A novel kernel based approach to arbitrary length symbolic data with application to type 2 diabetes risk

Predictive modeling of clinical data is fraught with challenges arising from the manner in which events are recorded. Patients typically fall ill at irregular intervals and experience dissimilar intervention trajectories. This results in irregularly sampled and uneven length data which poses a problem for standard multivariate tools. The alternative of feature extraction into equal-length vectors via methods like Bag-of-Words (BoW) potentially discards useful information. We propose an approach based on a kernel framework in which data is maintained in its native form: discrete sequences of symbols. Kernel functions derived from the edit distance between pairs of sequences may then be utilized in conjunction with support vector machines to classify the data. Our method is evaluated in the context of the prediction task of determining patients likely to develop type 2 diabetes following an earlier episode of elevated blood pressure of 130/80 mmHg. Kernels combined via multi kernel learning achieved an F1-score of 0.96, outperforming classification with SVM 0.63, logistic regression 0.63, Long Short Term Memory 0.61 and Multi-Layer Perceptron 0.54 applied to a BoW representation of the data. We achieved an F1-score of 0.97 on MKL on external dataset. The proposed approach is consequently able to overcome limitations associated with feature-based classification in the context of clinical data

Evaluation of the environmental noise levels in Abuja Municipality using mobile phones

Background: Noise remains a nuisance which impacts negatively on the physical, social and psychological wellbeing of man. It aggravates chronic illnesses like hypertension and other cardiopulmonary diseases. Unfortunately, increased activities from industrialization and technological transfers/drifts have tumultuously led to increased noise pollution in most of our fast growing cities today and hence the need for concerted efforts in monitoring and regulating our environmental noise.Objectives: To assess the equivalent noise level (Leq) in Abuja municipality and promote a simple method for regular assessment of Leq within our environment.Methods: This is a cross-sectional community based study of the environmental Leq of Abuja municipality conducted between January 2014 and January 2016. The city was divided into 12 segments including residential, business and market areas via the Abuja Geographic Information System. The major markets were captured separately on a different scale. Measurements were taken with the mobile phone softwares having validated this withExtech 407730 digital sound level meter, serial no Z310135 . Leq(A) were measured at different points and hours of the day and night. The average Leq(A) were classified according to localities and compared with WHO standard safety levels.Results: LeqD ranged 71-92dB(A); 42-79dB(A) and 69-90dB(A) in business/ parks, residential and market places respectively. The Night measurements were similar 18dB(A)-56dB(A) and the day-night Leq(A)=77.2dB(A) and 90.4dB(A) for residential and business zones.Conclusion: The night noise levels are satisfactory but the day and daynight levels are above the recommended tolerable values by WHO and therefore urgently call for awareness and legislative regulations

Testing the generalizability of ancestry-specific polygenic risk scores to predict prostate cancer in sub-Saharan Africa

Background Genome-wide association studies do not always replicate well across populations, limiting the generalizability of polygenic risk scores (PRS). Despite higher incidence and mortality rates of prostate cancer in men of African descent, much of what is known about cancer genetics comes from populations of European descent. To understand how well genetic predictions perform in different populations, we evaluated test characteristics of PRS from three previous studies using data from the UK Biobank and a novel dataset of 1298 prostate cancer cases and 1333 controls from Ghana, Nigeria, Senegal, and South Africa. Results Allele frequency differences cause predicted risks of prostate cancer to vary across populations. However, natural selection is not the primary driver of these differences. Comparing continental datasets, we find that polygenic predictions of case vs. control status are more effective for European individuals (AUC 0.608–0.707, OR 2.37–5.71) than for African individuals (AUC 0.502–0.585, OR 0.95–2.01). Furthermore, PRS that leverage information from African Americans yield modest AUC and odds ratio improvements for sub-Saharan African individuals. These improvements were larger for West Africans than for South Africans. Finally, we find that existing PRS are largely unable to predict whether African individuals develop aggressive forms of prostate cancer, as specified by higher tumor stages or Gleason scores. Conclusions Genetic predictions of prostate cancer perform poorly if the study sample does not match the ancestry of the original GWAS. PRS built from European GWAS may be inadequate for application in non-European populations and perpetuate existing health disparities

Nigerian Population Research on Environment, Gene and Health (NIPREGH) - objectives and protocol

Sub-Saharan Africa is currently undergoing an epidemiological transition from a disease burden largely attributable to communicable diseases to that resulting from a combination of both communicable and chronic non-communicable diseases. Data on chronic disease incidence, lifestyle, environmental and genetic risk factors are sparse in this region. This report aimed at providing relevant information in respect to risk factors that increase blood pressure and lead to development of intermediate cardiovascular phenotypes. We presented the rationale, objectives and key methodological features of the Nigerian Population Research on Environment, Gene and Health (NIPREGH) study. The challenges encountered in carrying out population study in this part of the world and the approaches at surmounting them were also presented. The preliminary data as at 20 November 2013 showed that out of the 205 individuals invited starting from early April 2013, 160 (72 women) consented and were enrolled; giving a response rate of 78%. Participants' age ranged from 18 to 80 years, with a mean (SD) of 39.8 (12.4) years and they were of 34 different ethnic groups spread over 24 states out of the 36 states that constitute Nigeria. The mean (SD) of office and home blood pressures were 113.0 (15.2) mm Hg systolic, 73.5 (12.5) mm Hg diastolic and 117.3 (15.0) mm Hg systolic, and 76.0 (9.6) mm Hg diastolic, respectively. Forty-three (26.8%) participants were hypertensive and 8 (5.0%) were diabetic. In addition to having the unique potential of recruiting a cohort that is a true representative of the entire Nigerian population, NIPREGH is feasible and the objectives realisable.status: publishe

Nigerian Population Research on Environment, Gene and Health (NIPREGH) - objectives and protocol

Sub-Saharan Africa is currently undergoing an epidemiological transition from a disease burden largely attributable to communicable diseases to that resulting from a combination of both communicable and chronic non-communicable diseases. Data on chronic disease incidence, lifestyle, environmental and genetic risk factors are sparse in this region. This report aimed at providing relevant information in respect to risk factors that increase blood pressure and lead to development of intermediate cardiovascular phenotypes. We presented the rationale, objectives and key methodological features of the Nigerian Population Research on Environment, Gene and Health (NIPREGH) study. The challenges encountered in carrying out population study in this part of the world and the approaches at surmounting them were also presented. The preliminary data as at 20 November 2013 showed that out of the 205 individuals invited starting from early April 2013, 160 (72 women) consented and were enrolled; giving a response rate of 78%. Participants' age ranged from 18 to 80 years, with a mean (SD) of 39.8 (12.4) years and they were of 34 different ethnic groups spread over 24 states out of the 36 states that constitute Nigeria. The mean (SD) of office and home blood pressures were 113.0 (15.2) mm Hg systolic, 73.5 (12.5) mm Hg diastolic and 117.3 (15.0) mm Hg systolic, and 76.0 (9.6) mm Hg diastolic, respectively. Forty-three (26.8%) participants were hypertensive and 8 (5.0%) were diabetic. In addition to having the unique potential of recruiting a cohort that is a true representative of the entire Nigerian population, NIPREGH is feasible and the objectives realisable

Removing the mask on hypertension (REMAH) study: Design; quality of blood pressure phenotypes and characteristics of the first 490 participants

Purpose: Previous studies that evaluated the prevalence of hypertension in Nigeria were either clinic based, non-standardized or did not include out-of-clinic blood pressure (BP) measurement. Materials and Methods: We selected a rural and an urban community in one state in each of the 6 geopolitical zones of Nigeria. Five consecutive BP of adults older than 18 years were measured in the clinic following which, each participant was provided with a home BP device to obtain duplicate morning and evening BP for 3 days. Result: Out of 556 invited from Anambra State, South-East Nigeria, 490 (88%) consented. Overall, more women participated in both rural (115 vs 61, p < .0001) and urban (213 vs 101; p < .0001) sites. About 35.9% of participants had their home BP monitored. Of the 4890 clinic BP readings, 29.8%, 16.3%, 16.6%, 16.4% and 20.8% ended in 0,2,4,6 and 8 digits respectively. Only 0.8% ended in odd numbers. Of the identical BP readings,5 (0.20%), 6 (0.25%), 56 (2.30%) and 316 (12.9%) SBP and 8 (0.33%), 17 (0.70%), 93 (3.80%), 319 (13.1%) DBP had no difference in five, four, three and two values of the five consecutive readings. Conclusion: REMAH is feasible and the quality of BP will ensure that the final results are robust

Prevalence and Determinants of Masked Hypertension Among Black Nigerians Compared With a Reference Population

Hitherto, diagnosis of hypertension in sub-Saharan Africa was largely based on conventional office blood pressure (BP). Data on the prevalence of masked hypertension (MH) in this region is scarce. Among individuals with normal office BP (<140/90 mm Hg), we compared the prevalence and determinants of MH diagnosed with self-monitored home blood pressure (≥135/85 mm Hg) among 293 Nigerians with a reference population consisting of 3615 subjects enrolled in the International Database on Home Blood Pressure in Relation to Cardiovascular Outcomes. In the reference population, the prevalence of MH was 14.6% overall and 11.1% and 39.6% in untreated and treated participants, respectively. Among Nigerians, the prevalence standardized to the sex and age distribution of the reference population was similar with rates of 14.4%, 8.6%, and 34.6%, respectively. The mutually adjusted odds ratios of having MH in Nigerians were 2.34 (95% confidence interval, 1.39-3.94) for a 10-year higher age, 1.92 (1.11-3.31) and 1.70 (1.14-2.53) for 10- or 5-mm Hg increments in systolic or diastolic office BP, and 3.05 (1.08-8.55) for being on antihypertensive therapy. The corresponding estimates in the reference population were similar with odds ratios of 1.80 (1.62-2.01), 1.64 (1.45-1.87), 1.13 (1.05-1.22), and 2.84 (2.21-3.64), respectively. In conclusion, MH is as common in Nigerians as in other populations with older age and higher levels of office BP being major risk factors. A significant proportion of true hypertensive subjects therefore remains undetected based on office BP, which is particularly relevant in sub-Saharan Africa, where hypertension is now a major cause of death.status: publishe

HemoTypeSC, a low-cost point-of-care testing device for sickle cell disease: promises and challenges

Background Sickle cell disease (SCD) is a neglected burden of growing importance. >312,000 births are affected annually by sickle cell anaemia (SCA). Early interventions such as newborn screening, penicillin prophylaxis and hydroxyurea can substantially reduce the mortality and morbidity associated with SCD. Nevertheless, their implementation in African countries has been mostly limited to pilot projects. Recent development of low-cost point-of-care testing (POCT) devices for sickle haemoglobin (HbS) could greatly facilitate the diagnosis of those affected. Methods We conducted the first multi-centre, real-world assessment of a low-cost POCT device, HemoTypeSC, in a low-income country. Between September and November 2017, we screened 1121 babies using both HemoTypeSC and HPLC and confirmed discordant samples by molecular diagnosis. Findings We found that, in optimal field conditions, the sensitivity and specificity of the test for SCA were 93.4% and 99.9%, respectively. All 14 carriers of haemoglobin C were successfully identified. Our study reveals an overall accuracy of 99.1%, but also highlights the importance of rigorous data collection, staff training and accurate confirmatory testing. It suggests that HPLC results might not be as reliable in a resource-poor setting as usually considered. Interpretation The use of such a POCT device can be scaled up and routinely used across multiple healthcare centres in sub-Saharan Africa, which would offer great potential for the identification and management of vast numbers of individuals affected by SCD who are currently undiagnosed

Marked variability in institutional deliveries and neonatal outcomes during the COVID-19 lockdown in Nigeria

Background The coronavirus disease 2019 (COVID-19) pandemic and the interventions to mitigate its spread impacted access to healthcare, including hospital births and newborn care. This study evaluated the impact of COVID-19 lockdown measures on newborn service utilization in Nigeria. Methods The records of women who delivered in hospitals and babies admitted to neonatal wards were retrospectively reviewed before (March 2019–February 2020) and during (March 2020–February 2021) the COVID-19 pandemic lockdown in selected facilities in Nigeria. Results There was a nationwide reduction in institutional deliveries during the COVID-19 lockdown period in Nigeria, with 14 444 before and 11 723 during the lockdown—a decrease of 18.8%. The number of preterm admissions decreased during the lockdown period (30.6% during lockdown vs 32.6% pre-lockdown), but the percentage of outborn preterm admissions remained unchanged. Newborn admissions varied between zones with no consistent pattern. Although neonatal jaundice and prematurity remained the most common reasons for admission, severe perinatal asphyxia increased by nearly 50%. Neonatal mortality was significantly higher during the COVID-19 lockdown compared with pre-lockdown (110.6/1000 [11.1%] vs 91.4/1000 [9.1%], respectively; p=0.01). The odds of a newborn dying were about four times higher if delivered outside the facility during the lockdown (p<0.001). Conclusions The COVID-19 lockdown had markedly deleterious effects on healthcare seeking for deliveries and neonatal care that varied between zones with no consistent pattern