July 2023 - Bmegradstudents-list

[Bmeroundtable-list] Summer Seminar Announcement - Wed., July 12
by Gelfand, Johanna K 07 Jul '23

07 Jul '23

[cid:image001.jpg@01D9B014.B713C160] BME Summer Seminar Series Wednesday, July 12th, 2023 9:30-10:30 AM EST Via Zoom Meeting - link below* Evaluation links: Jonathan Huang: https://purdue.ca1.qualtrics.com/jfe/form/SV_2ajxgeQ8kXEsW8K<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> Julio Rivera-De Jesus: https://purdue.ca1.qualtrics.com/jfe/form/SV_5tBP8zyfLDdo5Ei<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> Identification of Cell Type-Specific eQTLs through Empirical Bayes Regression Jonathan Huang (Yunlong Liu/Bumsoo Han, advisors) [Jonathan Huang] Abstract: Advances in technologies over the past few decades have shed light on the underlying genetics linked with neurological diseases. One tool, genome-wide association studies (GWAS), has been powerful in identifying loci associated with these diseases. However, because most GWAS identified variants are found within the non-coding regions of the DNA, it remains difficult to determine their functionality. A method to evaluate the effect of these variants on gene expression is through expression quantitative trait loci (eQTL). Both of these methods traditionally lack the granularity to tackle the issue of tissue heterogeneity and the role both neurons and glia play in disease. To address this, we utilize pseudo-bulked single cell RNA and multiomic data from the caudate of 161 patients from the Collaborative Studies on Genetics of Alcoholism (COGA) Study to identify the functional variants specific to cell-types found within the brain. Here, we use an empirical Bayesian regression model to identify eQTL and cell type-specific eQTL in six cell types: DRD1 and DRD2 expressing neurons, astrocytes, microglia, oligodendrocytes, and oligodendrocyte progenitor cells. Our preliminary results show that our method offers several improvements over the standard ordinary least squares regression model. First, using single cell multiomic data to identify cell type-specific enhancer-promoter pairs (ARCs) can enrich for functional variants within peak regions that actively contribute to gene expression. Second, the model can borrow gene expression information from shared cell types to estimate a prior distribution to improve the power of the analysis. Finally, when used in conjunction with ARC information, we can selectively borrow information from comparable cell types with a higher likelihood of improving the ability to identify eQTL and cell type-specific eQTL. Our study provides a method to overcome traditional barriers in identifying eQTL to investigate the effect of genetic variants on gene expression at a cell type-specific level. Microfluidic-based Assays for Environmental Monitoring of Waterborne Pathogens Julio Rivera-De Jesus (Jacqueline Linnes, advisor) [cid:image008.jpg@01D9B014.D375FDA0] Abstract: Waterborne pathogens, such as Vibrio cholerae (V. cholerae), manifest as severe gastrointestinal infections affecting 7.15 million people annually. Developing water monitoring platforms capable of detecting V. cholera and other waterborne pathogens in the environment would enable prevention for resource-limited communities where these pathogens are endemic. Methods for detecting V. cholerae in the environment require laborious protocols and expensive equipment, such as a polymerase chain reaction (PCR) machine. Nonetheless, advances in molecular biology, such as loop-mediated isothermal amplification (LAMP), can reduce the required infrastructure to detect diseases. Microfluidic diagnostics enable fast, near-patient, sample-to-answer devices capable of functioning without conventional lab-scale resources. Here, we present the use of plastic and paper microfluidic devices constructed and bonded by different modes. We use cyclic olefin-polymer (COP) in a smartphone-based assay that records fluorescent particles' Brownian motion and computes their diffusion coefficient through image correlation. COP is used due to its optical transmissibility making it feasible for fluorescence-based assay; however, the bonding methods may affect optical clearance or the assay. We demonstrate a comparison in image quality based on the average intensity of the smartphone videos of 400 nm streptavidin-coated beads within the sealed COP chips through different means, as well as successful amplification. For the paper-based device, the lateral flow assay (LFA) can accurately detect V.cholerae up to 100 cells/reaction. However, to detect the pathogen on-site, the sample must be filtrated to compensate for the low concentrations available in environmental water sources. Currently, we are developing an integrated microfluidic paper analytical device for enrichment, capture, amplification, and detection of V. cholerae on-site. Here we adapt and improve existing assays to increase their viability for field testing and environmental monitoring of waterborne pathogens. *Join Zoom Meeting https://purdue-edu.zoom.us/j/98231659969?pwd=T21Oa1B6QzFyQzFvckMzS1doNGlJUT…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> Meeting ID: 982 3165 9969 Passcode: biomedical Liz Rowen She/Her Graduate Program Assistant Weldon School of Biomedical Engineering Martin C. Jischke Hall of Biomedical Engineering 206 S. Martin Jischke Drive West Lafayette, IN 47907-2032 o: 765-494-1197 [7054E290]<https://www.purdue.edu/?utm_source=signature&utm_medium=email&utm_campaign=…> -- Bmeroundtable-list mailing list Bmeroundtable-list(a)ecn.purdue.edu https://engineering.purdue.edu/ECN/mailman/listinfo/bmeroundtable-list

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Weldon Graduate Program Announcements July 5th, 2023
by Siemers, Tammy R 05 Jul '23

05 Jul '23

[4,354 Breaking News Photos and Premium High Res Pictures - Getty Images] Weldon Graduate Program Announcements July 5th, 2023 * Career and Internship Opportunities * Graduate Professional Development Newsletter (June 23) * Leadership Development Program - open to all postdocs and early career PhDs * NextProf Pathfinder Workshop OCT. 22-24, 2023 | Ann Arbor, MI * Graduate Professional Development Newsletter (June 30) * Design Your Career On-Line Tool - Yale's Office of Career Strategy * Workshops and Deadlines * News from You Career and Internship Opportunities Internship Positions * Fit and Wear Test Engineer, New Balance<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fjobs.newb…> * ARC Usability Engineering Co-op, GE Healthcare<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fjobs.geca…> * Manufacturing Engineering Co-op/Intern, Infraredx<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.linke…> * Biomedical Engineering Co-op, Novartis<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.linke…> Postdoctoral Positions * Research Fellow, Physiology and Biomedical Engineering, Mayo Clinic<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fjobs.mayo…> * Post-Doctoral Associate, Biomedical Engineering, University of Minnesota<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhr.myu.um…> * NPA Website: https://careers.nationalpostdoc.org/jobs/<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcareers.n…> Full Time Positions * Operations Professional Development Program, Abbott<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jobs.…> * Senior/Staff Algorithm Engineer, Computer Vision, Noah Medical<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.simpl…> * Senior Engineer, R&D, Medical Device, Microfluidics, Novo Nordisk<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcareers.n…> * Engineer, Scientist II, Manufacturing Sciences, Thermo Fisher<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fjobs.ther…> * Sterilization Quality Engineer, Medical Device, Transmedics<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.simpl…> * Senior/Principal Scientist, Enzyme Engineering, BioMap<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.simpl…> * Associate Scientist, Strain Engineering, Willow Biosciences<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.simpl…> * R&D Engineer III, Simulation and Modeling, Align<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fjobs.alig…> * Biomedical Engineer, Regulatory Affairs Specialist, Radlink<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.simpl…> * Assistant/Associate Scientist, Bioengineering, California Institute for Quantitative Biosciences<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Faprecruit…> * Biomedical Engineer, Oakwood Labs<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.simpl…> * mRNA, Engineer, Scientist, Vaccine, Sanofi<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fjobs.sano…> * Process Engineer II, Medtronic<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmedtronic…> * Purdue Start-up Job Board<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurduefou…>-Foundry Start Up Companies Looking to Hire * ACTS Career Center<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcareers.a…>-Association for Clinical and Translational Science * Academic Careers<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Facademicc…> * Doc Jobs<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.docjo…>-Jobs beyond traditional clinical and academic roles Graduate Professional Development Newsletter (June 23) Graduate Professional Development Newsletter (June 23)<https://mailimages.purdue.edu/vo/?FileID=5ecfd549-30b7-4fd3-9b70-9146404a72…> Leadership Development Program - open to all postdocs and early career PhDs The Office of Education, Training, & International Services (OETIS) is excited to announce applications are being accepted for the Foundations of Leadership Program, a Torrey Pines Leadership Development Program at Sanford Burnham Prebys! This year-long program, originally established in 2015, is designed specifically for postdocs and early career PhDs. The purpose of the program is to learn more about your leadership style and the styles of others towards understanding how you and your current/future teams can succeed. Major topics that will be discussed in the context of leadership include: communication styles, conflict management, leadership strengths, influencing others, and negotiation. To learn more about the program, see attached flyer and visit http://sbpleaders.org/SitePages/Foundations.aspx<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsbpleaders…>. Space is limited! To apply, visit http://sbpleaders.org/SitePages/Foundations.aspx<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsbpleaders…> and complete the online application form. If accepted into the program, participants will pay a $285 fee that covers all program expenses and assessments. Application Deadline: July 11, 2023 @ 11:59 pm PT We recognize that as a year-long program, this may appear to be a large time commitment, but keep in mind that the program meets virtually only once a month (~4 hrs) on Friday mornings from August 2023 to June 2024. Project and self-study time will be at your discretion. If you have concerns about your ability to participate, do not hesitate to contact us (sbpleaders(a)sbpdiscovery.org<mailto:sbpleaders@sbpdiscovery.org>). NextProf Pathfinder Workshop OCT. 22-24, 2023 | Ann Arbor, MI The NextProf Pathfinder Workshop is intended for rising 1st and 2nd year PhD students and those in a Master's program intending to apply for a PhD program. The workshop prepares participants for a successful career in academia, and offers information on what it takes to build a competitive graduate school record to obtain a faculty position in academia/the professoriate. Participant application deadline: July 20th Find more information here: https://nextprofpathfinder.engin.umich.edu/<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fnextprofp…> Design Your Career On-Line Tool - Yale's Office of Career Strategy This effective and engaging online tool<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Focs.yale.…> is based on original concepts developed at Stanford University to apply Design Thinking principles to career decision-making and honed further by the advisors of Yale's Office of Career Strategy. The tool can be accessed directly through the Yale Office of Career Strategy website<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Focs.yale.…> through the Design Your Career Button at the top, or you may link directly to this page<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Focs.yale.…> Graduate Professional Development Newsletter (June 30) Graduate Professional Development Newsletter (June 30)<https://mailimages.purdue.edu/vo/?FileID=9923127b-a352-416b-91b1-c92c7ea302…> Workshops and Deadlines Here are some upcoming workshops and deadlines more detailed information about the workshops will be sent out separately closer to the event. July 6th NSF Fellowship Help Session (Enroll Here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgspd.gosi…>) July 7th Power & Control Workshop (CARE<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgspd.gosi…>) July 7th Postdoc Orientation (Enroll Here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgspd.gosi…>) July 7th Summer Lecture Series: A Conversation with Dr. Janice Lee (Register Here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.train…>) July 11th Deadline to apply for Torrey Pines Leadership & Development Program (Apply Here<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsbpleaders…>) July 14th RCR: Discipline-Specific Training (Enroll Here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgspd.gosi…>) July 14th Dr. Eliseo Perez-Stable: My Career Path to NIHMD: Health Disparities & Diversity (Register<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.train…>) July 18th Publishing a Scientific Paper (Enroll Here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgspd.gosi…>) July 18th NSF Fellowship Life Sciences Panel (Enroll Here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgspd.gosi…>) July 18th NSF Fellowship Physical and Computational Sciences Panel (Enroll Here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgspd.gosi…>) July 18th Fellowship Office Hour for Grad Students and Postdocs (Enroll Here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgspd.gosi…>) July 19th NSF Fellowship Engineering Panel (Enroll Here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgspd.gosi…>) July 19th NSF Fellowship Social Sciences and Education Panel (Enroll Here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgspd.gosi…>) July 19th NIH Graduate & Professional School Fair (Register Here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.train…>) July 20th NSF Fellowship Agriculture Panel (Enroll Here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgspd.gosi…>) July 20th Business Meal Etiquette (Enroll Here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgspd.gosi…>) July 20th NSF Fellowship Help Session (Enroll Here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgspd.gosi…>) July 24th Budgeting and Saving Money (Enroll Here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgspd.gosi…>) July 24th-Aug. 1st Virtual NIH Graduate & Professional School Fair (Register Here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.train…>) July 25th Computational Fellowships Info Session (Enroll Here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgspd.gosi…>) July 26th How to Find and Prepare for Fellowship Applications (Enroll Here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgspd.gosi…>) July 26th NDSEG (Defense Research) Fellowship Info Session (Enroll Here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgspd.gosi…>) July 27th Postdoc Grant Writing: All About NSF (Enroll Here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgspd.gosi…>) July 27th NSF Fellowship Help Session (Enroll Here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgspd.gosi…>) July 24th-25th Facilitating Entering Mentoring Workshop (CIMER<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsites.goo…>) Aug. 11th Deadline to apply for Stanford Biodesign Innovation Fellowship (Apply here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbiodesign…>) News from You Please inform Tammy of honors, awards, or other accolades (to include having a paper published) you receive so that the Weldon School may recognize your accomplishments. Send the complete information - specific title and nature of the award, name of conference or event at which award was given, date of said event, photograph if available, etc. - to tsiemers(a)purdue.edu<mailto:tsiemers@purdue.edu>. Tammy Siemers She/Her Associate Director, Graduate Education Weldon School of Biomedical Engineering 206 S. Martin Jischke Drive, West Lafayette, IN 47907-2032 o: 765-496-0294 Achiever, Relator, Includer, Restorative, Developer [233FFCD4]<https://www.purdue.edu/?utm_source=signature&utm_medium=email&utm_campaign=…>

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BME Master's Defense Announcement for Clarisse Zigan (D. Chan, Advisor)
by May, Sandra M 05 Jul '23

05 Jul '23

BME Master's Defense Announcement for Clarisse Zigan (D. Chan, Advisor) Everyone is invited to attend the public presentation beginning at 3:00pm Title: Exploring Changes to Matrix Mechanics and Composition of Chondrocyte-laden Hydrogels Defense Date: July 18th Defense Time: 3:00pm Defense Type: In person at MJIS 2001 or virtual at https://purdue-edu.zoom.us/j/99312080091?pwd=RnBkMSs3eHViZ0F3Kyt4Vlhqdld2UT…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> Meeting ID: 993 1208 0091 Passcode: 411736 Committee: Dr. Deva Chan, Chair; Dr. Alex Chortos, Dr. Douglas Brubaker Abstract: To explore the mechanisms of cellular mechanotransduction, it is necessary to employ biomaterials that effectively merge biofunctionality with appropriate mechanical characteristics. Agarose is a standard biopolymer used in cartilage mechanobiology but lacks necessary adhesion motifs for cell-matrix interactions to complete mechanostransduction studies. Collagen type I is a natural biomaterial used in cartilage mechanotransduction studies but creates an environment much softer than native cartilage tissue. In these studies, agarose is blended at two final concentrations (2% w/v and 4% w/v) with collagen type I (2 mg/mL). Our ultimate goal is to determine whether a composite hydrogel of agarose and collagen can create a mechanically and biologically suitable matrix for chondrocyte studies. First, hydrogels were characterized by rheologic and compressive properties, contraction, and structural homogeneity. Following baseline characterization, primary murine chondrocytes were embedded (1 x 106 cells/mL) within the hydrogels to assess the longer-term in vitro impact on matrix mechanics, cell proliferation, sulfated glycosaminoglycan (sGAG) content, and cellular morphology. To begin probing questions about physiologic loading conditions that chondrocytes experience in vivo, a custom compression loading system was validated using cell-laden hydrogels. Briefly, the 4% agarose - 2mg/mL collagen I hydrogel composites were able to retain chondrocyte morphology over 21 days in culture, resulted in continual sGAG production, and had bulk mechanics similar to that of the stiffest hydrogel material tested, indicating this hydrogel class may be promising towards developing an effective hydrogel for chondrocyte mechanotransduction and mechanobiology studies, a critical step towards a fuller understanding of cell-matrix interactions.

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BME PhD Defense Announcement for Thomas L. Jenkins (D. Little, advisor)
by May, Sandra M 05 Jul '23

05 Jul '23

BME PhD Defense Announcement for Thomas L. Jenkins (D. Little, advisor) Everyone is invited to attend the public presentation beginning at 10:00am. Title: Optimizing Engineered Tendon Development via Structural and Chemical Signaling Cues Date: July 11, 2023 Time: 10:00am Location: Drug Discovery Lobby Conference Room & Zoom - https://purdue-edu.zoom.us/j/97765911603?pwd=NTM2WnpFYVJSMjhVakoxWi9LMktFZz…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> Meeting ID: 977 6591 1603 Passcode: 857381 Committee: Dianne Little, Chair; Julie C. Liu; Marxa L. Figueiredo; Russell P. Main; Sarah Calve Abstract: The rotator cuff is a group of four muscles and tendons in the shoulder that function to lift and rotate the arm. Rotator cuff tendon tears are increasingly common: more than 545,000 rotator cuff surgeries occur annually in the US. However, treatment is often complicated by disorganized collagen matrix formed via fibrosis and results in high re-tear rates. Tendon tissue engineering seeks to solve the problem using biomaterials to promote neo-tendon formation to augment repair or regenerate tendon. However, while current biomaterials provide the opportunity to improve tendon healing, they frequently still exhibit fibrosis in preclinical studies. Therefore, a critical need exists to understand the mechanisms of aligned collagen formation when designing biomaterials for tendon tissue engineering. Matrix architecture and transient receptor potential cation channel subfamily V member 4 (TRPV4) regulate aligned collagen formation during tenogenesis in vitro, but the mechanism remains to be determined. Recently, TRPV4 stimulation was found to induce nuclear localization and activation of transcriptional co-activators Yes-associated protein (YAP). YAP expression is upregulated during tendon development, a process characterized by aligned collagen formation, and in response to physiological mechanical stimulation, suggesting it could play an important role in tendon. The objective of this work is to improve tissue engineering strategies and progress toward making a device that regenerate tendon after injury. Aim 1 incorporates tendon-derived matrix into synthetic polymer scaffolds to add biological signaling cues to induce tenogenesis. Aim 2 uses a 2D photolithography system (microphotopatterning) to optimize architectural and structural cues to promote stem cell differentiation toward tenogenic lineages. Aim 3 investigates dynamic tensile loading protocols to promote collagen matrix synthesis and improve engineered tendon mechanical function. Aim 4 investigates the role of TRPV4 and YAP in collagen alignment during engineered tendon development.

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Announcing the Trailblazers Symposium at Caltech, Division of Engineering and Applied Science
by Gelfand, Johanna K 03 Jul '23

03 Jul '23

(Sent to BME graduate students and post doctoral researchers) Dear colleague, The Division of Engineering and Applied Science (EAS) at Caltech is excited to announce the EAS Trailblazers Symposium, occurring November 2-3, 2023. This event seeks to recognize, and provide professional opportunities for, outstanding young researchers who are within 1-2 years of applying for a faculty position. We especially encourage applications from candidates who are committed to enhancing diversity, equity, and inclusion in the areas of research, teaching, and/or outreach. Further details are available at eastrailblazers.caltech.edu<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Feastrailb…>. I would like to ask your help in encouraging your most outstanding students and postdoctoral scholars to apply to our program. A flyer is attached to this email, which I hope can be posted on your campus. The deadline for applications is August 15, 2023. Thank you for your assistance in identifying candidates for our program. Sincerely, Harry Atwater Otis Booth Leadership Chair, Division of Engineering and Applied Science; Howard Hughes Professor of Applied Physics and Materials Science; Director, Liquid Sunlight Alliance

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[Bmeroundtable-list] BME Monday Roundtable - July 3, 2023
by Gelfand, Johanna K 03 Jul '23

03 Jul '23

[cid:image001.jpg@01D9AD8C.F13D8DB0] BME Monday ROUNDTABLE July 3, 2023 INTERIM HEAD’S NOTE I am starting this new position as Interim Head in the Weldon School of Biomedical Engineering at Purdue University. I am humbled to continue to have the wonderful opportunity to serve the Weldon School, its faculty, staff, and students. I hope to serve all of you better in the coming academic year in this role. UPCOMING IMPORTANT DATES Week of July 3 Tues., July 4: Official University Holiday. All offices and buildings closed. Wed., July 5: BME Summer Seminar, 9:30 a.m., via Zoom. Grigorii Rudakov (Tamara Kinzer-Ursem/Leopold Green, advisors) will present “Drug Delivery Through Blood-Brain Barrier: DNA Nano Lego for Grown-Ups” and Ankit Shah (Hugh Lee, advisor) will present “Advancing Smart Catheter Technology: Development of a 4-Axis 3D Printer for Direct Printing of Electronics on Curvilinear Surfaces.” Thurs., July 6: BME Master’s Defense Announcement for Zada B. Anderson (B. Duerstock and Thomas H. Everett IV, co-chairs), 2:00 p.m., via Zoom. Title of presentation: Cardiac Effects of Recurring Autonomic Dysreflexia. MJIS UPDATES Just a reminder: If you eat/snack in any of the seating areas in MJIS, please take a moment when you are finished to spray and wipe down the tables and make sure all trash is in the trash bins. We are seeing quite an infestation of ants that are attracted to food residue and crumbs! There are cleaning supplies available in each area. PLEASE remember to clean up after yourself each time. Also, we are seeing a lot of backpacks, bookbags and personal items being left in the sitting areas. The Purdue Police have notified us that the theft ring has made a reappearance on campus, and are working their way through campus building. This particular group works on a “theft by convenience” mode – entering unlocked offices, and taking whatever is readily available. If you have high school students or others working in your labs this summer, please make sure they keep their personal belongings on the provided hooks inside the secure lab block. Don’t allow yourself to be the victim of a convenience crime! Important deadlines and information Tues., July 11: BME IBSC PhD Defense Announcement for Mazin Hakim (L. Solorio, advisor), 3:00 p.m., MJIS 2001 and via Zoom. This defense is open only to those who have signed the Lilly NDA. Title: Platforms for Molecular Mechanisms and Improvement in Subcutaneous Injection of Biotherapeutics. Advisory Committee: Luis Solorio, Chair; Arezoo M. Ardekani; Julie C. Liu; Pavlos P. Vlachos. Join Zoom Meeting https://purdue-edu.zoom.us/j/94670872770?pwd=SmxaZjFlaSs3RXVPZWZsU3d3SXhsQT…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.googl…> Meeting ID: 946 7087 2770 Passcode: Mazin Sat. July 15th: Nominations submitted from faculty and staff for Purdue Engineering Fellows. The Purdue Engineering Fellows program is designed to recognize the accomplishments, contributions and potential of seven outstanding seniors who make a difference in the college and in the lives of others by bringing creative thinking to their academic activities, demonstrating distinctive problem-solving abilities, and are respected by their peers and faculty. In summary, Purdue Engineering Fellows will be students who demonstrate impressive abilities to think creatively and to develop innovative solutions to problems—whether in the classroom, in student life, or in the community. We are now asking our faculty and staff to submit nominations through the Qualtrics survey: https://purdue.ca1.qualtrics.com/jfe/form/SV_7ZZLY4ioCfXwjb0<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> by July 15th. Students must be in their senior year and graduating in May of 2024 (December grads are not eligible). Upon graduation, each recipient will receive $20,000 to use as they see fit. A nomination letter and copy of the student’s resume are required for full consideration. Contact Darshini Render (render(a)purdue.edu) if you have questions, including verifying your student nominee eligibility. You can find information about previous Purdue Engineering Fellows here: https://engineering.purdue.edu/Engr/AboutUs/News/Spotlights/2022/2022-0923-… Mon., July 24: Final Grade Entry Begins. (Ends promptly at 5:00 p.m., Tues., August 8th). Wed., Sept. 6: BMES Early Bird Registration Deadline! Register now to lock in savings with early-bird pricing for the 2023 BMES Annual Meeting (to be held in Seattle, WA, October 11-14). Thousands of biomedical engineers will attend this year’s meeting to learn, collaborate, and network. As a BMES member, you can save more than 10% with reduced early bird rates, so if you’re not already a member, now would be a good time to join! Click here for details: https://mailchi.mp/e3958bb463f2/o8cvhb9q5x-9335625?e=ea10e317a2<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailchi.m…> NOTE: We recommend booking your room at the Hyatt Regency Seattle because it’s closer to the convention center AND it’s where university receptions will be held (in addition to some being held inside the convention center). Here’s the link to reserve with the $259 discount rate. This rate only lasts until the allotted number of rooms have been sold. https://www.hyatt.com/en-US/group-booking/SEARS/G-BMES<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.hyatt…> Fri., Sept. 8: Abstract Submission Deadline for The Trauma THOMPSON Challenge. The primary goal of The Trauma THOMPSON Challenge is to encourage research to build better algorithms for autonomous instruction systems in uncontrolled and austere environments, especially for life-saving procedures. The envisioned algorithms include action recognition, action anticipation, procedure recognition, and visual question answering (VQA). The challenge participation details are below. Committee Updates Academic Programs Update Summer Grading Deadlines: 1. Final Grading windows are found here<https://www.purdue.edu/registrar/faculty/grading/index.html>: * Full 12-week summer session (includes all undergrad and grad-level research students) * Grade entry begins at 8 a.m. Monday July 24th and ends promptly at 5 p.m. Tuesday August 8th. 2. [cid:image002.png@01D9AD8C.F13D8DB0] Guidance on Final grading<https://nam04.safelinks.protection.outlook.com/ap/w-59584e83/?url=https%3A%…> 3. Now is the perfect time for faculty to take the 15 minutes to get all your required certifications up to date BEFORE the deadline approaches. * FERPA * GLBA * Data Handling * Protecting SSNs 4. This page<https://www.purdue.edu/registrar/faculty/grading/PWL-grade-entry-update.htm…> provides myPurdue grade entry instructions. 5. This page<https://www.purdue.edu/brightspace/Docs/Grades/SubmitFinalGradesToBanner.ph…> provides BrightSpace final grade submission instructions. * Those not making the deadline must use the Grade Change Workflow to submit a grade for each student. * Instructions may be found here<https://www.purdue.edu/registrar/faculty/grading/Grade_Change_Workflow.html…>. Resources and further information BME Summer Seminar, Wed., July 5, 9:30 a.m., via Zoom. Grigorii Rudakov (Tamara Kinzer-Ursem/Leopold Green, advisors) will present “Drug Delivery Through Blood-Brain Barrier: DNA Nano Lego for Grown-Ups” and Ankit Shah (Hugh Lee, advisor) will present “Advancing Smart Catheter Technology: Development of a 4-Axis 3D Printer for Direct Printing of Electronics on Curvilinear Surfaces.” *Join Zoom Meeting https://purdue-edu.zoom.us/j/98231659969?pwd=T21Oa1B6QzFyQzFvckMzS1doNGlJUT…<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> Meeting ID: 982 3165 9969, Passcode: biomedical Drug Delivery Through Blood-Brain Barrier: DNA Nano Lego for Grown-Ups Abstract: Treating brain-related diseases non-invasively poses a significant challenge, primarily due to the highly impermeable nature of the Blood-Brain Barrier (BBB). The BBB acts as a filter, preventing the passage of most artificial materials larger than 100 nm. Additionally, the substantial proton gradient between the brain and blood flow further complicates drug delivery. However, the field of nanomaterials offers promising solutions to overcome these obstacles, thanks to their small sizes and extensive research spanning over 50 years. Numerous approaches and materials have been investigated to enhance BBB permeability, including polymeric, organic, and inorganic nanoparticles, as well as composite nanomaterials. Despite these efforts, achieving efficient drug transport through the BBB remains a significant challenge. In this study, we focus on utilizing DNA nanomaterials, known for their exceptional biocompatibility, to facilitate the delivery of dyes into the brain. Specifically, we employ DNA tetrahedra, which are extensively studied and possess excellent physical rigidity. Our research investigates the impact of various factors, such as size, structure, receptor-mediated endocytosis pathway, and DNA chirality, on the efficiency of drug delivery. Our ultimate goal is to optimize this approach and achieve maximum delivery efficiency while ensuring high biocompatibility. To assess efficiency, we consider factors such as stability (both biological and physical), toxicity, and the quantity of dye delivered through both passive and active diffusion. The outcomes of this study hold significant potential. Firstly, we aim to gain insights into the most efficient method of drug delivery through the BBB using the most biocompatible material available. Additionally, our research contributes to the advancement of DNA bionanotechnology, paving the way for further developments in this field. Ultimately, our work represents a crucial milestone towards effectively treating brain-related diseases by enabling efficient drug delivery to the brain. This text was edited with chatGPT. Evaluation link for Grigorii Rudakov: https://purdue.ca1.qualtrics.com/jfe/form/SV_2rjC90vn9ZYFw0K<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> Advancing Smart Catheter Technology: Development of a 4-Axis 3D Printer for Direct Printing of Electronics on Curvilinear Surfaces Abstract: The demand for flexible conformal electronics on curvilinear surfaces for health monitoring and therapeutic applications has emerged due to the curvilinear nature of human anatomy. This research focuses on developing a 4-axis 3D printer designed specifically to address challenges associated with the conformal manufacturing of electronics on catheter surfaces for smart catheter applications. The goal is to eliminate complex lithography transfer techniques and overcome issues related to adhesion, surface geometry mismatch, material wastage, and other common problems in traditional fabrication methods. The key innovation of this device is its ability to directly print electronics on the catheter surface, transforming the catheter into a print bed. Leveraging the catheter's rotational movement and automatic height detection with specialized control system algorithms, the printer ensures precise nozzle positioning regardless of the catheter's surface geometry. Directly printing electronics onto catheters enables the development of advanced functionalities, including integrated sensors, wireless communication modules, and therapeutic devices. Additive manufacturing and the versatility of different inks and nanomaterials allow for incorporating a wide range of functionalities into these conformal medical devices. We have demonstrated printing encrypted chipless RFID antennas, microheaters, flow sensors, pH sensors, strain sensors, and flexible conducting traces directly on catheters, unlocking the potential for smart implantable catheters. This advancement enhances monitoring, diagnostics, and treatment capabilities while reducing the complexity and costs associated with traditional manufacturing techniques. The 4-axis printing approach provides customization and adaptability, allowing for patient-specific and tailored electronic devices on catheters. Evaluation link for Ankit Shah: https://purdue.ca1.qualtrics.com/jfe/form/SV_8GrFpXuRHzrgy2O<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> BME Master’s Defense Announcement for Zada B. Anderson (B. Duerstock and Thomas H. Everett IV, co-advisors), Thurs., July 6, 2:00 p.m., via Zoom. Title of presentation: Cardiac Effects of Recurring Autonomic Dysreflexia. Advisory Committee: Bradley S. Duerstock and Thomas H. Everett IV, co-chairs, Riyi Shi Abstract: Persons with a spinal cord injury (SCI) above the sixth thoracic vertebrae commonly experience autonomic dysreflexia (AD), 90 percent of individuals with this level of injury are susceptible to AD which is associated with an increase in sympathetic nerve activity. Left untreated AD causes a paroxysmal rise in blood pressure that may result in seizures, heart attack, or even death. This project investigates how AD affects QT interval, RR interval, P wave height, heart rate, and QRS width both during an event and long term to help identify potential cardiac risks for individuals with SCI who experience chronic AD. Sympathetic tone has been shown to influence QT interval changes that can be indicative of an increased risk of arrhythmia, which can be exacerbated by recurring episodes of AD. A rat spinal cord injury model at the T3 level undergoing colorectal distention (CRD) was used to induce AD. Electrophysiological recordings from an implanted ECG sensor and noninvasive skin nerve activity (SKNA) sensor array during normal baseline and three trials of CRD were collected on days 5, 7, 9, 11, 14, 16, 19, and 21 post-SCI. QT interval measurements were taken for 2 minutes of baseline and for 2 minutes after the initiation of each CRD trial. Corrected QT interval (QTc) was calculated using normalized Bazett’s formula to account for the impact of heart rate on QT interval. It was found that the rats’ susceptibility and reaction to AD events varied between subacute (5-14 days) and chronic phases of SCI. During the chronic phase the incidence of AD events increased during regular occurrences of CRD as indicated by above-threshold (≥15 mmHg) blood pressure spikes. AD events also resulted in increased QT interval short term variability marking an increased risk of arrythmias. Baseline P-wave height and QTc interval were also increased resulting in potentially detrimental cardiac effects. This rat model showed that humans who experience recurrent AD during the chronic phase of SCI may be at increased risk for arrythmia. Location: Zoom - https://purdue-edu.zoom.us/j/93427795215<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> Fri., Sept. 8: Abstract Submission Deadline for The Trauma THOMPSON Challenge. The primary goal of The Trauma THOMPSON Challenge is to encourage research to build better algorithms for autonomous instruction systems in uncontrolled and austere environments, especially for life-saving procedures. The envisioned algorithms include action recognition, action anticipation, procedure recognition, and visual question answering (VQA). The challenge participation details are below. We cordially welcome and invite you to take part in The Trauma THOMPSON Challenge at MICCAI 2023, which will be held in Vancouver, BC on October 12, 2023. ***************************************************************** Event: The Trauma THOMPSON Challenge Location: Co-located with MICCAI 2023 (Satellite Event) Date: October 12, 2023 TIME: AM Session Abstract Submission Deadline: September 8th, 2023 Paper Submission Deadline: September 15th, 2023 Challenge Website: https://thompson-challenge.grand-challenge.org<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fthompson-…> ***************************************************************** Challenge Overview: The primary goal of The Trauma THOMPSON Challenge is to encourage research to build better algorithms for autonomous instruction systems in uncontrolled and austere environments, especially for life-saving procedures. An AI-based guidance system does not only enhance the capabilities of untrained personnel to deliver diagnosis or resuscitative care in austere environments but also increases their confidence to undertake psychologically daunting procedures. This dataset would allow the study of human actions and intentions from the first-person view in the medical domain (refer to egocentric datasets of medical procedures). To the best of our knowledge, our dataset is the first egocentric view dataset of life-saving intervention (LSI) procedures with detailed annotations by medical professionals. We have collected over 200 procedure videos with environment, simulator, and type variability. Based on this dataset, the challenge we propose involves multiple tasks to encourage participants across the globe to design impactful algorithms with applications to medicine. The envisioned algorithms include action recognition, action anticipation, procedure recognition, and visual question answering (VQA). The challenge participation details are available on our challenge website<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fthompson-…>. Call for Participation and Papers: There will be 2 tracks for this challenge and a total of 4 challenge tasks. All accepted papers will be included in the MICCAI challenge proceedings (Lecture Notes in Computer Science (LNCS) volume in the challenges subline). We have a leaderboard for each task and submitting a paper (min 6 pages, max 12 pages, LNCS format) is mandatory for a corresponding submission in any task to be eligible in the official ranking. ● Track 1 o Task 1: Action Recognition o Task 2: Action Anticipation o Task 3: Procedure Recognition ● Track 2 We have prizes for top performing teams in each task and the best paper award. The details are available on our challenge website<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fthompson-…>. Important Dates ● Train data release: 11:59 PM EST, Jul. 6th, 2023  ● Test data release: 11:59 PM EST, Aug. 15th, 2023  ● Participation declaration form deadline: 11:59 PM EST, Aug. 25th, 2023 (Data confidentiality agreement required) - All teams must enter before this date! ● Deadline for results submission: 11:59 PM EST, Sep. 1st, 2023 ● Submit your inference code + checkpoint: 11:59 PM EST, Sep. 5th, 2023 ● Abstract submission: 11:59 PM EST, Sep. 8th, 2023 ● Full Paper submission deadline: 11:59 PM EST, Sep. 15th, 2023 ● Winner announcement: 11:59 PM EST, Sep. 22nd, 2023 ● Conference date: AM session, Oct. 8th, 2023 Organizing Committee ● Nina Jiang, Purdue University ● Yupeng Zhuo, Purdue University ● Juan Wachs, Purdue University ● Andrew W. Kirkpatrick, University of Calgary ● Jessica McKee, University of Calgary ● Kyle Couperus, The Geneva Foundation ● Christopher Colombo, The Geneva Foundation ● Eleanor Birch, Madigan Army Medical Center ● Chad Gorbatkin, Madigan Army Medical Center ● Oanh Tran, The Geneva Foundation ● Jonah Beck, The Geneva Foundation ● DeAnna DeVane, The Geneva Foundation Contact If you have any questions about the Trauma THOMPSON Challenge, please email Nina Jiang (jiang841(a)purdue.edu<mailto:jiang841@purdue.edu>), Yupeng Zhuo (zhuoy(a)purdue.edu<mailto:zhuoy@purdue.edu>), and Oanh Tran (otran(a)genevausa.org<mailto:otran@genevausa.org>). ***Disclaimers: The views expressed are those of the author(s) and do not reflect the official policy of the Department of the Army, the Department of Defense, or the U.S. Government. -- Bmeroundtable-list mailing list Bmeroundtable-list(a)ecn.purdue.edu https://engineering.purdue.edu/ECN/mailman/listinfo/bmeroundtable-list

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