Generate publications list from BibTeX file

[matt-graham]

Uses pybtex to generate a HTML publication list from a BibTeX file containing publication details for inclusion on website.

The note field in BibTeX file is used to store section names to organize publications under to reflect current publications page. Compared to the current publications list, this adds a few extra details (abbreviated author list, publication year and journal) - see example output below.

We could potentially make each publication entry expandable with additional details such as full author list, abstract and bibtex entry listed when expanded if that would be useful? @tbhallett tagging you for thoughts on what it would be useful to include!

Example output

Overview of the model

• Hallett et al (2024). A Healthcare Service Delivery and Epidemiological Model for Investigating Resource Allocation for Health: The Thanzi La Onse Model. medRxiv.

Analyses using the model

• Mangal et al (2024). Assessing the effect of health system resources on HIV and tuberculosis programmes in Malawi: a modelling study. The Lancet Global Health.
• Mangal et al (2024). A Decade of Progress in HIV, Malaria, and Tuberculosis Initiatives in Malawi. medRxiv.
• Molaro et al (2024). The potential impact of declining development assistance for healthcare on population health: projections for Malawi. medRxiv.
• Molaro et al (2024). A new approach to Health Benefits Package design: an application of the Thanzi La Onse model in Malawi. PLOS Computational Biology.
• Mohan et al (2024). Factors associated with medical consumable availability in level 1 facilities in Malawi: a secondary analysis of a facility census. The Lancet Global Health.
• She et al (2024). The changes in health service utilisation in Malawi during the COVID-19 pandemic. PLOS ONE.
• Colbourn et al (2023). Modeling Contraception and Pregnancy in Malawi: A Thanzi La Onse Mathematical Modeling Study. Studies in Family Planning.
• Manning Smith et al (2022). Estimating the health burden of road traffic injuries in Malawi using an individual-based model. Injury Epidemiology.
• Mangal et al (2021). Potential impact of intervention strategies on COVID-19 transmission in Malawi: a mathematical modelling study. BMJ Open.
• Hawryluk et al (2020). The potential impact of including pre-school aged children in the praziquantel mass-drug administration programmes on the S.haematobium infections in Malawi: a modelling study. medRxiv.

Healthcare seeking behaviour

• Ng'ambi et al (2022). Socio-demographic factors associated with early antenatal care visits among pregnant women in Malawi: 2004–2016. PLOS ONE.
• Ng'ambi et al (2020). A cross-sectional study on factors associated with health seeking behaviour of Malawians aged 15+ years in 2016. Malawi Medical Journal.
• Ng'ambi et al (2020). Factors associated with healthcare seeking behaviour for children in Malawi: 2016. Tropical Medicine & International Health.

[matt-graham]

Script now updated to output publication list as a list of <details> elements with summary showing {summarized_authors} ({year}). {title}. {venue}. as previously and expandable details showing a table which additional lists publication type (currently Journal article or Pre-print though could easily be expanded to for example conference proceedings / posters / talks etc., PhD theses), DOI, publication date, full author list and abstract. Example of output is as follows:

Example output

Overview of the model

• Hallett et al. (2024). A Healthcare Service Delivery and Epidemiological Model for Investigating Resource Allocation for Health: The Thanzi La Onse Model. medRxiv.

  Type	Pre-print
  DOI	10.1101/2024.01.04.24300834
  Date	January 2024
  Authors	Timothy B. Hallett, Tara D. Mangal, Asif U. Tamuri, Nimalan Arinaminpathy, Valentina Cambiano, Martin Chalkley, Joseph H. Collins, Jonathan Cooper, Matthew S. Gillman, Mosè Giordano, Matthew M. Graham, William Graham, Eva Janoušková, Britta L. Jewell, Ines Li Lin, Robert Manning Smith, Gerald Manthalu, Emmanuel Mnjowe, Sakshi Mohan, Margherita Molaro, Wingston Ng’ambi, Dominic Nkhoma, Stefan Piatek, Paul Revill, Alison Rodger, Dimitra Salmanidou, Bingling She, Mikaela Smit, Pakwanja D. Twea, Tim Colbourn, Joseph Mfutso-Bengo, and Andrew N. Phillips.
  Abstract	Background Decisions need to be made in all healthcare systems about the allocation of available resources with the aim of improving population health. Evidence is needed for these decisions, which can have enormous consequences for population health, especially in lower-income settings. Methods We address this need using an individual-based simulation model of healthcare need and service delivery that we have developed for Malawi, drawing on demographic, epidemiological and routine healthcare system data (on facilities, staff, and consumables). We compare the model’s simulated outputs with available data and estimate the impact that the healthcare system is having currently. We analyse the effects of improvements in healthcare access, clinician performance and consumables availability. Findings Malawi’s healthcare system averted 40 million Disability-Adjusted Life-Years (DALYs) in the five-year period to end-2019, which is half of the total DALYS that the population (total size: 19 million in 2020) would otherwise incur. This impact is strongly focussed on young children (mediated largely by programmes addressing respiratory infections, HIV/AIDS and malaria) and also by the HIV/AIDS and TB programmes (among adults). More services seem to be delivered than would be expected based on the number of staff and expected time needed for services. Nevertheless, the additional services that are provided (through service times being reduced or additional HCW hours worked) account for half the impact of the healthcare system (i.e., ∼20 million DALYS averted). If system improvements gave ill persons immediate access to healthcare, led to optimal referral and diagnosis accuracy, and eliminated consumable stock-outs, the overall impact of the healthcare system could increase by up to ∼30% (12 million more DALYS averted). Conclusions The healthcare system in Malawi generates substantial health gains to the population with very limited resources. Strengthening interventions could potentially increase these gains considerably and so should be a priority for investigation and investment. A detailed individual-based simulation model of healthcare service delivery is a valuable tool for healthcare system planning and for evaluating proposals for healthcare system strengthening.

Analyses using the model

• Mangal et al. (2024). A Decade of Progress in HIV, Malaria, and Tuberculosis Initiatives in Malawi. medRxiv.

  Type	Pre-print
  DOI	10.1101/2024.10.08.24315077
  Date	October 2024
  Authors	Tara Danielle Mangal, Margherita Molaro, Dominic Nkhoma, Timothy Colbourn, Joseph H. Collins, Eva Janoušková, Matthew M. Graham, Ines Li Lin, Emmanuel Mnjowe, Tisungane E. Mwenyenkulu, Sakshi Mohan, Bingling She, Asif U. Tamuri, Pakwanja D. Twea, Peter Winskill, Andrew Phillips, Joseph Mfutso-Bengo, and Timothy B. Hallett.
  Abstract	Objective Huge investments in HIV, TB, and malaria (HTM) control in Malawi have greatly reduced disease burden. However, the joint impact of these services across multiple health domains and the health system resources required to deliver them are not fully understood. Methods An integrated epidemiological and health system model was used to assess the impact of HTM programmes in Malawi from 2010 to 2019, incorporating interacting disease dynamics, intervention effects, and health system usage. Four scenarios were examined, comparing actual programme delivery with hypothetical scenarios excluding programmes individually and collectively. Findings From 2010-2019, HTM programmes were estimated to have prevented 1.08 million deaths and 74.89 million DALYs. An additional 15,600 deaths from other causes were also prevented. Life expectancy increased by 13.0 years for males and 16.9 years for females.The HTM programmes accounted for 24.2% of all health system interactions, including 157.0 million screening/diagnostic tests and 23.2 million treatment appointments. Accounting for the anticipated health deterioration without HTM services, only 41.55 million additional healthcare worker hours were required (17.1% of total healthcare worker time) to achieve these gains. The HTM programme eliminated the need for 123 million primary care appointments, offset by a net increase in inpatient care demand (9.4 million bed-days) that would have been necessary in its absence. Conclusions HTM programmes have greatly increased life expectancy, providing direct and spillover effects on health. These investments have alleviated the burden on inpatient and emergency care, which requires more intensive healthcare provider involvement.

• Mangal et al. (2024). Assessing the effect of health system resources on HIV and tuberculosis programmes in Malawi: a modelling study. The Lancet Global Health.

  Type	Journal article
  DOI	10.1016/S2214-109X(24)00259-6
  Date	October 2024
  Authors	Tara D Mangal, Sakshi Mohan, Timothy Colbourn, Joseph H Collins, Mathew Graham, Andreas Jahn, Eva Janoušková, Ines Li Lin, Robert Manning Smith, Emmanuel Mnjowe, Margherita Molaro, Tisungane E Mwenyenkulu, Dominic Nkhoma, Bingling She, Asif Tamuri, Paul Revill, Andrew N Phillips, Joseph Mfutso-Bengo, and Timothy B Hallett.
  Abstract	Background Malawi is progressing towards UNAIDS and WHO End TB Strategy targets to eliminate HIV/AIDS and tuberculosis. We aimed to assess the prospective effect of achieving these goals on the health and health system of the country and the influence of consumable constraints. Methods In this modelling study, we used the Thanzi la Onse (Health for All) model, which is an individual-based multi-disease simulation model that simulates HIV and tuberculosis transmission, alongside other diseases (eg, malaria, non-communicable diseases, and maternal diseases), and gates access to essential medicines according to empirical estimates of availability. The model integrates dynamic disease modelling with health system engagement behaviour, health system use, and capabilities (ie, personnel and consumables). We used 2018 data on the availability of HIV and tuberculosis consumables (for testing, treatment, and prevention) across all facility levels of the country to model three scenarios of HIV and tuberculosis programme scale-up from Jan 1, 2023, to Dec 31, 2033: a baseline scenario, when coverage remains static using existing consumable constraints; a constrained scenario, in which prioritised interventions are scaled up with fixed consumable constraints; and an unconstrained scenario, in which prioritised interventions are scaled up with maximum availability of all consumables related to HIV and tuberculosis care. Findings With uninterrupted medical supplies, in Malawi, we projected HIV and tuberculosis incidence to decrease to 26 (95% uncertainty interval [UI] 19–35) cases and 55 (23–74) cases per 100 000 person-years by 2033 (from 152 [98–195] cases and 123 [99–160] cases per 100 000 person-years in 2023), respectively, with programme scale-up, averting a total of 12·21 million (95% UI 11·39–14·16) disability-adjusted life-years. However, the effect was compromised by restricted access to key medicines, resulting in approximately 58 700 additional deaths (33 400 [95% UI 22 000–41 000] due to AIDS and 25 300 [19 300–30 400] due to tuberculosis) compared with the unconstrained scenario. Between 2023 and 2033, eliminating HIV treatment stockouts could avert an estimated 12 100 deaths compared with the baseline scenario, and improved access to tuberculosis prevention medications could prevent 5600 deaths in addition to those achieved through programme scale-up alone. With programme scale-up under the constrained scenario, consumable stockouts are projected to require an estimated 14·3 million extra patient-facing hours between 2023 and 2033, mostly from clinical or nursing staff, compared with the unconstrained scenario. In 2033, with enhanced screening, 188 000 (81%) of 232 900 individuals projected to present with active tuberculosis could start tuberculosis treatment within 2 weeks of initial presentation if all required consumables were available, but only 8600 (57%) of 15 100 presenting under the baseline scenario. Interpretation Ignoring frailties in the health-care system, in particular the potential non-availability of consumables, in projections of HIV and tuberculosis programme scale-up might risk overestimating potential health impacts and underestimating required health system resources. Simultaneous health system strengthening alongside programme scale-up is crucial, and should yield greater benefits to population health while mitigating the strain on a heavily constrained health-care system. Funding Wellcome and UK Research and Innovation as part of the Global Challenges Research Fund.

• Molaro et al. (2024). The potential impact of declining development assistance for healthcare on population health: projections for Malawi. medRxiv.

  Type	Pre-print
  DOI	10.1101/2024.10.11.24315287
  Date	October 2024
  Authors	Margherita Molaro, Paul Revill, Martin Chalkley, Sakshi Mohan, Tara Mangal, Tim Colbourn, Joseph H. Collins, Matthew M. Graham, William Graham, Eva Janoušková, Gerald Manthalu, Emmanuel Mnjowe, Watipaso Mulwafu, Rachel Murray-Watson, Pakwanja D. Twea, Andrew N. Phillips, Bingling She, Asif U. Tamuri, Dominic Nkhoma, Joseph Mfutso-Bengo, and Timothy B. Hallett.
  Abstract	Development assistance for health (DAH) to Malawi will likely decrease as a fraction of GDP in the next few decades. Given the country’s significant reliance on DAH for the delivery of its healthcare services, estimating the impact that this could have on health projections for the country is particularly urgent. We use the Malawi-specific, individual-based “all diseases – whole health-system” Thanzi La Onse model to estimate the impact this could have on health system capacities, proxied by the availability of human resources for health, and consequently on population health outcomes. We estimate that the projected changes in DAH could result in a 7-15.8% increase in disability-adjusted life years compared to a scenario where health spending as a percentage of GDP remains unchanged. This could cause a reversal of gains achieved to date in many areas of health, although progress against HIV/AIDS appears to be less vulnerable. The burden due to non-communicable diseases, on the other hand, is found to increase irrespective of yearly growth in health expenditure, if assuming current reach and scope of interventions. Finally, we find that greater health expenditure will improve population health outcomes, but at a diminishing rate.

• Molaro et al. (2024). A new approach to Health Benefits Package design: an application of the Thanzi La Onse model in Malawi. PLOS Computational Biology.

  Type	Journal article
  DOI	10.1371/journal.pcbi.1012462
  Date	September 2024
  Authors	Margherita Molaro, Sakshi Mohan, Bingling She, Martin Chalkley, Tim Colbourn, Joseph H. Collins, Emilia Connolly, Matthew M. Graham, Eva Janoušková, Ines Li Lin, Gerald Manthalu, Emmanuel Mnjowe, Dominic Nkhoma, Pakwanja D. Twea, Andrew N. Phillips, Paul Revill, Asif U. Tamuri, Joseph Mfutso-Bengo, Tara D. Mangal, and Timothy B. Hallett.
  Abstract	An efficient allocation of limited resources in low-income settings offers the opportunity to improve population-health outcomes given the available health system capacity. Efforts to achieve this are often framed through the lens of “health benefits packages” (HBPs), which seek to establish which services the public healthcare system should include in its provision. Analytic approaches widely used to weigh evidence in support of different interventions and inform the broader HBP deliberative process however have limitations. In this work, we propose the individual-based Thanzi La Onse (TLO) model as a uniquely-tailored tool to assist in the evaluation of Malawi-specific HBPs while addressing these limitations. By mechanistically modelling—and calibrating to extensive, country-specific data—the incidence of disease, health-seeking behaviour, and the capacity of the healthcare system to meet the demand for care under realistic constraints on human resources for health available, we were able to simulate the health gains achievable under a number of plausible HBP strategies for the country. We found that the HBP emerging from a linear constrained optimisation analysis (LCOA) achieved the largest health gain—∼8% reduction in disability adjusted life years (DALYs) between 2023 and 2042 compared to the benchmark scenario—by concentrating resources on high-impact treatments. This HBP however incurred a relative excess in DALYs in the first few years of its implementation. Other feasible approaches to prioritisation were assessed, including service prioritisation based on patient characteristics, rather than service type. Unlike the LCOA-based HBP, this approach achieved consistent health gains relative to the benchmark scenario on a year- to-year basis, and a 5% reduction in DALYs over the whole period, which suggests an approach based upon patient characteristics might prove beneficial in the future.

• She et al. (2024). Health workforce needs in Malawi: analysis of the Thanzi La Onse integrated epidemiological model of care. Human Resources for Health.

  Type	Journal article
  DOI	10.1186/s12960-024-00949-2
  Date	September 2024
  Authors	Bingling She, Tara D. Mangal, Margaret L. Prust, Stephanie Heung, Martin Chalkley, Tim Colbourn, Joseph H. Collins, Matthew M. Graham, Britta Jewell, Purava Joshi, Ines Li Lin, Emmanuel Mnjowe, Sakshi Mohan, Margherita Molaro, Andrew N. Phillips, Paul Revill, Robert Manning Smith, Asif U. Tamuri, Pakwanja D. Twea, Gerald Manthalu, Joseph Mfutso-Bengo, and Timothy B. Hallett.
  Abstract	To make the best use of health resources, it is crucial to understand the healthcare needs of a population—including how needs will evolve and respond to changing epidemiological context and patient behaviour—and how this compares to the capabilities to deliver healthcare with the existing workforce. Existing approaches to planning either rely on using observed healthcare demand from a fixed historical period or using models to estimate healthcare needs within a narrow domain (e.g., a specific disease area or health programme). A new data-grounded modelling method is proposed by which healthcare needs and the capabilities of the healthcare workforce can be compared and analysed under a range of scenarios: in particular, when there is much greater propensity for healthcare seeking.

• Mohan et al. (2024). Factors associated with medical consumable availability in level 1 facilities in Malawi: a secondary analysis of a facility census. The Lancet Global Health.

  Type	Journal article
  DOI	10.1016/S2214-109X(24)00095-0
  Date	June 2024
  Authors	Sakshi Mohan, Tara D Mangal, Tim Colbourn, Martin Chalkley, Chikhulupiliro Chimwaza, Joseph H Collins, Matthew M Graham, Eva Janoušková, Britta Jewell, Godfrey Kadewere, Ines Li Lin, Gerald Manthalu, Joseph Mfutso-Bengo, Emmanuel Mnjowe, Margherita Molaro, Dominic Nkhoma, Paul Revill, Bingling She, Robert Manning Smith, Wiktoria Tafesse, Asif U Tamuri, Pakwanja Twea, Andrew N Phillips, and Timothy B Hallett.
  Abstract	Background Medical consumable stock-outs negatively affect health outcomes not only by impeding or delaying the effective delivery of services but also by discouraging patients from seeking care. Consequently, supply chain strengthening is being adopted as a key component of national health strategies. However, evidence on the factors associated with increased consumable availability is limited. Methods In this study, we used the 2018–19 Harmonised Health Facility Assessment data from Malawi to identify the factors associated with the availability of consumables in level 1 facilities, ie, rural hospitals or health centres with a small number of beds and a sparsely equipped operating room for minor procedures. We estimate a multilevel logistic regression model with a binary outcome variable representing consumable availability (of 130 consumables across 940 facilities) and explanatory variables chosen based on current evidence. Further subgroup analyses are carried out to assess the presence of effect modification by level of care, facility ownership, and a categorisation of consumables by public health or disease programme, Malawi's Essential Medicine List classification, whether the consumable is a drug or not, and level of average national availability. Findings Our results suggest that the following characteristics had a positive association with consumable availability—level 1b facilities or community hospitals had 64% (odds ratio [OR] 1·64, 95% CI 1·37–1·97) higher odds of consumable availability than level 1a facilities or health centres, Christian Health Association of Malawi and private-for-profit ownership had 63% (1·63, 1·40–1·89) and 49% (1·49, 1·24–1·80) higher odds respectively than government-owned facilities, the availability of a computer had 46% (1·46, 1·32–1·62) higher odds than in its absence, pharmacists managing drug orders had 85% (1·85, 1·40–2·44) higher odds than a drug store clerk, proximity to the corresponding regional administrative office (facilities greater than 75 km away had 21% lower odds [0·79, 0·63–0·98] than facilities within 10 km of the district health office), and having three drug order fulfilments in the 3 months before the survey had 14% (1·14, 1·02–1·27) higher odds than one fulfilment in 3 months. Further, consumables categorised as vital in Malawi's Essential Medicine List performed considerably better with 235% (OR 3·35, 95% CI 1·60–7·05) higher odds than other essential or non-essential consumables and drugs performed worse with 79% (0·21, 0·08–0·51) lower odds than other medical consumables in terms of availability across facilities. Interpretation Our results provide evidence on the areas of intervention with potential to improve consumable availability. Further exploration of the health and resource consequences of the strategies discussed will be useful in guiding investments into supply chain strengthening. Funding UK Research and Innovation as part of the Global Challenges Research Fund (Thanzi La Onse; reference MR/P028004/1), the Wellcome Trust (Thanzi La Mawa; reference 223120/Z/21/Z), the UK Medical Research Council, the UK Department for International Development, and the EU (reference MR/R015600/1).

• She et al. (2024). The changes in health service utilisation in Malawi during the COVID-19 pandemic. PLOS ONE.

  Type	Journal article
  DOI	10.1371/journal.pone.0290823
  Date	January 2024
  Authors	Bingling She, Tara D. Mangal, Anna Y. Adjabeng, Tim Colbourn, Joseph H. Collins, Eva Janoušková, Ines Li Lin, Emmanuel Mnjowe, Sakshi Mohan, Margherita Molaro, Andrew N. Phillips, Paul Revill, Robert Manning Smith, Pakwanja D. Twea, Dominic Nkhoma, Gerald Manthalu, and Timothy B. Hallett.
  Abstract	Introduction The COVID-19 pandemic and the restriction policies implemented by the Government of Malawi may have disrupted routine health service utilisation. We aimed to find evidence for such disruptions and quantify any changes by service type and level of health care. Methods We extracted nationwide routine health service usage data for 2015–2021 from the electronic health information management systems in Malawi. Two datasets were prepared: unadjusted and adjusted; for the latter, unreported monthly data entries for a facility were filled in through systematic rules based on reported mean values of that facility or facility type and considering both reporting rates and comparability with published data. Using statistical descriptive methods, we first described the patterns of service utilisation in pre-pandemic years (2015–2019). We then tested for evidence of departures from this routine pattern, i.e., service volume delivered being below recent average by more than two standard deviations was viewed as a substantial reduction, and calculated the cumulative net differences of service volume during the pandemic period (2020–2021), in aggregate and within each specific facility. Results Evidence of disruptions were found: from April 2020 to December 2021, services delivered of several types were reduced across primary and secondary levels of care–including inpatient care (-20.03% less total interactions in that period compared to the recent average), immunisation (-17.61%), malnutrition treatment (-34.5%), accidents and emergency services (-16.03%), HIV (human immunodeficiency viruses) tests (-27.34%), antiretroviral therapy (ART) initiations for adults (-33.52%), and ART treatment for paediatrics (-41.32%). Reductions of service volume were greatest in the first wave of the pandemic during April-August 2020, and whereas some service types rebounded quickly (e.g., outpatient visits from -17.7% to +3.23%), many others persisted at lower level through 2021 (e.g., under-five malnutrition treatment from -15.24% to -42.23%). The total reduced service volume between April 2020 and December 2021 was 8 066 956 (-10.23%), equating to 444 units per 1000 persons. Conclusion We have found substantial evidence for reductions in health service delivered in Malawi during the COVID-19 pandemic which may have potential health consequences, the effect of which should inform how decisions are taken in the future to maximise the resilience of healthcare system during similar events.

• Colbourn et al. (2023). Modeling Contraception and Pregnancy in Malawi: A Thanzi La Onse Mathematical Modeling Study. Studies in Family Planning.

  Type	Journal article
  DOI	10.1111/sifp.12255
  Date	2023
  Authors	Tim Colbourn, Eva Janoušková, Ines Li Lin, Joseph Collins, Emilia Connolly, Matt Graham, Britta Jewel, Fannie Kachale, Tara Mangal, Gerald Manthalu, Joseph Mfutso-Bengo, Emmanuel Mnjowe, Sakshi Mohan, Margherita Molaro, Wingston Ng'ambi, Dominic Nkhoma, Paul Revill, Bingling She, Robert Manning Smith, Pakwanja Twea, Asif Tamuri, Andrew Phillips, and Timothy B. Hallett.
  Abstract	Malawi has high unmet need for contraception with a costed national plan to increase contraception use. Estimating how such investments might impact future population size in Malawi can help policymakers understand effects and value of policies to increase contraception uptake. We developed a new model of contraception and pregnancy using individual-level data capturing complexities of contraception initiation, switching, discontinuation, and failure by contraception method, accounting for differences by individual characteristics. We modeled contraception scale-up via a population campaign to increase initiation of contraception (Pop) and a postpartum family planning intervention (PPFP). We calibrated the model without new interventions to the UN World Population Prospects 2019 medium variant projection of births for Malawi. Without interventions Malawi's population passes 60 million in 2084; with Pop and PPFP interventions. it peaks below 35 million by 2100. We compare contraception coverage and costs, by method, with and without interventions, from 2023 to 2050. We estimate investments in contraception scale-up correspond to only 0.9 percent of total health expenditure per capita though could result in dramatic reductions of current pressures of very rapid population growth on health services, schools, land, and society, helping Malawi achieve national and global health and development goals.

• Manning Smith et al. (2022). Estimating the health burden of road traffic injuries in Malawi using an individual-based model. Injury Epidemiology.

  Type	Journal article
  DOI	10.1186/s40621-022-00386-6
  Date	July 2022
  Authors	Robert Manning Smith, Valentina Cambiano, Tim Colbourn, Joseph H. Collins, Matthew Graham, Britta Jewell, Ines Li Lin, Tara D. Mangal, Gerald Manthalu, Joseph Mfutso-Bengo, Emmanuel Mnjowe, Sakshi Mohan, Wingston Ng’ambi, Andrew N. Phillips, Paul Revill, Bingling She, Mads Sundet, Asif Tamuri, Pakwanja D. Twea, and Timothy B. Hallet.
  Abstract	Road traffic injuries are a significant cause of death and disability globally. However, in some countries the exact health burden caused by road traffic injuries is unknown. In Malawi, there is no central reporting mechanism for road traffic injuries and so the exact extent of the health burden caused by road traffic injuries is hard to determine. A limited number of models predict the incidence of mortality due to road traffic injury in Malawi. These estimates vary greatly, owing to differences in assumptions, and so the health burden caused on the population by road traffic injuries remains unclear.

• Mangal et al. (2021). Potential impact of intervention strategies on COVID-19 transmission in Malawi: a mathematical modelling study. BMJ Open.

  Type	Journal article
  DOI	10.1136/bmjopen-2020-045196
  Date	July 2021
  Authors	Tara Mangal, Charlie Whittaker, Dominic Nkhoma, Wingston Ng'ambi, Oliver Watson, Patrick Walker, Azra Ghani, Paul Revill, Timothy Colbourn, Andrew Phillips, Timothy Hallett, and Joseph Mfutso-Bengo.
  Abstract	Background COVID-19 mitigation strategies have been challenging to implement in resource-limited settings due to the potential for widespread disruption to social and economic well-being. Here we predict the clinical severity of COVID-19 in Malawi, quantifying the potential impact of intervention strategies and increases in health system capacity. Methods The infection fatality ratios (IFR) were predicted by adjusting reported IFR for China, accounting for demography, the current prevalence of comorbidities and health system capacity. These estimates were input into an age-structured deterministic model, which simulated the epidemic trajectory with non-pharmaceutical interventions and increases in health system capacity. Findings The predicted population-level IFR in Malawi, adjusted for age and comorbidity prevalence, is lower than that estimated for China (0.26%, 95% uncertainty interval (UI) 0.12%–0.69%, compared with 0.60%, 95% CI 0.4% to 1.3% in China); however, the health system constraints increase the predicted IFR to 0.83%, 95% UI 0.49%–1.39%. The interventions implemented in January 2021 could potentially avert 54 400 deaths (95% UI 26 900–97 300) over the course of the epidemic compared with an unmitigated outbreak. Enhanced shielding of people aged ≥60 years could avert 40 200 further deaths (95% UI 25 300–69 700) and halve intensive care unit admissions at the peak of the outbreak. A novel therapeutic agent which reduces mortality by 0.65 and 0.8 for severe and critical cases, respectively, in combination with increasing hospital capacity, could reduce projected mortality to 2.5 deaths per 1000 population (95% UI 1.9–3.6). Conclusion We find the interventions currently used in Malawi are unlikely to effectively prevent SARS-CoV-2 transmission but will have a significant impact on mortality. Increases in health system capacity and the introduction of novel therapeutics are likely to further reduce the projected numbers of deaths.

• Hawryluk et al. (2020). The potential impact of including pre-school aged children in the praziquantel mass-drug administration programmes on the S.haematobium infections in Malawi: a modelling study. medRxiv.

  Type	Pre-print
  DOI	10.1101/2020.12.09.20246652
  Date	December 2020
  Authors	Iwona Hawryluk, Tara Mangal, Andrew Nguluwe, Chikonzero Kambalame, Stanley Banda, Memory Magaleta, Lazarus Juziwelo, and Timothy B. Hallett.
  Abstract	Background Mass drug administration (MDA) of praziquantel is an intervention used in the treatment and prevention of schistosomiasis. In Malawi, MDA happens annually across high-risk districts and covers around 80% of school aged children and 50% of adults. The current formulation of praziquantel is not approved for use in the preventive chemotherapy for children under 5 years old, known as pre-school aged children (PSAC). However, a new formulation for PSAC will be available by 2022. A comprehensive analysis of the potential additional benefits of including PSAC in the MDA will be critical to guide policy-makers. Methods We developed a new individual-based stochastic transmission model of Schistosoma haematobium for the 6 highest prevalence districts of Malawi. The model was used to evaluate the benefits of including PSAC in the MDA campaigns, with respect to the prevalence of high-intensity infections (\textgreater 500 eggs per ml of urine) and reaching the elimination target, meaning the prevalence of high-intensity infections under 5% in all sentinel sites. The impact of different MDA frequencies and coverages is quantified by prevalence of high-intensity infection and number of rounds needed to decrease that prevalence below 1%. Results Including PSAC in the MDA campaigns can reduce the time needed to achieve the elimination target for S. haematobium infections in Malawi by one year. The modelling suggests that in the case of a lower threshold of high-intensity infection, currently set by WHO to 500 eggs per ml of urine, including PSAC in the preventive chemotherapy programmes for 5 years can reduce the number of the high-intensity infection case years for pre-school aged children by up to 9.1 years per 100 children. Conclusions Regularly treating PSAC in the MDA is likely to lead to overall better health of children as well as a decrease in the severe morbidities caused by persistent schistosomiasis infections and bring forward the date of elimination. Moreover, mass administration of praziquantel to PSAC will decrease the prevalence among the SAC, who are at the most risk of infection.

Healthcare seeking behaviour

• Ng'ambi et al. (2022). Socio-demographic factors associated with early antenatal care visits among pregnant women in Malawi: 2004–2016. PLOS ONE.

  Type	Journal article
  DOI	10.1371/journal.pone.0263650
  Date	February 2022
  Authors	Wingston Felix Ng'ambi, Joseph H. Collins, Tim Colbourn, Tara Mangal, Andrew Phillips, Fannie Kachale, Joseph Mfutso-Bengo, Paul Revill, and Timothy B. Hallett.
  Abstract	Introduction In 2016, the WHO published recommendations increasing the number of recommended antenatal care (ANC) visits per pregnancy from four to eight. Prior to the implementation of this policy, coverage of four ANC visits has been suboptimal in many low-income settings. In this study we explore socio-demographic factors associated with early initiation of first ANC contact and attending at least four ANC visits (“ANC4+”) in Malawi using the Malawi Demographic and Health Survey (MDHS) data collected between 2004 and 2016, prior to the implementation of new recommendations. Methods We combined data from the 2004–5, 2010 and 2015–16 MDHS using Stata version 16. Participants included all women surveyed between the ages of 15–49 who had given birth in the five years preceding the survey. We conducted weighted univariate, bivariate and multivariable logistic regression analysis of the effects of each of the predictor variables on the binary endpoint of the woman attending at least four ANC visits and having the first ANC attendance within or before the four months of pregnancy (ANC4+). To determine whether a factor was included in the model, the likelihood ratio test was used with a statistical significance of P\textless 0.05 as the threshold. Results We evaluated data collected in surveys in 2004/5, 2010 and 2015/6 from 26386 women who had given birth in the five years before being surveyed. The median gestational age, in months, at the time of presenting for the first ANC visit was 5 (inter quartile range: 4–6). The proportion of women initiating ANC4+ increased from 21.3% in 2004–5 to 38.8% in 2015–16. From multivariate analysis, there was increasing trend in ANC4+ from women aged 20–24 years (adjusted odds ratio (aOR) = 1.27, 95%CI:1.05–1.53, P = 0.01) to women aged 45–49 years (aOR = 1.91, 95%CI:1.18–3.09, P = 0.008) compared to those aged 15–19 years. Women from richest socio-economic position ((aOR = 1.32, 95%CI:1.12–1.58, P\textless 0.001) were more likely to demonstrate ANC4+ than those from low socio-economic position. Additionally, women who had completed secondary (aOR = 1.24, 95%CI:1.02–1.51, P = 0.03) and tertiary (aOR = 2.64, 95%CI:1.65–4.22, P\textless 0.001) education were more likely to report having ANC4+ than those with no formal education. Conversely increasing parity was associated with a reduction in likelihood of ANC4+ with women who had previously delivered 2–3 (aOR = 0.74, 95%CI:0.63–0.86, P\textless 0.001), 4–5 (aOR = 0.65, 95%CI:0.53–0.80, P\textless 0.001) or greater than 6 (aOR = 0.61, 95%CI: 0.47–0.79, \textless 0.001) children being less likely to demonstrate ANC4+. Conclusion The proportion of women reporting ANC4+ and of key ANC interventions in Malawi have increased significantly since 2004. However, we found that most women did not access the recommended number of ANC visits in Malawi, prior to the 2016 WHO policy change which may mean that women are less likely to undertake the 2016 WHO recommendation of 8 contacts per pregnancy. Additionally, our results highlighted significant variation in coverage according to key socio-demographic variables which should be considered when devising national strategies to ensure that all women access the appropriate frequency of ANC visits during their pregnancy.

• Ng'ambi et al. (2020). A cross-sectional study on factors associated with health seeking behaviour of Malawians aged 15+ years in 2016. Malawi Medical Journal.

  Type	Journal article
  DOI
  Date	2020
  Authors	Wingston Ng'ambi, Tara Mangal, Andrew Phillips, Tim Colbourn, Dominic Nkhoma, Joseph Mfutso- Bengo, Paul Revill, and Timothy B. Hallett.
  Abstract	IntroductionHealth seeking behaviour (HSB) refers to actions taken by individuals who are ill in order to find appropriate remedy. Most studies on HSB have only examined one symptom or covered only a specific geographical location within a country. In this study, we used a representative sample of adults to explore the factors associated with HSB in response to 30 symptoms reported by adult Malawians in 2016.MethodsWe used the 2016 Malawi Integrated Household Survey dataset. We fitted a multilevel logistic regression model of likelihood of ‘seeking care at a health facility’ using a forward step-wise selection method, with age, sex and reported symptoms entered as a priori variables. We calculated the odds ratios (ORs) and their associated 95% confidence intervals (95% CI). We set the level of statistical significance at P < 0.05.Results Of 6909 adults included in the survey, 1907 (29%) reported symptoms during the 2 weeks preceding the survey. Of these, 937 (57%) sought care at a health facility. Adults in urban areas were more likely to seek health care at a health facility than those in rural areas (AOR = 1.65, 95% CI: 1.19–2.30, P = 0.003). Females had a higher likelihood of seeking care from health facilities than males (AOR = 1.26, 95% CI: 1.03–1.59, P = 0.029). Being of higher wealth status was associated with a higher likelihood of seeking care from a health facility (AOR = 1.58, 95% CI: 1.16–2.16, P = 0.004). Having fever and eye problems were associated with higher likelihood of seeking care at a health facility, while having headache, stomach ache and respiratory tract infections were associated with lower likelihood of seeking care at a health facility.ConclusionThis study has shown that there is a need to understand and address individual, socioeconomic and geographical barriers to health seeking to increase access and appropriate use of health care and fast-track progress towards Universal Health Coverage among the adult population.

• Ng'ambi et al. (2020). Factors associated with healthcare seeking behaviour for children in Malawi: 2016. Tropical Medicine & International Health.

  Type	Journal article
  DOI	10.1111/tmi.13499
  Date	2020
  Authors	Wingston Ng'ambi, Tara Mangal, Andrew Phillips, Tim Colbourn, Joseph Mfutso-Bengo, Paul Revill, and Timothy B. Hallett.
  Abstract	Objective To characterise health seeking behaviour (HSB) and determine its predictors amongst children in Malawi in 2016. Methods We used the 2016 Malawi Integrated Household Survey data set. The outcome of interest was HSB, defined as seeking care at a health facility amongst people who reported one or more of a list of possible symptoms given on the questionnaire in the past two weeks. We fitted a multivariate logistic regression model of HSB using a forward step-wise selection method, with age, sex and symptoms entered as a priori variables. Results Of 5350 children, 1666 (32%) had symptoms in the past two weeks. Of the 1666, 1008 (61%) sought care at health facility. The children aged 5–14 years were less likely to be taken to health facilities for health care than those aged 0–4 years. Having fever vs. not having fever and having a skin problem vs. not having skin problem were associated with increased likelihood of HSB. Having a headache vs. not having a headache was associated with lower likelihood of accessing care at health facilities (AOR = 0.50, 95% CI: 0.26–0.96, P = 0.04). Children from urban areas were more likely to be taken to health facilities for health care (AOR = 1.81, 95% CI: 1.17–2.85, P = 0.008), as were children from households with a high wealth status (AOR = 1.86, 95% CI: 1.25–2.78, P = 0.02). Conclusion There is a need to understand and address individual, socio-economic and geographical barriers to health seeking to increase access and use of health care and fast-track progress towards Universal Health Coverage.

The docs/tlo_publications.py script now also additionally has an optional --update-from-zotero argument to update the local docs/publication.bib BibTeX file from the current items in the tlomodel Zotero group library by querying the Zotero web API. To allow compatibility with BibTeX files pulled from the Zotero web API which don't include attached notes in the note field unlike a local export using the Better BibTeX extension, the section names used to organize the publications are now included as tags / keywords on the Zotero entries rather than as a note.

The workflow for updating / adding publications would then be

1. Add or update publications to tlomodel Zotero group library using web or desktop apps.
2. Run python docs/tlo_publications.py --update-from-zotero if you have requirements in docs/requirements.txt installed locally or tox -e update-publications if not.
3. Stage and commit any changes to docs/publications.bib on a new branch and open a pull-request.

[matt-graham]

Weirdly one of the tests in tests/test_simulation.py initially failed but then passed on a re-run without any changes. As this PR doesn't change anything in the actual package code I suspect the initial failure was not connected to this PR but instead suggests there may be some non-determinism that has slipped through which is causing intermittent failures on suspend / resume?

[tbhallett]

Thanks VERY VERY much for all this @matt-graham --- it seems a fabulous solution to me.

I like the way the publications are displayed with the 'fold out' for additional info.

Two quick questions:

1. Could the workflow for adding publications be simplified, so that when the website is regenerated, it pulls from the Zotero library at that point? This would reduce the amount of steps/friction in adding a publication?

2. If we want to 'self-publish' a report or something ourselves.... Can we just add it to the Zotero Group library with a pdf attachment, and that will then be accessible through our website?

[matt-graham]

1. Could the workflow for adding publications be simplified, so that when the website is regenerated, it pulls from the Zotero library at that point? This would reduce the amount of steps/friction in adding a publication?

We could do something like this but there are a couple of downsides

• With the current solution the docs/publications.bib file is version controlled and is a separate 'ground-truth' for the publications. This means that means if we accidentally delete / edit information on the Zotero group library or Zotero / the group library become unavailable in future, we will still have a complete record of all the data required in the repository, and could also reconstruct the Zotero library from this data if necessary (as you can import from BibTeX file to Zotero). If we just download the bibliography data from Zotero each time we regenerate the website, we will only have the most recent version available, and this could end up as a incomplete / corrupted version.
• By requiring changes to the website to be made via a pull request we guard against malicious updates to the publication information getting published to the website. If we pull automatically from Zotero, that would mean for example if one of the Zotero accounts with access to the group library were compromised then the URL fields of the items could be updated to point to malware / spam links etc. With the current approach even if this happened we would have a chance to spot this when reviewing the PR which updates the publication data file.

From a technical side pulling in the Zotero data automatically when rebuilding / deploying the website would be simple to do with current implementation, but because of above my inclination would be to stick with the slightly more clunky but safer approach we have at the moment.

2. If we want to 'self-publish' a report or something ourselves.... Can we just add it to the Zotero Group library with a pdf attachment, and that will then be accessible through our website?

I think technically this should be possible, as the Zotero API does nominally seem to support downloading attachments files but I don't seem to be able to get this to work with group library currently (for example this API call for a specific attachment item in library returns a HTTP 404 not found status). We could still support this in a roundabout way by having the files stored locally on the repository or on some other URL but then we would need someway to link the filename in the repository to Zotero item. For this sort of use-case it might be better to just rely on existing research archive options such as Zenodo or insitutional equivalents to allow uploading a report and then just indexing this with Zotero (which should generally be able to automatically pull in the metadata).

[matt-graham]

I've added documentation on new process for adding publications to website to wiki: https://github.com/UCL/TLOmodel/wiki/Adding-or-updating-publications-on-website

I'll merge this in now.