Examining potential confounding factors in gene expression analysis of human saliva and identifying potential housekeeping genes.

Isolation of RNA from whole saliva, a non-invasive and easily accessible biofluid that is an attractive alternative to blood for high-throughput biodosimetry of radiological/nuclear victims might be of clinical significance for prediction and diagnosis of disease. In a previous analysis of 12 human samples we identified two challenges to measuring gene expression from total RNA: (1) the fraction of human RNA in whole saliva was low and (2) the bacterial contamination was overwhelming. To overcome these challenges, we performed selective cDNA synthesis for human RNA species only by employing poly(A)+-tail primers followed by qRT-PCR. In the current study, this approach was independently validated on 91 samples from 61 healthy donors. Additionally, we used the ratio of human to bacterial RNA to adjust the input RNA to include equal amounts of human RNA across all samples before cDNA synthesis, which then ensured comparable analysis using the same base human input material. Furthermore, we examined relative levels of ten known housekeeping genes, and assessed inter- and intra-individual differences in 61 salivary RNA isolates, while considering effects of demographical factors (e.g. sex, age), epidemiological factors comprising social habits (e.g. alcohol, cigarette consumption), oral hygiene (e.g. flossing, mouthwash), previous radiological diagnostic procedures (e.g. number of CT-scans) and saliva collection time (circadian periodic). Total human RNA amounts appeared significantly associated with age only (P ≤ 0.02). None of the chosen housekeeping genes showed significant circadian periodicity and either did not associate or were weakly associated with the 24 confounders examined, with one exception, 60% of genes were altered by mouthwash. ATP6, ACTB and B2M represented genes with the highest mean baseline expression (Ct-values ≤ 30) and were detected in all samples. Combining these housekeeping genes for normalization purposes did not decrease inter-individual variance, but increased the robustness. In summary, our work addresses critical confounders and provides important information for the successful examination of gene expression in human whole saliva.

Clean Cut (adaptive, multimodal surgical infection prevention programme) for low-resource settings: a prospective quality improvement study.

BACKGROUND: Clean Cut is an adaptive, multimodal programme to identify improvement opportunities and safety changes in surgery by enhancing outcomes surveillance, closing gaps in surgical infection prevention standards, and strengthening underlying processes of care. Surgical-site infections (SSIs) are common in low-income countries, so this study assessed a simple intervention to improve perioperative infection prevention practices in one. METHODS: Clean Cut was implemented in five hospitals in Ethiopia from August 2016 to October 2018. Compliance data were collected from the operating room focused on six key perioperative infection prevention standards. Process-mapping exercises were employed to understand barriers to compliance and identify locally driven improvement opportunities. Thirty-day outcomes were recorded on patients for whom intraoperative compliance information had been collected. RESULTS: Compliance data were collected from 2213 operations (374 at baseline and 1839 following process improvements) in 2202 patients. Follow-up was completed in 2159 patients (98·0 per cent). At baseline, perioperative teams complied with a mean of only 2·9 of the six critical perioperative infection prevention standards; following process improvement changes, compliance rose to a mean of 4·5 (P < 0·001). The relative risk of surgical infections after Clean Cut implementation was 0·65 (95 per cent c.i. 0·43 to 0·99; P = 0·043). Improved compliance with standards reduced the risk of postoperative infection by 46 per cent (relative risk 0·54, 95 per cent c.i. 0·30 to 0·97, for adherence score 3-6 versus 0-2; P = 0·038). CONCLUSION: The Clean Cut programme improved infection prevention standards to reduce SSI without infrastructure expenses or resource investments.

Ethiopia's transforming wheat landscape: tracking variety use through DNA fingerprinting.

Ethiopia is the largest wheat producer in sub-Saharan Africa yet remains a net importer. Increasing domestic wheat production is a national priority. Improved varieties provide an important pathway to enhancing productivity and stability of production. Reliably tracking varietal use and dynamics is a challenge, and the value of conventional recall surveys is increasingly questioned. We report the first nationally representative, large-scale wheat DNA fingerprinting study undertaken in Ethiopia. Plot level comparison of DNA fingerprinting with farmer recall from nearly 4000 plots in the 2016/17 season indicates that only 28% of farmers correctly named wheat varieties grown. The DNA study reveals that new, rust resistant bread wheat varieties are now widely adopted. Germplasm originating from CGIAR centres has made a significant contribution. Corresponding productivity gains and economic benefits have been substantial, indicating high returns to investments in wheat improvement. The study provides an accurate assessment of wheat varietal status and sets a benchmark for national policy-makers and donors. In recent decades, the Ethiopian wheat landscape has transformed from local tetraploid varieties to widespread adoption of high yielding, rust resistant bread wheat. We demonstrate that DNA fingerprinting can be applied at scale and is likely to transform future crop varietal adoption studies.

Using phenotypic distribution models to predict livestock performance.

Livestock production systems of the developing world use indigenous breeds that locally adapted to specific agro-ecologies. Introducing commercial breeds usually results in lower productivity than expected, as a result of unfavourable genotype by environment interaction. It is difficult to predict of how these commercial breeds will perform in different conditions encountered in e.g. sub-Saharan Africa. Here, we present a novel methodology to model performance, by using growth data from different chicken breeds that were tested in Ethiopia. The suitability of these commercial breeds was tested by predicting the response of body weight as a function of the environment across Ethiopia. Phenotype distribution models were built using machine learning algorithms to make predictions of weight in the local environmental conditions based on the productivity for the breed. Based on the predicted body weight, breeds were assigned as being most suitable in a given agro-ecology or region. We identified the most important environmental variables that explained the variation in body weight across agro-ecologies for each of the breeds. Our results highlight the importance of acknowledging the role of environment in predicting productivity in scavenging chicken production systems. The use of phenotype distribution models in livestock breeding is recommended to develop breeds that will better fit in their intended production environment.

Genetic characterization of Echinococcus species in eastern Ethiopia.

Cystic echinococcosis (CE) is a neglected zoonotic disease with considerable economic and public health burden worldwide, particularly affecting developing countries like Ethiopia. To initiate effective prevention and control of CE, comprehensive data on the local lifecycles of the various species/genotypes of Echinococcus are needed. In the present study, conducted in eastern Ethiopia, a total of 1106 livestock animals were examined at three slaughterhouses, which resulted in combined prevalence of morphologically and molecularly confirmed CE of 8.4% (75/891) in cattle, 1.1% (1/95) in sheep, 0.0% (0/95) in goats and 12.0% (3/25) in camels. All cystic lesions recovered during post mortem examination were assessed for cyst condition and underwent molecular characterization by PCR and sequencing of a 1081 bp fragment of the mitochondrial cox1 gene. A total of 175 cysts belonged to E. granulosus s.s. (n = 165), E. ortleppi (n = 6) and E. canadensis G6/7 (n = 4). Of all examined cysts, only 14 were fertile and contained protoscoleces, all from the lungs of cattle: 5 were E. granulosus s.s., 6 E. ortleppi and 3 E. canadensis G6/7. In sheep, only one sterile liver cyst of E. granulosus s.s. was found, while in camels seven sterile or caseated/calcified cysts of E. granulosus s.s. and E. canadensis G6/7 were found in liver and lungs. In conclusion, the prevalence of CE was rather low compared to other regions of Ethiopia, and, based on the number of fertile cysts, three Echinococcus spp. contributed almost equally to transmission. Cattle seem to be, epidemiologically, the most important livestock species. Our data provide a substantial basis for more detailed investigations of the transmission dynamics of CE in the study area.

Predictors of E-cigarette Use Among Young Australian Women.

INTRODUCTION: E-cigarette use is controversial worldwide. The majority of previous studies on e-cigarette use were not gender specific. This study aimed to identify the predictors of e-cigarette use among young Australian women. METHODS: This study used cross-sectional data from the 1989-1995 cohort of the Australian Longitudinal Study on Women's Health. In 2015, study participants (N=8,915) aged 19-26 years completed an online survey. Multivariable logistic regression was used to identify predictors of e-cigarette use. Data were analyzed in 2018. RESULTS: The prevalence of ever and past-year e-cigarette use among young Australian women was 11.1% and 6.4%, respectively. More than a quarter of past-year and ever e-cigarette users were never cigarette smokers. Use of e-cigarettes in the past year was associated with younger age (AOR per year increase=0.87, 95% CI=0.82, 0.93); financial difficulty (AOR=0.68, 95% CI=0.54, 0.87); being an ex-smoker (AOR=5.05, 95% CI=3.64, 7.01) or current cigarette smoker (AOR=10.01, 95% CI=7.77, 12.89); drinking at a level of lifetime risk of harm from alcohol-related disease or injury (AOR=1.23, 95% CI=1.01, 1.53). Ever e-cigarette use showed similar associations and was also associated with rural residence (AOR=0.74, 95% CI=0.60, 0.91) and intimate partner violence (AOR=1.44, 95% CI=1.17, 1.76). CONCLUSIONS: The high prevalence of e-cigarette use among never cigarette smokers has significant public health implications. Interventions to curb the use of e-cigarettes among young Australian women should focus on risk factors, such as early age, cigarette smoking, alcohol use, and intimate partner violence.

Effectiveness of pharmacotherapy for smoking cessation: protocol for umbrella review and quality assessment of systematic reviews.

BACKGROUND: In the long term, smoking cessation can decrease the risk of cancer, stroke, and heart attacks and improve overall survival. The aim of the proposed umbrella review is to summarize existing systematic reviews that assessed the effects of pharmacological interventions for smoking cessation and to evaluate the methodological quality of previously conducted systematic reviews. METHODS: Databases such as the Cochrane Library, PubMed, MEDLINE, EMBASE, CINAHIL PsychINFO Web of Science, Conference Papers Index, Scopus, and Google Scholar will be used to retrieve reviews. Systematic reviews which included only randomized control trials will be considered in this review. The primary outcome will be prolonged abstinence from smoking for a minimum of 6 months follow-up, and the secondary outcome will be point abstinence rate from smoking of less than 6 months follow-up but more than 7 days. Methodological quality of the included reviews will be assessed using the Assessment of Multiple Systematic Reviews 2 (AMSTAR 2) tool, which contains 16 domains. Two authors will screen the titles and abstracts of all reviews obtained by the search strategy, assess the full text of selected articles for inclusion, and extract data independently. The quality appraisal will be also assessed by two authors (AM, CC) independently, and Cohen's Kappa statistic will be used to assess inter-ratter agreement. The findings of the study will be narrated qualitatively to describe the effect of different pharmacotherapy on smoking cessation. DISCUSSION: The World Health Organization recommends treatment of tobacco dependence as one approach in its comprehensive tobacco control policy. To date, many trials and systematic reviews have been conducted to assess the effectiveness of pharmacotherapy for smoking cessation. Therefore, the findings of the umbrella review will improve clinical decision-making and be used as a baseline for future studies. SYSTEMATIC REVIEW REGISTRATION: PROSPERO CRD42017080906.

Estimation of indirect genetic effects in group-housed mink (Neovison vison) should account for systematic interactions either due to kin or sex.

Social interactions among individuals are abundant, both in wild and in domestic populations. With social interactions, the genes of an individual may affect the trait values of other individuals, a phenomenon known as indirect genetic effects (IGEs). IGEs can be estimated using linear mixed models. Most IGE models assume that individuals interact equally to all group mates irrespective of relatedness. Kin selection theory, however, predicts that an individual will interact differently with family members versus non-family members. Here, we investigate kin- and sex-specific non-genetic social interactions in group-housed mink. Furthermore, we investigated whether systematic non-genetic interactions between kin or individuals of the same sex influence the estimates of genetic parameters. As a second objective, we clarify the relationship between estimates of the traditional IGE model and a family-based IGE model proposed in a previous study. Our results indicate that male siblings in mink show different non-genetic interactions than female siblings in mink and that this may impact the estimation of genetic parameters. Moreover, we have shown how estimates from a family-based IGE model can be translated to the ordinary direct-indirect model and vice versa. We find no evidence for genetic differences in interactions among related versus unrelated mink.

Effects of albendazole on the clinical outcome and immunological responses in helminth co-infected tuberculosis patients: a double blind randomised clinical trial.

Despite several review papers and experimental studies concerning the impact of chronic helminth infection on tuberculosis in recent years, there is a scarcity of data from clinical field studies in highly endemic areas for these diseases. We believe this is the first randomised clinical trial investigating the impact of albendazole treatment on the clinical and immunological outcomes of helminth co-infected tuberculosis patients. A randomised, double-blind, placebo-controlled trial of albendazole (400mg per day for 3 days) in helminth-positive tuberculosis patients was conducted in Gondar, Ethiopia. The primary outcome was clinical improvement (ΔTB score) after 2 months. Among secondary outcomes were changes in the levels of eosinophils, CD4+ T cells, regulatory T cells, IFN-γ, IL-5 and IL-10 after 3 months. A total of 140 helminth co-infected tuberculosis patients were included with an HIV co-infection rate of 22.8%. There was no significant effect on the primary outcome (ΔTB score: 5.6±2.9 for albendazole versus 5.9±2.5 for placebo, P=0.59). The albendazole-treated group showed a decline in eosinophil cells (P=0.001) and IL-10 (P=0.017) after 3 months. In an exploratory analysis after 12 weeks, the albendazole treated group showed a trend towards weight gain compared with the placebo group (11.2±8.5 kg versus 8.2±8.7 kg, P=0.08)). The reductions in eosinophil counts and IL-10 show that asymptomatic helminth infection significantly affects host immunity during tuberculosis and can be effectively reversed by albendazole treatment. The clinical effects of helminth infection on chronic infectious diseases such as tuberculosis merit further characterisation.

Indirect genetic effects and kin recognition: estimating IGEs when interactions differ between kin and strangers.

Social interactions among individuals are widespread, both in natural and domestic populations. As a result, trait values of individuals may be affected by genes in other individuals, a phenomenon known as indirect genetic effects (IGEs). IGEs can be estimated using linear mixed models. The traditional IGE model assumes that an individual interacts equally with all its partners, whether kin or strangers. There is abundant evidence, however, that individuals behave differently towards kin as compared with strangers, which agrees with predictions from kin-selection theory. With a mix of kin and strangers, therefore, IGEs estimated from a traditional model may be incorrect, and selection based on those estimates will be suboptimal. Here we investigate whether genetic parameters for IGEs are statistically identifiable in group-structured populations when IGEs differ between kin and strangers, and develop models to estimate such parameters. First, we extend the definition of total breeding value and total heritable variance to cases where IGEs depend on relatedness. Next, we show that the full set of genetic parameters is not identifiable when IGEs differ between kin and strangers. Subsequently, we present a reduced model that yields estimates of the total heritable effects on kin, on non-kin and on all social partners of an individual, as well as the total heritable variance for response to selection. Finally we discuss the consequences of analysing data in which IGEs depend on relatedness using a traditional IGE model, and investigate group structures that may allow estimation of the full set of genetic parameters when IGEs depend on kin.

Insulin-requiring diabetes in Ethiopia: associations with poverty, early undernutrition and anthropometric disproportion.

BACKGROUND/OBJECTIVES: Most insulin-requiring diabetes patients in Ethiopia have an atypical form of the disease, which resembles previous descriptions of malnutrition-related diabetes. As so little is known about its aetiology, we have carried out a case-control study to evaluate its social and nutritional determinants. SUBJECTS/METHODS: Men and women with insulin-requiring diabetes (n=107), aged 18-40 years, were recruited in two centres, Gondar and Jimma, 750 km northwest and 330 km southwest of the capital, Addis Ababa, respectively. Controls of similar age and sex (n=110) were recruited from patients attending other hospital clinics. RESULTS: Diabetes was strongly associated with subsistence farming, odds ratio=3.5 (95% confidence interval: 1.5-7.8) and illiteracy/low levels of education, odds ratio=4.0 (2.0-8.0). Diabetes was also linked with a history of childhood malnutrition, odds ratio=5.5 (1.0-29.0) the mother's death during childhood, odds ratio=3.9 (1.0-14.8), and markers of poverty including poorer access to sanitation (P=0.004), clean water (P=0.009), greater overcrowding (P=0.04), increased distance from the clinic (P=0.01) and having fewer possessions (P=0.01). Compared with controls, people with diabetes had low mid upper arm circumference, body mass index (BMI) and fat/lean body mass (P<0.01). In addition, men with the disease tended to be shorter, were lighter (P=0.001), with reduced sitting height (P=0.015) and reduced biacromial (P=0.003) and bitrochanteric (P=0.008) diameters. CONCLUSIONS: Insulin-requiring diabetes in Ethiopia is strongly linked with poor education and markers of poverty. Men with the disease have associated disproportionate skeletal growth. These findings point towards a nutritional aetiology for this condition although the nature of the nutritional deficiency and its timing during growth and development remains obscure.

Insulin-requiring diabetes in rural Ethiopia: should we reopen the case for malnutrition-related diabetes?

AIMS/HYPOTHESIS: We evaluated the incidence of insulin-requiring diabetes in a rural area of sub-Saharan Africa. METHODS: Health surveillance data from a chronic disease programme in two zones of Ethiopia, Gondar and Jimma, were studied. The two zones have a population of more than 5,000,000 people. RESULTS: In Gondar Zone (1995-2008) and Jimma Zone (2002-2008) 2,280 patients presented with diabetes, of whom 1,029 (45%) required insulin for glycaemic control at diagnosis. The annual incidence of insulin-requiring diabetes was 2.1 (95% CI 2.0-2.2) per 100,000 and was twice as high in men (2.9 per 100,000) as in women (1.4 per 100,000). In both sexes incidence rates peaked at the age of 25 to 29 years. Incidence rates in the urban areas of Gondar and Jimma were five times higher than in the surrounding rural areas. Patients with insulin-requiring diabetes from rural and urban areas had a very low BMI and most were subsistence farmers or unemployed. CONCLUSIONS/INTERPRETATION: The typical patient with diabetes in rural Ethiopia is an impoverished, young adult male with severe symptoms requiring insulin for glycaemic control. The low incidence rates in rural compared with urban areas suggest that many cases of this disease remain undiagnosed. The disease phenotype encountered in this area of Africa is very different from the classical type 1 diabetes seen in the West and most closely resembles previous descriptions of malnutrition-related diabetes, a category not recognised in the current WHO Diabetes Classification. We believe that the case for this condition should be reopened.

Primary care treatment of epilepsy in rural Ethiopia: causes of default from follow-up.

BACKGROUND: In 1998, we set up nurse-led epilepsy clinics in five rural health centres around Gondar in northern Ethiopia. Despite good treatment outcomes, two years after registration only 40% of patients were still under follow-up. AIM: The purpose of this study was to examine the causes of default and factors that might improve adherence to follow-up. METHOD: The study was carried out at one of the five health centres. Patients who had defaulted from follow-up were identified from the clinic register. Trained enumerators visited the patients' villages and administered a questionnaire to the patients, or relatives if the patient was not available. RESULTS: 113 patients were traced. 28 (25%) had died and 21 (19%) had moved from the area. Of the remaining 64 patients, seven were accessing treatment from another source and 13 were in remission off treatment. 44 patients were still experiencing seizures and were on no treatment or had reverted to traditional remedies. The main reason given for default, in 44% of the patients, was difficulty in travelling to the health centre. 12% claimed that they preferred traditional remedies and 9% felt that they had not been improved by medical treatment. CONCLUSION: Despite decentralisation of care to rural health centres, the most common reason for default was the distance to travel to the health centre. Further decentralisation of care to a community level coupled with improved education may reduce default from follow-up.

The prevalence and characteristics of physical and sensory disabilities in Northern Ethiopia.

PURPOSE: To identify disabilities and to determine their prevalence, age of onset and perceived cause in one urban and three rural areas in Northern Ethiopia. METHOD: A community based cross-sectional study of households that were selected by systematic sampling. Trained enumerators identified individuals with physical disabilities or epilepsy who were 5 years of age or older. RESULTS: The overall prevalence of disability in 4214 individuals was 4.9%. The more common forms were walking difficulty (1.7%), loss of vision in one or both eyes (1.5%), hand dysfunction (0.8%) and epilepsy (0.7%). Information provided by the interviewees revealed a pattern of early onset, with injury and infection prominent as perceived causes. The importance of injury and infections was confirmed by the findings in half the people with disability, who were examined by a surgeon. CONCLUSIONS: Disability is a major public health problem and more facilities for rehabilitation and social support are needed. Measures that are needed to reduce the prevalence include health promotion, preventing injury, widening immunization coverage, better childhood nutrition and effective treatment for infection and injury. Further research should include younger children, cover a wider range of disability and use more sensitive means to detect hearing loss.

Access to diabetes treatment in northern Ethiopia.

Treatments for diabetes in Ethiopia are at present only available in hospitals so many patients must travel great distances to obtain insulin, tablets, and diabetes education. We reviewed all 496 people with diabetes attending the diabetic clinic at Gondar Hospital (281 with Type 1 (insulin-dependent) diabetes mellitus (DM) and 215 with Type 2 (non-insulin-dependent) DM. Half of the patients came from rural areas, all but 3 of them travelling more than 20 km, one-quarter of them more than 100 km and 33 patients (13%) more than 180 km. It is likely that many patients who fail to attend from the more distant areas have died. We are developing a scheme which would enable diabetic patients to be treated at rural health centres by nurses trained in the principles of diabetes care which could greatly improve the outlook for diabetic patients in Ethiopia.

Seroprevalence of HIV-1 and syphilis antibodies in blood donors in Gonder, Ethiopia, 1989-1993.

Data are presented from serologic screening for human immunodeficiency virus type 1 (HIV-1) in all blood donors (n = 3,696) in Gonder, Ethiopia, between 1989 and 1993. The crude seroprevalence was 10.6% in men (326 of 3,066) and 11.9% in women (75 of 630). Seroprevalence in male donors increased from 3.8% in 1989 to 16.0% in 1993 (p = 0.001); in female donors, seroprevalence increased from 7.0% in 1989 to 16.8% in 1992 (p = 0.002) and decreased to 13.4% in 1993. Syphilis seroreactivity increased from 4.8% in 1991 to 9.2% in 1993 (p = 0.02). HIV-1-seropositive donors were more likely to be seroreactive for syphilis than HIV-1-negative donors (odds ratio = 2.36; 95% confidence interval, 1.73-3.22). Therefore, there is an urgent need for control programs for both infections.