Research & Thesis

Visualizing brain size evolution in platyrrhine monkeys: a skull reconstruction, endocast extrapolation, and volume comparison of Cebupithecia sarmientoi :: Lilas Armstrong-Davies

In 2018, at the paleontological site La Venta, Colombia, the first complete monkey skull from the Middle Miocene epoch (11-13 MYA) was recovered. Paleontologists identified the skull as Cebupithecia sarmientoi, an extinct species of platyrrhine monkey whose skull was only previously known by teeth and mandible fragments. C. sarmientoi is most likely related to the Pitheciidae family of platyrrhine monkeys but has a noticeably smaller cranial cavity. This discrepancy indicates that C. sarmientoi had a smaller brain size than its extant relatives. To confirm the relative brain size, a digital 3D model of the fossil was reconstructed and a cast of the cranial cavity, or endocast, was created. The volume of the endocast was compared to 16 closely related living species of platyrrhine monkey using an RMA regression and the relative brain sizes were placed in evolutionary trees. This is the first study to attempt to extrapolate an endocast after a skull reconstruction and the workflow was assessed for future research. These visualizations of C. sarmientoi are the first of their kind and provide new insights on the rate and timing of brain size increase in platyrrhine monkey evolution. The visualizations will contribute to scientific publications on the C. sarmientoi discovery and enhance public understanding and interest in evolution and paleontology.

Thesis Student

Preceptor

Department Advisor

MRI Artifact Detection: Schematic Design in Perceptual Training for Radiological Board Exam Preparation :: Courtney Brendal

MRI physics and clinical comprehension of artifacts, or the spectrum of visual anomalies that can occur in all types of imaging modalities, are cornerstone subjects in the American Board of Radiology CORE Exam. Use of perceptual training is important in developing radiologists’ abilities to detect artifacts on images but is underutilized in radiology education resources. This thesis project outlines the creation and investigation of the novel use of representational schematic images of MRI artifacts for perceptual training. The results of this study inform the direction of a web-based, interactive learning resource that radiology residents and other learners would find useful and engaging to use.

We created an online Qualtrics survey and distributed it to medical students and radiology residents in the Johns Hopkins University School of Medicine (JHUSOM). Study participants were randomized to interact with only the schematic images, only the MRI images, or a combination of the two image types. There was no significant difference in participant pre/post-test performance and engagement survey feedback across all three test conditions, which suggests that studying schematic images could be equally as useful as studying from MRI images. Participants praised the resource for its use of concise and manageable visuals and explanations. Respondents suggested adding more MRI artifact image examples for additional reference and creating a glossary for radiology terminology that could accommodate beginner learners.

With these insights, we used the content from the Qualtrics pre-and-post-tests to design an interactive quiz using Unity. Additionally, we also incorporated our artifact image media into a downloadable PDF reference sheet and Anki deck for students to review for their CORE Exam study needs. These resources will be hosted on teamrads.com, JHUSOM’s open education radiology website.

Thesis Student

Preceptor

Department Advisor

Endoscopic Endonasal Skull Base Surgery for Pituitary Lesions: An AI-Assisted Creative Workflow to Develop an Animated Educational Resource for Patients and Physicians :: Hao Wen Gilbert Chen

Endoscopic endonasal skull base surgery (EESBS) is a complex surgical approach used to access and remove pituitary lesions and tumors through the anatomically complex sinonasal corridor. Many patients find it difficult to understand and conceptualize the nuanced anatomy, surgical technique, and the substantial postoperative side effect and symptom profile associated with this minimally invasive surgical procedure.

Effective perioperative counseling is challenging in the setting of time-constrained preoperative visits and by the abstract surgical technique in an anatomical region that is unfamiliar to most patients. The goal of this project was to create an interactive and accessible resource available for both patients and surgeons alike to help improve perioperative counseling and patient education. This research involved using an Artificial Intelligence assisted workflow to create a series of 2D animations that aim to explain the treatment process using engaging, educational, and easy-to-understand content. Animations were designed to provide patients with an immersive experience to help explain relevant anatomy as well as preoperative, surgical, and postoperative treatment phases. The resulting narrated, 2D “cut paper” style animations are a resource to assist physicians with patient communication and education needs. Given its modular design, this resource can be edited or updated to reflect changes in surgical techniques and can be adapted into interactive e-learning materials.

Recognizing that generative Artificial Intelligence (AI) reached public awareness in early 2023 as a powerful tool for generating new content including text, images, and audio from existing online data, this project aimed to incorporate this novel technology to enhance patient education over traditional approaches. With the implementation of an AI-assisted creative workflow, we utilized 1) an AI art generator for style inspiration, 2) an AI chatbot for assistance in script drafting, and 3) an AI voice synthesizer for audio narration. The research also addresses some of the potential risks and concerns associated with applying AI-assisted tools to patient education content creation. By implementing these new technologies in the creative workflow, this research provides valuable insights into when and how to appropriately apply AI technology while creating patient education content. The use of AI-assisted technologies in creating patient educational resources represents an exciting new development in the field of medical communication.

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Preceptor

Department Advisor

VISUALIZING MIPSA: Exploring Web-based User Experience Design in Teaching and Promoting Molecular Technology :: Anna Mai

This thesis explores the potential of web-based user experience in teaching and promoting a novel molecular technology, Molecular Indexing of Proteins by Self Assembly (MIPSA), which is a scalable and low-cost solution for comprehensive antibody profiling. Despite its potential applications, there are no existing visuals that explain the complex science of MIPSA. To address this gap, a website was developed with animations, graphics, and concise content to educate and engage the target audience of researchers and investors in biotechnology.

The website is the first of its kind to explain and visualize the concept of MIPSA using multimedia and the multimedia learning theory. The website aims to deliver the didactic content in an engaging and comprehensible way by employing website design principles, multimedia and the multimedia learning theory. A focus group was held with researchers and students at Johns Hopkins to assess the effectiveness of the website, and results showed high ratings for overall effectiveness, navigation, content organization, and visual appeal. The project’s implications for biocommunication and the promotion of a new molecular technology are discussed, along with suggestions for future studies…

Thesis Student

Preceptor

Department Advisor

Understanding the Cellular Mechanisms of Parkinson’s Disease: An Interactive Learning Module :: Gyyoung Oh

As the second most common neurodegenerative disorder, Parkinson’s disease (PD) is still being thoroughly researched. The complex cellular mechanisms of PD are responsible for its many symptoms, such as tremors, difficulties with balance, and constipation. An immense amount of information about PD has been discovered, but much of it remains among the scientific research community. There is a need for resources to educate PD patients, caretakers, and students about specific reasons behind diagnoses and symptoms. In addition, existing resources also do not allow audiences to customize their learning process.

This project aims to provide an effective interactive learning module that allows users to choose the order and rate at which they absorb  Information. In particular, it aims to teach users about the cellular mechanism of parthanatos that causes many of the symptoms of PD. Using 3D models and animations, it was developed as a WebGL (Web Graphics Library) web application created with Unity. Cinema4D was used to convert
molecular structure data into 3D models.

The goal of the interactive learning modules is to provide the first step in filling the gap in existing resources and educating all users about parthanatos, whether it is to supplement an existing knowledge background or start from the beginning. In future additions to the modules, other cellular pathways can be added to expand the educational content of the project.

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Preceptors

Department Advisor

Illustrating and Evaluating a New Visual Procedural Guide for Central Line Placement :: Elizabeth G. Siedell

Central venous catheterization, or central line, is a small catheter placed in a vein for long-term drug therapy or dialysis. It is a common procedure learned and performed across many medical fields, with over 5 million central lines inserted every year in the United States alone. However, improper insertion can be lethal, and complications affect patient quality of life, hospital days, and costs. Immediate complications, including vascular, cardiac, and pulmonary, are directly related to improper procedure technique. Proper central line procedural guidance and training optimizes patient safety and decreases complications.

Traditionally, most clinical procedural guides are text-heavy manuals with few diagrams, which can be difficult to learn from or referenced during a procedure. In this project, we aimed to address this issue by creating a visual guide for venous catheterization so that medical trainees and practitioners can more safely and efficiently perform the procedure. We also created an IRB-approved study to compare text-only instruction against the novel visual guide through a simulated central line procedure in the Johns Hopkins Simulation Center. Using the two instructional methods, our study assessed time spent on procedure, accuracy of procedure, eye-tracking data, and postsurvey feedback.

We analyzed trends in the survey data to find differences in survey A (given to the users who used the text-only guide) and survey B (given to users who used the illustrated guide). The preliminary trends from the survey show reduced cognitive load and task load in participants who used the illustrated guide. Survey results also showed a trend in strong user preference for the illustrated guide compared to the text-only guide. Common feedback was in favor of the visual guide or expressing the need for visuals if they received the text-only guide. Our study suggests the importance of illustrated procedural guides in both user preference and in reducing user cognitive load. Moving forward, the study will continue to run and our findings could inform a better standard for creating healthcare procedural guides. Additionally, we plan to publish our research in a peer-reviewed journal to further advocate for the necessity of visual procedural guides.

Thesis Student

Preceptor

Department Advisor

Improving Simulation Task Training: A Novel Interactive Resource and 3D Printing Provide Customizable Solutions for Increasing Fidelity and Lowering Costs :: Emily Simpson

Abscess incision and drainage (I & D) is a common procedure used for treating skin abscesses. This procedure can relieve pain and accelerate healing of an abscess; however, if performed inadequately, infection can spread. Medical simulation devices, called task trainers, permit learners to manually practice the skills and steps of a procedure. Abscess incision and drainage task trainers function as a bridge between book learning and practicing on a real patient.

Abscess task trainers are expensive; commercial trainers range from $30 – $150 per single-use device. Furthermore, they are available only in limited skin tone options. Limited exposure to skin tone and body mass diversity restricts adequate healthcare training. Simulation centers also may encounter supply chain issues when ordering abscess incision and drainage task trainers. To prevent this, a simulation center must order the trainers months in advance, however, some commercial trainers have a short shelf life. Instructions for several do-it-yourself alternatives exist, but the resulting task trainers are low fidelity and can be complicated to create.

To address these limitations, we developed a new method of abscess task trainer creation, including the design of a 3D printed base. The abscess task trainers created for this project are lower cost compared to commercial alternatives, and allow customizable fidelity, such as variety of skin tones, body mass, and the ability to add inflammation. To help simulation center facilitators navigate this  customizability, we designed a novel interactive resource to allow users to select different options for the components of the abscess task trainer: the base, skin, color, drainage, and details. Based on the choices selected, a user receives customized instructions for abscess task trainer creation. Ultimately, the goal of this project was improved abscess incision and drainage training through cost reduction, increased fidelity, and greater diversity options, which results in better patient healthcare.

Thesis Student

Preceptor

Department Advisor

Personalized Visualization of Congenital Heart Disease for Communication with Families :: Miranda Stano

Congenital heart diseases (CHD) appear in about 1 in 110 live births in the United States. Depending on the disease presentation, CHD can be a life-threatening condition and require prompt surgical intervention after birth. Due to the physiologic complexity of CHDs, it can be difficult for families to obtain an adequate understanding of their child’s condition. Furthermore, many CHD cases present as rare, patient-specific anomalies. Illustrations and 3D models are available for patient families to review when discussing care for CHD. However, approximately 50% of CHD phenotypes fall outside of typical disease spectra. In these cases, available visualizations have limited effectiveness in communicating the intricacies of variant pediatric heart defects.

To address these issues with CHD patient education, an application was designed for the customizing and sharing 3D heart models. Patient and physician workflows were defined. 3D models exhibiting two commonly occurring CHD types were extracted from CT and MRI datasets and refined for web-viewing to demonstrate the application’s model bank. A prototype animation demonstrating interactive components was produced to outline application functionality. Physicians specializing in CHD care were consulted at each stage of development. A patient family interview was approved by the Institutional Review Board and conducted to better understand the CHD treatment experience and receive feedback on design components.

This project, which has resulted in the design and visual assets for a novel CHD model customization tool, may guide the development of a multifaceted, fully operational application. This project has identified a means of improving the surgical consent process for CHD patients.

Thesis Student

Preceptor

Department Advisor

2023 Thesis Presentations

The Thesis Presentations of the MBI Class of 2023 will be held on Tuesday, May 23rd, 2023, 2:00-4:00 PM (EDT), both in-person in the Chevy Chase Auditorium and with a Live broadcast to the Department’s YouTube Page. The students will present to their faculty, preceptors and those able to join us live.

Alumni, students, and the public are invited to participate through YouTube Live Chat. A Q&A with Audience questions and Typed questions from the YouTube Chat will be held at the end of each presentation.

Links to the YouTube Live event will be shared to the Department’s social media accounts: Facebook, LinkedIn, Instagram, and Twitter.

Thank you for taking a look at the research into the art of biomedical visualization from the MBI Class of 2023!

An Animated Portrayal of Normal Placentation and the Pathophysiology of Placenta Accreta Spectrum :: Jason Brady

Placenta accreta spectrum (PAS) is a potentially life-threatening condition in which the placenta is abnormally adherent to the uterus. PAS is categorized according to the depth of myometrial invasion; in placenta accreta, the placenta attaches to the myometrium; placenta increta invades the myometrium; and placenta percreta penetrates through the myometrium and/or uterine serosa, and may invade surrounding tissues and adjacent organs including the urinary bladder, vagina, and pelvic vasculature (Kilcoyne, 2017). An unplanned delivery in a PAS patient may be catastrophic due to massive peripartum hemorrhage, increased risk of ureteral and bladder injury, and pulmonary embolism (Silver, 2018).

The incidence of PAS has quadrupled since the 1980s, from one in 1,250 births to one in 272 births (Obstetric Care Consensus, 2018). The primary cause of PAS is prior cesarean delivery (Silver, 2018). Cesarean delivery accounted for 31.8% of all deliveries in the US in 2020 (National Vital Statistics Report, 2020). Maternal mortality rates for PAS are as high as 7% (Rosner, 2010); however, women treated in specialized tertiary care centers are less likely to require large volume blood transfusions, undergo subsequent surgical procedures, or experience concomitant morbidity (Wright, 2013). Despite these benefits, only 23% of obstetricians refer suspected PAS patients to these specialized centers (Einerson, 2019).

Few educational resources exist describing normal placental development and the pathophysiology and clinical management of PAS. Accessible visual media resources are needed for patients and healthcare providers to increase awareness of this condition, to facilitate communication between patients and referring physicians, and to educate patients about treatment options at tertiary referral centers.

A six-minute animation was created. This novel educational resource depicts normal placental development, detailing the invasive nature of placental trophoblasts and their ability to remodel and enlarge maternal blood vessels. Subsequently, the pathophysiology of PAS is demonstrated at the cellular level with 3D animation. Degrees of PAS (accreta, increta, percreta) are defined and illustrated. The animation describes the importance of preplanning a delivery and surgical treatment at a specialized tertiary care center with a multidisciplinary team.

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Preceptor

Department Advisor

Exploring the Sinonasal Cavity in Three Dimensions: Teaching Otolaryngology Surgical Trainees Clinical Anatomy Using a Web-based Learning Resource :: Shirley Li

Endoscopic sinus surgery is the most common procedure to restore normal sinus function in chronic sinus disease and is performed in a small complex anatomical space intimate to critical structures (i.e. eyes, anterior cranial fossa, and major head and neck vessels). Otolaryngology surgical trainees must therefore have a thorough three-dimensional (3D) understanding of the sinonasal space to avoid disorientation when surgically navigating through a limited endoscopic view.

However, learning of this anatomical region is hampered by the complexity of anatomy as well as limitations in current teaching resources. Commonly used two-dimensional (2D) visualizations include static illustrations and radiological CT imaging that poorly convey the 3D nature of the space. The author could not find any existing educational resources employing 3D visualization of the sinonasal space.

Web-based multimedia resources, such as online sinus surgery videos are widely used as a learning tool with novel clinical training modules developed to facilitate correlation of anatomical knowledge in radiological visualization and endoscopic surgical view. However, these resources lack correlation among the different types of media and the spatial relationships of clinically relevant structures in 3D space is not fully correlated to static 2D visualizations.

In this project, we propose creating a web-based interactive resource offering a comprehensive and multidimensional visualization of the sinonasal cavity. This resource will consist of two learning modes: i) In Explore Mode, fully interactable 3D schematic and CT-segmented models are presented alongside 2D axial and coronal CT image series, allowing users to navigate the sinonasal cavity in 3D space and bridge the gap between 3D and 2D visualizations. ii) In Clinical Mode, surgical video clips are featured in addition to a schematic 3D model and CT image series, improving spatial orientation during surgery by correlating 3D and 2D visualizations of the sinonasal cavity from a clinical perspective.

The authors of this research postulate such a resource can improve clinical training outcomes among otolaryngology surgical trainees.

Thesis Student

Preceptor

Department Advisor

Animating a Novel Mechanism of Cell Migration: Signal Transduction Excitable Networks (STEN) :: Jiyu Kelly Lim

Life is dynamic. Cells are constantly changing shape. Many do so by displaying a variety of protrusions that not only vary their appearance but also play a key role in important cellular activities such as cell migration, division, and phagocytosis. These protrusions manifest in unique shapes and sizes, ranging from finger-like filopodia to sheet-like lamellipodia.

It is well known that these protrusions drive outward from the cell body by a combination of actin polymerization and actomyosin-based contractions, referred to as “cytoskeletal activity”.

However, what determines the shape, and hence the identity of the protrusions, has remained a mystery until recently.

In recent years, a research team in the Johns Hopkins University Department of Cell Biology discovered a novel mechanism: Signal Transduction Excitable Network (STEN). It was found that STEN, a signaling network consisting of receptors, small GTPase proteins, and phosphoinositide lipids, determines the locations and lateral dimensions of cellular protrusions. Without STEN, cytoskeletal activity only produces transient, small extensions, or “puncta” which are ineffective in moving or reshaping cells. Manipulating the signal network can lead to alterations of the cytoskeletal system and morphing of the shape of the cell. Increasing or decreasing signal transduction activity can elevate or decrease the speed and range of wave propagation respectively, converting pseudopodia into wider lamellipodia, or narrower filopodia.

This novel finding provides a direction for future biomedical research as it shows STEN plays a critical role in cell migration and morphology, and dysregulation of this system can lead to the development of a variety of diseases including cancer, and developmental and metabolic abnormalities.

However, the mechanism of STEN is difficult to succinctly explain due to its three-dimensional, dynamic nature. Current teaching materials are limited to simple line diagrams and crude confocal microscopy videos and photographs, none of which are adequate to allow for in-depth understanding of this intricate process.

To solve this challenge, I propose a narrative 3D animation that can help learners visualize and comprehend this novel mechanism. To maximize didactic efficacy, 2D images will be created to supplement the animation, and designed to be used independent of the animation if desired.

Thesis Student

Preceptor

Department Advisor

Rethinking the Evolution of Temporal Fenestrae in Turtles: An Interactive Application for Comparative Anatomy and Phylogenetics :: Annelis Gabriela Rivera-Del Río

The question of turtle origins is among the oldest and most debated problems in vertebrate systematics. A key factor in this debate is the pattern of temporal fenestration in the skull, which has long been central to amniote evolutionary hypotheses. Recently, there has been robust evidence supporting turtles as having evolved within the diapsid radiation, which includes all other living reptiles. This requires that the anapsid skull in turtles is secondarily derived. ‘Transitional’ fossils that support this theory were elusive until the Middle Permian reptile Eunotosaurus africanus was re-examined using computed tomography (CT) in 2015. Eunotosaurus exhibits features that help reconcile the gap between turtles and other reptiles, but how it does so is still misunderstood. This misconception is attributed to the complexity of the evolutionary concepts involved and a need for more intuitive visuals describing the complex architecture of the Eunotosaurus skull.

This thesis communicates the importance of Eunotosaurus to the study of turtle origins through a novel digital reconstruction and a 3D interactive web application. The first of its kind, this reconstruction utilizes best practices for restoring a fossil’s antemortem shape. It is then implemented in an application focused on contextualizing this taxon in the ‘tree of life.’ This application provides a valuable learning resource for students and investigators as it contributes to virtual paleontology, evolutionary science pedagogy, and functional morphology.

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Preceptor

Department Advisor

Understanding Percutaneous Cholangioscopy: Designing and Evaluating Novel Multimedia Tools for Patients and Physicians :: Jennifer A. Wang

Percutaneous cholangioscopy is a minimally invasive interventional radiology (IR) procedure that can be an alternative treatment for patients with complex gallstones who are not candidates for traditional surgical intervention. Interventional radiologists anecdotally find that few patients and referring physicians are familiar with this procedure, precluding some patients from this treatment option.

With the paucity of accessible educational materials on this topic, we created a patient education pamphlet and video animation to explain percutaneous cholangioscopy to both patients and referring physicians. We ran a pilot study to compare a text-only explanation of the procedure against a text and images explanation. Learning was assessed through pre/post-testing and engagement was measured using Likert-scale surveys. We recruited family and friends (non-physician group) to represent our intended patient population and received 19 total responses. We also recruited 20 IR residents (physician group) as our representative referring physician population and received 12 responses.

To analyze our data, we performed f-tests and t-tests to check for differences in pre/post test scores and engagement survey scores. The pilot survey showed that both text-only explanations and text with images explanations improved test scores in the non-physician group, and there was no significant difference in their final scores. The physician group scored high regardless of intervention. In both the physician and non-physician groups, a majority of participants preferred the explanation of percutaneous cholangioscopy that included visuals aids. The most common feedback we received pertained to the value of learning from our visuals or requesting visuals be added if they did not receive any.

Our pilot test suggests the importance of including visuals in the explanation of new procedures such as percutaneous cholangioscopy. Next, we will investigate this further through an IRB-approved study planned to test larger samples of patients of the procedure and possible referring physicians. Our study could inform best practices for developing patient education materials in interventional radiology. Additionally, the multimedia we create will be made available online to help raise awareness of percutaneous cholangioscopy and help improve understanding of the procedure in both patients and physicians.

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Preceptor

Department Advisor

3D Visualization of Genetic Mutations in Pancreatic Intraepithelial Neoplasia :: Ting I Wang

Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest forms of cancer in the United States and is often diagnosed in advanced stages with poor prognosis. A new workflow called CODA that uses machine learning to reconstruct pancreas pathology, from precursor lesions to PDAC, has been established to study PDAC in humans in three-dimensions. Although the genetic mutations that drive PDAC are known, there exists little information regarding 3D spatial distribution of these mutations. Once defined in 3D, these mutations would need to be visualized in a clear and organized way.

The application of genetic sequencing to 3D-constructed precursor lesions in the human pancreas afforded a novel opportunity to develop tools to visualize complex genetic changes in three dimensions. Each lesion was subdivided for deeper resolution of lesion heterogeneity. The visualization developed took a 3D scatter plot approach. Genetic mutations were represented by mapped objected spaced equally throughout the precursor lesions. Each genetic mutation was assigned a color. Object size was used to represent prevalence of each genetic mutation in 4 distinct 3D precursor lesions in each gene sequencing region. Four visualization outputs were created, including still images, turntable videos, an interactive platform, and a promotional image. The interactive platform includes a 3D interactive model that a user can rotate and scale, togglable genetic mutation representations, and a switch between “prevalence” and “no prevalence” modes. Modeling was done using 4D® and ZBrush®. Unity was used for lighting, materials, and creation of the 3D interactive platform.

This thesis project experimented with ways in which data commonly visualized in a 2D manner could be visualized in a 3D space. The visualization represents a first step in understanding tumorigenesis in three dimensions and its contributing factors as related to tumor microenvironments in human.

Thesis Student

Preceptor

Department Advisor

2022 Thesis Presentations

The Thesis Presentations of the Class of 2022 were held on Friday, April 22, 2021, 3:00-5:00 PM (EDT), both in-person in the Chevy Chase Auditorium and with a Live broadcast to the Department’s YouTube Page. The students presented to their faculty, preceptors and those able to join us live.

Alumni, students, and the public were invited to participate through YouTube Live Chat. Guests typed questions into the Chat window of the YouTube Live Broadcast, and a special Q&A was held at the end of all presentations to answer posted questions.

Links to the YouTube Live event will be shared to the Department’s social media accounts: Facebook, LinkedIn, Instagram, and Twitter.

Thank you for taking a look at the research into the art of biomedical visualization from the MBI Class of 2022!

Visualizing Glaucoma: Accurately Characterizing and Depicting Visual Loss via Virtual Reality :: EMILY CHENG

Glaucoma is the leading cause of global irreversible blindness, affecting more than 70 million people worldwide between the ages of 40 – 80. Tests to diagnose and understand the impact of disease are well established, however the actual patient experience of glaucoma-affected vision has been confined to epidemiologic descriptions of function and imprecise visualization of what the patient sees. Many patients diagnosed with early-stage glaucoma are prescribed life-long therapies, yet they experience minimal visual distortions. The eventual, long-term impact of glaucoma on their activities of daily living and quality of life eludes them, reducing chances for treatment compliance. Furthermore, the limited visual depiction of the disease may prevent providers and family members from providing empathetic care and support.

Existing visualizations portraying the first-person experience of glaucoma suffer from methodological shortcomings. Most current representations are static, 2D images that do not correlate with patient-specific visual field (VF) impairment; these images do not capture or address the variability of vision loss and its effects on the patient’s ability to decipher visual information. Moreover, most have not been derived from a systematic, patient-centered approach. Thus, there is a need for better methods to visualize disease from the patient perspective, and new ways to communicate that experience.

This research protocol accomplished these goals through a two-phase process: Phase 1 involved characterizing the visual experiences of several patients with unilateral, moderate to severe glaucoma via a series of custom eye assessments and interviews. Patients with unilateral disease then corroborated the visual differences between their glaucoma-affected and normal eyes. Phase 2 depicted the resulting data through virtual reality (VR) eye-tracking technology in order to demonstrate dynamic aspects of the disease. The final VR application includes: (i) a real-time video feed which represents to patients various glaucoma patient visual field loss patterns derived from our pool of characterized patient data, (ii) an immersive environment for visual search tasks with the option to toggle off representations of the disease state, and (iii) a patient education module with animations outlining the physiology of glaucoma, including links between disease pathology and findings in common tests used to identify and assess progression of disease.

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Preceptor

Department Advisor

Mapping the Tumor Vasculome: A novel interactive 3D visualization of computationally-derived tumor hemodynamics :: LAURA EKL

Breast cancer is currently the second major cause of death for women in the US (American Cancer Society 2019). New research has highlighted the significance of the tumor ‘vasculome’ in the progression, metastatic potential, and prognosis of breast tumors (Junttila and de Sauvage 2013). The vasculome encompasses an interdependent web of morphological (i.e. diameter, length, microvascular density), functional (i.e., oxygenation, shear stress, flow rate) and other complementary data (e.g., genomic profiles) that characterize a vascular tree. The vasculome shapes the tissue microenvironment, and specifically in cancer, results in the creation of a unique tumor microenvironment (TME). This TME exerts selection pressure on cancer cell populations and profoundly impacts their survival, proliferation, metastatic potential, and response to therapy.

Advances in multiscale imaging and computer modeling have enabled a recent study that characterizes the vasculome in an ensemble of preclinical breast tumors (Stamatelos and Bhargava, et al. 2019). The main objective of this project was to create an interactive web-based platform for 3D visualization of the tumor vasculome, i.e., the morphological and functional parameters generated during the prior study.

PlayCanvas was used to visualize the vasculome data for normal tissue as well as for breast tumor xenografts via an interactive, web-based platform. The 3D visualizations were supplemented by didactic text and illustrations that were created to provide the user with an understanding of the fundamental morphological and hemodynamics concepts addressed. This interactive application enables new insights into the relationships between different vasculome parameters, and how they can shape the TME. This project is a first step towards a novel ‘visual atlas’ that will be used to map the vasculomes of different tumor models and tissue types.

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Preceptor

Department Advisor

Walking the Line: Examining an Illustration of A.L. 288-1 for Anatomical Accuracy and its Implications for Studying Australopithecine Locomotion :: KURT ESENWEIN

After over 45 years, since Dr. Donald Johanson’s famed discovery of “Lucy” (A.L. 288-1), a debate in the scientific community still endures over the nature of her bipedal gait. Did Australopithecus afarensis walk upright more as a great ape, with significant hip and knee flexion (the Bent-Hip Bent-Knee [BHBK] walking hypothesis), or was her gait closer to a modern human’s?

At the heart of this debate is a single pen-and-ink line drawing, first published in an article by Drs. J. Stern and R. Susman on australopithecine locomotion (Stern and Susman, 1983). Despite the decades of arguments that have followed, this lone twodimensional fossil reconstruction has never been tested. This project compares the with a contemporary 3D model of A.L. 288-1, and deciding if the Stern and Susman (1983) figure, which has been crucial to BHBK proponents, is indeed anatomically accurate.

To test the drawing’s accuracy, casts of A.L. 288-1’s innominate and sacrum were scanned using high-resolution computed tomography (UHR CT). This produced a 3D mesh which was compared to the original illustration. In the end, it was not possible to match the drawing to the model. Though it demonstrates nothing about australopithecine gait in itself, it undermines the BHBK hypothesis which is derived from the drawing, since it contains flawed anatomy. The flaws are likely due to the source material provided to the artist, demonstrating the importance of the collaboration between scientists and illustrators, and their ability to understand one another.

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Preceptor

Department Advisor

The Most Difficult Teachable Moment: Autopsy Consenting :: SORA JI

Medical and clinical discoveries through autopsies have informed hundreds of studies elucidating pathophysiological developments of diseases, which are crucial for improving medical treatment. At Johns Hopkins Hospital (JHH), all families of patients who have been inpatients within the past year have the right to an autopsy. This service requires consent of the deceased patient’s next-of-kin. It is important for clinicians to provide empathy while effectively communicating the medical significance and benefits an autopsy can provide for the patients’ families, when asking for consent. However, clinicians frequently find themselves unprepared for this important conversation for two main reasons: 1) lack of training opportunities and 2) lack of educational materials organizing the process of asking for autopsy.

To meet the need for educational material and training opportunities, we envisioned a systematic learning experience with three main components: 1) a training module webpage, 2) a quick reference mobile app, and 3) a printed pocket guide. Contents for each component were selected in consultation with a JHH pathologist and clinicians experienced in obtaining autopsy consent. The webpage includes well organized information and interactive simulations to help clinicians learn and retain the material. This knowledge is reinforced by utilizing a mobile app, which enables easy access to necessary information right before or while the clinician is requesting an autopsy consent from the patient’s family. Finally, the hand-held pocket guide provides visual support for not only the clinicians, but also for the families when determining the correct next-of-kin, discussing how the autopsy will affect the funeral, and informing the next steps families should prepare for once their consent is given.

Through the novel use of Standardized Patients and interactive-media-building software alongside 2D illustrations, we have developed prototype resources designed for effective information delivery. This opportunity has shed light on the potential use of such hybrid media in creating highly effective medical visualization resources, in this case, to improve the communication in requesting autopsy consent at the Johns Hopkins Hospital.

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Preceptor

Department Advisor

Reimagining Delivery of Midlife Womens Healthcare :: EMILY SLAPIN LUFKIN

Between competing time demands, a healthcare system that is difficult to navigate, and limited information directed to their demographic, it is often difficult for perimenopausal women to access quality healthcare. The result is insufficient preventative care and unsatisfactory health outcomes for women in their post-reproductive years.

The Johns Hopkins Women’s Wellness and Healthy Aging Program is a new model for delivering midlife women’s healthcare that offers streamlined scheduling, interdisciplinary coordination and communication, a patient navigator to help establish patient’s relationships with providers in multiple specialties, and a personalized patient roadmap for healthy aging.

The rise in mobile communications over the last decade has revolutionized the way we access information. Social media has become an important platform for reaching patients, particularly underserved populations (Welch et al. 2016). Attention spans are shorter, making brief explainer videos an effective way to educate a patient population (Krämer and Böhrs 2016).

The research question this project addresses is whether brief explainer videos and illustrations on social media are effective at educating patients about this new model of integrated care. Patient stakeholder feedback was solicited at the beginning of the project to determine the most burdensome aspects of accessing quality healthcare and the health topics of most concern to middle-aged women. Subsequent rounds of stakeholder feedback were integral to the iterative process of creating the visuals and determining their efficacy. Two animations and a suite of 20 illustrations were created using the Adobe Creative Suite addressing health concerns of the perimenopausal population such as healthy aging, reducing risk of cardiovascular disease and cancer, maintaining mental health and cognitive function, and treatment of menopausal symptoms.

Patient stakeholder feedback determined that short explainer videos and illustrations on social media can be an effective tool to educate patients. Educated and engaged patients often have better health outcomes (Paterick et al. 2017). This new model of healthcare delivery and mode of educating patients have the potential to improve healthcare outcomes and decrease healthcare costs for women during their post-reproductive years.

Thesis Student

Preceptor

Department Advisor

Teaching MRI Physics: Creating media with a focus on the Radiology CORE Exam :: EMILY WU

MRI physics is an important component of radiology training and the American Board of Radiology CORE exam. There is a need for improved learning resources on the topic, but current literature does not provide much information about what types of study materials residents value or creating effective media for teaching MRI physics. This thesis project explores the MRI physics resource needs of radiology residents, creates new media based on the results, and establishes the basis for a future study to test its efficacy.

An online needs assessment survey was created and distributed to current members and recent graduates of the Johns Hopkins diagnostic radiology residency program. Respondents reported that current MRI physics resources were confusing and lacked diagrams and animations. The results indicated that residents desire resources with appealing visuals and simplified details. Questions banks and practice questions were consistently rated as the most helpful resources, but webpages with animations, videos, and webpages with diagrams were also ranked highly.

We created a 10-minute animation introducing the fundamentals of MRI physics, incorporating feedback from the needs assessment. This project aims to fulfill the need for visually appealing MRI physics resources to help residents learn these concepts, and to inform educators and content creators about how to improve the quality of educational materials on the subject. After this project, we have also planned for a follow-up study to evaluate the thesis animation in comparison to other media modalities, with the goal of evaluating how radiology residents best prefer to study for the CORE exam.

Thesis Student

Preceptor

Department Advisor

Educating Patients: Communicating the Gut-Brain Connection in Parkinson’s Disease using Multimedia :: SUSIE YUN

Parkinson’s disease (PD) is a type of synucleinopathy that is characterized by abnormal accumulation of α-synuclein (α-syn) aggregates in neurons (Challis et al. 2020). The misfolded α-syn triggers self-aggregation into neurotoxic amyloid fibrils that can be transmitted from cell to cell, ultimately causing neurodegeneration (Kim et al. 2019). Mounting evidence suggests that for a majority of PD patients, this process can originate in the gut and ascend to the brain via the vagus nerve (Kim et al. 2019). Once in the brain, α-syn pathology propagates to reach the midbrain leading to motor dysfunction.

Since PD is mostly known as a motor disorder, its non-motor symptoms often go undetected. By the time patients begin exhibiting motor symptoms, the disease is usually advanced to the extent that only symptoms can be treated (Dawson et al. 2019). Recent studies suggest that non-motor symptoms, particularly those associated with gastrointestinal (GI) dysfunction may appear as many as 20 years prior to neurological symptoms (Challis et al. 2020). It is important for the public, especially those with chronic GI complications to understand how prolonged GI symptoms may indicate early-stage PD.

However, two factors currently hinder education in this area: (i) scientific research papers are difficult to understand particularly for readers without a scientific background; and (ii) current visual resources for this topic are limited to schematic, often confusing diagrams and inaccurate anatomical and molecular images. In particular, spatial relationships between the gut and the brain are difficult to depict in 2D. And, no effective didactic 3D visualizations exist to address this important public health topic.

I propose an interactive platform of (i) a foundational 2D teaching module on the scientific background and pathogenesis of PD, and (ii) a narrative 3D animation highlighting recent studies of the gut-brain connection in PD. Learners will navigate at their own pace through the introductory learning module prior to viewing the more complex material.

Thesis Student

Preceptors

Department Advisor

2021 Thesis Presentations

The Thesis Presentations of the Class of 2021 was held on April 16, 2021, 3:00-5:00 PM (EDT). This year’s presentation were held remotely with a Live broadcast to the Department’s YouTube Page. The students presented to their faculty and preceptors.

Alumni, students, and the public were invited to participate through YouTube Live. Guests typed questions into the Chat window of the Live Broadcast, and a special Q&A was held at the end of all presentations to answer posted questions.

Links to the YouTube Live event will be shared to the Department’s social media accounts: Facebook, LinkedIn, Instagram, and Twitter.

Creating a Game-Based Learning Tool for Optimizing Intra-Hospital Disaster Response :: NOELLE E. BURGESS

Preparing for disasters such as Mass Casualty Incidents (MCIs), whether of natural or human origin, are of increasing concern. When these incidents occur, hospitals are overrun with an influx of new patients and day-to-day operations are interrupted. Concurrently, increased demand for intensive care resources can outpace the ability of hospital staff to organize appropriately. In such events, efficient management of space (emergency rooms, operating rooms), medical staff, and supplies (blood, hospital beds) is imperative for reducing injury, illness and saving lives.

The Johns Hopkins Bloomberg School of Public Health recently identified key disaster categories for which United States hospitals need to be prepared: Large-scale natural disasters, complex MCIs, and catastrophic health events. Each category poses its own set of challenges for effective management of operations and resources.

During a complex MCI, demand for space, staff, and supplies quickly expand beyond the bounds of Emergency Departments (ED). Although many training tools exist for both the field and ED, surprisingly few exist for hospital-wide disaster response. Programs that do exist come in the form of infrequent, costly, and time-intensive large-scale simulations. A game-based instructional modality was developed to practice the medical knowledge, teamwork, and complex decision making required by multidisciplinary teams. As part of this research, a physical board game was developed using an iterative design approach. Additionally, a wireframe prototype of a complimentary digital version was developed using the Waterfall design approach. Both these options were chosen to reduce training costs, and increase training frequency and efficacy compared to large-scale MCI simulations.

The purpose of this project is to create an accessible and cost-effective game-based disaster readiness training tool specifically for intra-hospital personnel. The desired outcome is to increase efficiency and effectiveness of intra-hospital disaster response for MCI. For this project, a mass-shooting scenario has been selected as the focus of gameplay.

Thesis Student

Preceptors

Department Advisor

Prostate Carcinogenesis: Depicting a Proposed Pathway for Prostate Cancer Precursor Lesion Development Using 3D Animation :: WILLIAM GUZMAN JR.

Prostate cancer is one of the most common malignant neoplasms among men in Western countries (De Marzo et al. 2017). In 2020, there will be an estimated 191,930 American men diagnosed with prostate cancer, an almost 10% increase from 2019 (Siegel et al. 2020). Visual resources for understanding of the pathogenesis of prostate cancer development, and specifically the development of prostate cancer precursor lesions, are limited. A visual void exists between prostate cancer Pathologists presenting histological findings and those with differing prostate cancer specialties. Furthermore, prostate cancer is typically studied using two-dimensional microscopy slides, and it is often difficult to explain new three-dimensional spatial hypotheses and findings to those outside of the pathology field.

Recent pathological evidence suggests a new role for prostate infections and inflammation in prostate cancer development. This novel hypothesis has the potential to challenge the dogma that high grade prostatic intraepithelial neoplasia (HGPIN) serves as the direct precursor to prostate cancer development. Rather, new molecular pathologic evidence indicates that an inflammation-associated lesion termed proliferative inflammatory atrophy (PIA) may directly transition to prostate cancer. 3D visualization of prostate cancer is novel and important in itself due to the multi-focal and atypical pattern of growth, and it is consequently challenging to communicate this new prostate cancer precursor lesion development model.

To address the lack of comprehensive histological research representation, a 3D mechanism of disease animation was constructed which portrays a new proposition for precursor lesion development using novel radical prostatectomy specimen data. The animation outlines and describes the harmful effects inflicted upon luminal epithelium caused by bacterial toxins, such as colibactin, as well as oxidants produced by immune cells induced by chronic inflammation. By improving visual understanding of histological data, this 3D animation provides a platform to further clarify the current knowledge of prostate cancer in the context of bacterial infections and chronic inflammation.

Thesis Student

Preceptors

Department Advisor

Technical Advisor

Visualizing Cochlear Specializations that Enhance Protection of Hearing Function in Bats :: JAMIE LYNN PETERSON

The cochlea is a fluid-filled coil of the inner ear that transforms sound waves into electrical signals for processing in the brain. The mammalian auditory system is most commonly studied using the mouse, Mus musculus, due to anatomical similarities of the cochlea between auditory generalists, such as mice and humans. Auditory specialists, such as bats, exhibit unique resistance to age-related hearing loss, or presbycusis. This adaptation enables bats to navigate while flying with echolocation throughout their lifetime. Studying comparative cochlea anatomy can aid in understanding specializations of the mammalian auditory system and hearing loss among species. There is a significant gap in available educational resources for comparative cochlea anatomy focusing on bats and mice.

The purpose of this project was to develop an interactive educational resource for comparative cochlea anatomy of the big brown bat, Eptesicus fuscus and Mus musculus with a 3D overview animation depicting labeled cochlea models. Segmentations of histological and micro-CT data were modified and sculpted to build idealized anatomical models suitable for teaching purposes. A separate section of the interactive allows the user to explore comparative cochlear anatomy of bats and mice as related to hearing loss. The user interface and interactivity were coded to allow exploration of bat and mouse cochlea regions and intuitive navigation between sections about specific anatomical structures and bat hearing loss research. The results of this project provide a didactic and accessible visualization for auditory researchers, graduate students, and lay audiences to review basic cochlear anatomy, compare cochlear anatomy of bats and mice, and strengthen their understanding of human age-related and noise-induced hearing loss.

Comparative Cochlea Anatomy Module and 3D Models

Thesis Student

Preceptors

Department Advisor

3D Reconstruction of Fossilized Skull of South American Miocene Monkey Homunculus patagonicus: An Augmented Reality for Field Application :: KELLYN SANDERS

For most Miocene taxa, primate fossil evidence consists of broken cranial bones, teeth, and jaws. Studying these fossils is difficult due to the damage and distortion during geological stress. During fossilization the soft tissue preservation of these specimens is usually nonexistent. Homunculus patagonicus is an unusual primate from the Miocene epoch (~17 million years old) of extreme southern Argentina. The first associated cranium and mandible of this species will allow the most complete reconstruction of the adaptations of any early platyrrhine. To reconstruct the diet of such extinct mammals, the jaws, skull and muscles of mastication provide insight into how food properties influence skull morphology over evolutionary time (Perry, 2018). This project allows the use of comparative anatomy to learn how H. patagonicus lived, and its relationship to its environment through an examination of dietary adaptations.

Using extant analogs, correlations can be made between muscle and bone dimensions providing informed inferences about feeding behaviors in fossils. Inferences can be validated because, “Diet and mastication are closely tied to hard anatomy” (Perry, 2008). Thus, access to data from living analogs makes reconstructions of mastication especially justifiable for early primates (Perry, 2008). This data can be then used to recreate the magnitude and orientation of the force produced by the adductor muscles. These variables can be used to better understand the properties of foods and how they relate to food processing anatomy and behavior (Perry et al. 2011).

This project leverages digital visualization techniques to provide an interactive application using the digital fossil reconstruction of Homunculus patagonicus. The reconstruction of the skull and jaw adductor muscles are implemented through an interactive iOS application in addition to the original CT fossil data, extant distribution maps, and primate phylogeny. This application will not only provide researchers, students and the general public a learning resource but will also contribute to the fields of virtual paleontology, biocommunication and plastic surgery, especially facial reconstruction.

Thesis Student

Preceptors

Department Advisor

Visualizing HOPE: Encouraging HIV-Positive Organ Transplantation Using Novel Modular Animations :: MORGAN SUMMERLIN

HIV+ candidates in need of organ transplantation face an increased risk of mortality while on the organ waitlist and decreased access to transplantation compared to HIV-uninfected (HIV-) candidates. Fortunately, HIV+ donor organs can now legally be transplanted into HIV+ recipients, thanks to the HIV Organ Policy Equity (HOPE) Act of 2013, which reverses an outdated ban and unlocks a pool of organs from an estimated 300-500 HIV+ deceased donors in the US annually. However, challenges in the current organ donation system and stigma against HIV present barriers to HOPE implementation and the potential for life-saving HIV+ donor to HIV+ recipient (HIV-to-HIV) organ transplantation. In collaboration with transplant surgeons, infectious disease healthcare providers, organ donation community consultants, and medical illustrators, a novel animation workflow was developed to create HOPE education materials. The animations, targeted to potential donors and recipients with HIV, healthcare providers, and professionals in the organ donation community are intended to promote awareness and ultimately increase the rate of HIV-to-HIV transplantation.

To efficiently communicate to these critical audiences, the animation process was streamlined by combining overlapping information into reusable components and addressing each audience with a customized call-to-action clip. The results of this project provide two individual animations addressed to (1) people living with HIV and (2) professionals in the organ donation community. The animations consist of reusable clips that explain the background information of the HOPE Act, the potential biological risks of HIV-to-HIV transplantation, and a concluding statement that reminds the viewer that their participation is essential to continue the success of the HOPE Act. Each animation concludes with an individualized call-to-action segment that inspires viewers to make a change.

By informing these critical audiences through inclusive and educational animations, this project aims to reduce stigma in HIV+ organ donor referrals and registration and to encourage participation in HIV-to-HIV transplantation.

Thesis Student

Preceptors

Department Advisor

Content Advisor

Personalizing Hospital-based Stroke Education: Designing a Novel Recovery App to Prepare Stroke Patients for the Transition Home :: HELEN TANG

Stroke is a leading cause of adult disability in the United States. It is a complex disease for which timely intervention and treatment has the highest yield. Individualized patient education is crucial for optimizing recovery, preventing recurrence, and improving patient outcomes. Current hospital-based education is largely paper-based and suboptimal for meeting the varied, yet precise educational needs of the stroke patients and their care partners (carers). To augment the current education program, the multidisciplinary stroke team at the Johns Hopkins Comprehensive Stroke Center is building a mobile app that will provide individualized, interactive, and accessible education to prepare hospitalized stroke patients and their carers for the transition from hospital to home. This thesis project lays groundwork for the development of the app by designing its overall structure and navigation, and by prototyping specific paths demonstrating key features and functions of the app.

User-centered methodology was implemented to focus each stage of app design on the fulfillment of unmet learning needs of stroke patients and carers in acute hospital care and after hospital discharge. Key identified needs were synthesized into four enabling objectives and the underlying information architecture that informed the scope and structure of the app. Digital prototypes of seven key tasks that translated the abstract groundwork into concrete visuals were developed in an iterative and collaborative process with stakeholders.

The core features designed were (i) personalization of daily educational content, (ii) actionable recovery goal-setting, (iii) progress tracking, and (iv) improved two-way communication between patient and care team. Corresponding information architecture, interactive digital prototypes, and a model for progressive personalization were constructed. Together, these contributions provide the foundation for development of the first iteration of the app, and serve as valuable communication tools for continued collaboration and planning between stakeholders. The user-centered methodology imparted structure and strategy to the design process, while iteration enabled adaptability to new insights. Frequent usability testing, inquiry, and collaboration with stakeholders were essential to design refinement. The continued use of these methods during app development will maximize usability and efficacy of this novel personalized educational resource for early stroke recovery.

Thesis Student

Preceptor

Content Advisor

Department Advisor

Optimizing e-Learning in genetics: creating and comparing three categories of multimedia :: JENNY WANG

Online learning is rapidly expanding in the United States. One feature of online learning is the increased use of animations, especially in the sciences. However, there are contradictions within the literature regarding the effectiveness of animations in scientific education. Some studies claim that animation is the best modality for teaching scientific topics, while others have shown that it increases cognitive load, leading to reduced effectiveness. This thesis will test these opposing positions by measuring the effectiveness (retention and engagement) across three types of multimedia that we created: (i) a 6 minute 38 second traditional 2D animation, (ii) a 6 minute 43 second whiteboard animation, and (iii) an 8 minute 11 second PowerPoint video edited together from lecture videos. This three-way comparative approach will determine intrinsic differences and similarities across multimedia.

We recruited study participants from Amazon Mechanical Turk (N=168), split into six groups of 28 differentiated by video order. Retention and engagement scores were collected via survey in JHM Qualtrics. Using single factor ANOVA, we found no difference (p < 0.05) among the three modalities for retention. However, whiteboard animation performed better with word recall than the other two videos, suggesting that simultaneous narration with written text leads to better learner outcomes. We also found that the two animation formats performed better (p < 0.05) than the PowerPoint lecture for engagement (enjoyment, attention, understanding). This project aims to provide insight for e-Learning creators into which modalities work best for engaging and teaching learners while also considering monetary costs.

Thesis Student

Preceptor

Content Advisor

Department Advisor

2020 Thesis Presentations

The Thesis Presentations of the Class of 2020 were held on April 17, 2020, 3:00-5:00 PM (EDT). This year’s presentation were held remotely with a Live broadcast to the Department’s YouTube Page. The students presented to their faculty and invited alumni, students, and staff from Johns Hopkins Medicine as well as the public to participate through YouTube Live. Links to the YouTube Live event were be shared to the Department’s other social media accounts: Facebook, LinkedIn, Instagram, and Twitter.

Order of Presenters: Jamie Peterson, Helen Tang, Jenny R. Wang, William Guzman Jr., Kellyn Sanders, Morgan Summerlin, and Noelle Burgess.