SACEMA Newsletter: December 2019

We wish all our friends, colleagues, students and collaborators a Blessed Holiday Season and a Prosperous New Year!

NEWS

SACEMA/The Conversation Africa science communication awards

SACEMA in collaboration with The Conversation Africa hosted a writing competition for SACEMA-affiliated masters, doctoral and postdoctoral students. Students were invited to submit an 800-word article about their research. Final judging was done by The Conversation Africa and the winners of the awards were announced at the SACEMA Research Days meeting on 12 September 2019. Click here to read more.

Notification of relapse and other previously treated tuberculosis in the 52 health districts of South Africa

SACEMA Senior Researcher Dr Florian Marx published a manuscript entitled “Notification of relapse and other previously treated tuberculosis in the 52 health districts of South Africa” in the August edition of the International Journal of Tuberculosis and Lung Disease (IJTLD). The manuscript reports findings from an ecological analysis conducted in collaboration with colleagues at the Desmond Tutu TB Centre (Faculty of Medicine and Health Sciences). The study used data from South Africa’s electronic tuberculosis (TB) register and showed that in several South African health districts, former TB patients, in particular those with a history of previous successful TB treatment, contribute considerably to the notified burden of tuberculosis. The study complements ongoing mathematical modelling research aiming to project the population-level impact and cost-effectiveness of TB preventive and case-finding interventions targeted to former TB patients. Click here to read more.

Further For more information contact: Florian Marx at fmarx@sun.ac.za

Performance comparison of the Maxim and Sedia Limiting Antigen Avidity assays for HIV incidence surveillance.

SACEMA researchers Alex Welte and Joseph Sempa, together with colleagues from the Consortium for the Evaluation and Performance of HIV Incidence Assays (CEPHIA) published a manuscript in the July edition of PlosOne entitled “Performance comparison of the Maxim and Sedia Limiting Antigen Avidity assays for HIV incidence surveillance”. The study compares the two manufacturers, Maxim Biomedical and Sedia Biosciences Corporation, who supply CDC-approved versions of the HIV-1 LAg assays for detecting ‘recent’ HIV infection in cross-sectional incidence estimation. Click here to read more.

Postdoc is awarded University of Oxford, African-Oxford Initiative (AfOx) collaborative research and travel grant

Postdoctoral Research Fellow, Olugbenga Oluwagbemi won the University of Oxford, African-Oxford Initiative (AfOx) collaborative research and travel grant after his research proposal titled “Treatment As Prevention (TASP) and Treatment After Infection (TAI) interventions: Developing a multi-modelling approach towards malaria elimination”, was selected by the awarding panel. He spent 4 weeks (June-July, 2019), in the Malaria Atlas Project (MAP) research group, Big Data Institute, University of Oxford and was hosted by Prof. Peter Gething. Click here to read more.

Congratulations to our graduates

Abdul-Karim Iddrisu graduated from the University of Cape Town with a PhD in Statistics. His dissertation, titled “Sensitivity analysis approaches for incomplete longitudinal data in a multi-centre clinical trial”, was supervised by Prof Freedom Gumedze of the University of Cape Town.

Wanja Chabaari graduated from Stellenbosch University with an MSc in Mathematics. Her thesis, titled “Understanding women’s engagement in HIV care after initiating antiretroviral therapy during pregnancy in South Africa”, was supervised by Professor Rachid Ouifki from the University of Pretoria, Dr Amina Eladdadi of the College of Saint Rose, USA and Prof Juliet Pulliam of SACEMA.

Arrivals and departures

Olatunji Adetokunboh joined SACEMA in September as a Researcher/National Public Health Liaison. Prior to joining SACEMA, he worked as Technical Advisor and Manager for various HIV and Reproductive Health projects in South Africa and Nigeria. He also worked with Cochrane SA, South African Medical Research Council and Centre for Evidence-based Health Care, Stellenbosch University. Olatunji is a medical doctor with masters and doctoral degrees in clinical epidemiology and epidemiology respectively. His research focuses on evidence synthesis and multilevel modelling approaches to infectious disease epidemiology, with special interest in vaccine-preventable diseases and HIV infection in sub-Saharan Africa.

Roxanne Beauclair also joined SACEMA in September. In her role as National Public Health Liaison she is attempting to understand what unmet modelling needs South African public health stakeholders have, and which of these are priorities for decision-making. Roxanne is also a specialist in applying biostatistical methods to epidemiological data. She received training from Ghent University in Belgium (PhD) and the University of Cape Town (MPH). She has been involved in an analytical capacity for several different epidemiological studies of HIV in Southern Africa. Recently, she has become an R enthusiast and enjoys learning new ways to improve upon statistical programmes by creating clean, reproducible, and legible code.

We are sad to say goodbye to Nadia Rhode, who is leaving SACEMA at the end of December. Nadia filled in as temporary SACEMA Administrator for the past five months while the position vacated by Amanda October was being advertised and filled. We will miss her bubbly personality and contagious smile. We wish Nadia the very best for the future!

SCIENTIFIC ACTIVITIES

SACEMA researchers attend South African National Blood Transfusion Congress

“Adapt. Innovate. Advance.” This was the theme for the 35th South African National Blood Transfusion Congress held at Sun City in August, which was attended by SACEMA’s Director Juliet Pulliam, SACEMA Postdoctoral Fellow Larisse Bolton, and SACEMA Research Associate Eduard Grebe. Hosted by the South African Society for Blood Transfusion, The South African National Blood Service (SANBS) and Western Cape Blood Service (WCBS) came together with international representatives from the transfusion medicine and blood systems research community to share the latest advances and research outputs. Click here to read more .

SACEMA delegation attends Modelling in the Context of African Health (MoCAH) Conference

Professors Juliet Pulliam and John Hargrove, along with their respective PhD students, James Azam and Elisha Are, attended the Modelling in the Context of African Health Conference held at Durban, South Africa from 14-16 October. This was a joint conference of the University of Kwazulu-Natal, under the African Health and Big Data flagships, and the CoE-MaSS. Click here to read more .

PhD student attends Future of Science Conference at AIMS Rwanda in Kigali

SACEMA PhD student, Elisha Are won a full travel grant to attend the “Future of Science conference” in Kigali from 7-9 July 2019. Organized by the African Institute for Mathematical Sciences (AIMS) Rwanda, the conference was meant to create an informal environment where postgraduate students, as well as young researchers, can interact with world-leading researchers in various science disciplines. The three-day conference featured several talks and a panel discussion session.

Apart from enjoying every bit of his stay in the beautiful city of Kigali, Elisha also took advantage of the conference to catch up with old friends and broaden his research network. Elisha (right) with Chilperic (MMED 2018, Alumnus).

Hargrove and Vale work on tsetse fly biology

In late October 2019, John Hargrove went to Zimbabwe and worked for 10 days with Professor Glyn Vale, SACEMA Research Associate and long-time colleague in the world of tsetse biology. Both are part of BBSRC project: “Epidemiological consequences of reproductive senescence in long-lived vector”, involving field work in Zimbabwe, data analysis and the development of epidemiological and evolutionary theory. The team is headed by Bristol University’s Dr Sinead English, who was supposed to accompany Hargrove and Vale on a field trip to Rekomitjie Research Station in the Zambezi Valley. In the event, the continuing decline in the Zimbabwean economy means that it is no longer feasible for the government to carry out research at Rekomitjie. Accordingly, Hargrove and Vale spent their time together working on data arising from the Project and in the development of new publications. It is to be hoped that matters will improve in Zimbabwe in the not too distant future, to the point where research can be resuscitated at Rekomitjie.

EVENTS

Introduction to R: Management, Exploration, and Communication of data

Dr Roxanne Beauclair of SACEMA and Data Yarn in Pretoria presented this intensive five-day course at SACEMA. The course took place at the Stellenbosch Institute for Advanced Study (StIAS), from 12 to 16 August 2019. The course was designed to suit graduate students or professionals who are familiar with statistical analysis, have managed or interacted with datasets using other software platforms, and were familiar with programming in another language other than R. Click here to read more .

An introduction to the Joint Modelling of Longitudinal and Survival Data, with Applications in R

Professor Dimitris Rizopoulos of the Erasmus Medical Center Rotterdam presented this intensive three-day course at SACEMA. The course took place at the Stellenbosch Institute for Advanced Study (StIAS), from 14 to 16 October 2019. The course was aimed at applied researchers and graduate students. The lectures were focused on how joint models are used in practice, key assumptions behind them, and how they can be utilized to extract relevant information from the data. This course was aimed at applied researchers and graduate students.

An introduction to the CHPC, 06 November 2019

Inus Scheepers from the Centre for High Performance Computing (CHPC) in Cape Town presented a half day workshop for SACEMA staff and students. The workshop was aimed at introducing participants to the CHPC and guiding them on how to submit jobs to the cluster. Click here to read more

SACEMA Research Days, 9-12 September 2019

SACEMA’s annual Research Days meeting was held over four days at the Protea Hotel, Technopark near Stellenbosch. A total of sixty-nine people participated in the meeting, including SACEMA bursary holders, their supervisors, and postgraduate students from the Biochemistry Department working with Prof Jacky Snoep, the SACEMA-affiliated South African Research Chair (SARChI). Click here to read more .

UPCOMING EVENTS

Mathematical Modelling Research to Guide Decision Making for Tuberculosis Control in South Africa, 27-28 January 2020
Software Engineering for Applied Mathematical Sciences (SEAMS), 20-31 January 2020