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  • My mid-year reflection on my arrival at UCT and how my honours year is going so far.

    By Thato Makena

    When I first arrived at UCT, I felt like I had stepped into shoes that were too big for my feet. I had a very intense perception of UCT, and I somewhat had an inferiority complex towards the people around me. In essence, my imposter syndrome made me feel like my presence at UCT was a mistake, like they had accepted me by mistake.

    The very first bioinformatics assignment that was given to me was something I did not expect. We were required to edit some code and change the graphics of a certain game. I came from a biological background with absolutely no coding experience, and so I felt like we were being thrown into the deep end until I realised that the very same people I had done my undergrad with were making progress with the assignment, and so I thought, hmm? I am the problem. Am I the dumb one? Did I overestimate my abilities by applying for this degree? But it was already too late, the fees were paid, and the accommodation contracts were signed.


    After a conversation with a fellow classmate, I realised that I was not the only person feeling this way, matter of fact, the majority of the class felt the same way, but everyone was just putting on a brave face. Through that conversation, I realised that a defeatist mindset was not going to get me anywhere and that I needed to change my attitude towards the challenges I was facing. That meant being vocal and asking questions when I felt lost, speaking to my lecturers, and sharing my notes so that others could share with me. Active participation and not trying to tackle things alone, that is what changed the game for me.
    As time went on, everything started to make sense. I finally started to understand what honours were about. It was not about the content and the marks; it was about understanding complex concepts and gaining non-tangible skills. Our main lecturer would never give us due dates, and it just felt wrong, but at some point, I realised that he did that so that we would feel no pressure, so that we would learn to manage our own work in our own time, so that we could apply the many skills and concepts that we would learn in the different modules to the complex assignments he would give us.


    Everything just started to make sense the second I stopped trying so hard to be perfect. When I allowed myself to be confused, when I allowed myself to be embarrassed, when I allowed myself to reach out to strangers for help, when I texted people/group chats first. Now I feel confident, I feel like I belong, I feel like there is a reason why UCT saw my average marks and still decided to take me in. I no longer feel inferior, and I no longer feel like I was accepted by mistake. Instead, I feel proud, and I feel lucky to be here.


    Yes, I’ve learnt a lot of new science stuff, but I also learnt a lot about myself, and I feel like most of the positive changes have been internal. I cannot wait to reflect on my growth at the end of this course.

  • AI in healthcare: The controversies hindering its great potential

    By Thato Makena

    The human population is at the highest it has ever been, and potentially the highest it will ever be. Globally, surveys estimate that around 50-70% of healthcare professionals suffer from burnout, stress from increased workloads and an unhealthy work-life imbalance. This is concerning because people’s lives are in the hands of the very same people.
    Artificial intelligence is an increasingly popular tool that simplifies and enhances the way we live and work, but despite the concerning stats above and the increase in investments for AI in healthcare and medicine, there are still so many barriers and controversies preventing its implementation in real life.

    By conducting a systematic review using search terms like “AI/Machine learning/Deep learning” combined with “Health/Medicine” on platforms like PubMed and Google Scholar, it is easy to gauge the multiple ways in which AI can potentially revolutionise and augment the healthcare industry. Such a review also highlighted three key limitations and concerns surrounding using AI in this industry, and it is those points that keep it in a preclinical space and prevent its
    implementation in real-life settings.

    Technical challenges, such as data handling and management, are a major issue. Healthcare deals with sensitive and private information, which is an issue because AI models rely on very large datasets. Incentivising and promoting the shift from prioritising individual treatments to overall patient outcomes can promote data sharing, which will result in better and more reliable/accurate AI models.

    Ethical concerns like patient privacy, consent and accountability are also major roadblocks. Prioritising the anonymisation of patient data as well as informed consent from patients is key. Patients should be aware that their data is being used to train AI models. Accountability is also a concern; if a patient is harmed because of decisions made using these technologies, who bears the responsibility?


    Lastly, social concerns surrounding AI are also an issue. There is a growing concern that AI will take over people’s jobs, which is a massive misunderstanding and overestimation/overexpectation of what AI can do. Involving all stakeholders in its implementation can help lessen fears around AI, and by using frameworks and visualisation tools to explain why the technology made the decision it made can build trust in the technology.


    Overall, it is understandable why lots of AI-based technologies are stuck in the pre-clinical and experimental stages of implementation. Co-operation between physicians, scientists, legal and ethical bodies, as well as the public, is needed for this to work. Prioritising patient care over the excitement of new and ground-breaking technology is also very important. Slow, careful and stepwise adoption of AI into the healthcare industry is just as important.


    Addressing all concerns and misunderstandings surrounding AI is crucial because, at the end of the day its purpose is to re-engineer jobs and allow healthcare workers to focus on the more innately human, emotional and unpredictable aspects of medicine.

    References:

    1. Peng, Z. and Ren, X. (2024) ‘Application and development of artificial intelligence-based
      Medical Imaging Diagnostic Assistance System’, International Journal of Biology and Life
      Sciences, 6(1), pp. 39–43. doi:10.54097/sb3m1m17.
    2. Aung, Y.Y., Wong, D.C. and Ting, D.S. (2021) ‘The promise of Artificial Intelligence: A
      review of the opportunities and challenges of artificial intelligence in Healthcare’, British
      Medical Bulletin, 139(1), pp. 4–15. doi:10.1093/bmb/ldab016.

  • Finding my path in the world of research

    By Baphiwe Mlondo

    The first day of honours orientation felt like stepping into a new world. I was initially registered for Bioinformatics, but soon realised it wasn’t what I truly wanted. I had always pictured myself in a wet lab, so I made the switch to biomedical forensic science. This decision brought me a sense of relief and excitement. Jumping into research was like diving into the deep end. There was no gradual transition; I quickly found myself in a fast-paced environment filled with tons of work. At times, I felt lost, unsure of what I was doing. But that uncertainty also sparked my curiosity. Discovering something new every day became the highlight of my experience.

    The coursework was more engaging than in my undergraduate studies. We had lively discussions that allowed me to hear my colleagues’ perspectives on our field’s direction. It was rewarding to see how our studies applied to real-world situations. Having a solid support system made my honours journey smoother. Family, friends, and supervisors provided encouragement, and connecting with colleagues from different streams helped me find a community I can lean on. It was comforting to know that others understood what I was going through. However, there were challenges beyond my control, such as financial issues. Being partially funded meant having outstanding fees and not receiving meal allowances. Thankfully, programs like the UCT Food Sovereignty initiative provided much-needed support. Overall, this honours journey has taught me about adaptability and the importance of community. Each day brings new lessons, and I’m learning to embrace change while relying on those around me.

  • The Deep Learning Renaissance in Forensic Identification

    By Baphiwe Mlondo

    In the world of law enforcement and crime-solving, the ability to accurately identify human remains can be a matter of justice and closure. Traditional methods used to determine a decedent’s age, sex, ancestry, and stature often rely heavily on the expertise of forensic anthropologists. However, these methods are not without their flaws; they introduce a level of subjectivity that can lead to inconsistencies.

    The need for more reliable identification methods has never been more pressing. As wrongful identifications can have devastating consequences, researchers are turning to artificial intelligence (AI) and deep learning to enhance forensic analysis. These technologies offer the promise of more objective and efficient methods, reducing human bias in the process.

    Recent research by Yi et al. (2021) has explored the potential of deep convolutional neural networks (DCNNs) to analyse chest radiographs for age and sex estimation. Their study utilised a substantial dataset of 112,120 chest X-rays, balanced between male and female subjects across various age groups. The DCNN was trained on this data, having first been pre-trained on the ImageNet database to build a robust foundational understanding.

    The results were compelling. The model effectively identified key anatomical features, revealing that it focused on the sternum and upper ribs in 94% of images during sex estimation, with no activation in breast tissues (Figure 1). For age estimation, the DCNN highlighted specific bony structures in 56% of cases for individuals under and over 18 years (Figure 2) and emphasised the diaphragmatic region in 62% of images for ages 11–18 (Figure 3). These findings indicate that the model learned meaningful patterns associated with biological differences, validating its potential as an objective alternative in forensic identification.

    While the promise of these advancements is exciting, challenges remain. Ensuring the model’s accuracy across diverse populations and ongoing evaluation of its effectiveness in real-world scenarios are critical. As we stand at the crossroads of technology and forensic science, deep learning holds the potential to redefine how we approach the identification of human remains, paving the way for a future marked by precision and reliability.

    Figure 1.  Heatmaps for deep convolutional neural networks focusing on the sternum and upper ribs for prediction of female and male sex

    Figure 2. Heatmaps for deep convolutional neural networks focusing on bony structures to determine the age

    Figure 3. Heatmaps for deep convolutional neural networks focusing on the diaphragmatic region to determine the age

    References

    Yi, P.H., Wei, J., Kim, T.K., Shin, J., Sair, H.I., Hui, F.K., Hager, G.D. & Lin, C.T. 2021. Radiology “forensics”: determination of age and sex from chest radiographs using deep learning. Emergency Radiology. 28(5):949-954.

  • FROM BONES TO BYTES: HOW DEEP LEARNING IS TRANSFORMING FORENSIC IDENTIFICATION

    By Baphiwe Mlondo

  • Finding Answers, Facing Challenges: Parents’ Experiences with Genetic Testing for DEE

    By Anna Butler

    Parenting small children is hard enough – chickenpox, tantrums and stepping on lego in the middle of the night! Now imagine a real curveball: your child suddenly develops epileptic seizures. You’ve seen all the doctors and tried every medication, but nothing seems to work. Being in and out of the hospital affects your quality of life, and you’re unsure how to manage it. On top of this, your child appears to have developmental delays, and you’re not sure if these are related to the seizures or not.

    This is a real experience faced by families of children affected by developmental and epileptic encephalopathies (DEE), a group of epilepsy disorders characterised by medication-resistant seizures starting in early and childhood as well as developmental deficits.

    Genetic testing DEE patients has revolutionised management of these disorders. It allows for a genetic diagnosis to be made, meaning that doctors can focus on treating the underlying problem rather than symptoms alone. While much research has explored the clinical benefit of genetic testing, less is known about its emotional impact on parents.

    To address this gap, a multidisciplinary research team from the University of New South Wales conducted the first study looking into psychosocial effects of genetic testing in DEE. They recruited 25 parents of children who had undergone genetic testing for DEE. Methods included semi-structured interviews and two questionnaires: the Quality-of-Life Scale (family version) (QoL-FV) and the Genetic Counselling Satisfaction Scale (GCSS). The interview results were analysed for emerging themes which were compared with the survey findings to gain a fuller picture of parents’ experiences.

    The study revealed that parents valued compassionate genetic counselling, and that it contributed to increased hope and processing of the diagnosis. However, they also reported significant stress after receiving results, largely due to feelings of uncertainty about their child’s future and lack of diagnosis-specific resources. Many of the parents felt isolated initially but indicated that participating in peer support groups and connecting with other families helped to adapt to the diagnosis.

    This study highlights that genetic testing is more than just a medical process – it is an emotional journey for families. While a genetic diagnosis can bring long-awaited answers and relief from uncertainty, it can also create new stresses and unanswered questions. Ongoing genetic counselling, paired with clear and accessible information, can help families process the diagnosis and plan for the future. Just as importantly, connecting with others who share similar experiences provides comfort and reduces the sense of isolation many parents feel.

    Reference:

    Nevin, S.M., Wakefield, C.E., Barlow‐Stewart, K., McGill, B.C., Bye, A., Palmer, E.E., Dale, R.C., Gill, D., Kothur, K., Boggs, K., Le Marne, F., Beavis, E., Macintosh, R. and Sachdev, R. (2021). Psychosocial impact of genetic testing on parents of children with developmental and epileptic encephalopathy. Developmental Medicine & Child Neurology, 64(1), 95–104. doi:https://doi.org/10.1111/dmcn.14971.

  • Decoding the genetics of childhood epilepsy: Insights from developmental and epileptic encephalopathy patients

    By Anna Butler

  • Reflection: Learning to Learn

    By Karabo Tisane

    My honours year has been a fluctuating learning curve. Just when I thought I had conquered a moment of confusion, another layer of complexity revealed itself. If this year has taught me anything, it’s that learning is rarely linear, learning is an ever-evolving process that requires humility, persistence and willingness to embrace not knowing. I have learned that asking questions is not a weakness but a necessary step in developing true understanding.


    The modular structure of the honours programme exposed me to a broad spectrum of topics, from the intricacies of gene expression in Hox genes to the futuristic realities of organ engineering. It felt like a roller coaster of abstract, yet feasible scientific concepts. And yet the most rewarding part was realising that these concepts were not isolated. There was always a connection between them. Recognising those connections became a personal highlight. The ability to link knowledge across disciplines made me appreciate not just the content but how science itself is beautifully interconnected.


    On of the steepest challenges I faced this year was the academic writing process. No one prepared me for how isolating it can feel to sit with mountains of literature and synthesise it into something original. The discipline, time management and internal motivation required to complete a writing assignment have stretched me in ways I did not expect. Most of all I have come out the other end with a powerful new skill, the ability to communicate complex science concepts with clarity and confidence.


    Of course, honours has not only been about reading and writing. One of the most exciting aspects of this year was stepping into the lab. Being trusted with a meaningful, hands-on research task was daunting but mostly thrilling. After years of reading dry method sections in scientific papers I finally got to do some of the techniques myself. Learning how to perform real laboratory procedures transformed my understanding of experimental science from abstract to
    tangible. An experience I will forever cherish.


    In the end. Honours has been rigorous, demanding and at times overwhelming, but above all its been deeply rewarding. Every fall, every moment of doubt or confusion was part of a bigger learning pathway. I have come to see those moments not as setbacks but as necessary steps in becoming more reflective, capable and resilient scientist. Honours did not just teach me about melatonin, genetics or lab protocols, it taught me how to learn. And that is a skill I will carry forward, long after the year is over.

  • Melatonin- More than just a sleeping hormone

    By Karabo Tisane

    Melatonin is a hormone primarily produced by the pineal gland in the brain (1). Its secretion is stimulated by darkness, and its maximal circulating peak concentration is typically observed between 2-4am. This rhythmic endogenous secretion is regulated by the suprachiasmatic nuclei which form part of the brain’s internal clock that is sensitive to light and dark cues. Melatonin therefore plays a central role in stabilising and strengthening the circadian rhythms which are natural internal processes that regulate the sleep-wake cycle.

    Due to melatonin being mainly secreted at night it is known as the sleep hormone. People with various sleep disorders and mood disorders have dysfunction in melatonin physiology. As a result, synthetic melatonin is prescribed for insomnia, and it is commonly used to treat jet lag. However, the role of melatonin extends far beyond regulating sleep.

    To better understand these broader functions, several review articles were consulted. The authors compiled original papers from PubMed and Scopus databases, and key words like “melatonin”, “Mediterranean diet”, “Antioxidant food”, just to name a few were used to come up with papers to review. A reverse search through the reference lists of relevant articles was also used to ensure comprehensive coverage of the topic. The collective findings from these reviews offered a more expansive understanding of melatonin’s role in human health.

    One of melatonin’s most remarkable properties is its potent antioxidant power which is significantly more potent than Vitamin E at neutralising harmful reactive oxygen species. The antioxidant properties of melatonin contribute to a wide range of health benefits, including protection of the heart and brain, slowing cellular ageing, and reducing damage after injury in multiple organs. Melatonin is effective in reducing early cognitive decline and has anti-ageing capabilities as well as immune modulatory effects due to its ability to enter cells.

    Melatonin plays a role in glucose metabolism through modulation of the glucose transporters, helping the body to absorb glucose after meals. This contributes to improved glucose tolerance, reduced risk of obesity and diabetes. On the other hand, melatonin inhibits glucose transporters 2 which are found in cancer cells and are responsible for supporting tumour growth. The potential anticancer effects of melatonin surely can’t be ignored, highlighting the importance of understanding its natural sources and how we can harness them.

    Figure 1: Functions of melatonin in the body.

    And here’s something you might not know, melatonin is also found in food (2). That means you may be able to enjoy its benefits without reaching for a supplement. Foods rich in melatonin include nuts, milk, fish grapes, wine and tropical fruits which are all able to raise serum melatonin levels and enhance antioxidant activity in the body.

    Figure 2. Increased serum melatonin levels 120 minutes after consumption of tropical fruits (3)

    While melatonin is best known for helping us sleep, it is increasingly recognised as a multifunctional hormone with important roles in metabolism, cell protection, and even cancer biology. As research continues, we may uncover even more reasons to appreciate this nighttime hormone both in the lab and on our plates. Future studies may help clarify how dietary melatonin contributes to health and how individual factors influence its effectiveness and optimal intake. Fuel the Boss in You, One Melatonin Bite at a Time.

    References

    1. Munoz-Jurado A, Escribano BM. Presence of melatonin in foods of daily consumption:The benefit of this hormone for health. Food Chemistry. 2024;458:140172.2.
    2. Pereira GA, Gomes Domingos AL, Aguiar ASd. Relationship between food consumptionand improvements in circulating melatonin in humans: an integrative review. Critical Reviews inFood Science and Nutrition. 2022;62(3):670-8.3.
    3. Sae-Teaw M, Johns J, Johns NP, Subongkot S. Serum melatonin levels and antioxidantcapacities after consumption of pineapple, orange, or banana by healthy male volunteers.Journal of pineal research. 2013;55(1):58-64.

  • From Bite to Bloodstream

    By Karabo Tisane