BME WEEKLY ROUNDTABLE

February 19, 2024

INTERIM HEAD’S NOTE

The College of Engineering approved our submission for the one-time University employee recognition payments of $1,500. Among those excellent BME employees on the list we submitted, there were 3 faculty colleagues, 2 Executive/Management/Professional staff colleagues, 1 Support/Service staff colleague, 12 graduate students, and 1 post doc. Congratulations to them. Thank you all for nominating our wonderful colleagues. For more information,

https://www.purdue.edu/newsroom/purduetoday/releases/2023/Q4/university-announces-additional-details-on-employee-recognition-plan.html?utm_source=sfmcPT&utm_medium=email&utm_campaign=231130PurdueToday&utm_term=University+announces+additional+details+on+employee+recognition+plan&utm_id=826115&sfmc_id=0038c00002tv2n2AAA

As you know, there will be three Head Candidates to visit our school and our campus in the coming two weeks. I want to thank the search committee for their work. More importantly, I want to thank Jo Gelfand for the great work she is doing to ensure successful visitation of these candidates. It is not an easy task given the amount of work she has to do and the limited bandwidth she has dealing with so many other things.
A working group has been formed to develop transparent procedures for teaching load and assignments. An email will be sent to the entire faculty on Tuesday to provide an update on this.
We are looking for an instructional lab supervisor to serve our educational missions in Indianapolis. Please make your recommendation if you know someone whom you think may be a good fit.

UPCOMING IMPORTANT DATES

Week of February 19

Mon., Feb. 19 – Fri., Feb. 23: Fulbright Week. Purdue's Fulbright Week will start you on your way to applying for the Fulbright U.S. Student Program. Fulbright U.S. Student Grants offer a fully funded post-baccalaureate year to study, research, or teach abroad. Sessions will be held in-person with a virtual option unless otherwise noted. Sessions are a mix of in-person and remote offerings. See below for details.

Mon., Feb. 19: IU School of Medicine Center for Diabetes and Metabolic Diseases Enrichment Seminar Series, 12:00 p.m., R4-101 (Indianapolis) and via Zoom. Chris Harle, PhD, Professor and Department Chair, Health Policy and Management, IU Richard M. Fairbanks School of Public Health and Research Scientist, Regenstrief Institute Center for Biomedical Informatics and Lauren Lembcke, Team Lead, Data Core Services, Regenstrief Institute Center for Biomedical Informatics will present “Building Real-World Data and Analytic Services for Diabetes and Metabolic Disease Research Impact.” Zoom link: https://iu.zoom.us/j/87501979533#success

Tues., Feb. 20: Purdue Engineering Distinguished Lecture Series, Lecture at 1:30 p.m. and Panel at 2:30 p.m., ARMS Atrium. Russell Allgor, Vice President and Chief Scientist, Worldwide Operations at Amazon.com will present “Structuring Amazon’s outbound network to scale.” Hosted by the College of Engineering and the School of Industrial Engineering. Register here: https://purdue.ca1.qualtrics.com/jfe/form/SV_7P75FDaroDkuwVo?utm_source=delivra&utm_medium=email&utm_campaign=PEDLS%20-%20Russell%20Allgor%20-%20Feb%2020%2C%202024&utm_id=45804663

Tues., Feb. 20: Environmental and Ecological Engineering Research Seminar, 10:30 a.m., POTR 234 (Fu Room). Peter J. Vikesland, PhD, Nick Prillaman Professor of Civil and Environmental Engineering, Virginia Tech will present “Nanobiotechnology Enabled Sensing of Current and Emerging Pandemic Threats.”

Wed., Feb. 21: BME Distinguished Seminar Series: 9:30 a.m., MRGN 121 and via Zoom. Leonardo A. Rivera-Rivera, PhD, Associate Scientist, Department of Medicine and Medical Physics, Wisconsin Alzheimer’s Disease Research Center, University of Wisconsin – Madison will present “Elucidating cerebrovascular disease pathways to cognitive decline with neurofluid imaging.”

Wed., Feb. 21: Seminar for Neurotrauma and Diseases, 4:00-5:00 p.m., DLR 131 and via Zoom. Vijay Rangachari, PhD, Professor of Biophysical Chemistry, University of Southern Mississippi will present “α-synculein modulates TDP-43 phase transitions to induct heterotypic amyloids – Implications in Neurodegenerative diseases.” Zoom link: http://bit.ly/42hhhJG The seminar series is sponsored by the Center for Paralysis Research and Plexon.

Thurs., Feb. 22: BME PhD Defense Announcement for Neal Patel (V. Rayz, Chair), 10:30 a.m., MJIS 2001 and via Zoom. Title: Characterization of Neurofluid Flow using Physics-Guided Enhancement of 4D flow MRI.

Thurs., Feb. 22: Seminars in Hearing Research, 12:00 noon, Nelson Hall – 1215. Samantha Hauser, AUD, CCC-A, PhD Candidate will present “Towards Precision Diagnostics for Complex Sensorineural Hearing Loss.”

Thurs., Feb. 22: BMS 692/CPB 697 Graduate Seminar, 12:30 p.m., LYNN 1136. Grace Mulia, Graduate RA, BMS will present “Development of Targeted Interleukin-27 to Treat Acute Respirator Distress Syndrome.” Gada Daffaalla Awdalkreem, Graduate RA, CPB, will present “Development of Small Cell Neuroendocrine Prostate Cancer Mouse Cell Line Model.” Jhon Martinez, Graduate Student, BME, will present “Mechanistic Investigations of Neuronal Network Activity Changes Utilizing an in vitro Model of Blast-induced TBI.” This seminar series is sponsored by the Department of Basic Medical Sciences, College of Veterinary Medicine.

MJIS ALERT

MJIS Air Handling Shutdown, Tues., March 12 beginning at 7:30 AM and lasting until approx. 3:00 PM for preventative maintenance of the building’s air systems. This includes air ventilation supplies to all public, classroom and research areas, including chemical fume hoods. There should be NO chemicals used anywhere! All chemical fume hood activity should terminate by 5 PM Monday March 11th. You must make sure all chemical containers are sealed at that time. Chemical fume hoods will have notices posted - do not resume activity until BME staff have verified that work is complete, and have removed postings.

2024 BME Research Symposium: Innovations in Biomedical Engineering

BMEGSA is excited to announce the 2024 BME Research Symposium to be held on April 16th, 2024 in the Hall for Discovery Learning Research (DLR) in Room 131 from 9:30 a.m. – 4:30 p.m.

Abstracts submissions are now open! All BME-affiliated undergraduate, post-bacs, and graduate students are welcomed to submit an abstract. The submission is open to both West Lafayette and Indianapolis campus. All abstract submissions are due by March 19th at 11:59pm on the submission portal. We encourage all students to apply, and please ensure your abstract follows the directions provided in this email. There will be cash prizes and awards for the top oral and poster presentations!

For all attendees, please complete the registration form for the BME Symposium, which can be found here. There is no cost to register for the symposium.

If you have any questions, please reach out to Brendan (bbkazu@purdue.edu) or Lizzy (frazie34@purdue.edu) via email.

Graduate Recruiting

Purdue’s College of Engineering Graduate Recruitment office will be recruiting in Colombia from February 18th to March 1st. Colleen Coulter, Assistant Director of Graduate Recruitment, plans to visit Bucaramanga, Pereira, and Bogota with a group from EducationUSA. She will connect with Purdue-specific partners in Barranquilla (U. Del Norte), Cali (ICESI U.), and Medellín (U. EAFIT). If you have faculty and/or students in Colombia that you want Colleen to connect with during this trip, please alert her by email: clc@purdue.edu.

Upcoming important deadlines and information

Wed., Feb. 28: BME Distinguished Seminar Series, 9:30 a.m., MRGN 121 and via Zoom. John Oshinski, Professor of Radiology & Imaging Sciences and Biomedical Engineering, Emory University/Georgia Tech will present “Measuring Neural Dynamics with MRI.”

Thurs., Feb. 29: BME PhD Defense Announcement for Lexi Petrucciani (E. Pienaar, advisor). Everyone is invited to attend the public presentation beginning at 7:00 am in MJIS 2001 and via Zoom. Title: Agent-Based Modeling of Cell Culture Granuloma Models: The Role of Structure, Dimension, Collagen, and Matrix Metalloproteinases

Thurs., Feb. 29: BME PhD Defense Announcement for Luke Brennan (J. Linnes and N. Rodriguez, co-advisors). Everyone is invited to attend the public presentation beginning at 12:30 pm in Lilly Hall of Life Sciences (LILY) room 1117 or via Zoom. Title: HPV Rapid Diagnostic Test Development through Human-centered Design.

Fri., March 1: Indiana Human-Centered Design for Health Seminar Series, 12:00 p.m. via Zoom. Lean about research and best practices in HCD and health, promote the diverse HCD expertise in Indiana, and build a community of HCD researchers and practitioners focused on health, in Indiana and beyond. The speaker will be Andrew Miller, Associate Professor and Chair, Department of Hunan-Centered Computing, IUPUI. Register and learn about upcoming seminars at healthtechquitylab.org/hcd-seminar

Wed., March 6: BME PhD Preliminary Exam Announcement for Damilola C. Lawore (D. Brubaker and L. Green, co-advisors). Everyone is invited to attend the public presentation beginning at 2:30 PM in MJIS 2001. Title: Characterizing the anticancer potential of vaginal microbes and metabolites.

Wed., March 6: Purdue Engineering Distinguished Lecture Series. Karen Willcox, Director, Oden Institute for Computational Engineering and Sciences, Associate Vice President for Research, and Professor of Aerospace Engineering and Engineering Mechanics, The University of Texas at Austin will present “From Reduced-Order Modeling to Scientific Machine Learning: How Computational Science is Enabling the Design of Next-Generation Engineering Systems.” This seminar is hosted by the College of Engineering, and School of Mechanical Engineering. Register at bit.ly/pedls-willcox

Fri., March 8: Bottorff Graduate Fellowship Program Applications due. Please see the attached Bottorff Fellowship application form for Summer 2024. The Bottorff Graduate Fellowship Program is designed to increase the number of Purdue doctoral engineering students focused on medical technology innovation and clinical translation. Funds to support a summer clinical immersion experience are available to help students gain clinical exposure at the Indiana University School of Medicine (IUSM). This full-time 8-week summer clinical immersion experience will be followed by a fall class focused on biomedical product translation (BME 56100 Preclinical and Clinical Study Design or BME 59500 Biomedship). Finally, a spring Regulatory class will help fellows understand the workings of the US FDA and other regulatory agencies and the steps needed for clinical translation. Applications are due by Friday, March 8^th.

Contact Aaron Lottes (lottes@purdue.edu) or Craig Goergen (cgoergen@purdue.edu) for questions about the program.

Mon., March 11 – Friday, March 15: Spring Break.

Tues., March 12: MJIS Air Handling Shutdown, beginning at 7:30 AM and lasting until approx. 3:00 PM for preventative maintenance of the building’s air systems. This includes air ventilation supplies to all public, classroom and research areas, including chemical fume hoods. There should be NO chemicals used anywhere! All chemical fume hood activity should terminate by 5 PM Monday March 11th. You must make sure all chemical containers are sealed at that time. Chemical fume hoods will have notices posted - do not resume activity until BME staff have verified that work is complete, and have removed postings.

Mon., March 18: Engineering in Medicine Pediatrics Research Symposium, 10:00 am – 3:00 pm, Joseph E. Walther Hall, R3 C203, 980 W. Walnut St, Indianapolis. The day will include scientific sessions, networking, a poster session and expert panels on industry partnerships, leveraging resources, and success stories. Register by March 7^th: https://redcap.link/nixel8sz The Symposium is sponsored by Crossroads Pediatric Device Consortium, The Indiana University School of Medicine, and Purdue University College of Engineering.

Tues., March 19: Abstracts submissions for the 2024 BME Research Symposium: Innovations in Biomedical Engineering are due by March 19th at 11:59pm on the submission portal. All BME-affiliated undergraduate, post-bacs, and graduate students are welcomed to submit an abstract. The submission is open to both West Lafayette and Indianapolis campuses. We encourage all students to apply, and please ensure your abstract follows the directions provided in this email. There will be cash prizes and awards for the top oral and poster presentations! The Symposium will take place on April 16 in the Hall for Discovery Learning, Room 131. If you have any questions, please reach out to Brendan (bbkazu@purdue.edu) or Lizzy (frazie34@purdue.edu) via email.

Thurs., April 4: 19^th Annual Garnet E. Peck Symposium, France A. Cordova Recreational Sports Center. Registration now open: www.purdue.edu/conferences/Peck2024 . The Peck Symposium will showcase the digital transformations occurring in the pharmaceutical industry. Presentations include the latest developments in discovery, data analysis, process development and the application of AI in the pharmaceutical industry, as well as a poster session and 3-minute student thesis competition. Chaired by Dr. Nathaniel Milton, Professor of Practice. Questions? Email Cindy Everhart, IMPH Communications & Events Coordinator, ceverha1@purdue.edu

Sat., April 6: E-Waste Day, 8:00 a.m. – 2:00 p.m., Tippecanoe County Fairgrounds (1190 Teal Road, Lafayette). Our bi-annual e-waste event is back on April 6th from 8am-2pm at the Tippecanoe County Fairgrounds! This event includes FREE electronics recycling, paper shredding, and medicine disposal for Tippecanoe County residents!

Details on E-waste Recycling: Tippecanoe County residents may bring in electric and electronic devices such as TVs, computers, laptops, vacuum cleaners, printers, etc. for recycling at no charge. We will NOT accept items with refrigerant such as AC units, refrigerators, dehumidifiers, or freezers. We will NOT accept large appliances such as washing machines or stoves. Those can be recycled at Oscar Winski Scrap Metal at 2407 N 9th St. All attendees must show proof of Tippecanoe County residency to receive free service.
Details on paper shredding: A paper shredding truck will be on-site to accept up to two banker boxes of paper to shred and recycle from each car. Just pull up, dump your box in the bin, and that's it! Paper clips, staples, folders, and file tabs are A-OK! Please remove binders and alligator clips.
Details on medicine take-back: The Tippecanoe County Sheriff's Department will also be here to accept any unused or expired medicines. Over-the-counter and prescription (including controlled substances) are accepted. It will be dumped out onsite, so bring it loose if possible! All of your medicines will be destroyed and disposed of safely. We will not take liquids, needles of any kind, insulin, or powders.
We will have volunteers on hand to unload your electronics. Please have them packed in your vehicle in an easy-to-unload manner so that we can keep the line of cars moving.

Wed., April 10: Purdue Engineering Distinguished Lecture Series. Jeffrey Dean, Google Senior Fellow and SVP of Google Research and Google Health, Google Research will present “Machine Learning, AI and Applications of AI.” This seminar is hosted by the College of Engineering, and Elmore Family School of Electrical and Computer Engineering. Register at bit.ly/pedls-dean

Fri., June 7: Indiana Human-Centered Design for Health Seminar Series, 12:00 p.m. via Zoom. Lean about research and best practices in HCD and health, promote the diverse HCD expertise in Indiana, and build a community of HCD researchers and practitioners focused on health, in Indiana and beyond. The speaker will be Youngbok Hon, Professor, Herron School of Art and Design, IUPUI. Register and learn about upcoming seminars at healthtechquitylab.org/hcd-seminar

Resources and further information

Mon 2/19 Kickoff Event HCRN 1066

6-7:30pm Giant Leaps Toward a (Ful)Bright Future: Celebrating 10 Years of Fulbright Success through NISO

Tues 2/20 Information Sessions HCRS 1076

1:30pm Fulbright for Graduate Students

2:30pm 2025-26 English Teaching Assistant Grants

5:30pm 2025-26 Research and Study Grants

Wed 2/21 Information Sessions HCRS 1054

4:30pm 2025-26 Research and Study Grants

5:30pm 2025-26 English Teaching Assistant Grants

6:30pm Fulbright for STEM majors

Thurs 2/22 Duhme Hall Living Room

6-7:30pm Fulbright: Around the World in 90 Minutes

Fri 2/23 WALC 2051

10:00-11:00 am Fulbright Scholar Grants (Faculty only)

All sessions are 45 minutes unless noted

Additional information available at: https://www.purdue.edu/niso/fulbright/fulbrightweek.html

Abstract: The world is emerging from the darkest days of the COVID-19 pandemic. This pandemic, caused by the global spread of the SARS-Cov-2 virus, has illustrated the poor performance of existing monitoring approaches whose aim is to quantify the environmental aspects of such dissemination. Recent advances in both nanotechnology and biotechnology, however, enable the development of novel alternatives, are more sensitive and potentially more cost-effective than existing approaches. In this presentation, we will present work conducted to design and test plasmonic and nanopore-based platforms for detection of both current (SARS-Cov-2) and emerging (influenza and antimicrobial resistant organisms), pandemic threats in both water and air.

Abstract: While Alzheimer’s disease (AD) is the most prevalent cause of dementia, postmortem examinations reveal that at least half of clinically diagnosed AD patients exhibit cerebrovascular disease (CVD), potentially contributing to cognitive impairment and dementia. Despite this association, the mediation pathways between AD, related dementias, and vascular disease remain poorly understood, and treatments often overlook the multi-etiological nature of dementia. To provide insights into AD and CVD relationships, non-invasive Magnetic Resonance Imaging (MRI) is being utilized in longitudinal studies involving AD risk-enriched populations. However, current clinically available MRI techniques lack sensitivity and specificity to address key vascular hypotheses in such studies. MRI methods commonly employed today, such as fluid attenuation and susceptibility imaging only indirectly characterize CVD and cannot inform on the dynamic neurofluid flow and vascular motion phenomena that are hypothesized to interact with AD related pathology. This presentation will introduce a variety of MRI strategies designed to improve the characterization of CVD in the context of aging and AD, including a description of challenges associated with technical and physiological variability. Findings from risk-enriched populations and biomarker-confirmed AD patients will also be presented.

Biography: I obtained a Bachelor of Science in Applied Physics from the University of Puerto Rico – Humacao. Subsequently, I completed my Ph.D. in Physics at UW-Madison, focusing on the optimization of MRI methods for assessing cerebrovascular hemodynamics under the guidance of Dr. Oliver Wieben. Following my doctoral studies, I pursued a post-doctoral fellowship at the same institution, where I worked on accelerated Non-Cartesian sampling acquisition and constrained image reconstruction methods for neuroimaging. This included work on motion-encoded pulse sequences and contrast-enhanced MRI, supervised by Dr. Kevin M. Johnson. Currently, I serve as an Associate Scientist at the Wisconsin Alzheimer’s Disease Research Center at UW-Madison. In this role, I collaborate closely with investigators from the Departments of Medical Physics, Radiology, Medicine, and Kinesiology. My research interests revolve around the development of sensitive markers for the characterization of cerebrovascular health, employing innovative MRI methods across various stages from data acquisition and image reconstruction to post-processing strategies.

~ BME Host: Vitaliy Rayz ~

Zoom link: https://purdue-edu.zoom.us/j/98045041653?pwd=S3E4czF3d2RWNkdybUtWbzJ5MHpZQT09

Note: Students registered for the seminar are expected to attend in-person.

Thesis Committee: Dr. Vitaliy Rayz (Chair), Dr. Edward Delp, Dr. A.J. Schwichtenberg, and Dr. Michael Markl

Abstract: Cerebrospinal fluid (CSF) plays a diverse role within the skull including cushioning the brain, regulating intracranial pressure, and clearing metabolic waste via the glymphatic system. Disruptions in CSF flow have long been investigated for hydrocephalus-related diseases such as idiopathic normal pressure hydrocephalus (iNPH). Recently, changes in CSF flow have been implicated in neurodegenerative disorders such as Alzheimer’s disease (AD) and Parkinson’s disease. It remains difficult to obtain in vivo measurements of CSF flow which contribute to disease initiation, progression, and treatment. Three-directional phase-contrast MR imaging (4D flow MRI) has been used to measure CSF velocities within the cerebral ventricles. However, there remain challenges in balancing acquisition time, spatiotemporal resolution, and velocity-to-noise ratio. This is complicated by the low velocities and long relaxation times associated with CSF flow. Additionally, flow-derived metrics associated with cellular adaptations and transport rely on near-wall velocities which are poorly resolved and noisy. To address these challenges, we have applied physics-guided neural networks (PGNN) to super-resolve and denoise synthetic 4D flow MRI of CSF flow within the 3rd and 4th ventricles using novel physics-based loss functions. These loss functions are specifically designed to ensure that high-resolution estimations of flow fields are physically consistent and temporarily coherent. We apply these PGNN to various test cases including synthetically generated 4D flow MRI in the cerebral ventricles and vasculature, in vitro 4D flow MRI acquired at two resolutions in 3D printed phantoms of the 3rd and 4th ventricles, and in vivo 4D flow MRI in a healthy subject. Lastly, we apply these physics-guided networks to investigate blood flow through cerebral aneurysms. These techniques can empower larger studies investigating the coupling between arterial blood flow and CSF flow in conditions such as iNPH and AD.

Zoom link: https://iu.zoom.us/j/88597603864

Abstract: Although sensorineural hearing loss (SNHL) is a single audiometrically defined clinical category, animal models and human temporal-bone studies show that individuals have highly complex SNHL pathologies, with variable combinations of inner and outer hair cell (IHC/OHC) injury, reduced endocochlear potential (EP), and cochlear synaptopathy. An umbrella diagnosis of SNHL belies the diversity of possible underlying cochlear pathophysiology profiles and the associated divergent listening outcomes among patients with similar audiograms. Current clinical tools and guidelines do not adequately capture this diversity in hearing, hindering individualized audiological management and treatments. To address this problem, we are testing a battery of physiological biomarkers rather than a single metric of hearing. Our coordinated battery in multiple preclinical chinchilla models of SNHL and in humans with SNHL allows for an investigation of not only isolated pathologies but considers the potential interactions between the many sources of cochlear dysfunction in complex SNHL. In addition to physiological assessment, human subjects complete behavioral measures of speech perception that place varying degrees of demand on peripheral and central factors to assess functional differences in hearing. Efforts to increase the precision of diagnostic tools in audiology, initial findings from this study, and challenges related to cross-species integration will be presented.

This year’s SHRP schedule is available here: https://purdue.edu/TPAN/hearing/shrp_schedule

Titles and abstracts of all SHRP talks are here: https://purdue.edu/TPAN/hearing/shrp_abstracts

Abstract: Brain tissue and cerebral spinal fluid (CSF) move in response to changes in blood pressure/flow over the cardiac cycle. This is referred to as Neural Dynamics. Magnetic resonance imaging (MRI) can be used to study CSF flow pulsations using phase contrast magnetic resonance (PCMR). We have recently developed an MRI method to measure motion of the brain parenchyma using displacement encoding with simulated echoes (DENSE). We applied PCMR and DENSE to look at coupling of CSF flow and brain motion in the setting of Chiari Malformation, a disease where the cerebellar tonsils drop below the foramen magnum. MRI scans were performed in a series on 100+ Chiari Malformation patients where ~half underwent treatment by posterior fossa decompression surgery. We examined changes in neural dynamics (CSF flow and brain motion) between healthy subjects and Chiari Malformation patients, and in Chiari Malformation patients before and after surgery. The goal of the project is to: 1) understand pathophysiology of Chiari Malformation, 2) predict effects of surgery on neural dynamics, and 3) develop better methods of selecting patients for surgical treatment.

Biography: John Oshinski, PhD is a Professor of Radiology & Imaging Sciences at Emory and Biomedical Engineering at Emory University and Georgia Tech. He was trained as a mechanical Engineer and has spent 25 years using imaging and experimental and computational fluid mechanics to study the relationship between hemodynamics and vascular disease in the clinical environment. His research program focuses on developing new imaging and modelling applications that improve the diagnosis of cardiovascular disease, influence patient care decisions, and enable a better understanding of basic cardiacvascular physiology and pathophysiology. Dr. Oshinski also serves as director of the Emory Center for Systems Imaging (CSI), and integrated core facility that houses all the research imaging equipment in the Emory school of Medicine (3T and 7T human MRI scanners, human PET/CT and PET/MR scanners, animal MRI and PET/CT, cyclotron, and Radiopharmacy).

~ BME Host: Vitaliy Rayz ~

Zoom link: https://purdue-edu.zoom.us/j/99721542345?pwd=SnpHdjhWWlFWTmVMSzd1WS9teC9NZz09

Note: Students registered for the seminar are expected to attend in-person.

Thurs., Feb. 29: BME PhD Defense Announcement for Lexi Petrucciani (E. Pienaar, advisor). Everyone is invited to attend the public presentation beginning at 7:00 am in MJIS 2001 and via Zoom. Title: Agent-Based Modeling of Cell Culture Granuloma Models: The Role of Structure, Dimension, Collagen, and Matrix Metalloproteinases

Advisory Committee: Elsje Pienaar (Chair), Tamara Kinzer-Ursem, Nan Kong, Nelita du Plessis, Bradley Allen

Abstract: Tuberculosis (TB) remains a global public health crisis, causing over 10 million new infections and 1.3 million deaths in 2022 alone. TB is caused by Mycobacterium tuberculosis (Mtb), which initiates heterogeneous pathology in the lungs, including granulomas and cavities. Granulomas are organized structures of immune cells, traditionally thought to contain bacteria. Cavities are pathological spaces caused by the destruction of extracellular matrix (ECM), which can worsen disease outcomes and cause long-lasting pulmonary impairment. In vitro methods are commonly used to study host-pathogen interactions in Mtb infection, and recent developments have led to models that represent the TB granuloma environment more closely than traditional cell culture. These advances include the development of 3D models and the inclusion of physiological ECM components like collagen. Increasing complexity has been accomplished in a piece-wise manner – minimally necessary components are included to minimize cost while maintaining throughput and tractability. This creates a need for tools to analyze these systems and, more importantly, integrate the independent data created. We developed an agent-based model to characterize multiple in vitro models of TB and apply it to 1) separate the contributions of dimension and structure to bacterial control in granuloma-like spheroids and 2) explore how the interactions of collagen and matrix metalloproteinases (MMP) contribute to clinically relevant outputs such as bacterial load and ECM destruction. The model provides insights into the role of granuloma structure and the conflicting results of MMP inhibition, generating new hypotheses to be tested in tandem with in vitro models.

Zoom link: https://purdue-edu.zoom.us/j/9607220370

Thurs., Feb. 29: Purdue University 3^rd Annual Health Equity Summit, 8:00 am to 3:00 pm, PMU North and South Ballrooms. Hosted by Dr. Jerome Adams and Purdue’s Health Equity Initiatives Team with Indiana CTSI. The event will feature Francis S. Collins, MD, PhD, Senior Investigator at the National Human Genome Research Institute and former Director of the National Institutes of Health. What to expect: Lunch and collaborative opportunities at NO cost, innovative health equity topics, and poster session with awards ceremony. Register for the event today at https://web.cvent.com/event/aa2fe096-8206-4093-85f2-6c22e8baad1c/summary

Thurs., Feb. 29: BME PhD Defense Announcement for Luke Brennan (J. Linnes and N. Rodriguez, co-advisors). Everyone is invited to attend the public presentation beginning at 12:30 pm in Lilly Hall of Life Sciences (LILY) room 1117 or via Zoom. Title: HPV Rapid Diagnostic Test Development through Human-centered Design.

Advisory Committee: Jacqueline Linnes, Co-Chair; Natalia M. Rodriguez, Co-Chair; Mohit Verma; Monica L. Kasting; Aaron C. Ermel

Abstract: Almost every case of cervical cancer in the United States is medically preventable with vaccination and proper screening, yet many Americans are insufficiently screened. Over 12 thousand American women suffered from cervical cancer in 2018¹ causing 4 thousand deaths, with over a third in women who had never received a routine screening test².

New, sensitive testing techniques for cervical cancer screening are facilitating HPV testing without evaluating the cells collected in the sample by eye. This opens the door to new, accessible methods of screening such as rapid testing in clinic and at home, self-sampling, and mail-in testing. As cervical cancer morbidity and mortality is largely a result of healthcare inequities, these methods may have a significant impact on cervical cancer outcomes.

The goal of this project is to create a proof-of-concept, sample-to-answer rapid test to be used for cervical cancer screening in Indiana outpatient clinics. We began the project by conducting interviews and a survey to explore Indiana clinician perspectives on cervical screening methods such as self-sampling, rapid testing, and home-based screening. Clinicians preferred in-clinic testing with same-visit results, in the hopes that face-to-face explanation of results and scheduling follow-up care in person would improve patient retention for these important follow-up tests. To create such a test, we augmented an isothermal nucleic acid amplification method that copies 13 of the 14 high-risk human papillomavirus (hrHPV) types with an endogenous b-globin sample control and a simple colorimetric lateral flow strip (LFS) readout. When tested with HPV 16 the assay achieved a limit of detection of 1000 HPV copies per reaction, which would detect endocervical samples deemed ‘sufficient’ by clinical guidelines. It also performs in endocervical cells using methods and equipment that could be implemented in an outpatient clinic. The final test accepts swabs or brushes of endocervical cells, lyses them in 5 minutes, copies the target DNA and a sample adequacy control, and delivers the readout within 40 minutes on an LFS readout. Future directions for this assay include soliciting feedback from clinicians and other stakeholders about the prototype developed, adapting the assay to interferents of clinical endocervical samples, and adding probes for other HPV types, such as HPV 18 and eventually the other hrHPV types.

Zoom Link: https://iu.zoom.us/j/5867035107?omn=82114505547

Wed., March 6: BME PhD Preliminary Exam Announcement for Damilola C. Lawore (D. Brubaker and L. Green, co-advisors). Everyone is invited to attend the public presentation beginning at 2:30 PM in MJIS 2001. Title: Characterizing the anticancer potential of vaginal microbes and metabolites.

Thesis Committee members: Dr. Douglas Brubaker, Ph.D. (Co-chair); Dr. Leopold Green, Ph.D. (Co-chair); Dr. Luis Solorio, Ph.D.; Dr. Quihong He, Ph.D.

Abstract: The vaginal microbiome plays a crucial role in the risk, progression, and treatment of female cancers, yet our understanding of its complex dynamics remains incomplete. There's a pressing need to develop systematic approaches to unravel how vaginal microbiome components and their products interact with host cells, particularly regarding their therapeutic potential. In response, we propose the Pharmacobiome, a systems biology framework that quantitatively assesses the similarity between vaginal microbes/products and known drugs/small molecules based on their impact on host cellular responses. To test this, we will analyze published vaginal microbiome multi-omics data and establish host vaginal epithelial gene and protein signatures linked to each profiled vaginal microbe/metabolite. We will first compare the established vaginal signatures to FDA-approved anticancer drug perturbation gene signatures to characterize the Anticancer Vaginal Pharmacobiome. Then we compare the established host vaginal epithelial gene and protein signatures to the gene expression profiles associated with human monocyte-to-macrophage polarization to identify vaginal microbes/metabolites with the potential to induce macrophage polarization. Finally, we will engineer a macrophage-bacterial symbiont, where we will embed bacteria in the macrophages, serving as therapeutic controllers against cancer cells. Overall, our proposed research endeavors to overcome the obstacle of lacking knowledge regarding the functions of various microbial species identified in the vaginal environment. This research would underscore the Pharmacobiome's potential in delineating the anticancer therapeutic aspects of vaginal microbiome constituents, with implications extending to diverse cancers, microbiomes, and disease contexts.

BME Distinguished Seminar Series, 9:30 a.m., MRGN 121 (NOTE LOCATION CHANGE) or via Zoom.

Zoom link: https://purdue-edu.zoom.us/j/5593290378?pwd=eFBOZFlNTU50ZDA2S2gwcnpyOWIwUT09

Note: Students registered for the seminar are expected to attend in-person.

Week #	Date	Speaker	Title	Host	Website
7	2/21/2024	Anne Robertson	Distinguished Service Professor, Department of Mechanical Engineering and Materials Science, Swanson School of Engineering, University of Pittsburgh	Vitaliy Rayz	https://www.engineering.pitt.edu/people/faculty/anne-robertson/
8	2/28/2024	John Oshinsk	Professor in the Emory/Georgia Tech Department of Biomedical Engineering and Department of Radiology and Imaging Sciences, Emory University School of Medicine	Vitaliy Rayz	https://www.cores.emory.edu/csic/about/faculty-staff/oshinski-john.html
9	3/6/2024	Melissa Kemp	Carol Ann and David D. Flanagan Professor, Georgia Cancer Coalition Distinguished Cancer Scholar, Georgia Tech	Elsje Pienaar	https://bme.gatech.edu/bme/faculty/Melissa-Kemp
10	3/20/2024	Jerome Mertz	Professor, Biomedical Engineering, Boston University	Krishna Jayant	https://www.bu.edu/csn/profile/jerome-mertz/
11	3/27/2024	Mikhail G. Shaprio	Professor of Chemical Engineering, Caltech	Krishna Jayant	https://cce.caltech.edu/people/mikhail-g-shapiro
12	4/3/2024	Jennifer Linderman	Pamela Raymond Collegiate Professor of Engineering, University of Michigan	Kinzer-Ursem Pienaar	https://che.engin.umich.edu/people/linderman-jennifer/
13	4/10/2024	Victor Barocas	Professor, Department of Biomedical Engineering, University of Minnesota	Deva Chan	https://cse.umn.edu/bme/victor-barocas
14	4/17/2024	Kim “Avrama” Blackwell	Professor and DEO of Roy J. Carver Department of Biomedical Engineering	Kinzer-Ursem	https://ibi.gmu.edu/faculty-directory/kim-avrama-blackwell/
15	4/24/2024	Stacey Finley	Nichole A. and Thuan Q. Pham Professor and Associate Professor of Biomedical Engineering, Chemical Engineering and Materials Science, and Quantitative and Computational Biology, USC	Kinzer-Ursem Pienaar	https://viterbi.usc.edu/directory/faculty/Finley/Stacey

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Postdoctoral Fellow Opportunity – IUSM Emergency Medicine

The laboratory of Dr. Nathan J. Alves, PhD, within the Department of Emergency Medicine at the Indiana University School of Medicine (IUSM), is seeking a highly motivated and independent post-doctoral research fellow. Dr. Alves is a Chemical and Biomolecular Engineer, Associate Professor and the Director of Translational Research for the Department of Emergency Medicine in addition to having an affiliate faculty appointment at Purdue University in Biomedical Engineering. The Alves Lab explores highly interdisciplinary research interests applying engineering and biophysical principles and designs to create translational technologies and treatments in the area of blood coagulation and fibrinolysis. The primary focus of research in the laboratory is to develop targeted clot digesting therapeutic agents to more safely digest clinically relevant blood clots to treat pulmonary embolism (PE, blood clots in the lungs), deep vein thrombosis (DVT), and ischemic stroke. This interdisciplinary research utilizes diverse enzyme assays, chemical synthesis, blood clot formation and digestion assays under shear, and other novel testing/delivery platforms that include multivalent branched molecules and nanoparticle drug delivery systems. Projects Include: (1) Leveraging multivalency to modulate enzyme activity and improve inhibitor selectivity (nanoparticle drug delivery and targeting). (2) Ex-vivo flowing models of clot digestion under shear using in-vivo like fluorescently labeled blood clots from human whole blood. (3) Development of novel fibrinolytic diagnostics tools to assess coagulation state. (4) Mouse models of clot formation/targeting/digestion utilizing intravital microscopy. (5) Study the effects of environmental microplastic exposure on coagulation/fibrinolysis. Projects are funded both externally and internally.

For additional information and to apply, go to: https://indiana.peopleadmin.com/postings/19651

Attachments:

BME_Symposium_Flyer

2024 03 18 EiM symposium flyer