µL (IQR 18.0-34.0) and the median density of P. vivax infections (n = 28) was 16.4 parasites/µL (IQR 8.8-55.1). Gametocyte densities by (mRNA-based) qRT-PCR were strongly associated with total parasite densities for both P. falciparum (correlation coefficient = 0.83, p = 0.010) and P. vivax (correlation coefficient = 0.58, p = 0.010). Antibody titers against P. falciparum AMA-1 and MSP-119 were higher in individuals who were P. falciparum parasite positive in both surveys (p < 0.001 for both comparisons). DISCUSSION: This study adds to the available evidence on the wide-scale presence of submicroscopic parasitaemia by quantifying submicroscopic parasite densities and concurrent gametocyte densities. There was considerable heterogeneity in the occurrence of P. falciparum and P. vivax infections and serological markers of parasite exposure between the examined low endemic settings in Ethiopia

Micro water harvesting for climate change mitigation: Trade-offs between health and poverty reduction in Northern Ethiopia

Water harvesting is an important tool for mitigating the adverse effects of climate change. This report investigates the trade-offs between health and poverty reduction by considering the impacts of water harvesting on health in Tigray region, northern Ethiopia. In particular, we assess the prevalence of malaria in association with ponds and wells. Moreover, the determinants of malaria incidence are explored with multivariate analysis. Additionally, we investigate people¿s willingness to pay (WTP) for improved malaria control using a contingent valuation method (CVM). In particular, we applied a double-bounded dichotomous choice CV surveys to elicit households¿ WTP for improved health services to control malaria. With interval regression, the WTP was explained as a function of household characteristics, health and health service conditions, and village level factors. The malaria prevalence rate is very high, more than 30 percent in low land communities, although rates are higher after rainy season. This suggests that ponds and wells are important factors in determining the prevalence of malaria. Better conditions of housing and toilet type, availability of bed nets reduce incidence. Pond and well ownership affects the WTP for improved malaria control in a negative and positive way respectively indicating differences in their economic attractiveness. WTP decreases with altitude and thus malaria incidence. Education and household asset holding generally increases WTP for improved health services. The results suggest that valuation results on household¿s WTP in poor economies may be underestimated because of cash constraint. Consequently, alternative payment vehicles in eliciting households¿ WTP have to be considered. Similarly, the estimated mean WTP for the external health cost of wells and ponds may be underestimated. In our case, ponds and wells are not fully exploited, as our results suggest that they do not contribute to household income or welfare. In that case, the presence of ponds and wells pose high external costs to the econom

Past eight-year malaria data in Gedeo zone, southern Ethiopia: trend, reporting-quality, spatiotemporal distribution, and association with socio-demographic and meteorological variables.

BACKGROUND: Informed decision making is underlined by all tiers in the health system. Poor data record system coupled with under- (over)-reporting of malaria cases affects the country's malaria elimination activities. Thus, malaria data at health facilities and health offices are important particularly to monitor and evaluate the elimination progresses. This study was intended to assess overall reported malaria cases, reporting quality, spatiotemporal trends and factors associated in Gedeo zone, South Ethiopia. METHODS: Past 8 years retrospective data stored in 17 health centers and 5 district health offices in Gedeo Zone, South Ethiopia were extracted. Malaria cases data at each health center with sociodemographic information, between January 2012 and December 2019, were included. Meteorological data were obtained from the national meteorology agency of Ethiopia. The data were analyzed using Stata 13. RESULTS: A total of 485,414 suspected cases were examined for malaria during the previous 8 years at health centers. Of these suspects, 57,228 (11.79%) were confirmed malaria cases with an overall decline during the 8-year period. We noted that 3758 suspected cases and 467 confirmed malaria cases were not captured at the health offices. Based on the health centers records, the proportions of Plasmodium falciparum (49.74%) and P. vivax (47.59%) infection were nearly equivalent (p = 0.795). The former was higher at low altitudes while the latter was higher at higher altitudes. The over 15 years of age group accounted for 11.47% of confirmed malaria cases (p < 0.001). There was high spatiotemporal variation: the highest case record was during Belg (12.52%) and in Dilla town (18,150, 13.17%, p < 0.001) which is located at low altitude. Monthly rainfall and minimum temperature exhibited strong associations with confirmed malaria cases. CONCLUSION: A notable overall decline in malaria cases was observed during the eight-year period. Both P. falciparum and P. vivax were found at equivalent endemicity level; hence control measures should continue targeting both species. The noticed under reporting, the high malaria burden in urban settings, low altitudes and Belg season need spatiotemporal consideration by the elimination program

Gametocyte Sex Ratio: The Key to Understanding Plasmodium falciparum Transmission?

A mosquito needs to ingest at least one male and one female gametocyte to become infected with malaria. The sex of Plasmodium falciparum gametocytes can be determined microscopically but recent transcriptomics studies paved the way for the development of molecular methods that allow sex-ratio assessments at much lower gametocyte densities. These sex-specific gametocyte diagnostics were recently used to examine gametocyte dynamics in controlled and natural infections as well as the impact of different antimalarial drugs. It is currently unclear to what extent sex-specific gametocyte diagnostics obviate the need for mosquito feeding assays to formally assess transmission potential. Here, we review recent and historic assessments of gametocyte sex ratio in relation to host and parasite characteristics, treatment, and transmission potential

Semi-high-throughput detection of Plasmodium falciparum and Plasmodium vivax oocysts in mosquitoes using bead-beating followed by circumsporozoite ELISA and quantitative PCR.

BACKGROUND: The malaria infection status of mosquitoes is commonly determined by microscopic detection of oocysts on the dissected mosquito midgut. This method is labour-intensive, does not allow processing of large numbers of mosquitoes and can be challenging in terms of objective classification of oocysts. Here, a semi-high-throughput bead-beating ELISA method is proposed for detection of the circumsporozoite protein (CSP) followed by confirmation by quantitative PCR (qPCR). METHODS: Cultured Plasmodium falciparum gametocytes were offered to Anopheles stephensi mosquitoes and examined by microscopy. After bead-beating, mosquito homogenate was examined by CSP-ELISA and 18S qPCR. As negative controls, mosquitoes that were offered a heat-inactivated gametocyte blood meal were used. The CSP-ELISA/qPCR methodology was applied to high and low-intensity infections of cultured P. falciparum gametocytes. A similar methodology optimized for P. vivax was used on mosquitoes that were offered blood from Ethiopian donors who were naturally infected with P. vivax. RESULTS: There was considerable variation in CSP-ELISA signal and qPCR values in mosquitoes with low oocyst intensities. There was a strong agreement mosquito positivity by CSP-ELISA and by qPCR in mosquitoes that fed on cultured P. falciparum material (agreement 96.9%; kappa = 0.97) and naturally infected P. vivax parasite carriers [agreement 92.4% (kappa = 0.83)]. CONCLUSIONS: The proposed bead-beating CSP-ELISA/qPCR methodology considerably increases throughput for the detection of mosquito infection. qPCR remains necessary to confirm infections in mosquitoes with low CSP-ELISA signal. This methodology may prove particularly useful for studies where very low mosquito infection prevalence is expected and study sites where experience with oocyst detection is limited