Towards a methodology for addressing missingness in datasets, with an application to demographic health datasets

Missing data is a common concern in health datasets, and its impact on good decision-making processes is well documented. Our study's contribution is a methodology for tackling missing data problems using a combination of synthetic dataset generation, missing data imputation and deep learning methods to resolve missing data challenges. Specifically, we conducted a series of experiments with these objectives; $a)$ generating a realistic synthetic dataset, $b)$ simulating data missingness, $c)$ recovering the missing data, and $d)$ analyzing imputation performance. Our methodology used a gaussian mixture model whose parameters were learned from a cleaned subset of a real demographic and health dataset to generate the synthetic data. We simulated various missingness degrees ranging from $10 \%$, $20 \%$, $30 \%$, and $40\%$ under the missing completely at random scheme MCAR. We used an integrated performance analysis framework involving clustering, classification and direct imputation analysis. Our results show that models trained on synthetic and imputed datasets could make predictions with an accuracy of $83 \%$ and $80 \%$ on $a)$ an unseen real dataset and $b)$ an unseen reserved synthetic test dataset, respectively. Moreover, the models that used the DAE method for imputed yielded the lowest log loss an indication of good performance, even though the accuracy measures were slightly lower. In conclusion, our work demonstrates that using our methodology, one can reverse engineer a solution to resolve missingness on an unseen dataset with missingness. Moreover, though we used a health dataset, our methodology can be utilized in other contexts.Comment: 16 pages and references, 5 figures and four tables, Paper accepted for presentation at SACAIR 2022 in Stellenbosch, Westen Cape, South Afric

The relation of preventive dental behaviors to periodontal health status

. Current recommendations for periodontal health maintenance emphasize toothbrushing, flossing and periodic dental checkups. The purposes of this study were to examine (1) the effects of these practices on periodontal health and (2) the relationships of demographic and socioeconomic variables with these behaviors and with periodontal health. Adults ( n = 319) in the Detroit, Michigan tri-county area were asked how frequently they performed the 3 preventive behaviors. Levels of plaque, gingivitis, calculus, and periodontal attachment were then assessed during in-home dental examinations. There were no statistically significant differences in these health measures between those with acceptable and unacceptable brushing behavior. About 20% of the subjects reported acceptable flossing behavior, and these individuals had significantly less plaque and calculus than other participants. Over 3/4 of subjects reported having a dental checkup at least 1 × a year, and these persons were found to have significantly less plaque, gingivitis, and calculus compared to less frequent attenders. Acceptable brushing behavior was not associated with any particular demographic or socio-economic characteristic, while differences in acceptable flossing behavior were found among age groups. Frequencies of yearly dental checkups varied significantly within every demographic and socioeconomic characteristic.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75510/1/j.1600-051X.1994.tb00303.x.pd

Household Effects of School Closure during Pandemic (H1N1) 2009, Pennsylvania, USA

To determine the effects of school closure, we surveyed 214 households after a 1-week elementary school closure because of pandemic (H1N1) 2009. Students spent 77% of the closure days at home, 69% of students visited at least 1 other location, and 79% of households reported that adults missed no days of work to watch children

Effects of coronavirus disease pandemic on tuberculosis notifications, Malawi

The coronavirus disease (COVID-19) pandemic might affect tuberculosis (TB) diagnosis and patient care. We analyzed a citywide electronic TB register in Blantyre, Malawi and interviewed TB officers. Malawi did not have an official COVID-19 lockdown but closed schools and borders on March 23, 2020. In an interrupted time series analysis, we noted an immediate 35.9% reduction in TB notifications in April 2020; notifications recovered to near prepandemic numbers by December 2020. However, 333 fewer cumulative TB notifications were received than anticipated. Women and girls were affected more (30.7% fewer cases) than men and boys (20.9% fewer cases). Fear of COVID-19 infection, temporary facility closures, inadequate personal protective equipment, and COVID-19 stigma because of similar symptoms to TB were mentioned as reasons for fewer people being diagnosed with TB. Public health measures could benefit control of both TB and COVID-19, but only if TB diagnostic services remain accessible and are considered safe to attend.Peer reviewe

Social gradient in the cost of oral pain and related dental service utilisation among South African adults

Background: Oral pain affects people's daily activities and quality of life. The burden of oral pain may vary across socio-economic positions. Currently, little is known about the social gradient in the cost of oral pain among South Africans. This study therefore assessed the social gradient in the cost of oral pain and the related dental service utilisation pattern among South African adults. Methods: Data were obtained from a nationally representative cross-sectional survey of South African adults ?16 year-old (n = 2651) as part of the South African Social Attitudes Survey conducted by the South African Human Sciences Research Council. The survey included demographic data, individual-level socio-economic position (SEP), self-reported oral health status, past six months' oral pain experience and cost. The area-level SEP was obtained from the 2010 General Household Survey (n = 25,653 households) and the 2010/2011Quarterly Labour Force Survey conducted in South Africa. The composite indices used for individual-level SEP (? = 0.76) and area-level SEP (? = 0. 88) were divided into tertiles. Data analysis was done using t-tests and ANOVA. Significance was set at p < 0.05. Results: The prevalence of oral pain among the adult South Africans was 19.4 % (95 % CI = 17.2-21.9). The most commonly reported form of oral pain was 'toothache' (78.9 %). The majority of the wealthiest participants sought care from private dental clinics (64.7 %), or from public dental clinics (19.7 %), while the poorest tended to visit a public dental clinic (45 %) or nurse/general medical practitioner (17.4 %). In the poorest areas, 21 % responded to pain by 'doing nothing'. The individual expenditure for oral pain showed a social gradient from an average of ZAR61.44 spent by those of lowest SEP to ZAR433.83 by the wealthiest (national average ZAR170.92). Average time lost from school/work was two days over the six-month period, but days lost was highest for those living in middle class neighbourhoods (3.41), while those from the richest neighbourhood had lost significantly fewer days from oral pain (0.64). Conclusions: There is a significant social gradient in the burden of oral pain. Improved access to dental care, possibly through carefully planned universal National Health Insurance (NHI), may reduce oral health disparities in South Africa.Scopus 201

Lung cancer diagnosed following an emergency admission: exploring patient and carer perspectives on delay in seeking help

Purpose Compared to others, patients diagnosed with lung cancer following an emergency, unplanned admission to hospital (DFEA) have more advanced disease and poorer prognosis. Little is known about DFEA patients’ beliefs about cancer and its symptoms or about their help-seeking behaviours prior to admission. Methods As part of a larger single-centre, prospective mixed-methods study conducted in one University hospital, we undertook qualitative interviews with patients DFEA and their carers to obtain their understanding of symptoms and experiences of trying to access healthcare services before admission to hospital. Interviews were recorded and transcribed. Framework analysis was employed. Results Thirteen patients and 10 carers plus 3 bereaved carers took part in interviews. Three patient/carer dyads were interviewed together. Participants spoke about their symptoms and why they did not seek help sooner. They described complex and nuanced experiences. Some (n = 12) had what they recalled as the wrong symptoms for lung cancer and attributed them either to a pre-existing condition or to ageing. In other cases (n = 9), patients or carers realised with hindsight that their symptoms were signs of lung cancer, but at the time had made other attributions to account for them. In some cases (n = 3), a sudden onset of symptoms was reported. Some GPs (n = 6) were also reported to have made incorrect attributions about cause. Conclusion Late diagnosis meant that patients DFEA needed palliative support sooner after diagnosis than patients not DFEA. Professionals and lay people interpret health and illness experiences differently

Risk assessment to groundwater of pit latrine rural sanitation policy in developing country settings

Parallel global rise in pit-latrine sanitation and groundwater-supply provision is of concern due to the frequent spatial proximity of these activities. Study of such an area in Malawi has allowed understanding of risks posed to groundwater from the recent implementation of a typical developing-country pit-latrine sanitation policy to be gained. This has assisted the development of a risk-assessment framework approach pragmatic to regulatory-practitioner management of this issue. The framework involves water-supply and pit-latrine mapping, monitoring of key groundwater contamination indicators and surveys of possible environmental site-condition factors and culminates in an integrated statistical evaluation of these datasets to identify the significant factors controlling risks posed. Our approach usefully establishes groundwater-quality baseline conditions of a potentially emergent issue for the study area. Such baselines are foundational to future trend discernment and contaminant natural attenuation verification critical to policies globally. Attribution of borehole contamination to pit-latrine loading should involve, as illustrated, the use of the range of contamination (chemical, microbiological) tracers available recognising none are ideal and several radial and capture-zone metrics that together may provide a weight of evidence. Elevated, albeit low-concentration, nitrate correlated with some radial metrics and was tentatively suggestive of emerging latrine influences. Longer term monitoring is, however, necessary to verify that the commonly observed latrine-borehole separation distances (29–58 m), alongside statutory guidelines, do not constitute significant risk. Borehole contamination was limited and correlation with various environmental-site condition factors also limited. This was potentially ascribed to effectiveness of attenuation to date, monitoring of an emergent problem yet to manifest, or else contamination from other sources. High borehole usage and protective wall absence correlated with observed microbiological contamination incidence, but could relate to increased human/animal activity close to these poorly protected boreholes. Additional to factors assessed, a groundwater-vulnerability factor is recommended that critically relies upon improved proactive securing of underpinning data during borehole/latrine installations. On-going concerns are wide ranging, including poorly constrained pit-latrine input, difficulties in assessing in-situ plume natural attenuation and possible disposal of used motor oils to latrines

Evaluating a Measure of Social Health Derived from Two Mental Health Recovery Measures: The California Quality of Life (CA-QOL) and Mental Health Statistics Improvement Program Consumer Survey (MHSIP)

Social health is important to measure when assessing outcomes in community mental health. Our objective was to validate social health scales using items from two broader commonly used measures that assess mental health outcomes. Participants were 609 adults receiving psychological treatment services. Items were identified from the California Quality of Life (CA-QOL) and Mental Health Statistics Improvement Program (MHSIP) outcome measures by their conceptual correspondence with social health and compared to the Social Functioning Questionnaire (SFQ) using correlational analyses. Pearson correlations for the identified CA-QOL and MSHIP items with the SFQ ranged from .42 to .62, and the identified scale scores produced Pearson correlation coefficients of .56, .70, and, .70 with the SFQ. Concurrent validity with social health was supported for the identified scales. The current inclusion of these assessment tools allows community mental health programs to include social health in their assessments

Responding to salinity in a rural African alluvial valley aquifer system : to boldly go beyond the world of hand-pumped groundwater supply?

Effective response to groundwater salinity in the developing world may critically safeguard drinking-water supplies. Groundwater resources throughout rural Africa are exploited by a vast and increasing number of hand-pumped boreholes for community supply. Our research in TA Ngabu (Shire Valley), Southern Malawi aims to: define groundwater-salinity problem occurrence within its semi-arid alluvial-valley aquifer setting and rural developing-world context; critique current capacity to respond; and, to discuss future response options - in particular considering the need to explore alternative options that boldly go beyond the world of hand-pumped groundwater supply. Salinity problem definition was achieved through survey of 419 hand-pumped boreholes that revealed widespread brackish groundwater causing non-potable (unpalatable) drinking-water supplies. Persistent non-functionality or abandonment of boreholes was typically ascribed to salinity. Whilst salinity is conceptualised to arise from shallow-groundwater evaporation, formation-evaporite dissolution and faulted-area upwelling, sparse data locally renders attribution of salinity sources to individual boreholes difficult. There is a significant need to better resolve the vertical distribution of salinity. Problem response capacity was hampered by multiple factors, including, sector inertia, low drilling costs compromising water-point integrity, and lack of technical vision for alternatives. Various recommendations are made to improve response capacity continuing to work at the hand-pump supply scale. However, in areas where salinity is significant, exploring the feasibility of other options is advocated in conjunction with technical capacity development. Groundwater options may utilise high borehole yields possible from alluvial aquifers, grossly under-exploited by hand pumps. Groundwater at depth, albeit of unknown quality typically, or pipeline transfers of probable good-quality groundwater from valley-margin units, should be considered. Surface-water pipeline supplies may be viable for (growing) population centres. Canal-fed irrigation schemes (pending for the area), should be multiple-use, protective of groundwater and embrace pipeline drinking-water supply and managed-aquifer-recharge opportunities. Advancing desalination technologies, although presently unaffordable, should be kept under review

Impact of COVID-19 on tuberculosis notifications in Blantyre Malawi: an interrupted time series analysis and qualitative study with healthcare workers.

COVID-19 may impact on tuberculosis (TB) diagnosis and care. We analysed a city-wide electronic TB register in Blantyre, Malawi and interviewed TB officers. Malawi had no official “lockdown” but closed schools and borders on 23 March 2020. In interrupted time series analysis, there was an immediate 35.9% reduction in TB notifications (95% CI 22.0 to 47.3%) in April, which recovered to near pre-pandemic numbers by December 2020, but with 333 (95% CI 291 to 375) fewer cumulative notifications than anticipated. Women and girls were impacted (30.7% fewer cases, 95% CI 28.4 to 33.0%) more than men and boys (20.9% fewer, 95% CI 18.5 to 23.3). Fear of COVID-19 infection, temporary facility closure, inadequate protective equipment and COVID-19 stigma with similar presenting symptoms to TB were mentioned. Public health measures could benefit both TB and COVID-19, but only if diagnostic services remain accessible and are considered safe to attend