Tag: Research

I Went to South Africa for Three Months

On July 23, 2022

Our Arrival:

I remember the green of it first. Lush foliage like I have never known before, spread out in shades of lime and sage coating the dusty dirt below. Inseparable from the foliage, the land was smothered with the scent of Earth. It was the most natural smell I could imagine of the outdoors, and yet it was so unfamiliar to me. These weren’t the standard-issue sod sold en-masse in the farmlands of suburbia near my house. These were native grasses, lush and tall and alive.

I had just entered South Africa. Michelle, a classmate, and I were at the start of our ten-week internship program for the partial completion of our respective Master of Science in Global Health degrees. We were both interning with Pact, an international non-profit with a headquarters in Pretoria, South Africa, whose mission focuses on reducing HIV incidence in orphans, vulnerable children, and youth across the country. This was my first time leaving the United States in 7 years, and my first time living in another country for an extended period. I was glad I wasn’t alone.

My first week in South Africa was a myriad of adjustments. Some were small: learning to walk 20 minutes through the neighborhood without sidewalks, adjusting to the exchange rate, cars driving on the opposite side of the road. Others were greater, like learning to live 16 hours and 8,000 miles away from those I love and adjusting to the 7-hour time difference that went along with it. It took a full week and 3 nauseating episodic migraines just to feel like myself again. On our third day in South Africa, Michelle and I made our first commute to the Pact office. We dressed ourselves up and hailed a $3.00 Uber to trek the 15-minute drive to HQ. We had picked out our hotel to be close to where we’d be working, but quickly realized that even the smallest distances on a map were simply unwalkable, which was a combination of the city’s lack of sidewalks and the large and complex roadways which made the journey on foot much longer than it appeared. Squeezed into a VW, we watched through the spiderweb-like cracks of the front window as we passed shopping malls and suburban complexes, secured with gates and electric fences. As we slowed to a stop at one of the lights, locally known as robots, I stared out the window as street vendors, women with children, and business employees walked between the stopped cars, selling car chargers and surgical masks, begging for money, or handing out flyers. Our driver closed the windows, and I turned to stare at the seat ahead

Working at Pact:

I remember the Pact office next. Michelle and I arrived excited but exhausted, still sloughing off the remnants of jetlag. Despite our exhaustion and confusion, we were greeted by every single person in the Pact office, who were all genuinely excited and pleased to meet us.

Christel, our supervisor and liaison with Georgetown, led us around the office and showed us to our two adjacent office spaces near the break room. After receiving our access key, the Wi-Fi password, and a new notebook, I ventured to the kitchen and had my first taste of a South African specialty: rooibos tea.

Despite the excitement of my arrival in an unfamiliar office, there was an aura of calm that surrounded the work life here. As someone used to the harried speed of employment in an American office, I was disquieted by the peace at which the faculty moved about in this space. Though the attitude was leisurely, it was clear everyone still valued the quality of their work equal to that of their personal lives, and everyone on the team was courteous and accommodating. Though Michelle and I needed to jump several hurdles to complete our projects, every member of the Pact team worked with us to help us succeed. Whether that meant ensuring access to data, driving us to research sites, or providing feedback on our papers, everyone was eager to collaborate even if it meant putting other projects on hold. This genuine passion for work every day is something I know I want to take with me as I move into positions in the future.

Exploring South Africa:

The third thing I remember is the wildlife. When I was 16 years old, I worked my first job as a staff member for the Long Island Game Farm, a petting zoo that boasted pony rides, donkeys, zebra, and a giraffe. I saw these animals every day during the summer I worked there, but they were always enclosed, and moved like clockwork, slowly walking a memorized path around their pen.

During our stay in South Africa, Michelle and I ventured on at least half a dozen hikes across Pretoria and Cape Town. I was astonished during the first of our hikes when we were able to walk, without fences or barriers, next to a herd of zebra and ostriches, left free to roam the reserve. Seeing these animals in their element: surrounded by fields of grasses with room to roam and explore at-will is an experience I will never forget. Every hike I took in South Africa I hoped to catch a glimpse of more wildlife. On one walk, I was lucky enough to catch a glimpse of a pair of giraffes underneath the shade of a nearby tree. Though I had seen giraffes before, I found a simple pleasure in seeing these magnificent creatures roaming on their own; I remembered they are real and beautiful creatures, not just spectacles kept to be watched.

In addition to the various hikes I went on during my stay, I also had the pleasure of going on a couple of game drives at a nearby wildlife reserve. Though this game drive was a much more guided experience than our walks, I still had the pleasure of finding a group of rhinos or a buffalo through the coverage of the bush. These tours were not the planned promenades around different mass enclosures like any safari I had experienced in the States. It was a 2.5-hour drive, sometimes on dirt roads and sometimes off them, trying to track down lions or elephants who had their own travel agenda. On these drives I saw rhinos, lions, buffalo, wildebeests, zebra, kudu, monkeys, water monitors, guinea fowl, and springbok. (I even saw a few penguins during my visit to Cape Town). All of which, I could never hope to see outside a zoo back home.

Finishing my Research:

The last thing I’ll remember about South Africa is completing my scholarly paper. During my ten-week internship with Pact, I had the opportunity to complete a research protocol which would constitute my final assignment to earn my master’s degree from Georgetown University. My project was to complete the first analysis of Pact’s Pilot Girl/Boy Index Survey.

The Girl/Boy Index was launched in 2018 to several schools across the Gauteng and Northwest Provinces of South Africa to assess children’s behaviors and circumstances surrounding topics like nutrition, education, psycho-social support, and HIV/AIDS. For my project, I analyzed children’s responses to these questions, and specifically how they were impacted by factors like gender, location, and age, and how some of these answers might be related to knowledge of a child’s own HIV status and childhood/teen pregnancy.

Though I am grateful for every step of completing this project, there were certainly times at which I was hit by the weight of the analyses I was completing. Many of these children were facing harsh challenges and circumstances I can barely imagine handling myself. In one section of the survey, students were permitted to write a free response to expand on any aspects of their home life they felt they need support for. While some students wrote about how they needed uniforms or equipment to join the local soccer team, other students had more emotional requests:

“I need help so that I can concentrate at school. I fail to concentrate at school since I got a baby boy because I have to look after him and the schoolwork as well. I cannot do everything, so I need someone to help me get through this and how to manage everything on my own.”

Writing a paper that will hopefully be used to empower programs for students and disadvantaged youth, like those run by Pact, was a sincere honor. While I was able to learn new skills and methods to use to better myself and advise my future projects, I am most proud at the notion that my research might have an impact on the school children of South Africa. Completing this project and working with the people at Pact reminded me of a simple truth: good science means nothing if it can’t be used for the greater good.

What Went Wrong With Covid?

By Kayla Nikc

On December 26, 2021

In COVID-19, Personal

It’s a simple question, and probably one which many of us have asked each other and ourselves the past 20 months. How can this world, with its advanced researchers, extensive public health protocols, and past pandemic experience, have been so unprepared for the COVID-19 pandemic? People have blamed poor communication, public noncompliance, even the scientists themselves, but none can completely cover the worsening of the pandemic alone.

For one of my graduate classes this semester, Quantitative Evidence for Infectious Disease Research, I was tasked with answering this question. Instead of limiting my response to any one of the reasons we might jump to for worsening the pandemic, I decided to focus on the scientific community, and the communication of research to the public.

If you’re familiar with scientific research and the scientific method, you’ll know that the process begins with a hypothesis. Many times, there are more than one. The null hypothesis is the hypothesis being tested. The null hypothesis can be any theory, but in epidemiology it will essentially state that there is no causal relationship between a cause and an outcome. For example, a null hypothesis about smoking and lung cancer could posit that there is no causal association between smoking and lung cancer. The data then will either support the null hypothesis or give scientists a cause to reject it. This is where an alternative hypothesis is needed. An alternative hypothesis would state that there is some causal association between cause an outcome, and could say that smoking is a cause for lung cancer.

Epidemiologists and biostatisticians will usually analyze the impact of cause and effect through something called “significance testing“. With this method, the scientists will select a certain significance level, which is the value for which a p-value less than or equal to it is considered statistically significant. The p-value is a measure of probability that the observed difference could have occurred only by chance. Usually, the significance level is set to 0.05, meaning any experiment with a probability of having occurred only by chance equal to 5% or less, would be statistically significant. This is why in some papers you might see researchers state they are 95% confident in their results. Sometimes, these p-values are accompanied by a confidence interval, which is the range of possible values of the estimate being calculated at 95% confidence. In the truest interpretation, according to frequentist statistics, the 95% confidence interval will include the true effect in at least 95% of replications of the process of obtaining the data.

These results have caveats, however. Experiments need to have a large enough sample size to accurately develop results, and the model chosen to analyze the data needs to be correct for the experiment. Unfortunately, this is not always the case in published studies, and many epidemiologists have previously published reports cautioning authors and readers against the common misinterpretations in significance testing (read more here, here, and here). Though published, the COVID-19 pandemic only highlighted this issue further, and many controversial topics over the past 20 months, including the impact of mask-wearing, the contagiousness, or R-naught of the pandemic, and the effectiveness of medications like hydroxychloroquine or ivermectin have fallen victim to these misinterpretations, exacerbating misunderstanding and mistrust of public health authorities.

In the paper attached below, I explore how key publications studying these controversial features of the COVID-19 pandemic succeed or fail in conveying the accuracy and strength of their results to other scientists and, by extension, the public at large. To quote my conclusion:

In a time when scientific results can and should be shared as quickly as possible, researchers and publishers have an additional responsibility to ensure their methods are clearly stated and all results clearly indicate confidence interval ranges and limitations in addition to the basic “significance”

While I am by no means an expert in epidemiology, I feel that this analysis can elucidate how a healthy dose of skepticism is necessary even in scientific quantitative research. Often, we may take for granted the black and white answers of pure science. We can see research as logical and absolute, but there is plenty of room for uncertainty, as the COVID-19 pandemic has shown. I hope this article helps to explain some of the confusion to any readers, and might equip you with the knowledge to approach future papers with questions and determine for yourself how reliable the results are.

Thank you.

What-Went-Wrong-WIth-COVID Download

My First Journal Publication

By Kayla Nikc

On December 26, 2021

In Personal

This post has been a long time coming, but with the end of senior year (I graduated!) and the continuation of graduate school, I haven’t had time to announce the results properly yet. This past spring, I submitted a paper I wrote for my climate change ecology class on how different newspaper platforms have used climate-centered language throughout the years. I created graphs to understand how word-usage might vary by year, season, and publisher, and ultimately concluded that talk about climate change is mostly affected by the political leaning of the news platform and extreme short-term, rather than sustained long-term, temperature anomalies.

The paper in its full length can be found HERE, on page 19.

discourse around the topic. I know its a little bit unusual for an analysis on climate change, but one of my favorite aspects of college was combining lessons from my classes each semester into final papers. As a linguistics major, this one happens to combine my interests of language and climate change.

Though it was published in a first-edition campus journal, I am so proud to have officially published my first peer-reviewed paper. Though this may be the first, be on the lookout for more as I prepare a paper for publication in the new year…

Happy Holidays to everyone reading and I hope everyone has a warm and healthy New Year!

COVID-19 Variants and What They Mean for the New Vaccines

By Kayla Nikc

On January 7, 2021

In COVID-19

Last month, the FDA approved two vaccines, from Pfizer and Moderna respectively, to begin the process of immunization against COVID-19 across the United States. Despite this major milestone in protective measures, there is a new coronavirus curveball: variants of the already deadly virus.

Most recently, the London variant has made headlines after confirmed cases of the virus in California, Colorado, and Florida, but the WHO has also recorded other variants, such as 501Y.V2 in South Africa. But what do these variants mean for the long-awaited vaccines and their potential protections?

How do Virus Mutations Arise?

In order to understand how these COVID-19 variants might impact the efficacy of the Pfizer and Moderna vaccines, one must first understand how viruses mutate in the first place.

Viruses, though not considered living, contain genetic information in the form of DNA or RNA. DNA, which stands for Deoxyribose nucleic acid, is the genetic compound which forms a signature double-helix and is the primary means of storing genetic information in our cells. RNA, or ribonucleic acid, is another variation of nucleotides. One of the key differences between DNA and RNA is the number of hydroxyl, or -OH groups, on each of their sugar molecules, seen in the image below, with the DNA sugar on the left and the RNA sugar on the right.

https://www.technologynetworks.com/genomics/lists/what-are-the-key-differences-between-dna-and-rna-296719

While the lack of a single hydroxyl group may not seem like it would make a lot of difference, the structure of DNA is far more stable than that of RNA, and this variation in reactivity dictates the roles of DNA and RNA wherever they are used. DNA, with its greater stability, is able to store genetic information for long periods of time and harbor limited mutations, a necessary trait to achieve proper gamete production and cell replication. The greater reactivity of RNA also has its benefits. As a reproducible intermediary, RNA can transport genetic information throughout a cell to be used and then quickly degraded according to a cell’s needs.

Every time genetic information is replicated, there is the possibility that there will be a mutation, either a deletion, insertion, or substitution of one type of nucleic acid for another. DNA polymerases, involved in replication, are able to proofread the insertion of bases to reduce the possibility of these mistakes in the DNA. RNA polymerases lack this ability, meaning any change to the RNA could cause a change in the structure or function of any proteins performing operations throughout the cell.

What Does This Have to do with COVID-19?

As I stated earlier, viruses also make use of DNA and RNA, though usually they will only use one or the other depending on the particular virus’ reproductive strategy. The primary goal of any virus is to produce as many copies of itself as possible and to spread those copies to as many cells as possible. DNA viruses, like herpesvirus, smallpox virus, and papillomavirus, prioritize larger genomes, with greater stability than their RNA virus counterparts, which allows them to encode many proteins to aid in their invasion into a given cell. These viruses, however, owing to their stability and their DNA polymerases, are also less likely to mutate, meaning that vaccines aimed at protecting against these viruses are likely to remain successful for years.

RNA viruses, instead, make use of their greater likelihood for mutation as a way to adapt to the host around them. The flu, part of the Orthomyxoviridae family of viruses, is one example of RNA viruses. The rapid mutations of the flu resulting from its instability as an RNA virus is why there is a new recommended flu shot every fall.

Coronavirus is another example of an RNA virus, which, as we’ve seen, can also rapidly mutate, which, without appropriate distancing and masking to reduce infection rates, could prevent the timely release of an effective vaccine. If COVID-19 is allowed to continue to spread and replicate, new variants have the ability to outpace our vaccine development abilities.

What the Experts Think:

As of now, evolutionary biologists and other experts remain hopeful that the vaccines created by Moderna and Pfizer will continue to be effective against the London and South African variants, however, these results remain inconclusive. According to Nature.com, researchers hope to have more information about the variants and the possible effects on vaccine efficacy by next week. For now, though, adhering to social distancing and masking recommendations from the WHO remains imperative, not only to ensure the health and safety of you and those around you, but also to reduce the opportunity for the generation of future variations.