Our Research Updates in Archways give a snapshot of the Rice ARCHES Initiative’s current work, research progress, and future directions
Adapting for Pandemic Safety
This week Russell Ku, a Research Assistant in the BMED Lab, tells us about precautions the Project CHROMA team is taking based on CDC guidelines.
After the unprecedented COVID-19 pandemic began, Rice University began implementing a system of precautions that are based on CDC guidelines to prevent the spread of the virus and keep community members safe.
These include weekly testing for all members of the Rice community who interact with campus, use of personal protective equipment such as masks and face shields on all parts on campus- both indoors and outdoors, physical distancing, and increasing cleaning and disinfection of buildings, all of which apply to the CHROMA lab as well.
Image: Rice University offers fast and free COVID-19 testing to all students, faculty, and staff each week.
More specifically to the CHROMA lab, the team also made efforts to reduce visit times and physical contact as much as possible to keep our participants safe.
We now give participants links to online questionnaires or printed copies so that they can complete them in the comfort of their own homes and eliminated most high-contact measurements, such as blood pressure, height and weight, and waist measurements. We also give participants the option of electronic or no-contact delivery of some pre-visit forms.
Although Texas has ended its mask mandate and lifted restrictions on building capacity limits, Rice University has not changed its protocols. All of the above-mentioned precautions are still in effect. Any changes that may be made in the future will follow the university’s Research Reactivation Program guidelines.
See https://coronavirus.rice.edu/ for more information on how Rice is minimizing COVID-19 transmission risk on campus and keeping the community safe!
Posted in Blog Posts, COVID-19 | Comments Off on Research Update: April 2021
Scientists have turned the structure of the coronavirus into music
Thursday, April 23, 2020
Our third journal club is online! Feel free to join the discussion remotely in the comments below. One of our participants in Project CHROMA suggested the following research that combines science and music to study the coronavirus:
Vineeth Venugopal (2020) “Scientists have turned the structure of the coronavirus into music,” Science 10.1126/science.abc0657.
Researchers at MIT have created a musical representation of the amino acid sequence and structure of the COVID-19 spike protein (based on protein data bank entry 6VSB published by Wrapp et al. 2020) using a technique known as sonification.
The team led by Markus Buehler transposed the vibrational frequencies of the 20 natural amino acids to an audible spectrum in order to assign a musical note to each amino acid, thus creating a 20-tone “amino acid scale.” To create the COVID-19 spike protein musical score, the notes were played on a Japanese koto. The volume and duration of each note were defined by the secondary and higher-order folded structure of the protein. Heat-induced molecular vibrations were represented by unique sounds as well. A neural network was then used to generate music compositions that captured the relationships between amino acid sequence and protein structure.
It’s apparently faster using this technique rather than traditional molecular dynamics modeling to search for sites where antibodies or drugs could bind on the viral protein — researchers simply have to compare the musical scores of the sonified structures.
This musical technique is also a great way to communicate the significance of protein sequences and their folded structure to the public!
Read more about this sonification method developed by the research team:
Chi-Hua Yu, Zhao Qin, Francisco J Martin-Martinez, and Markus J Buehler (2019) “A Self-Consistent Sonification Method to Translate Amino Acid Sequences into Musical Compositions and Application in Protein Design Using Artificial Intelligence,” ACS Nano, 13(7): 7471-7482.
Importance of Regulating Stress, Social Support, and Sleep during COVID-19
A collection of news articles featuring Project CHROMA Principle Investigator, Dr. Christopher Fagundes, on the importance of regulating stress, social support, and sleep to make you less prone to COVID-19.
We hope everyone is regulating their stress, social support and sleep this weekend! Check out this piece from Discover Magazine and Dr. Fagundes about how these factors can affect the immune system.https://t.co/c8CXSVbbw4
Additionally, he was featured in the Houston Chronicle, where he continued to offer tips for people to follow. We’re thankful for the opportunity to spread awareness in the Houston community during this time. Read his article here: https://t.co/9Jq5v1hqsN
As we continue to adjust to the ongoing COV-19 situation and the new Stay Home – Work Safe order, Dr. Fagundes shares some tips to mitigate the risk factors for COV-19 on Forbes.
Dr. Fagundes shares how stress and loneliness can impact your risk of getting COV-19 & some ways we can mitigate the harmful effects of loneliness and stress during this critical time – an extremely important topic as we adjust to the current pandemic. https://t.co/TRd8sR8QoTpic.twitter.com/TK3L5R0vJq
Playing unfamiliar music to patients could improve music therapy outcomes.
Music can promote brain healing, but scientists are still trying to understand which types of music work best for each patient.
Ajwad Creative/DigitalVision Vectors/Getty Images
When Melia Bonomo wants to kick back and relax, she turns to music and the gentle melodies of pop star Ed Sheeran. Like many people, the physicist feels her mood lift with certain tunes, a change doctors exploit to improve the health of patients with cognitive impairments. But some patients are unresponsive to music therapy. And it remains unclear exactly what restorative changes music actually induces in the brain. New results from Bonomo, a graduate student at Rice University, Texas, and her colleagues suggest that clues to both of these problems lie in how the brain responds to a listener’s favorite tune. Bonomo was set to share her findings in a session on the physics of the brain at the March Meeting of the American Physical Society earlier last month. (The meeting was canceled due to concerns about the new coronavirus disease, COVID-19, but Physics is reporting on some of the results that would have been presented.)
“Music therapy doesn’t work for everybody,” says Bonomo, who collaborated with researchers at Houston Methodist Hospital’s Center for Performing Arts Medicine. “We wanted to see if we could better understand why that is from how a person’s brain processes music.”
In the study, Bonomo and her colleagues used functional magnetic resonance imaging (fMRI) to monitor the neuronal activity of 25 people as they listened to six audio excerpts. Each person’s set list included their favorite song, a Bach concerto, and an old newscast by Walter Cronkite. The team then translated the resulting fMRI images into network-like maps, with one map for each excerpt per person. To make these maps, the researchers divided the brain into 84 regions and drew a connecting line between two regions if they had similar patterns of activity during an audio excerpt.
Bonomo looked first at the brain maps of participants listening to their favorite songs. Within these networks, she noticed that some regions were more strongly connected with each other than others, forming a “community.” She then found that the networks fell into two categories: those where there were many connections between different communities and those where there were fewer. And interestingly, the category for a participant’s map was predictive of how they would respond to the other five sound clips.
She and her colleagues found that when a participant’s “favorite-song” network had many intercommunity connections but few intracommunity ones, the distribution of connections changed significantly for each of the other excerpts. But when the opposite was true, these connections tended to stay in place, unless the participant was listening to the most unfamiliar sound clips. (For the people in the study, the least known excerpts were a melody from a Japanese opera and a passage of foreign language speech.)
Bonomo and colleagues made network-like representations of brain activity in response to music. The maps indicate that the brain’s response to a favorite song (left)—specifically, the types of connections between regions of activity—predicts how it will respond to other music (center and right).
The fact that networks with more isolated communities are harder to disrupt is well known in network theory, explains Bonomo. Seeing this effect in the brain’s response to music tells us that, for some, forming new neuronal connections—something the brain needs to do to compensate for an injury, for example—may require a bigger auditory stimulus. That could have implications for music therapy, where clinicians select music to foster neuronal connections and help the brain heal. Typically, therapists select popular melodies, such as the classical music of Bach or Beethoven, to stimulate a recovery. But the new study suggests that those pieces might not be the right ones to play for everyone, says Bonomo. Instead, unfamiliar music might be the best bet. Bonomo and her colleagues are currently testing this hypothesis in a study of people with mild cognitive impairment.
Although Bonomo’s work went unpresented at the March Meeting, she did share it on Twitter. Inspired by fellow physicist Douglas Holmes of Boston University, she condensed her planned talk into ten slides that she tweeted out under the hashtag #APS10slides10tweets. She hopes that the tweets will scroll across the screens of others studying how music impacts the brain. While she doesn’t know yet if that has happened, she said that sending the tweets “was a cool way to publicly share a snapshot of my research.”
What do stress, loneliness and lack of sleep have in common? They are all factors that can weaken your immune system and make you more susceptible to COVID-19, according to Rice University’s Christopher Fagundes, an associate professor in the department of psychological sciences who studies the link between mental and immune health.
Chris Fagundes. Photo by Jeff Fitlow.
“In my field, we have conducted a lot of work to look at what predicts who gets colds and different forms of respiratory illnesses, and who is more susceptible to getting sick,” Fagundes said. “We’ve found that stress, loneliness and lack of sleep are three factors that can seriously compromise aspects of the immune system that make people more susceptible to viruses if exposed. Also, stress, loneliness and disrupted sleep promote other aspects of the immune system responsible for the production of proinflammatory cytokines to over-respond. Elevated proinflammatory cytokine production can generate sustained upper respiratory infection symptoms.”
And while this previous research has centered on different cold and upper respiratory viruses, he said “there is no doubt” that these effects would be the same for COVID-19.
Previous studies have indicated that healthy, nonimmunocompromised people who spend less time around others and are exposed to the cold virus are significantly more likely to get sick and experience worse symptoms than those people who get out and socialize.
Fagundes said this can be explained by the way positive emotions buffer against stressors and evoke a favorable immune response, even while extroverted individuals are more likely to be around more people, possibly those who are carrying germs that could make them sick.
It’s an interesting paradox during the global COVID-19 pandemic, Fagundes said, when people are strongly encouraged and in some places required to stay at home to prevent the further spread of the virus.
Another major factor that impacts immune health is sleep deprivation, Fagundes said, which he noted has been demonstrated over and over in previous study of the topic.
“The overwhelming consensus in the field is that people who do not consistently get a good night’s sleep — 7-9 hours for adults, with variation on what is optimal — makes a person more likely to get sick,” he said.
Fagundes said that although alcohol use, certain jobs and other factors make some people more likely to have poor sleep, psychological stress has a tremendous impact on a person’s quality of sleep.
“It’s important also to note that when we talk about stress, we mean chronic stress taking place over several weeks, not a single stressful incident or a few days of stress,” Fagundes said. “An isolated stressful incident does not seem to make a person more susceptible to a cold or the flu.”
However, even absent of poor sleep, chronic stress alone is disruptive enough to the immune system to make people more likely to get sick, Fagundes said.
“Without question, previous work on this topic clearly demonstrates that chronic stress affects our immune system in a way that makes us more susceptible to viruses and colds,” he said. “Just think about college students who get sick after weeks of stress while studying for a big exam.”
Fagundes said the best ways to mitigate the harmful health effects of loneliness and stress during the COVID-19 pandemic are to stay connected with others through communication, particularly video calls.
“There is some evidence that it may be better to video conference versus having a regular phone call to reduce feelings of isolation,” he said. “There’s something about chatting with people and having them visually ‘with’ you that seems to be more of a buffer against loneliness.”
Fagundes also noted that it is important to keep a routine during stressful times.
“This will regulate your sleep and allow you to focus on immediate goals and plans,” he said. “In turn, you will overthink things less and feel more accomplished.”
And if you find yourself worrying nonstop about the situation, it can be helpful to set aside specific “worry times,” Fagundes said.
“People often worry and overthink things because their brain is telling them there is something to solve,” he said. “However, it can be counterproductive after a while. A good technique is to set aside 15 minutes a day where you allow yourself to worry, preferably with a pen and paper. After that, you aren’t allowed to think about the issue for the rest of the day.”
Fagundes said it is also sometimes helpful for people to identify inaccurate thoughts that reinforce negative thinking and emotions.
“People often convince themselves that a situation is much worse than it is by telling themselves things that are not true,” he said. “We call these cognitive distortions. For example, it is common to catastrophize a situation by convincing themselves that the worst-case scenario is the most likely scenario. When people learn to identify and then refute these thoughts, they often feel much better.”
Posted in COVID-19, News | Comments Off on How stress and loneliness can make you more likely to get COVID-19
Systematically Improving Espresso: Insights from Mathematical Modeling and Experiment
Thursday, March 19, 2020
Our second journal club was moved online! Feel free to join the discussion remotely in the comments below. Josh Hill from the department of Physics & Astronomy suggested the following paper that combines science and the culinary arts:
Michael Cameron, Dechen Morisco, Daniel Hofstetter, Erol Uman, Justin Wilkinson, Zachary Kennedy, Sean Fontenot, William Lee, Christopher Hendon, and Jamie M. Foster (2020) “Systematically Improving Espresso: Insights from Mathematical Modeling and Experiment,” Matter2(3):631-648.
The coffee industry is huge! In the U.S. alone, it provided 1.5 million jobs and accounted for 1.6% of the gross domestic profit in 2015. Espresso is the trickiest coffee beverage format in terms of maintaining a consistent yield and desirable flavor. The goal of this project was to develop a mathematical model of espresso extraction in order to optimize the espresso parameters at play for a reduction of the variation in taste and waste!
These espresso parameters are:
grind setting
coffee mass
water pressure and temperature
beverage volume
The model determined that variation in espresso drinks was not due to human variation, but rather due to non-uniform flow during espresso extraction related to coffee grind size. The team determined a critical minimum grind size that would homogenize the flow, increase extraction yield, and reduce drink variability. Interestingly, the extraction yield had a non-linear dependence on grind setting — this was attributed to a competing relationship between a finer grind leading to an increase in flow but also an increase in grind aggregation leading to partial clogging conditions that affect the flow.
Typically, 20g of dry coffee mass is used to make a single 40g espresso shot. However, the research team demonstrated that a barista can achieve highly reproducible espresso with the same 40g extraction yield by reducing the coffee mass to 15gand using a counter-intuitively coarser grind!
The mass reduction suggestions were implemented at a local cafe in Eugene, Oregon. Espresso drinks were prepared with 15g of specialty-grade coffee, rather than 20g. Firstly, there was a reduced order-to-delivery time since the shot brewing time was 14s rather than 20-30s. Secondly, the research team calculated that the cafe had saved $0.13 per drink given the lower coffee dry mass being used. This amounted to an increase in profit of $3,620 per year!
To summarize: The multi-scale mathematical model of espresso extraction enabled an understanding of the origin of the variation in espresso drinks. The research team made suggestions to minimize drink variation and dry coffee waste: (1) reduce the dry coffee mass used and (2) increase the grind size. Espresso yield and taste were both preserved, while the shot brewing time became faster.
These novel, model-based brewing protocols will contribute to creating a more sustainable coffee-consuming future!
Our “Project CHROMA Personnel” series in Archways highlights the key researchers behind the Rice ARCHES Initiative.
Kristi Parker, M.Ed.
This month Nyla Vela from the Department of Psychological Sciences interviews our Lab Manager in the Biobehavioral Mechanisms Explaining Disparities (BMED) Lab.
Earlier this week I got to sit down with our very own, Kristi Parker, the Lab Manager here at the BMED Lab, and she gave me the ins and outs of what its really like to oversee the incredible projects we have here.
Kristi, a California native who got her master’s in education at the University of Southern California, found herself drawn to the BMED lab due to her interest in Psychology. She says that she is very fascinated with the work the lab is doing regarding connecting the mind and the body.
Before we were lucky enough to have her however, she actually worked as a paralegal for 5 years!
Further, she began to tell me about what her job entails. In her words, she takes care of a lot of administrative work. From scheduling and working with grants to overseeing progress made by all the different projects under the lab’s wing, Kristi could be seen as the glue that keeps this lab together. Serving as an immediate liaison between Dr. Christopher Fagundes, our primary investigator, and the rest of the lab, we are always well informed and on top of our immediate goals as a team.
When asked about what she enjoys about her job, Kristi told me that she really enjoys the participant interaction aspect of the lab. She detailed a story about one participant who, when Project Heart was still doing home visits, would bake cookies and tell stories every visit.
Evidently, Kristi is a caring and hard-working figure here at the BMED Lab. If it weren’t for her, our lab would simply fall apart, so we are very grateful that her interest in learning about others landed her here with us!
Musical Sound Quality as a Function of the Number of Channels in Modern Cochlear Implant Recipients
Thursday, February 6, 2020
Our first journal club was a great success! We had students and postdocs in attendance from the departments of Physics & Astronomy, Applied Physics, Bioengineering, and Psychology. The interdisciplinary mix of trainees sparked some good discussions.
Melia Bonomo presented on the following paper:
Katelyn Berg, Jack Noble, Benoit Dawant, Robert Dwyer, Robert Labadie, Virginia Richards, and René Gifford (2019) “Musical Sound Quality as a Function of the Number of Channels in Modern Cochlear Implant Recipients,” Frontiers in Neuroscience 13:999.
Cochlear implant users consistently report musical sound quality impairments following implantation. Therefore, in this study, the objectives were to determine:
Number of channels needed for high level of musical sound quality (a) overall, and (b) for different genres: Alternative, Hip Hop/Rap, Jazz, Pop, R&B, Rock
Impact of device and patient factors on musical sound quality
Relationship between musical sound quality, speech recognition, and speech sound quality
The study contained 21 subjects who had been using cochlear implants for at least 6 months (cohort average usage was about 4 years). There were six electrode conditions — each subject’s clinical mapping, and then several in which certain electrodes were deactivated such that there were only 4, 8, 10, 12, or 16 active electrode channels. For each of these conditions, subjects listened to 15 song clips (30-seconds each) from 30 possible songs in the six different genres.
Musical quality was measured subjectively on a 1=very poor to 10=very good scale, for which subjects were asked to consider clarity, richness, and pleasantness and to not consider their familiarity or preference.
Overall, having at least 10 electrodes led to higher musical sound quality. For almost Alternative, Jazz, Pop, R&B, and Rock, there was a significant increase from 4 electrodes to 12 electrodes. A lack of significant increase during Hip Hop/Rap may be due to the musical complexity.
There was no significant impact from implant experience, the device manufacturer, electrode type, or the surgeon who performed the implantation. Patient’s musical sophistication was measured by the Ollen Index (which accounted for music knowledge and ability to play an instrument, sing, understand and create music, etc.) showed a positive correlation with music sound quality. However, when two musicians in the cohort were removed from the data, the correlation disappeared.
There was a positive correlation between speech recognition in both conditions and musical sound quality as well as between speech sound quality and music sound quality.
One of the limitations of the study was that it can be difficult to disentangle subjective musical sound quality from song preference. One way of alleviating this concern would be to break down the three sound qualities (clarity, richness, pleasantness) and ask about each specifically, rather than one combined question, and additionally ask about familiarity and preference to control for these factors.
A major limitation of the study was that these subjective music quality ratings could have been affected by the unfamiliar electrode manipulation and frequency bandwidth that cells are being stimulated for. One way of addressing this would be to look at speech quality as a function of the number of electrodes and used this to control for effect of lack of experience with the different electrode mappings. A second way of addressing this could be to allow participant to become accustomed to hearing with the new electrode mapping (e.g., listening to different speech until speech quality and recognition become comparable to their norm), and then test for music quality.
To summarize: Musical sound quality significantly increased from 4 to 10 channels, and for all genres except Hip Hop/Rap. Higher musical sound quality was not correlated with musical experience (after controlling for two musicians in cohort), cochlear implant experience, or device specifications. Musical sound quality was positively correlated with speech recognition and sound quality.
Music perception is rarely measured in the clinic, but it’s an important factor to consider when developing electrode mapping to preserve music appreciation!
Posted in Events, Journal Club | Comments Off on Journal Club: February 2020
Our Research Updates in Archways give a snapshot of the Rice ARCHES Initiative’s current work, research progress, and future directions.
Art & Science at the ARO Conference
This month, Melia Bonomo from the Department of Physics & Astronomy tells us about some unique art exhibits at the Association for Research in Otolaryngology conference.
Recently, I had the opportunity to attend the Association for Research in Otolaryngology (ARO)’s 2020 midwinter meeting in San Jose, California with the Raphael Lab. It was a really great opportunity to learn about current research in auditory neuroscience, especially for work relevant to Project CHROMA that is looking at how the ear and brain perceive and process music. An important aspect of doing scientific research is interacting with other scientists to share your results, discuss progress, learn about other work going on in your field, spark new ideas and research directions, and initiate new collaborations — communication really is key to scientific advancements.
In addition to research presentations and posters, there were several neat exhibits at ARO that combined the arts and sciences!
(1) Outside the San Jose McEnery Convention Center, there was a large-scale interactive sculpture (pictured above) called Idea Tree by artist Soo-in Yang, fabricated and installed by Demiurge, and engineered by ARUP. Demiurge give a great description of the connection between art and technology: “The sculpture accepts audio inputs – speech, song, ambient noise – and by interacting with and learning from participants using advanced AI and speech recognition software, these sounds are used to create a dynamic audio composition. Idea Tree is the embodiment of the idea that a convention center is a place where people gather to share ideas and concepts, forming the seeds for these ideas to grow and evolve.”
(2) Inside the Convention Center’s prefunction area, there was a multisensory art exhibit called “Your Eyes On My Ears,” in which visitors listened to accompanying audio while contemplating portraits of individuals wearing hearing aids or cochlear implants. This exhibit was put together by the Droit Pluriel and Foundation Pour l’Audition to provide a unique perspective on hearing loss.
“Your Eyes on My Ears” multisensory exhibit at the ARO conference in San Jose.
(3) One night of the conference there was a public outreach event at the San Jose Montgomery Theater, “Musae on the Brain: Women in Voice and Science,” which featured a performance by a local women’s vocal ensemble Musae followed by presentations by Sarah Schneider, a speech-language pathologist from UCSF who specializes in understanding and caring for the professional voice, and Dana Boebinger, an auditory neuroscientist from Harvard who studies how humans perceive complex sounds. There was a q&a period afterwards for discussion on how music arises from a combination of human voices, ears, and brains.
Also at ARO, I met Dr. Charles Limb and Dr. Karen Barrett of the The Sound and Music Perception Lab (University of California, San Francisco) who have a National Endowment for the Arts-funded Research Lab like us! Limb and Barrett are studying the cognitive and social processes of arts-based creativity, and how these processes affect learning-related outcomes. Check out their website for more information about their work: https://ohns.ucsf.edu/limb-lab.
Overall, the conference and the associated art exhibits made for a great experience — a big thank you to the Raphael group for supporting me to attend!
Posted in Blog Posts | Comments Off on Research Update: January 2020
Our “Tools of the Trade” series in Archways highlights the research technology and methodologies used by the Rice ARCHES Initiative.
Modularity of the Brain
This month Fengdan Ye from the Department of Physics & Astronomy discusses an analysis method being used to study brain activity in Project CHROMA.
In recent years of neuroscience research, it has become more and more popular to view the whole human brain as a functional network. The structure of the human brain network has been studied in relation to cognitive performance, as well as disease progression. Modularity is one of the many ways to quantify the structure of a human brain network, and it’s a concept I have been working with throughout my PhD.
What is modularity? To understand that, we first need a clear picture of what a whole-brain network looks like. A network consists of nodes and links. In our case, the nodes are different brain regions. These regions are usually defined from existing divisions of the human brain, which can be based on either anatomical or functional features of the brain. For example, Brodmann areas are brain regions defined based on the microscopic cellular composition of the brain. The links between these regions can be defined in many different ways. One popular way is to derive the links from functional magnetic resonance imaging (fMRI) data. Specifically, the Blood-oxygen-level-dependent (BOLD) imaging method in fMRI gives information on the level of activity of any brain regions at any given time. A link exists between two brain regions, if they show synchronized activity across a period of time. A link is absent if the activity of two brain regions is not coordinated.
Modularity quantifies how modular the brain network is. The higher the modularity, the more modular the network is. For example, let’s assume we have six brain regions A through F. If brain regions A, B, and C are all linked to each other, and D, E and F are all linked to each other, but there is no link between the first group (ABC) and the second group (DEF), then the network is very modular. Under the context of BOLD imaging, this means the brain has two distinct functional modules: one consists of ABC and the other DEF. The regions within each module always activate together, but regions across modules do not communicate functionally. On the other hand, if there are links between all six regions, then the network is less modular because it is harder to define which regions work more closely with each other. Below is another example of low- and high-modularity networks:
Image: Comparison of networks that have the same number of nodes (circles) and links (connecting lines) but different modularity (M) because of the network organizations.
In research, people not only look at the modularity value of a brain network, but also the compositions of the identified modules. This method has shed light on human cognitive and behavioral function, as well as prognosis and progression of diseases, such as stroke and Alzheimer’s disease.
For more in-depth reading:
O Sporns and RF Betzel (2016), Modular Brain Networks. Annu Rev Psychol, 67:614-640.
G Chen, HY Zhang, C Xie, G Chen, ZJ Zhang, GJ Teng, and SJ Li (2013), Modular reorganization of brain resting state networks and its independent validation in Alzheimer’s disease patients. Front Hum Neurosci, 7:456.
Posted in Blog Posts | Comments Off on Tools of the Trade II
