Duke Research Blog

Following the people and events that make up the research community at Duke.

HIV Can Be Treated, But Stigma Kills

Three decades ago, receiving an HIV diagnosis was comparable to being handed a death sentence. But today, this is no longer the case.

Advances in HIV research have led to treatments that can make the virus undetectable and untransmittable in less than six months, a fact that goes overlooked by many. Treatments today can make HIV entirely manageable for individuals.

However, thousands of Americans are still dying of HIV-related causes each year, regardless of the fact that HIV treatments are accessible and effective. So where is the disconnect coming from?

On the 30th anniversary of World AIDS Day, The Center for Sexual and Gender Diversity at Duke University hosted a series of events surrounding around this year’s international theme: “Know Your Status.”

One of these events was a panel discussion featuring three prominent HIV/AIDS treatment advocates on campus, Dr. Mehri McKellar, Dr. Carolyn McAllaster, and Dr. Kent Weinhold, who answered questions regarding local policy and current research at Duke.

From left to right: Kent Weinhold, Carolyn McAllaster, Mehri McKellar and moderator Jesse Mangold in Duke’s Center for Sexual and Gender Diversity

The reason HIV continues to spread and kill, Dr. McKellar explained, is less about accessibility, and more about stigma. Research has shown that stigma shame leads to poor health outcomes in HIV patients, and unfortunately, stigma shame is a huge problem in communities across the US.

Especially in the South, she said, there is very little funding for initiatives to reduce stigma surrounding HIV/AIDS, and people are suffering as a result.

In 2016, the CDC reported that the South was responsible for 52 percent of all new HIV diagnoses and 47 percent of all HIV-related deaths in the US.

If people living with HIV don’t feel supported by their community and comfortable in their environment, it makes it very difficult for them to obtain proper treatment. Dr. McKellar’s patients have told her that they don’t feel comfortable getting their medications locally because they know the local pharmacist, and they’re ashamed to be picking up HIV medications from a familiar face.

 

HIV/AIDS Diagnoses and Deaths in the US 1981-2007 (photo from the CDC)

In North Carolina, the law previously required HIV-positive individuals to disclose their status and use a condom with sexual partners, even if they had received treatment and could no longer transmit the virus. Violating this law resulted in prosecution and a prison sentence for many individuals, which only enforced the negative stigma surrounding HIV. Earlier this year, Dr. McAllaster helped efforts to create and pass a new version of the law, which will make life a lot easier for people living with HIV in North Carolina.

So what is Duke doing to help the cause? Well, In 2005, Duke opened the Center for AIDS Research (also known as CFAR), which is now directed by Dr. Kent Weinhold. In the last decade, they have focused their efforts mainly on improving the efficacy of the HIV vaccine. The search for a successful vaccine has been long and frustrating for CFAR and the Duke Human Vaccine Institute, but Dr. Weinhold is optimistic that they will be able to reach the realistic goal of 60 percent effectiveness in the future, although he shied away from predicting any sort of timeline for this outcome.

Pre-exposure prophylaxis or PrEP (photo from NIAID)

Duke also opened a PrEP Clinic in 2016 to provide preventative treatment for individuals who might be at risk of getting HIV. PrEP stands for pre-exposure prophylaxis, and it is a medication that is taken before exposure to HIV to prevent transmission of the virus. Put into widespread use, this treatment is another way to reduce negative HIV stigma.

The problem persists, however, that the people who most need PrEP aren’t getting it. The group that has the highest incidence of HIV is males who are young, black and gay. But the group most commonly receiving PrEP is older, white, gay men. Primary care doctors, especially in the South, often won’t prescribe PrEP either. Not because they can’t, but because they don’t support it, or don’t know enough about it.

And herein lies the problem, the panelists said: Discrimination and bias are often the results of inadequate education. The more educated people are about the truth of living with HIV, and the effectiveness of current treatments, the more empathetic they will be towards HIV-positive individuals.

There’s no reason for the toxic shame that exists nationwide, and attitudes need to change. It’s important for us to realize that in today’s world, HIV can be treated, but stigma kills.

Post by Anne Littlewood

Math on the Basketball Court

Boston Celtics data analyst David Sparks, Ph.D, really knew his audience Thursday, November 8, when he gave a presentation centered around the two most important themes at Duke: basketball and academics. He gave the crowd hope that you don’t have to be a Marvin Bagley III to make a career out of basketball — in fact, you don’t have to be an athlete at all; you can be a mathematician.

David Sparks (photo from Duke Political Science)

Sparks loves basketball, and he spends every day watching games and practices for his job. What career fits this description, you might ask? After graduating from Duke in 2012 with a Ph.D. in Political Science, Sparks went to work for the Boston Celtics, as the Director of Basketball Analytics. His job entails analyzing basketball data and building statistical models to ensure that the team will win.

The most important statistic when looking at basketball data is offensive / defensive efficiency, Sparks told the audience gathered for the “Data Dialogue” series hosted by the Information Initiative at Duke. Offensive efficiency translates to the number of points per possession while defensive efficiency measures how poorly the team forced the other offense to perform. These are measured with four factors: effective field goal percentage (shots made/ shots taken), turnover rate, successful rebound percentage, and foul rate. By looking at these four factors for both offensive and defensive efficiency, Sparks can figure out which of these areas are lacking, and share with the coach where there is room for improvement. “We all agree that we want to win, and the way you win is through efficiency,” Sparks said.

Since there is not a lot of room for improvement in the short windows between games during the regular season, a large component of Sparks’ job involves informing the draft and how the team should run practices during preseason.

David Sparks wins over his audience by showing Duke basketball clips to illustrate a point. Sparks spoke as part of the “Data Dialogue” series hosted by the Information Initiative at Duke.

Data collection these days is done by computer software. Synergy Sports Technology, the dominant data provider in professional basketball, has installed cameras in all 29 NBA arenas. These cameras are constantly watching and coding plays during games, tracking the locations of each player and the movements of the ball. They can analyze the amount of times the ball was touched and determine how long it was possessed each time, or recognize screens and calculate the height at which rebounds are grabbed. This software has revolutionized basketball analytics, because the implication of computer coding is that data scientists like Sparks can go back and look for new things later.

The room leaned in eagerly as Sparks finished his presentation, intrigued by the profession that is interdisciplinary at its core — an unlikely combination of sports and applied math. If math explains basketball, maybe we can all find a way to connect our random passions in the professional sphere.

The Importance of Evidence in Environmental Conservation

What counts as good evidence?

In medical research, a professional might answer this question as you would expect: evidence can be trusted if it is the result of a randomized, controlled, double-blind experiment, meaning the evidence is only as strong as the experiment design. And in medicine, it’s possible (and important) to procure this kind of strong evidence.

But when it comes to conservation, it’s a whole different story.

Dr. David Gill (photo from The Nicholas School)

The natural world is complicated, and far beyond our control. When studying the implications of conservation, it’s not so easy to design the kind of experiment that will produce “good” evidence.

David Gill, a professor in Duke’s Nicholas School for the Environment, recently led a study featured in the journal Nature that needed to  define what constitutes good evidence in the realm of marine conservation. Last Wednesday, he made a guest appearance in my Bass Connections meeting to share his work and a perspective on the importance of quality evidence.

Gill’s research has been centered around evaluating the effectiveness of Marine Protected Areas (or MPAs) as a way of protecting marine life. Seven percent of the world’s oceans are currently designated as MPAs, and by 2020, the goal is to increase this number to 10 percent. MPAs arguably have massive effects on ecosystem health and coastal community functioning, but where is the evidence for this claim?

Although past investigations have provided support for creating MPAs,  Gill and his team were concerned with the quality of this evidence, and the link between how MPAs are managed and how well they work. There have historically been acute gaps in study design when researching the effects of MPAs. Few experiments have included pre-MPA conditions or an attempt to control for other factors. Most of these studies have been done in hindsight, and have looked only at the ecological effects within the boundaries of MPAs, without any useful baseline data or control sites to compare them to.

As a result of these limitations, the evidence base is weak. Generating good evidence is a massive undertaking when you are attempting to validate a claim by counting several thousand moving fish.

Gill’s measure of ecosystem health includes counting fish. (Photo from Avoini)

So is there no way to understand the impacts of MPAs? Should conservation scientists just give up? The answer is no, absolutely not.

To produce better evidence, Gill and his team needed to design a study that would isolate the effects of MPAs. To do this, they needed to account for location biases and other confounding variables such as the biophysical conditions of the environment, the population density of nearby human communities, and the national regulations in each place.

The solution they came up with was to compare observations of current conditions within MPAs to “counterfactual” evidence, which is defined as what would have happened had the MPA not been there. Using statistical matching of MPAs to nearby non-MPA and pre-MPA sites, they were able to obtain high-quality results.

A happy sea turtle pictured in a marine protected area (photo from English Foreign and Commonwealth Office.)

The research showed that across 16,000 sampled sites, MPAs had positive ecological impacts on fish biomass in 71 percent of sites. They also discovered that MPAs with adequate staffing had far greater ecological impacts than those without, which is a pretty interesting piece of feedback when it comes to future development. It’s probably not worth it to create MPAs before there is sufficient funding in place to maintain them.

Gill doesn’t claim that his evidence is flawless; he fully admits to the shortcomings in this study, such as the fact that there is very little data on temperate, coldwater regions — mostly because there are few MPAs in these regions.

The field is ripe for improvement, and he suggests that future research look into the social impacts of MPAs and the implications of these interventions for different species. As the evidence continues to improve, it will be increasingly possible to maximize the win-wins when designing MPAs.

Conservation science isn’t perfect, but neither is medicine. We’ll get there.

Energy Week Kicks Off With Electric Bikes, Buses and More

Global warming is becoming a bigger issue every day. But have no fear – “Energy Week at Duke’ is here! The 2018 event featured everything from electric mountain bikes to the world’s most fuel-efficient vehicle.

To kick off the exciting week, eBike Central and Proterra founder Dale Hill rolled up to the Chemistry parking lot on Sunday to inform everyone about today’s latest tech that’s helping our planet become more sustainable.

eBike Central had a whole fleet of electric bikes, or “e-bikes,” on display for people to try out: mountain bikes, commuter bikes, cargo bikes and more. I tried out one of the mountain bikes and took it off-roading up a steep hill nearby (which I never would’ve been able to make up without the electric assist). Then just to mess around I tried out the “Packster 40,” which was equipped with a child seat in front of the handle bars. It was surprisingly maneuverable and went really fast.

Instead of having a throttle, these e-bikes work through pedal assist, meaning each time you pedal, the bike outputs additional power to the wheels. You can select from five different modes, ranging from “eco” (a 25 percent additional assist), to “turbo” (an extra 300 percent). You can reach top speeds of around 28 miles per hour without even breaking a sweat. What was really cool about the Packster 40 was that it could shift gears at a standstill, and you could add up to three seats if you’ve got triplets!

As you can see, e-bikes are a very eco-friendly and convenient mode of transportation. They allow for longer, faster commutes while also helping out the environment. The mountain bikes are appealing to a variety of riders, whether they have bad knees or just want the energy to do more laps per session. The batteries take about 4-6 hours to get a charge that lasts for 70 miles. Just within this past year, the mile range has increased by 30 percent, and that number is only growing. As the price for e-bikes goes down and their functionality improves, we’ll be seeing a lot more of them around.

E-bikes aren’t the only cool electric vehicle rising in popularity. Dale Hill gave an inspiring a talk on how his company Proterra is bringing positive change to public transit through their electrically powered buses. (pic: Duke Today)

Proterra decided to get involved with public transit because buses are ideal candidates for implementing battery electric vehicles. Buses operate on continuous routes, so it’s easy to watch them and monitor their performance. They come back to a common maintenance facility, operated on by a professional staff. And obviously they drive tons of people around every day, so cutting out fossil fuels for such a heavily used service could make a large-scale impact in the long run.

As the world’s urban density rapidly rises, it simply isn’t feasible for everyone to have cars. More and more people will need to turn to alternative methods, like the bus. By 2030, the majority of the world’s vehicles will be battery electric. Good thing is, not only are they more reliable than diesel ones, but they require much less maintenance . On top of that, they save a ton of money on gas. So not only are electric buses sustainable, but also a smart investment! It makes sense why Boston, New York City, San Francisco, Los Angeles and Austin have already all committed to having 100 percent electric bus fleets within the coming decades. And Proterra is playing a huge part in that. They currently account for 60 percent of all electric bus sales.

Duke itself is hopping on this electric vehicle train – by 2024 students will be riding a fully battery powered C1 between East and West Campus. This is another one of the sustainable steps Duke has been taking towards carbon neutrality.

The Duke Electric Vehicles team was also at the kickoff event, showcasing their vehicle that holds the Guinness World Record for most fuel-efficient vehicle. They did a couple of laps around the parking lot in the “hydrogen fuel cell car,” which gets the equivalent of 14,573 miles per gallon.

I encourage you guys to do your part in living sustainably. Maybe you could buy an electric bike, and effortlessly leave your friends dumbfounded in the dust on your way to school.

Will SheehanPost by Will Sheehan

 

 

 

 

Meet Dr. Sandra K. Johnson, Engineering “Hidden Figure”

When Dr. Sandra K. Johnson first tried her hand at electrical engineering during a summer institute in high school, she knew that she was born to be an electrical engineer. Now, as the first African-American woman to receive a Ph.D. in computer engineering in the United States, Johnson visited Duke to share her story as a “hidden figure” and inspire not just black women, but all students not to be discouraged by obstacles they may face in pursuit of their passion.

Though she did discuss her achievements, Johnson’s talk also made it clear that more than successes, it was the opposition she faced that most motivated her to persevere in electrical engineering. While pursuing a Master’s degree at Stanford, she met Dr. William Shockley, who in his free time was conducting research he believed would prove that African Americans were intellectually inferior to other races. Johnson had originally been planning on just finishing her program with a Master’s and then going into the workforce, but after hearing what this man was trying to prove, she decided she would prove to him that she was capable of doing anything that the non-black students in the same program could do. She finished the program with a Ph.D. in electrical engineering. She continued to make this declaration to anyone who didn’t believe she was capable: “before I leave this place, I will make a believer out of you.”

Dr. Johnson is the founder, CTO and CEO of Global Mobile Finance, Inc., a finance and tech startup based in Research Triangle Park, NC. Photo from BlackComputeHER.

While mapping out her own path to pursuing her goals, Johnson also firmly believed in making the path easier for other black people pursuing advanced degrees. When asked what the current generation of students could be doing to help themselves, she said to find mentors and to mentor others. Johnson shared an anecdote of sitting in a lab at Stanford waiting to begin an experiment when a man walked up to her and said she was in the wrong place. After talking to him for several minutes and showing him that she knew even more about the subject than he did and was in the right place, she told him that the next time someone who looked like her walked into the lab, not to be so sure of himself. Johnson went on to become an IBM Fellow, an IEEE Fellow, and a member of the prestigious Academy of Electrical Engineers. At the end of her talk, Johnson discussed what she believes is the best way to expedite change — to have people of color as founders and CEOs of major corporations that have the power to increase minority representation in their workforce. This is what she intends to do with her own company, Global Mobile Finance, Inc. If her current track record is any indication, there is no doubt her company will become a major corporation in the years to come, opening more doors for black women and other minorities pursuing their passions.

Post by Victoria Priester

Sean Carroll on the Evolution of Snake Venom

What’s in a snake bite?

According to University of Wisconsin-Madison evolutionary biologist Sean Carroll who visited Duke and Durham last week, a snake bite contains a full index of clues.

In his recent research, Carroll has been studying the adaptations of novelties in animal form, such as snake venom. Rattlesnakes, he explains, are the picture of novelty. With traits such as a limbless body, fangs, infrared pits, patterned skin, venom, and the iconic rattle, they represent an amazing incarnation of evolution at work.

Rattlesnakes: the picture of novelty (Photo from USGS)

Snake venoms contain a complex mixture of proteins. This mixture can differ in several ways, but the most interesting difference to Carroll is the presence or absence of neurotoxins. Neurotoxic venom has proven to be a very useful trait, because neurotoxins destroy the nervous tissue of prey, effectively paralyzing the animal’s respiratory system.

Some of today’s rattlesnake species have neurotoxic venom, but some don’t. So how did this happen? That’s what Carroll was wondering too.

Some genes within genomes, such as HOX genes, evolve very slowly from their original position among the chromosomes, and see very few changes in the sequence in millions of years.

But snake venom Pla2 genes are quite the opposite. In recent history, there has been a massive expansion of these genes in the snake genome, Carroll said. When animals evolve new functions or forms, the question always arises: are these changes the result of brand new genes or old genes taking on new functions?

Another important consideration is the concept of regulatory versus structural genes. Regulatory genes control the activity of other genes, such as structural genes, and because of this, duplicates of regulatory genes are generally not going to be a favorable adaptation. In contrast, structural gene activity doesn’t affect other genes, and duplicates are often a positive change. This means it is easier for a new structural gene to evolve than a regulatory one. Carroll explained.

Evolutionary Biologist Sean Carroll (Photo from seanbcarroll.com)

Carroll examined neurotoxic and non-neurotoxic snakes living in overlapping environments. His research showed that the most recent common ancestor of these species was a snake with neurotoxic venom. When comparing the genetic code of neurotoxic snakes to non-neurotoxic ones, he found that the two differed by the presence or absence of 16 genes in the metalloproteinase gene complex. He said this meant that non-neurotoxic venom could not evolve from neurotoxic venom.

So what is the mechanism behind this change? What could be the evolutionary explanation?

When Carroll’s lab compared another pair of neurotoxic and non-neurotoxic species in a different region of the US, they found that the two species differed in exactly the same way, with the same set of genes deleted as had been observed in the first discovery. With this new information, Carroll realized that the differences must have occurred through the mechanism of hybridization, or the interbreeding of neurotoxic and non-neurotoxic species.

Carroll’s lab is now doing the structural work to study if the genes that result in neurotoxic and  non-neurotoxic protein complexes are old genes carrying out new functions or entirely new genes. They are using venom gland organoids to look into the regulatory processes of these genes.

In addition to his research studying the evolution of novelties, Carroll teaches molecular biology and genetics at Madison and has devoted a large portion of his career to  storytelling and science education.

Meet New Blogger Anne Littlewood – Working on Biology and Puppies

My name is Anne Littlewood and I am a sophomore here at Duke. I grew up in San Francisco, spent a brief moment living on the island of Kauai, and finished high school in Pebble Beach, California. I am studying the intersection of biology and psychology here at Duke, in an effort to understand how biological mechanisms inform our interactions with the environment.

Snuggles in Puppy Kindergarten!

Outside the classroom, I can be found frequenting Duke’s beloved Puppy Kindergarten, where I work as a volunteer. Recently, I’ve become an Associate Editor for Duke’s literary magazine, The Archive. I love writing creatively, and it’s been so great to find a community of my literature- loving peers. I’m also participating in a Bass Connections project this year, and working on a team to evaluate the outcomes of different conservation interventions through the synthesis of an evidence gap map for World Wildlife fund.

Me and Cricket on Carmel Beach

Most of all I love to spend time outdoors, whether it’s exploring the mountains of North Carolina on a backpacking trip, lying in my hammock at Eno Quarry, or walking through the gardens each day on my way to class. I’m a huge animal lover, and I’m way too obsessed with my dog, a 12-pound cavalier King Charles spaniel named Cricket.

I’ve always been into science, but I think I really fell in love with Biology my freshman year of high school, when my all time favorite teacher, Mr. Cinti helped me extract my DNA one afternoon, just for fun. Writing is my passion, and I’m excited to explore my skills in a variety of genres this year. This blog is my first ever attempt at journalism/ science writing, and I’m excited to give it a try!

Cracking the Code on Credit Cards at Datathon 2018

Anyone who has ever tried to formulate and answer their own research question knows that it means entering uncharted waters. This past weekend the hundreds of students in Duke Datathon 2018 did just that, using only their computer science prowess and a splash of innovation.

Here’s how it worked: the students were provided three data sets by Credit Sesame, a free credit score estimator, and given eight hours to use their insight and computer science knowledge to interpret the data and create as much value for the company as they could. Along the way, Duke Undergraduate Machine Learning (DUML), the organization hosting the event, provided mentors and workshops to help the participants find direction and achieve their goals. 

Datathon participants attempting to derive meaning from the Credit Sesame Data

This year was the first such ‘Datathon’ event to take place at Duke. The event attracted big-name sponsors such as Google and Pinterest and was made possible by the DUML executive team, headed by co-presidents Rohith Kuditipudi and Shrey Gupta (to see a full list of event sponsors, click here).

DUML faculty advisor Dr. Rebecca Steorts said that even the planning of the event transcended disciplines: one of her undergraduate students and co-president of DUML, Shrey Gupta, found a way to utilize statistics to predict how many people would be attending. “It’s all about finding computational ways of combining disciplines to solve the problem,” Steorts said, and it’s very apparent that her students have taken this to heart.

The winning team (Jie Cai, Catie Grasse, Feroze Mohideen) presenting on how they can best gauge which customers are most “valuable” to Credit Sesame

After more than an hour of deliberations, the eight top teams were selected and five finalists were asked to present their findings to the judges. The winning team (Jie Cai, Catie Grasse, Feroze Mohideen) proposed a way to gauge which customers who create trial accounts are most likely to be profitable, by using a computer filtering program to predict likely customer engagement based on customer-supplied data and their interaction with the free trial. Other top teams discussed similar topics with different variations on how Credit Sesame might best create this profile to determine who the “valuable” customers are likely to be.

DUML hosts other events throughout the year to engage students such as their MLBytes Speaker Series and ECE Seminar Series. To learn more about Duke Undergraduate Machine Learning, click here.

by Rebecca Williamson

 

 

 

 

 

Considerations about AIDS from Brazilian literature

To know what illness is, you have to be ill first.

This was one of the points that post-doctoral student and essayist  Milena Mulatti Magri emphasized in her talk on Oct. 15. She was discussing Brazilian writer Caio Fernando Abreu’s writings about AIDS and its effect on groups who already faced societal prejudice before the breakout of AIDS in the 1980’s and 90’s, when patients were identified mainly as homosexual.

By studying research done by Professor Vladimir Safatle and physician and philosopher Georges Canguilhem, Magri has pieced together that health is seen as a form of normativity and disease as a deviation. Thus, ostracizing and excluding those who contract disease is seen as justifiable because they have deviated from what is seen as normal, even when the disease is not the fault of the patient.

Magri has also analyzed essays about the relationship between disease, metaphor and patient stigma, such as cancer patients who, in addition to combating the illness growing unwelcome inside their own bodies, also have to deal with social stigmas that come with disease, such as cancer as a representation for evil.

Brazilian author and columnist Caio Fernando Abreu. (Image from KD Frases.)

However, while Magri emphasized that social metaphors of different diseases should be deconstructed, she has also found that literature and personal writing can be a way to discuss and otherwise “incommunicable experience.”

During a time when it was seen as shameful to have AIDS, Caio Fernando Abreu began a biweekly publication of his health chronicles in the newspaper O Estado de São Paulo, which was one of the first instances of someone publicly discussing their experience with AIDS from the perspective of the ill person, as opposed to from the perspective of doctors or health experts.

Abreu’s columns confronted the difficulty of living with disease and living in proximity to death, and discuss the increased social prejudice as a result of the disease. Abreu also wrote a play called “O homem e amancha” (in English, “The Man and the Stain”), which is an intertextual reading of the famous Spanish novel Don Quijote de la Mancha. In her talk, Magri explained that “Mancha,” which in English means “stain,” can refer to both the home of Don Quijote before he sets off of on his adventures and the rare skin cancer that often accompanies AIDS called Kaposi Sarcoma, which forms lesions on the skin that resemble stains.

Abreu intended to use his own experiences to question the social prejudice against AIDS, and there Magri highlighted a marked change, even between his own writings at the beginning of his diagnosis compared to those at the end of his life, when he spoke openly and without metaphor about suffering that is amplified by social exclusion. 

Magri believes that Abreu’s writings were pioneering acts of courage, and that from his writing we learn to empathize rather than to judge and stigmatize.

Post by Victoria Priester

Victoria Priester

Coding: A Piece of Cake

Image result for cake

Imagine a cake, your favorite cake. Has your interest been piqued?

“Start with Cake” has proved an effective teaching strategy for Mine Cetinkaya-Rundel in her introduction-level statistics classes. In her talk “Teaching Computing via Visualization,” she lays out her classroom approaches to helping students maintain an interest in coding despite its difficulty. Just like a cooking class, a taste of the final product can motivate students to master the process. Cetinkaya-Rundel, therefore, believes that instead of having students begin with the flour and sugar and milk, they should dive right into the sweet frosting. While bringing cake to the first day of class has a great success rate for increasing a class’s attention span (they’ll sugar crash in their next classes, no worries), what this statistics professor actually refers to is showing the final visualizations. By giving students large amounts of pre-written code and only one or two steps to complete during the first few class periods, they can immediately recognize coding’s potential. The possibilities become exciting and capture their attention so that fewer students attempt to vanish with the magic of drop/add period. For the student unsure about coding, immediately writing their own code can seem overwhelming and steal the joy of creating.

Example of a visualization Cetinkaya-Rundel uses in her classes

To accommodate students with less background in coding, Cetinkaya-Rundel believes that skipping the baby steps proves a better approach than slowing the pace. By jumping straight into larger projects, students can spend more time wrestling their code and discovering the best strategies rather than memorizing the definition of a histogram. The idea is to give the students everything on day one, and then slowly remove the pre-written coding until they are writing on their own. The traditional classroom approach involves teaching students line-by-line until they have enough to create the desired visualizations. While Cetinkaya-Rundel admits that her style may not suit every individual and creating the assignments does require more time, she stands by her eat-dessert-first perspective on teaching. Another way she helps students maintain their original curiosity is by cherishing day one through pre-installed packages which allow students to start playing with visualizations and altering code right away.

Not only does Cetinkaya-Rundel give mouth-watering cakes as the end results for her students but she also sometimes shows them burnt and crumbling desserts. “People like to critique,” she explains as she lays out how to motivate students to begin writing original code. When she gives her students a sloppy graph and tells them to fix it, they are more likely to find creative solutions and explore how to make the graph most appealing to them. As the scaffolding falls away and students begin diverging from the style guides, Cetinkaya-Rundel has found that they have a greater understanding of and passion for coding. A spoonful of sugar really does help the medicine go down.  

    Post by Lydia Goff

Drug Homing Method Helps Rethink Parkinson’s

The brain is the body’s most complex organ, and consequently the least understood. In fact, researchers like Michael Tadross, MD, PhD, wonder if the current research methods employed by neuroscientists are telling us as much as we think.

Michael Tadross is using novel approaches to tease out the causes of neuropsychiatric diseases at a cellular level.

Current methods such as gene editing and pharmacology can reveal how certain genes and drugs affect the cells in a given area of the brain, but they’re limited in that they don’t account for differences among different cell types. With his research, Tadross has tried to target specific cell types to better understand mechanisms that cause neuropsychiatric disorders.

To do this, Tadross developed a method to ensure a drug injected into a region of the brain will only affect specific cell types. Tadross genetically engineered the cell type of interest so that a special receptor protein, called HaloTag, is expressed at the cell membrane. Additionally, the drug of interest is altered so that it is tethered to the molecule that binds with the HaloTag receptor. By connecting the drug to the Halo-Tag ligand, and engineering only the cell type of interest to express the specific Halo-Tag receptor, Tadross effectively limited the cells affected by the drug to just one type. He calls this method “Drugs Acutely Restricted by Tethering,” or DART.

Tadross has been using the DART method to better understand the mechanisms underlying Parkinson’s disease. Parkinson’s is a neurological disease that affects a region of the brain called the striatum, causing tremors, slow movement, and rigid muscles, among other motor deficits.

Only cells expressing the HaloTag receptor can bind to the AMPA-repressing drug, ensuring virtually perfect cell-type specificity.

Patients with Parkinson’s show decreased levels of the neurotransmitter dopamine in the striatum. Consequently, treatments that involve restoring dopamine levels improve symptoms. For these reasons, Parkinson’s has long been regarded as a disease caused by a deficit in dopamine.

With his technique, Tadross is challenging this assumption. In addition to death of dopaminergic neurons, Parkinson’s is associated with an increase of the strength of synapses, or connections, between neurons that express AMPA receptors, which are the most common excitatory receptors in the brain.

In order to simulate the effects of Parkinson’s, Tadross and his team induced the death of dopaminergic neurons in the striatum of mice. As expected, the mice displayed significant motor impairments consistent with Parkinson’s. However, in addition to inducing the death of these neurons, Tadross engineered the AMPA-expressing cells to produce the Halo-Tag protein.

Tadross then treated the mice striatum with a common AMPA receptor blocker tethered to the Halo-Tag ligand. Amazingly, blocking the activity of these AMPA-expressing neurons, even in the absence of the dopaminergic neurons, reversed the effects of Parkinson’s so that the previously affected mice moved normally.

Tadross’s findings with the Parkinson’s mice exemplifies how little we know about cause and effect in the brain. The key to designing effective treatments for neuropsychiatric diseases, and possibly other diseases outside the nervous system, may be in teasing out the relationship of specific types of cells to symptoms and targeting the disease that way.

The ingenious work of researchers like Tadross will undoubtedly help bring us closer to understanding how the brain truly works.

Post by undergraduate blogger Sarah Haurin

Post by undergraduate blogger Sarah Haurin

 

Creating a Gender Inclusive Campus: Reflecting on “Becoming Johanna”

Following Duke’s Oct. 4 screening of the 2016 documentary, “Becoming Johanna,” students, faculty, staff and community members in the audience were eager to ask questions of the panel, which included the film’s director/producer, Jonathan Skurnik, and even the film’s transgender subject, Johanna Clearwater herself.

Johanna Clearwater pictured with the film’s director/producer Jonathan Skurnik

The film showcases the heart-wrenching and empowering story of a latina transgender teenager growing up in Los Angeles. After beginning her transition at age 16, Johanna faced the rejection of her mother and intense opposition from school authorities. Soon after, she was abandoned by her family and entered the foster care system, where she was lucky to find a much more supportive family environment. After changing schools, she connected on a personal level with her school principal, Deb, who helped Johanna find a community where she felt understood and supported. This success story of self-advocacy and resilience in the face of abandonment and exclusion highlights the daily struggles of many transgender teenagers. For these individuals, becoming comfortable in their own skin is the end of a long and demanding journey, often made even more difficult by the ignorance and cruelty of society. Finding and following the path to authentic expression takes a huge amount of courage, as this route is often layered with adversity.

Before the screening, Duke clinical social worker Kristin Russel put the film in context for the audience, inviting our reflection with her words: “A well told story… is really what can help us bridge the unfortunate distance that can remain uncrossed and misunderstood if such stories are silenced.” Chief Diversity Officer for the School of Medicine Judy Seidenstein then introduced the film and facilitated the panel discussion.

After the film, the audience was invited to join the conversation. Questions came from every demographic of the crowd, and provided a nice sampling of opinions. Many audience members pointed out how important these conversations are, especially in a conservative state like North Carolina that has so recently struggled with the protection of LGBTQ rights with last year’s ‘Bathroom Bill.’ Specifically, the questions and comments from hospital staff and faculty from the School of Medicine gave a nice insight into the direction of support on campus for sexual and gender diversity.

Audience members reflect on the film with those nearby

Cheryl Brewer, the Associate Vice President of Nursing, told the room about the inclusion work that she is leading in the School of Nursing. They have developed a new core curriculum to promote acceptance and support of gender and sexual diversity through situational trainings. She noted that there have been some people that struggle with implicit biases more than others, but that the program has been a success overall.

Russell spoke briefly about her work with transgender and gender diverse youth in the clinical setting and emphasized the importance of having family support. Legally and psychologically, maintaining family involvement and support of patients is essential for treatment.

Events like this one reflect ongoing efforts to support sexual and gender diversity within and beyond Duke, by promoting conversation and increasing empathy through storytelling. Duke is well on the way to becoming a much more inclusive community, where everyone can feel a sense of belonging.

Guest post by Anne Littlewood

The Complicated Balance of Predators and Prey

If you knew there was a grizzly bear sitting outside the door, you might wait a while before going to fill up your water bottle, or you might change the way you are communicating with their other people in the room based on your knowledge of the threat.

Ecologists call this “predation risk,” in which animals that could potentially fall prey to a carnivore know this risk is present, and alter their habits and actions accordingly.

A yellow slider turtle.

A yellow slider turtle.

One way in which animals do this is through habitat use, such as a pod of dolphins that changes where they spend most of their time depending on the presence or absence of predators. Animals might also change their feeding habits and diving behavior because of predation risk.

Animals do this all of the time in the wild, but when predators are removed from ecosystems by hunting or over-fishing, the effect of their absence is felt all the way down the food chain.

For example, large amounts of algae growth on coral reefs can be traced back to over-fishing of large ocean predators such as sharks, who then don’t hunt smaller marine mammals like seals. As seal numbers increase, there are more of them to hunt smaller fish that feed on vegetation, which means fewer smaller fish or plankton to keep algal growth in check, and algae begins to grow unchecked.

Meagan Dunphy-Daly

Meagan Dunphy-Daly

This is a “trophic cascade” and it has large effects on ecosystems, Duke Marine Lab instructor Meagan Dunphy-Daly  t0ld the Sustainable Oceans Alliance last Thursday. She has performed research both in labs and in the field to study the effects that removing large predators have on marine ecosystems.

Dunphy-Daly discussed one lab experiment where 10 yellow-bellied slider turtle hatchlings were kept in tanks where they couldn’t see people or anything else on the outside. In real life, blue herons and other large birds prey on these turtle hatchlings, so the researchers made a model skull of a blue heron that they painted and covered with feathers.

Turtles are air-breathing, so each hatchling was given the option to sit where they could be at the surface of their tank and breathe, but this spot was also where the turtle hatchlings thought the bird beak might shoot down at any time to try to “eat” them.

Their options were to get air and risk getting hit by the bird beak, or diving down to the bottom of the tank to get food. During this experiment, Dunphy-Daly found that turtle hatchlings actually decreased their dive time and spent more time at the surface. If the turtles are continuously diving, they are expending lots of energy swimming back and forth between the surface and the bottom, she said, which means if the predator were to actually attack, they would have less energy left to use for a rapid escape.

Even when there is food at the bottom, when a predator is present, these turtles alter their activity by taking deep dives less frequently so as to not max out their aerobic limit before they actually need to escape a predator.

This is one way in which animals alter their behavior due to predation risk.

But let’s say that predators were disappearing in their real habitats, so turtles didn’t feel the need to build up these emergency energy reserves to escape them. They might dive down and feed more frequently, which would then decrease the amount of the vegetation they eat.

This in turn could have an effect on oxygen levels in the water because there would be fewer plants photosynthesizing. Or another species that feeds on the same plant could be out-competed by turtles and run out of food for their own populations.

The absence of large or small predators can have large impacts on ocean ecosystems through these complicated trophic cascades.

Victoria PriesterPost by Victoria Priester

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