Q&A: Methods for estimating genetic gain in sub-Saharan Africa and achieving improved gains.

Regular measurement of realized genetic gain allows plant breeders to assess and review the effectiveness of their strategies, allocate resources efficiently, and make informed decisions throughout the breeding process. Realized genetic gain estimation requires separating genetic trends from nongenetic trends using the linear mixed model (LMM) on historical multi-environment trial data. The LMM, accounting for the year effect, experimental designs, and heterogeneous residual variances, estimates best linear unbiased estimators of genotypes and regresses them on their years of origin. An illustrative example of estimating realized genetic gain was provided by analyzing historical data on fresh cassava (Manihot esculenta Crantz) yield in West Africa (https://github.com/Biometrics-IITA/Estimating-Realized-Genetic-Gain). This approach can serve as a model applicable to other crops and regions. Modernization of breeding programs is necessary to maximize the rate of genetic gain. This can be achieved by adopting genomics to enable faster breeding, accurate selection, and improved traits through genomic selection and gene editing. Tracking operational costs, establishing robust, digitalized data management and analytics systems, and developing effective varietal selection processes based on customer insights are also crucial for success. Capacity building and collaboration of breeding programs and institutions also play a significant role in accelerating genetic gains.

Impact of a short online course on the accuracy of non-ophthalmic diabetic retinopathy graders in recognising glaucomatous optic nerves in Vietnam.

PURPOSE: To test an online training course for non-ophthalmic diabetic retinopathy (DR) graders for recognition of glaucomatous optic nerves in Vietnam. METHODS: This was an uncontrolled, experimental, before-and-after study in which 43 non-ophthalmic DR graders underwent baseline testing on a standard image set, completed a self-paced, online training course and were retested using the same photographs presented randomly. Twenty-nine local ophthalmologists completed the same test without the training course. DR graders then underwent additional one-to-one training by a glaucoma specialist and were retested. Test performance (% correct, compared with consensus grades from four fellowship-trained glaucoma experts), sensitivity, specificity, positive and negative predictive value, and area under the receiver operating (AUC) curve, were computed. RESULTS: Mean age of DR graders (32.6±5.5 years) did not differ from ophthalmologists (32.3±7.3 years, p=0.13). Online training required a mean of 297.9 (SD 144.6) minutes. Graders' mean baseline score (33.3%±14.3%) improved significantly after training (55.8%±12.6%, p<0.001), and post-training score did not differ from ophthalmologists (58.7±15.4%, p=0.384). Although grader sensitivity reduced before [85.5% (95% CI 83.5% to 87.3%)] versus after [80.4% (78.3% to 82.4%)] training, specificity improved significantly [47.8 (44.9 to 50.7) vs 79.8 (77.3 to 82.0), p<0.001]. Grader AUC also improved after training [66.6 (64.9 to 68.3)] to [80.1 (78.5 to 81.6), p<0.001]. Additional one-to-one grader training by a glaucoma specialist did not further improve grader scores. CONCLUSION: Non-ophthalmic DR graders can be trained to recognise glaucoma using a short online course in this setting, with no additional benefit from more expensive one-to-one training. After 5-hour online training in recognising glaucomatous optic nerve head, scores of non-ophthalmic DR graders doubled, and did not differ from local ophthalmologists. Intensive one-to-one training did not further improve performance.

Glaucoma Treatment Patterns in Sub-Saharan Africa.

PRCIS: Physicians were most likely to recommend primary medical therapy upon diagnosis of glaucoma. Laser therapy was underutilized where they were available. Physicians were more likely to recommend surgery in severe glaucoma, laser therapy in mild glaucoma, while recommendation of medical therapy did not depend on glaucoma severity. PURPOSE: To characterize treatment patterns for newly diagnosed glaucoma in sub-Saharan Africa (SSA). METHODS: This was a multicenter cross-sectional study of adults newly diagnosed with glaucoma at 27 eye care centers in 10 African countries. In addition to demographic and clinical data, physician treatment recommendations (medication, laser, surgery, or no treatment) were recorded. Statistical analyses were performed using STATA version 14.0. RESULTS: Data from 1201 patients were analyzed. Physicians were most likely to recommend primary medical therapy upon diagnosis of glaucoma (69.4%), with laser (13.2%), surgery (14.9%), and no treatment (2.5%) recommended to the remaining patients. All sites had medical therapy available and most (25/27, 92.6%) could provide surgical treatment; only 16/27 (59.3%) sites offered laser, and at these sites, 30.8% of eyes were recommended to undergo primary laser procedures. As glaucoma severity increased, the laser was recommended less, surgery more, and medications unchanged. Patient acceptance of medical therapy was 99.1%, laser 88.3%, and surgery 69.3%. CONCLUSIONS: Medical therapy for first-line glaucoma management is preferred by most physicians in SSA (69%). Laser therapy may be underutilized at centers where it is available. These findings underscore the need for comparative studies of glaucoma treatments in SSA to inform the development of evidence-based treatment guidelines and of programs to reduce glaucoma blindness in SSA. Strategic approaches to glaucoma therapy in SSA must address the question of whether medical therapy is the most optimal first-line approach in this setting.

Estimating vaccine coverage in conflict settings using geospatial methods: a case study in Borno state, Nigeria.

Reliable estimates of subnational vaccination coverage are critical to track progress towards global immunisation targets and ensure equitable health outcomes for all children. However, conflict can limit the reliability of coverage estimates from traditional household-based surveys due to an inability to sample in unsafe and insecure areas and increased uncertainty in underlying population estimates. In these situations, model-based geostatistical (MBG) approaches offer alternative coverage estimates for administrative units affected by conflict. We estimated first- and third-dose diphtheria-tetanus-pertussis vaccine coverage in Borno state, Nigeria, using a spatiotemporal MBG modelling approach, then compared these to estimates from recent conflict-affected, household-based surveys. We compared sampling cluster locations from recent household-based surveys to geolocated data on conflict locations and modelled spatial coverage estimates, while also investigating the importance of reliable population estimates when assessing coverage in conflict settings. These results demonstrate that geospatially-modelled coverage estimates can be a valuable additional tool to understand coverage in locations where conflict prevents representative sampling.

Qualitative content analysis of Nigerian heads-of-state and presidents' inaugural addresses: text mining, topic modelling and sentiment analysis.

Political speech acts are critical for politicians launching a regime because they can provide information that can be used to control people's thoughts and opinions. The purpose of this study was to conduct a qualitative content analysis of the inaugural and ascension addresses of Nigerian heads of state and presidents. The textual data used in this analysis were the ascension and inaugural addresses of Nigerian Heads of State and Presidents from 1960 to 2019. They were extracted and analysed using text-mining techniques. Textual data were clustered about their topical content using Latent Dirichlet Allocation (LDA), and speech cohesion between these addresses was examined using a similarity matrix and heatmap. Furthermore, term frequency and association analyses were performed to examine the high-frequency terms (tokens) and the terms (tokens) that are strongly correlated within each of the ascension/inaugural addresses (corpus). The summarization of characters and words in the ascension and inaugural addresses reveals that the Civilian Presidents used more characters and words than the Military Heads of State. There was an increase in the number of characters and words in the ascension and inaugural addresses among those who had served the nation multiple times. The total sentiment score in the ascension/inaugural addresses from 1960 to 2019 by Civilian Presidents and Military Heads of State revealed that the Civilian Presidents expressed more trust, surprise, sadness, joy, fear, disgust and anticipation in their addresses than the Military Heads of State. The most occurring term (token) in the ascension/inaugural addresses was the word government which appeared 221 times. The most token in the corpus government was found to be moderately correlated with the following tokens: loss, existing and majority. Similarly, economic was found to be moderately correlated with these tokens: inflation, building, education, exchange, loan, workers and technical. In this study, all the ascension/inaugural addresses share similar topic distribution: as seen in Abacha's and Muritala's addresses; and Shonekan's inaugural address was very similar to Balewa, Azikwe and Babangida's addresses; Babangida's ascension, Abdulsalam's 1998 ascension, Jonathan's 2010 inaugural and Buhari's 2015 inaugural addresses discussed similar topics to Obasanjo's 1976 ascension address. The highest average sentiment score was observed in Obasanjo's 2003 inaugural address and the lowest score was in Buhari's 1983 ascension address. The sentiment score for the ascension/inaugural addresses showed that Civilian Presidents inaugural addresses expressed more positive, joy, trust and anticipation than Military Heads of State. These emotions showed that the Civilian President's inaugural addresses are better when compared to Military Heads of State in terms of the sentiment scores.

Clinical Characteristics and Stage at Presentation of Glaucoma Patients in Sub-Saharan Africa.

PRCIS: The initial presentation of glaucoma varies meaningfully across SSA. A comprehensive strategy with regional customization based on local differences is needed to reduce glaucoma blindness in SSA. PURPOSE: To explore regional variations in the presentation of newly diagnosed glaucoma in Sub Saharan Africa (SSA). METHODOLOGY: This was a multicenter, cross-sectional study in which newly diagnosed, consecutive, glaucoma patients aged older than or equal to 18 years were recruited from 27 eye clinics in 10 countries throughout SSA. Demographic and ophthalmic examination data were collected. Glaucoma severity was based on optic nerve head and visual field assessment. Statistical analyses were performed using STATA version 14.0. RESULTS: Among 1214 enrolled patients with newly diagnosed glaucoma from Western, Eastern, and Southern Africa, the overall mean (SD) age was 59.9 (17.1) years. More than half of all patients (716/1178; 60.8%) presented with severe glaucoma in the worse eye, and one-third (36.9%) had severe glaucoma in both eyes. Primary open angle glaucoma was the commonest form of glaucoma in all regions (77.4%). A family history of blindness (260/1204, 21.6%) was common. Patients from Western Africa had lower mean presenting intraocular pressure (26.4 [11.1] mm Hg, P <0.001), but had worse glaucoma in the better eye based on mean cup-disc ratio (0.8; P <0.001) and mean visual field mean deviation [10.4 (8.4)] dB, P =0.016) compared with other regions. Exfoliation glaucoma was more common in Eastern Africa (30/170=17.7%, P <0.001) compared with other regions. CONCLUSION: The initial presentation of glaucoma varies meaningfully across SSA. A comprehensive strategy with regional customization based on local differences is needed to reduce glaucoma blindness in SSA.

When Do Nigerian Women of Reproductive Age Initiate and What Factors Influence Their Contraceptive Use? A Contextual Analysis.

BACKGROUND: Contraceptive use initiation and continuation is one of the major interventions for reducing maternal deaths worldwide. Nigeria aimed to achieve a 27% prevalence rate of modern contraceptive uptake by 2020, however, this seems to have remained unachieved. The objective of this study was to investigate when Nigerian women initiate contraceptive use and its associated factors, using nationally representative data. METHODS: Data on 11,382 Nigerian women (aged 15-49 years) from the 2017 Performance Monitoring and Accountability 2020 (PMA2020) survey were used to determine the prevalence of lifetime contraceptive use. The Kaplan-Meier test was used to determine median time (years) to contraceptive uptake. In addition, the factors associated with contraceptive use were determined using multivariable logistic regression model. Statistical significance was determined at 5%. RESULTS: The prevalence of modern contraceptive use was 14.2%. There were disparities in the timing (years) of contraceptive use initiation across several women's characteristics. Women from urban residence, highest household wealth index, nulliparous, unmarried, and highly educated women had the minimum median time (years) to contraceptive use initiation. The multivariable logistic model showed that rural women were 26% less likely to initiate contraceptive use, when compared with the urban dwellers (OR= 0.74; 95% CI: 0.65, 0.84). Furthermore, married women were 24% less likely to initiate contraceptive use, when compared with the unmarried (OR= 0.76; 95% CI: 0.63, 0.93). In addition, geographical region, wealth, television source, ever given birth, education, age, and religion were significantly associated with contraceptive use. CONCLUSION: The prevalence of contraceptive use is low in Nigeria. There were differences in contraceptive use initiation among women of reproductive age in Nigeria. There is a need to adopt sustainable strategies to improve contraceptive uptake and to re-iterate the benefits of contraception, including providing enlightenment programs among key populations such as the rural dwellers and low income earners.

Management of possible serious bacterial infection in young infants where referral is not possible in the context of existing health system structure in Ibadan, South-west Nigeria.

INTRODUCTION: Neonatal infections contribute substantially to infant mortality in Nigeria and globally. Management requires hospitalization, which is not accessible to many in low resource settings. World Health Organization developed a guideline to manage possible serious bacterial infection (PSBI) in young infants up to two months of age when a referral is not feasible. We evaluated the feasibility of implementing this guideline to achieve high coverage of treatment. METHODS: This implementation research was conducted in out-patient settings of eight primary health care centres (PHC) in Lagelu Local Government Area (LGA) of Ibadan, Oyo State, Nigeria. We conducted policy dialogue with the Federal and State officials to adopt the WHO guideline within the existing programme setting and held orientation and sensitization meetings with communities. We established a Technical Support Unit (TSU), built the capacity of health care providers, supervised and mentored them, monitored the quality of services and collected data for management and outcomes of sick young infants with PSBI signs. The Primary Health Care Directorate of the state ministry and the local government led the implementation and provided technical support. The enablers and barriers to implementation were documented. RESULTS: From 1 April 2016 to 31 July 2017 we identified 5278 live births and of these, 1214 had a sign of PSBI. Assuming 30% of births were missed due to temporary migration to maternal homes for delivery care and approximately 45% cases came from outside the catchment area due to free availability of medicines, the treatment coverage was 97.3% (668 cases/6861 expected births) with an expected 10% PSBI prevalence within the first 2 months of life. Of 1214 infants with PSBI, 392 (32%) infants 7-59 days had only fast breathing (pneumonia), 338 (27.8%) infants 0-6 days had only fast breathing (severe pneumonia), 462 (38%) presented with signs of clinical severe infection (CSI) and 22 (1.8%) with signs of critical illness. All but two, 7-59 days old infants with pneumonia were treated with oral amoxicillin without a referral; 80% (312/390) adhered to full treatment; 97.7% (381/390) were cured, and no deaths were reported. Referral to the hospital was not accepted by 87.7% (721/822) families of infants presenting with signs of PSBI needing hospitalization (critical illness 5/22; clinical severe infection; 399/462 and severe pneumonia 317/338). They were treated on an outpatient basis with two days of injectable gentamicin and seven days of oral amoxicillin. Among these 81% (584/721) completed treatment; 97% (700/721) were cured, and three deaths were reported (two with critical illness and one with clinical severe infection). We identified health system gaps including lack of staff motivation and work strikes, medicines stockouts, sub-optimal home visits that affected implementation. CONCLUSIONS: When a referral is not feasible, outpatient treatment for young infants with signs of PSBI is possible within existing programme structures in Nigeria with high coverage and low case fatality. To scale up this intervention successfully, government commitment is needed to strengthen the health system, motivate and train health workers, provide necessary commodities, establish technical support for implementation and strengthen linkages with communities. REGISTRATION: Trial is registered on Australian New Zealand Clinical Trials Registry (ANZCTR) ACTRN12617001373369.

Providing oxygen to children and newborns: a multi-faceted technical and clinical assessment of oxygen access and oxygen use in secondary-level hospitals in southwest Nigeria.

BACKGROUND: Oxygen is an essential medical therapy that is poorly available globally. We evaluated the quality of oxygen therapy in 12 secondary-level Nigerian hospitals, including access to oxygen equipment, equipment functionality, healthcare worker knowledge and appropriateness of use. METHODS: We conducted a three-part evaluation of oxygen access and use involving: (1) facility assessment (including technical evaluation of oxygen equipment), (2) clinical audit (children and neonates admitted January 2014-December 2015) and (3) survey of healthcare worker training and experience on the clinical use of oxygen (November 2015). RESULTS: Oxygen access for children and newborns is compromised by faulty equipment, lack of pulse oximetry and inadequate care practices. One hospital used pulse oximetry for paediatric care. Eleven hospitals had some access to oxygen supplies. Testing of 57 oxygen concentrators revealed two (3.5%) that were 'fit for use'. Overall, 14.4% (3708/25 677) of children and neonates received oxygen some time during their admission; 19.4% (1944/10 000) of hypoxaemic children received oxygen; 38.5% (1217/3161) of children who received oxygen therapy were not hypoxaemic. CONCLUSIONS: Oxygen access for children in Nigerian hospitals is poor, and likely results in substantial excess mortality. To improve oxygen access for children globally we must focus on actual provision of oxygen to patients-not simply the presence of oxygen equipment at the facility level. This requires a systematic approach to improve both oxygen (access [including equipment, maintenance and affordability]) and oxygen use (including pulse oximetry, guidelines and continuing education).

The Factor Structure of the Adapted WHO Quality of Life BREF questionnaire in a sample of adolescents in Nigeria.

INTRODUCTION: The World Health Organization's Quality of Life Instrument (WHOQOL-BREF) is widely validated and popularly used in assessing perceived quality of life (QOL) of adolescents and the general population. Though the WHOQOL-BREF has been used in some studies in Nigeria, its theoretical structure has not been comprehensively investigated. This study examined the factor structure of the Adopted WHOQOL-BREF questionnaire and it theoretical structure in a large sample of adolescents in Nigeria. METHODS: Data on demographic characteristics and QOL were extracted from 1,963 adolescents who participated in a state-wide study on psychosocial functioning and quality of life of adolescents in Benue State, Nigeria. Descriptive statistics were used to present the distribution of the data while Cronbach's alpha and Polychoric ordinal alpha were used to describe the internal consistency (reliability) of the adapted WHOQOL-BREF and alpha value of 0.700 was considered reliable. Structural analysis was performed to extract the underlying factors while confirmatory factor analyses were used to assess some hypothesized structure of the adapted WHO-QOL BREF. Relative Chi-square test (χ2/df) value ≤3.0 was regarded a good fit while multiple fit indexes with values ≥0.90 (for acceptable fit) were used for assessing diverse aspects of the models. All analyses were performed at 5% significance level using IBM SPSS statistics version 20, R package and AMOS version 21. RESULTS: Participants were mostly male (54.8%) and 14.7±1.4 years old with 51.0% residing in rural areas. The overall internal consistency of the 4-factor model was 0.862 (for Cronbach's Alpha) and 0.989 (for Polychoric Alpha) while the 2-factor model had 0.870 (for Cronbach's Alpha) and 0.990 (for Polychoric Alpha). The Cattelle's Scree plot, Horn's parallel analysis and the confirmatory factor analysis revealed a 2-factor model as the best model for the WHO-QOL BREF. The 23-item 2-factor structure had a relative Chi-square test value χ2/df < 3 = 2.98, p < 0.001 with all fit indices within the acceptable range. CONCLUSION: The adapted WHO QOL BREF can be safely used to assess quality of life among Adolescents in Nigeria and related settings. Using the two factors extracted in the present study may yield better results in settings similar to the present study location.

Care seeking behaviour and aspects of quality of care by caregivers for children under five with and without pneumonia in Ibadan, Nigeria.

BACKGROUND: This study aimed to investigate the differences in reported care seeking behaviour and treatment between children with pneumonia and children without pneumonia with cough and/or difficult breathing. METHODS: Three hundred and two children aged 0-59 months with fast breathing pneumonia were matched with 302 children seeking care for cough and/or difficult breathing at four outpatient clinics in Ibadan, Nigeria. After follow up at home, Demographic and Health Survey (DHS) and Multiple Indicator Cluster Survey (MICS) questionnaires were administered in the community by trained field workers to gather information around care seeking delay, patterns of care seeking, appropriateness of care seeking and treatment provided once care was sought. Multivariable analysis was carried out to determine significant factors associated with care seeking delay. RESULTS: Children with pneumonia had a significantly longer delay (median = 3d) before seeking care than those without pneumonia (median = 2d; P = 0.001). The length of the delay was 21% (95% confidence interval (CI) = 1%-42%) greater in those aged 0-1 month and 11% (95% CI = 5%-42%) greater in those aged 2-11 months compared to those aged 12-59 months. The length of delay was 17% (95% CI = 5%-30%) greater in rural locations than urban ones, and 33% (95% CI = 7%-51%) shorter in fathers with only primary education compared to higher education, adjusted for covariates. The range of places where care was sought showed the same distribution in those with and without pneumonia. Twenty two per cent of those with pneumonia sought care first from inappropriate providers. The number of children for whom caregivers reported having received antibiotic treatment was 92% for those with pneumonia and 84% for those without pneumonia. CONCLUSIONS: Given that children with pneumonia and cough/cold had similar patterns of reported care seeking information gathered on care seeking (type of provider visited) from DHS and MICS surveys on those with 'symptoms of acute respiratory infection' in this setting provide a reasonably valid indication of care seeking behaviours in children with pneumonia. There are high levels of antibiotic overuse for children with cough/cold in this setting which risks worsening antibiotic resistance.

A prospective validation study in South-West Nigeria on caregiver report of childhood pneumonia and antibiotic treatment using Demographic and Health Survey (DHS) and Multiple Indicator Cluster Survey (MICS) questions.

BACKGROUND: Childhood pneumonia is the single largest infectious cause of death in children under five worldwide. Demographic and Health Surveys (DHS) and Multiple Indicator Cluster Surveys (MICS) provide health information on care sought for sick children in resource poor settings. Despite not being primarily designed to identify childhood pneumonia, there are concerns that reported episodes of "symptoms of acute respiratory infection" in DHS and MICS are often interpreted by other groups as a "proxy" for childhood pneumonia. Using DHS5 and MICS5 survey tools, this study aimed to assess how accurately caregivers report of "symptoms of acute respiratory infection" reflect pneumonia episodes and antibiotic use in children under five. METHODS: Children aged 0 to 59 months presenting with cough and/or difficult breathing were recruited from four study hospitals in Ibadan, Nigeria from August 2015 to March 2017. Children were assessed using World Health Organization (WHO) standard criteria by study physicians to identify whether they had pneumonia. Three hundred and two matched children in each category of 'pneumonia' and "no pneumonia" were followed up at home, either two or eight weeks later, using questions from DHS5 and MICS5 surveys to assess the accuracy of caregiver recall of pneumonia. RESULTS: The specificity of DHS5 and MICS5 questions for identifying childhood pneumonia were 87.4 (95% confidence interval (CI) = 83.1-91.0) and 86.1 (95% CI = 81.7-89.8) respectively and the sensitivity of questions were 37.1 (95% CI = 31.6-42.8) and 37.1 (95% CI = 31.6-42.8). Correct recall of antibiotic treatment was poor (kappa statistic = 0.064) but improved with the use of medicine pill boards (kappa statistic = 0.235). CONCLUSIONS: DHS5 and MICS5 survey questions are not designed to identify childhood pneumonia and this study confirms that they do not accurately discern episodes of childhood pneumonia from cough/cold in children under five. The proportion of pneumonia episodes appropriately treated with antibiotics cannot be accurately assessed using current DHS and MICS surveys. If these results are used to guide programmatic decisions, it is likely to encourage overuse and inappropriate prescribing of antibiotics for episodes of cough/cold. International agencies who continue to use these household data to monitor the proportion of children with pneumonia who receive antibiotic treatment should be discouraged from doing this as these data are likely to mislead national and global programmes. Medicine pill boards are used in a number of DHS surveys and should be promoted for wider use in national population surveys to improve the accuracy of antibiotic recall.

Psychometric properties and Confirmatory structure of the Strengths and difficulties questionnaire in a sample of adolescents in Nigeria.

Though the SDQ has been used in selected studies in Nigeria, its theoretical structure has not been fully and appropriately investigated in the setting. The present study employs Exploratory Factor Analysis (EFA) and Confirmatory Factor Analysis (CFA) to investigate the theoretical structure of the self-reported version of the SDQ in a sample of adolescents in Benue state, Nigeria. A total of 1,244 adolescents from different categories of secondary schools in Makurdi and Vandekya Local government areas of Benue state participated in the study. Preliminary data analyses were performed using descriptive statistics while the theoretical structure of the SDQ was assessed using EFA and CFA. Model fits were assessed using Chi-square test and other fit indices at 5% significance level. Participants were 14.19±2.45 (Vandekya) and 14.19±2.45 (Makurdi) years old. Results of the EFA and CFA revealed a 3-factor oblique model as the best model for the sample of adolescents studied (χ2/df =2.20, p<0.001) with all fit indices yielding better results. A correlated 3-factor model fits the present data better than the 5-factor theoretical model of the SDQ. The use of the original 5-factor model of the SDQ in the present setting should be interpreted with caution.