Pathogens for your pocket

08:05 a.m.

Maeve Doyle

PathogenAR, an application co-created by U of T grad Kristen Browne, was named Finalist in the 2020 Adobe Creativity Government Awards. The awards recognize government professionals who are making an impact through creativity and design.

“This is an innovative solution to what sounds to be a long-standing problem. The concept to use AR and be able to even present and discuss on the fly is what really makes this an outstanding entry,” wrote one assessor.

A 3D-modelling specialist, Browne created PathogenAR as part of a team at the National Institute of Allergy and Infectious Diseases (NIAID). The app allows users to carry around 3D-models of pathogens in their pockets.

“We thought we could create an application which would allow a user to carry around all the structures they needed. Something they could just bring out at a conference table and show their peers and say, this is what I’m trying to tell you about,” says Browne. “They’d be able to walk people through important features, interacting, highlighting, connecting to a projector. Then those people could download the app and walk through it themselves.”

Biomedical Communications alum Kristen Browne. Photo provided by K. Browne.

3D-model print files for download

“PathogenAR is a natural extension of the NIH’s 3D Print Exchange,” says Darrell Hurt, computational biologist, project lead and chief of the Bioinformatics and Computational Biosciences Branch of NIAID at the National Institute of Health (NIH).

The 3D Print Exchange is an interactive website for searching, sharing and downloading print files for 3D biomedical models.

Browne, a 2015 graduate of the Master of Science in Biomedical Communications, says that although colour 3D prints from the 3D Print Exchange’s library are a really great way to visualize protein structures, they’re not particularly portable. “They’re also really fragile and heavy, so carrying them around isn’t practical.”

For a solution, the 3D Print Exchange team turned to augmented reality, an increasingly popular technology that overlays computer visualizations onto the real world through a smartphone or tablet screen.

See a demo of PathogenAR on YouTube. “Experience pathogens in augmented reality. The PathogenAR app uses image-tracking-based interactivity as a convenient method for researchers and students to...”

Prototype module

The first module Influenza: A Universal Vaccine allows users to explore strategies that NIAID researchers are using to develop a single vaccine to target the many types of influenza virus.

“This is really high level data that ordinarily people would have a hard time interpreting, but because of PathogenAR, they can visualize it as long as they have a smartphone,” says Browne.

With a Merge Cube device–a foam cube inlaid with patterns recognized by a smartphone’s camera–users can even project and interact with 3D-models of the virus.

PathogenAR’s 3D model of the influenza virus projected onto a Merge Cube. (Marketing image. Not real game play.) Provided by K. Browne.

SARS-CoV-2

Browne says PathogenAR has been downloaded more than 300 times after being shared through NIH social platforms, and that feedback has been positive.

“That indicates that there definitely is interest and now we know we can build forward. How can we make this more engaging? Reduce barriers? Improve our storytelling? What subjects can have the most impact on people right now?” says Browne. “And, of course, that’s where SARS-CoV-2 comes up.”

In one module under development, the PathogenAR team is working to tell the story of one route to stopping the spread of SARS-CoV-2, the virus which causes COVID-19. It will allow users to explore the interaction between the viral spike protein and the host cell, and potentially better understand how scientists hope to disrupt the mechanism that allows the virus to enter a cell.

• BMC graduate answers the call to fight COVID-19

Ultimately, both the influenza and the SARS-CoV-2 modules will inform the public about viruses, immunity, and vaccines. “People can start to understand, oh, this is what a vaccine is. It’s not just a fluid that goes into my arm. It’s a functional entity,” says Browne.

While PathogenAR is all about molecular data right now, she says it won’t always be.

“We will likely be integrating models that come from medical imaging for stories about how pathogens affect the body, and maybe even one showing how the swab test for COVID-19 works using a model of the sinus from one of our collaborators. We can basically tell any story that lends itself to augmented reality.”

NIAID’s PathogenAR app is available for download from Google Play and the App Store.

Postcards for Beirut

11:42 a.m.

Maeve Doyle

Tuesday, August 4, 2020, Farah Hamade woke and checked her phone. Her family chat group was crammed with messages. "Is everyone okay?” And, “What happened?"

It was 6 p.m. local time in Beirut, Lebanon when the first blast occurred, The Washington Post reported. A stockpile of ammonium nitrate stored in a warehouse exploded in the city's port. A second, stronger explosion obliterated buildings and devastated the densely populated area. Hundreds of people dead. Thousands injured. Hundreds of thousands displaced.

Then the video appeared in Hamade’s feed.

"The footage was shocking. I was in utter disbelief. My family sent photos of damage to their offices and homes, of destruction in the streets that are so familiar to me. Thankfully my family is safe, but we all know someone who has been injured, left homeless or killed," says Hamade, a second year graduate student in the Master of Science in Biomedical Communications at the University of Toronto.

A second home

Lebanese-American, Hamade was born in San Francisco. She lived in multiple countries as she grew up but considers Lebanon her second home. "I grew up visiting family in Beirut multiple times a year for holidays and summers. A big part of my family lives in Beirut and the surrounding areas," she says.

In August 2019, one year before the Beirut explosions, Farah Hamade, MScBMC Class of 2020, poses for a photo in Lebanon. Photo provided by F. Hamade.

Her memories from Beirut are of family greetings at the airport, pillow forts in her grandmother's apartment, morning coffees on her aunt's balcony. "It's a city filled with life and creativity, nestled between the sea and the mountains," says Hamade.

Already worried by Lebanon’s current financial crisis and public protests, the biomedical visualization specialist says worries for her second home now include the coronavirus pandemic as victims made homeless by the catastrophe try to find shelter with family and friends.

Despite feeling overwhelmed and exhausted, Hamade says that she knows she can help, even from a distance, by raising funds and sharing news.

Crisis response

Hamra, Beirut 2017 by Farah Hamade: 4-by-6-inch copies of the postcard are available for suggested donations of $15 US or $20 Cdn.

Hamade is selling postcard prints of a watercolour sketch. The sketch depicts the view as she saw it in 2017 from her aunt's balcony in the Hamra neighbourhood of Beirut. She says that the sketch represents both a happy memory and a hopeful future.

"All the funds raised from the postcards will go to disaster relief efforts in Beirut. The first batch of donations will be going to the Lebanese Red Cross," says Hamade, who will make future donations to other NGOs working in the area.

To receive a postcard

“To donate, you can send funds via Venmo to farahamade, or by Paypal or eTransfer to farahamade@gmail.com. Include your mailing address to receive a postcard. You can also make donations directly to the Lebanese Red Cross,” she says.

Regardless of the reasons behind the catastrophe, Hamade says the important thing is that people are suffering and aid in the coming weeks is crucial. "I hope that these postcard prints will encourage people to donate and maybe even inspire them to visit Beirut one day."

Connaught New Researcher Award funds biomolecular visualization research

The Connaught Fund at the University of Toronto awarded Derek Ng a $20,000 Connaught New Researcher Award. Ng, who holds a PhD in molecular structural biology and is an assistant professor in the Biomedical Communications program, will use the award to fund his research into biomolecular visualization.

Dr. Derek Ng, assistant professor of biomedical communications, is a 2020 recipient of the prestigious Connaught New Researcher Award.

Ng says that due to rapid technological advances in molecular structural biology and bioinformatics, research scientists generate and have access to vast amounts of biomolecular data.

"Integrating, exploring, and extracting meaning from this great quantity and diversity of data is the challenge," he says.

With the Connaught New Researcher Award, Ng says that he will be able to study the role of visualization in the analytical processes, methods, and tools that molecular biologists currently use. Findings from this study will inform the creation of an evidence-based framework that can be used to guide the design and evaluation of future visual analytic tools to better support knowledge discovery in molecular structural biology.

A Further Honour for BMC Alum Dr. John Semple

On June 1st we wrote about Dr. John Semple receiving an Honorary Doctorate at OCADU. We recently learned that he also received another award: the Lavina Lickley Lifetime Achievement Award from the Department of Surgery at the University of Toronto.

The Lavina Lickley Lifetime Achievement Award “…recognizes faculty members who have demonstrated significant contributions to the Department of Surgery throughout their careers at the University of Toronto. These individuals will have provided a lifetime of exceptional professionalism through leadership, research, teaching, exemplary clinical care, administration or public service.”

Dr. Lickley was a pioneering cancer surgeon and researcher at Women’s College Hospital in Toronto. In her long and distinguished career she trained many surgeons, and mentored many researchers, one of whom was John Semple.

After receiving his BScAAM degree from the (then) Art as Applied to Medicine Department at U of T, Dr. Semple went on to earn his MD at McMaster University and received his surgical training and MSc at the University of Toronto.

He has gone on to become: a Professor of Surgery at the University of Toronto; Head of the Division of Plastic Surgery, Women’s College Hospital; Chair in Surgical Breast Cancer Research at the Canadian Breast Cancer Foundation; and many other positions and accolades to numerous to mention.

Jenkinson and Woolridge on visualizing the coronavirus in Le Devoir

Wednesday, June 3, 2020 - 9:30 a.m.

Jodie Jenkinson et Nick Woolridge de MScBMC à propos de l'image emblématique SARS-CoV-2, et la réalisation d'une vue en coupe pour révéler son intérieur. "D’où vient l’image emblématique du nouveau coronavirus?"

Obtenez toute l'histoire. https://bit.ly/3csiHWv

Jodie Jenkinson and Nicholas Woolridge of MScBMC on the iconic SARS-CoV-2 image, and on making a cutaway to reveal the virus' interior. "D’où vient l’image emblématique du nouveau coronavirus?"

Get the whole story. https://bit.ly/3csiHWv

OCADU awards honourary degree to Art as Applied to Medicine grad

Dr. John Semple, BScAAM 7T6 (Photo: uoftplasticsurgery.ca/directory/faculty/john-semple)

Monday, June 1, 2020 - 12:15 p.m.

OCAD University names Art as Applied to Medicine grad, Dr. John Semple, an honourary degree recipient. One of four to receive the honour, OCADU will award the degrees on Friday, June 12 at their virtual convocation ceremony.

Semple, graduated in 1976 with a Bachelor of Science in Art as Applied to Medicine from the University of Toronto. Both an artist, and a surgeon at Women’s College Hospital, he is internationally recognized for reconstructive surgery of the breast.

Founded in 1945, Art as Applied to Medicine began as a three-year diploma course. The three-year Bachelor of Science degree began in 1967. In 1990, the name Art as Applied to Medicine was changed to Biomedical Communications when the program became a Division in the Department of Surgery. The degree was elevated to the current 24-month Master of Science in Biomedical Communications (MScBMC) in 1993.

OCAD University is celebrating the honourary degree recipients "for their contribution to knowledge and culture in their creative fields, for their passionate belief in the importance of visual arts and design, and for their spirit of philanthropy in the cultural sector and beyond."

Get the whole story: https://bit.ly/2XkrnK8

BMC director awarded $200,000 research grant

Thursday, May 28, 2020 - 8:30 a.m.

Jodie Jenkinson, associate professor and director, Biomedical Communications program (Credit: D. Mazierski)

Canada's Social Sciences and Humanities Research Council (SSHRC) announced on May 20 the award of a two-year, $197,647 Partnership Development Grant to Jodie Jenkinson, associate professor and director of the Biomedical Communications program at the U of T Mississauga.

"Visualizations, interactives, simulations and animations are common learning resources in today's undergraduate science classroom," says Jenkinson. "But scientific accuracy, clarity and quality can really vary. There's also little known about how effective these multimedia learning tools really are."

Jenkinson puts this down to the gap between the communities who design the visualizations, the researchers who evaluate the learning materials and outcomes, and the instructors who rely on multimedia tools for teaching.

Jenkinson says the Partnership Develop Grant will allow her and co-applicants Gaël McGill of Harvard University and Susan Keen of the University of California, Davis to establish a partnership to engage these three communities in better integration of craft- and research-based knowledge in instructional multimedia design for undergraduate biology education.

The VISABLI (visualizations, interactives, simulations and animations in biology learning and instruction) partnership will establish a community of practice around science visualization. VISABLI will foster and sustain interdisciplinary communication and collaboration between the three stakeholder groups.

"The VISABLI partnership will contribute to the design of educational research protocols that better reflect real-world learning environments. We will work toward the development of improved standards of practice for the visualization design community, which will contribute to the creation of instructional tools for the modern biology classroom," says Jenkinson. "All of this will lead to better learning outcomes in undergraduate biology students."

Jenkinson, who conducts novel research into the role that visual complexity plays in learning, is also co-principal investigator on a National Science Foundation $500,000 US grant.

World Health Organization names BMC alumnus winner in Health for All Film Festival

Tuesday, May 19, 2020 - 8:00 a.m.

Maeve Doyle

maeve.doyle@utoronto.ca

Nitai Steinberg, PhD, MScBMC Class of 2019. (Submitted by: N. Steinberg)

Nitai Steinberg, a graduate of the Institute of Medical Science’s Biomedical Communications program at the U of T Mississauga, was named winner of the Student Prize in the World Health Organization’s inaugural Health for All Film Festival. Steinberg received the award for his animation Antibiotic Resistance. The film festival showcased the role of individuals and communities as champions for health and well-being. Steinberg’s entry was one of 1,265 entries received from 119 countries. As the Student Prize winner, he will receive a grant of $5,000 US. The head of the World Health Organization (WHO) Dr Tedros Ghebreyesus made the announcement Tuesday at an online virtual awards ceremony hosted in Geneva, Switzerland.

Misconceptions around antimicrobial resistance

“Antimicrobial resistance is the ability of bacteria to break down antibiotics and render them ineffective,” says Steinberg, who graduated in 2019. “This is a major threat to human health. Modern medicine depends on antibiotics. Without them, many diseases could no longer be treated. Invasive surgeries and organ transplants would not be possible,” he says.

Steinberg created the film under the supervision of Jodie Jenkinson, director of the Biomedical Communications program and with financial support from Jenkinson’s SSHRC Insight Grant. He says that his goal was to address two common misconceptions.

“According to a WHO survey, the majority of people have heard of antimicrobial resistance but think that it means the human body becomes tolerant to antibiotics when in fact it is the bacteria that are resistant,” says Steinberg. “They also believe that bacteria exposed to antibiotics become resistant to them gradually. Actually, some bacteria in a population are already resistant.”

He says that after antibiotic exposure, the sensitive bacteria die, but the resistant bacteria keep living and frequent antibiotic use makes them more and more prevalent. Bacteria spread in the environment and higher numbers of resistant bacteria, mean higher antibiotic resistance everywhere.

Dr. Ruediger Krech, WHO’s Director of Health Promotion and jurist, told Steinberg at the May 12 awards ceremony that he took a public health issue, broke down the complexity, spiced it up and made it inspiring. “You tell the AMR [antimicrobial resistance] story so that we as watchers want to see more. You’ve inspired and intrigued us and this can only be done by someone who knows both the science and the filmmaking,” said Krech.

Jenkinson, who conducts novel research in the role that visual complexity plays in learning, says that film and animation are powerful media for conveying understanding.

“Difficult concepts such as the natural selection of antibiotic resistant bacteria are more easily explained through visuals. Visualizations coupled with narration are better understood. Music connected to visuals can emphasize ideas such as randomness and sound cues can emphasize importance,” she says.

Understanding leads to action

With a greater understanding of antimicrobial resistance, Steinberg hopes that society will take action and limit the misuse of antibiotics.

The WHO will distribute Antimicrobial Resistance and the other winning submissions through public screenings at festival events and through its various social and web platforms.

Steinberg earned a PhD in microbiology from the Weizmann Institute of Science in Israel where he researched bacterial biofilms. He says he pursued a degree in Biomedical Communications to learn how to disseminate scientific knowledge.

“It is really important that people understand the scientific theory behind diseases and behind health policies. Without this knowledge, without this understanding, it is really hard to expect anyone to change,” he says.

The search for approved drugs to target SARS-CoV-2

Friday, May 1, 2020 - 9:30 a.m.

Maeve Doyle

maeve.doyle@utoronto.ca

Developing drug therapies and a vaccine is high priority now as COVID-19 impacts lives around the globe.

A team of applied scientists at Cyclica Inc. led by Vijay Shahani (MScBMC 1T5) has identified thousands of small molecule drugs that can potentially be repurposed to target the SARS-CoV-2 virus that causes COVID-19.

Dr. Vijay Shahani, Head of Applied Science at Cyclica Inc. (Photo submitted by V. Shahani.)

Of the almost 10,000 drugs they evaluated through machine learning and informatics, nearly 4,500 are either approved medicines already in use or experimental medicines, with associated safety data, currently being tested in phase II and phase III clinical trials.

“The key here is speed,” says Shahani, who earned a PhD in medicinal chemistry from UTM before returning to earn a Master of Science in Biomedical Communications.

Andrew Haller, an adjunct lecturer in the Department of Pharmacology and Toxicology at the University of Toronto, says a resource of approved drugs could potentially expedite COVID-19 treatments by months or even years.

"Using an already approved therapeutic would reduce the regulatory requirements to get into the clinic. On-market drugs have a lot of data associated with them and people understand the risks and methods of use of the drugs. You could deliver new therapeutics to battle COVID-19 in as little as a few months," says Haller, who is also founder and CEO of Phoenox Pharma, one of Cyclica’s local biotech partners.

Cyclica’s team has stored the collection of drugs they identified, along with protein data, in a searchable database named PolypharmDB. They developed the database using Cyclica’s deep learning engine MatchMaker, which predicts pairings of drugs to proteins.

“We used the literature surrounding infections caused by the previous viruses SARS and MERS  to propose potential host proteins that may serve as drug targets for SARS-CoV-2. We then queried PolypharmDB to select small molecules that are predicted to bind to those key proteins,” says Shahani.

“The results from PolypharmDB are small molecule drug candidates that MatchMaker predicted to be likely binders to key host proteins,” he says. 

MatchMaker predicted that the drug disopyramide, used to treat irregular heartbeats, will interact with a human protein involved in SARS-CoV-2 infection. “This prediction, if validated pre-clinically, could translate into an acute treatment for COVID-19."

Cyclica's AI technology predicted that the antiarrythmic drug disopyramide will interact with the human protein TMPRSS2 involved in SARS-CoV-2 infection. Vijay Shahani says that this prediction, if validated pre-clinically, could translate into an acute treatment for COVID-19. (Visualization submitted by V. Shahani.)

Cyclica is also offering their support to the research and academic communities working within the realm of COVID-19. 

"Let's say that there is another host protein identified by researchers as critically involved with a COVID-19 infection. What we can do is very quickly mine PolypharmDB and pull out ten, fifty, a hundred candidate drug molecules, all with safety data, that are likely to interact with that host protein. Depending on the target, that could be done in less than 24 hours," Shahani says.

Cyclica, a biotechnology company in Toronto, uses artificial intelligence to design new medicines and accelerate drug discovery efforts. Shahani says that they have had the ability to assess small molecule drugs for their off-target interactions for a while now.

"But we've applied it to smaller chemical libraries that our collaborators at U of T and Ryerson were interested in. Now, we have the chance to assess these existing medicines to see how they could make an impact on the current COVID-19 pandemic and that's what prompted us to build it out so quickly,” he says.

Researchers who have a target and a hypothesis and who wish to interact with Cyclica's technologies can complete and submit a form through their COVID-19 Response page: https://cyclicarx.com/covid19.

“To accelerate drug discovery is our mandate. The ultimate goal would be to try and validate some of these small molecule drugs in preliminary assays and then push them forward into the clinics if we can,” says Shahani. “I think we felt that we have an opportunity here to help save people's lives."

BMC graduate answers the call to fight COVID-19

Wednesday, April 16, 2020 - 2:54 p.m.

Maeve Doyle

maeve.doyle@utoronto.ca

Avesta Rastan, a 2019 graduate of the Master of Science in Biomedical Communications, contributed an infographic to the program's COVID-19 Visual Media Resource page .

Rastan, who specialized in biomedical visualization design, created the illustrated infographic for a general audience. She says that while there is widespread awareness of the virus, many people do not know how it affects the human body.

Rastan says that she researched the events that occur after infection to satisfy her own curiosity. "But I thought that if I was wondering this, others must be as well. As a medical illustrator, I felt responsible to act on this communication gap."

The infographic shows the journey of SARS-CoV-2 from the nose, mouth or eyes to the alveoli in the lungs. Carefully designed illustrations depict an alveolus as it transforms from healthy, to moderately, to severely infected. It also explains the body's own immune response after infection, which can lead to respiratory distress, septic shock, multi-organ failure and even death.

"I believe that understanding how COVID-19 can affect the human body empowers people to take action to protect themselves and others from getting infected," she says.

Rastan is a creative innovation associate at INVIVO Communications in Toronto. As part of the creative team there, she develops media for the healthcare and pharmaceutical industries. Rastan also owns and operates Azuravesta Design, a design, animation and biomedical communications studio.

"I hope that this piece makes the SARS-CoV-2 virus less of an invisible enemy and more of a physical entity that people can actively protect themselves against through the proper preventative measures shown in the infographic," she says. "Knowledge is power."

Rastan has made her COVID-19 infographic available for free use under a CC BY-ND license, and anyone can download it from her website for both digital and print media.