Project description:Classification is a common technique applied to 'omics data to build predictive models and identify potential markers of biomedical outcomes. Despite the prevalence of case-control studies, the number of classification methods available to analyze data generated by such studies is extremely limited. Conditional logistic regression is the most commonly used technique, but the associated modeling assumptions limit its ability to identify a large class of sufficiently complicated 'omic signatures. We propose a data preprocessing step which generalizes and makes any linear or nonlinear classification algorithm, even those typically not appropriate for matched design data, available to be used to model case-control data and identify relevant biomarkers in these study designs. We demonstrate on simulated case-control data that both the classification and variable selection accuracy of each method is improved after applying this processing step and that the proposed methods are comparable to or outperform existing variable selection methods. Finally, we demonstrate the impact of conditional classification algorithms on a large cohort study of children with islet autoimmunity.
Project description:BackgroundA school preventive chemotherapy (PC) program for soil-transmitted helminths (STHs) and schistosomiasis has operated in Huambo, Uige and Zaire provinces, Angola, since 2013 and 2014, respectively; complemented by a school water, sanitation and hygiene (WASH) program in a subset of schools from 2016. Conducted in 2021, this is the first impact assessment of the school program for the control of schistosomiasis and STHs.Methodology/principal findingsA two-stage cluster design was used to select schools and schoolchildren for parasitological and WASH surveys. The rapid diagnostic tests (RDTs), point of care circulating cathodic antigen (POC-CCA) and Hemastix, were used to estimate Schistosoma mansoni and Schistosoma haematobium prevalence, respectively. Kato Katz was used to detect STHs, and quantify STH and S. mansoni infections. Urine filtration was used to quantify S. haematobium infections. Prevalence, infection intensity, relative prevalence reduction and egg reduction rates were calculated for schistosomiasis and STHs. Cohen's Kappa co-efficient was used to assess agreement between RDTs and microscopy. Chi-square or Fisher's exact test was used to compare WASH indicators in WASH-supported and WASH-unsupported schools. Overall, 17,880 schoolchildren (599 schools) and 6,461 schoolchildren (214 schools) participated in the schistosomiasis and STH surveys, respectively. Prevalence of any schistosomiasis in Huambo was 29.6%, Uige 35.4%, and Zaire 28.2%. Relative reduction in schistosomiasis prevalence from 2014 for Huambo was 18.8% (95% confidence interval (CI) 8.6, 29.0), Uige -92.3% (95%CI -162.2, -58.3), and Zaire -14.0% (95%CI -48.6, 20.6). Prevalence of any STH in Huambo was 16.3%, Uige 65.1%, and Zaire 28.2%. Relative reduction in STH prevalence for Huambo was -28.4% (95%CI -92.1, 35.2), Uige -10.7% (95%CI -30.2, 8.8), and Zaire -20.9% (95%CI -79.5, 37.8). A higher proportion of WASH-supported schools had improved water sources, and toilet and handwashing facilities compared to WASH-unsupported schools.Conclusions/significanceThe limited impact this school program has had in controlling schistosomiasis and STHs identifies the need for a comprehensive understanding of individual, community, and environmental factors associated with transmission, and consideration for a community-wide control program.
Project description:BackgroundCurrent guidelines and targets for soil-transmitted helminth (STH) control focus on school-based deworming for school-age children, given the high risk of associated morbidity in this age group. However, expanding deworming to all age groups may achieve improved STH control among both the community in general and school-age children, by reducing their risk of reinfection. This trial aims to compare school-based targeted deworming with community-wide mass deworming in terms of impact on STH infections among school-age children.MethodsThe CoDe-STH (Community Deworming against STH) trial is a cluster-randomised controlled trial (RCT) in 64 primary schools in Dak Lak province, Vietnam. The control arm will receive one round of school-based targeted deworming with albendazole, while in the intervention arm, community-wide mass deworming with albendazole will be implemented alongside school-based deworming. Prevalence of STH infections will be measured in school-age children at baseline and 12 months following deworming. The primary outcome is hookworm prevalence in school-age children at 12 months, by quantitative PCR. Analysis will be intention-to-treat, with outcomes compared between study arms using generalised linear and non-linear mixed models. Additionally, cost-effectiveness of mass and targeted deworming will be calculated and compared, and focus group discussions and interviews will be used to assess acceptability and feasibility of deworming approaches. Individual based stochastic models will be used to predict the impact of mass and targeted deworming strategies beyond the RCT timeframe to assess the likelihood of parasite population 'bounce-back' if deworming is ceased due to low STH prevalence.DiscussionThe first large-scale trial comparing mass and targeted deworming for STH control in South East Asia will provide key information for policy makers regarding the optimal design of STH control programs.Trial registrationACTRN12619000309189 .
Project description:BackgroundHelminth infections caused by parasitic worms, including nematodes (roundworms), cestodes (tapeworms) and trematodes (flukes), can cause chronic symptoms and serious clinical outcomes if left untreated. The US military frequently conducts activities in helminth-endemic regions, particularly Africa, the Middle East and Southeast Asia. However, the military does not currently screen for these infections, and to date, no comprehensive surveillance studies have been completed to assess the frequency of helminth diagnoses in the military personnel and their families.MethodsTo determine the burden of helminth infections in the US Military Health System (MHS), we conducted a retrospective analysis of International Classification of Diseases (ICD)-9/10 diagnosis codes from all medical encounters in the MHS Data Repository (MDR) from fiscal years (FY) 2012 to 2018. Chart reviews were conducted to assign ICD diagnoses as incorrect, suspected, probable or confirmed based on the laboratory results and symptoms.ResultsAbstraction of MHS data revealed over 50 000 helminth diagnoses between FY 2012 and FY 2018. Of these, 38 445 of diagnoses were amongst unique subjects. After chart review, we found there were 34 425 validated helminth infections diagnosed amongst the unique subjects of US military personnel, retirees and dependents. Nearly 4000 of these cases represented infections other than enterobiasis. There were 351 validated strongyloidiasis diagnoses, 317 schistosomiasis diagnoses and 191 diagnoses of cysticercosis during the study period. Incidence of intestinal nematode infection diagnoses showed an upward trend, whilst the incidence of cestode infection diagnoses decreased.ConclusionsThe results of this study demonstrate that helminth infections capable of causing severe morbidity are often diagnosed in the US military. As helminth infections are often asymptomatic or go undiagnosed, the true burden of helminth infections in US military personnel and dependents may be higher than observed here. Prospective studies of US military personnel deployed to helminth-endemic areas may be indicated to determine if post-deployment screening and/or empirical treatment are warranted.
Project description:BackgroundThe crater lakes of Barombi Mbo and Barombi Kotto are well-known transmission foci of schistosomiasis and soil-transmitted helminthiasis having had several important control initiatives previously. To collect contemporary epidemiological information, a cross-sectional survey was undertaken inclusive of: signs and symptoms of disease, individual treatment histories, local water, sanitation and hygiene (WASH)-related factors and malacological surveillance, with molecular characterisation of specimens.MethodsAt each lake, a community cross-sectional survey was undertaken using a combination of stool and urine parasitological sampling, and interview with pro-forma questionnaires. A total of 338 children and adults participated. Material from snail and parasite species were characterised by DNA methods.ResultsEgg-patent prevalence of urogenital schistosomiasis was 8.7% at Barombi Mbo (all light-intensity infections) and 40.1% at Barombi Kotto (21.2% heavy-intensity infections). Intestinal schistosomiasis was absent. At Barombi Kotto, significantly more women reported signs and symptoms associated with female genital schistosomiasis. While there had been extensive recent improvement in WASH-related infrastructure at Barombi Mbo, water contact risk scores were higher among schistosomiasis-infected participants (P < 0.001) and at Barombi Kotto in general (P < 0.001). Across both lakes, mean prevalence of STH was very low (6.3%) evidencing an impressive decrease of 79.0% over the last decade; neither Strongyloides stercoralis nor Ascaris lumbricoides were found. A total of 29 freshwater sampling sites were inspected for snails, 13 in Barombi Mbo and 16 in Barombi Kotto; water chemistry differed significantly (P < 0.0001) between lakes for both mean pH (7.9 v. 9.6) and mean conductivity (64.3 μS v. 202.1 μS) respectively. Only two Bulinus camerunensis found on the central island of Barombi Kotto were observed to shed schistosome cercariae, but schistosome DNA was later detected in Bulinus sampled from both lakes as well as in Indoplanorbis exustus, an invasive species from Asia.ConclusionsSTH is currently at very low levels while urogenital schistosomiasis is of greatest concern at Barombi Kotto. This assessment highlights a unique opportunity for further study of the epidemiological dynamics at these crater lakes, to evaluate future intensified interventions both in terms of gaining and sustaining control at Barombi Kotto or in moving towards local interruption of transmission of both diseases at Barombi Mbo.
Project description:BACKGROUND: In 2004 Niger established a large scale schistosomiasis and soil-transmitted helminths control programme targeting children aged 5-14 years and adults. In two years 4.3 million treatments were delivered in 40 districts using school based and community distribution. METHOD AND FINDINGS: Four districts were surveyed in 2006 to estimate the economic cost per district, per treatment and per schistosomiasis infection averted. The study compares the costs of treatment at start up and in a subsequent year, identifies the allocation of costs by activity, input and organisation, and assesses the cost of treatment. The cost of delivery provided by teachers is compared to cost of delivery by community distributers (CDD). The total economic cost of the programme including programmatic, national and local government costs and international support in four study districts, over two years, was US$ 456,718; an economic cost/treatment of $0.58. The full economic delivery cost of school based treatment in 2005/06 was $0.76, and for community distribution was $0.46. Including only the programme costs the figures are $0.47 and $0.41 respectively. Differences at sub-district are more marked. This is partly explained by the fact that a CDD treats 5.8 people for every one treated in school. The range in cost effectiveness for both direct and direct and indirect treatments is quantified and the need to develop and refine such estimates is emphasised. CONCLUSIONS: The relative cost effectiveness of school and community delivery differs by country according to the composition of the population treated, the numbers targeted and treated at school and in the community, the cost and frequency of training teachers and CDDs. Options analysis of technical and implementation alternatives including a financial analysis should form part of the programme design process.
Project description:The World Health Organization recommends anthelminthic treatment for pregnant women after the first trimester in soil-transmitted helminth (STH) endemic regions to prevent adverse maternal-fetal consequences. Although studies have shown the high prevalence of infection in the Philippines, no research has evaluated deworming practices. We hypothesized that pregnant women are not receiving deworming treatment and we aimed to identify barriers to World Health Organization guideline implementation. We conducted key informant interviews with local Department of Health (DOH) administrators, focus group discussions with nurses, midwives, and health care workers, and knowledge, attitudes, and practices surveys with women of reproductive age to elicit perspectives about deworming during pregnancy. Key informant interviews revealed that healthcare workers were not deworming pregnant women due to inadequate drug supply, infrastructure and personnel as well as fear of teratogenicity. Focus group discussions showed that healthcare workers similarly had not implemented guidelines due to infrastructure challenges and concerns for fetal malformations. The majority of local women believed that STH treatment causes side effects (74.8%) as well as maternal harm (67.3%) and fetal harm (77.9%). Women who were willing to take anthelminthics while pregnant had significantly greater knowledge as demonstrated by higher Treatment Scores (mean rank 146.92 versus 103.1, z?=?-4.40, p<0.001) and higher Birth Defect Scores (mean rank 128.09 versus 108.65, z?=?-2.43, p?=?0.015). This study concludes that World Health Organization guidelines are not being implemented in the Philippines. Infrastructure, specific protocols, and education for providers and patients regarding anthelminthic treatment are necessary for the successful prevention of STH morbidity and mortality among pregnant women.
Project description:We use nonverbal and verbal emotion cues to determine how others are feeling. Most studies in vocal emotion perception do not consider the influence of verbal content, using sentences with nonsense words or words that carry no emotional meaning. These online studies aimed to validate 95 sentences with verbal content intended to convey 10 emotions. Participants were asked to select the emotion that best described the emotional meaning of the sentence. Study 1 included 436 participants and Study 2 included 193. The Simpson diversity index was applied as a measure of dispersion of responses. Across the two studies, 38 sentences were labelled as representing 10 emotion categories with a low degree of diversity in participant responses. Expanding current databases beyond basic emotion categories is important for researchers exploring the interaction between tone of voice and verbal content, and/or people's capacity to make subtle distinctions between their own and others' emotions.
Project description:BackgroundSoil-transmitted helminth (STH) infections remain highly endemic across the Philippines, and are believed to be important contributors to delayed cognitive development of school-aged children. Identification of communities where children are at risk of functional illiteracy is important for the attainment of Sustainable Development Goals target for literacy. We aimed to quantify the associations between the spatial variation of STH infections and functional literacy indicators adjusting for other important contributors, and identify priority areas in the Philippines in need of interventions.Methodology/principal findingsWe used data from 11,313 school-aged children on functional literacy indicators collected in 2008. Nested fixed-effects multinomial regression models were built to determine associations between STH endemicity and geographical distribution of functional literacy, adjusting for demographics, household level variables, and the prevalence of malaria. Bayesian multinomial geostatistical models were built to geographically predict the prevalence of each level of functional literacy. The number of school-aged children belonging to each of the functional literacy indicator classes was forecast for 2017. We estimated 4.20% of functional illiteracy burden among school-aged children in Mindanao might be averted by preventing T. trichiura infections. Areas predicted with the highest prevalence of functional illiteracy were observed in localised areas of the eastern region of the Visayas, and the south-eastern portion of Mindanao.Conclusions/significanceThe study demonstrates significant geographical variation in burden of functional illiteracy in school-aged children associated with STH infections suggesting that targeted helminth control could potentially promote the development of cognitive function of school-aged children in the Philippines. The benefits of a spatially targeted strategy should be tested by future studies.