[cid:image003.jpg@01D987F6.7607FD80] BME Monday ROUNDTABLE May 16, 2023 DEPUTY HEAD'S NOTE I apologize for the lateness. Honoring our graduates, Purdue celebrated spring 2023 graduation last Friday and this past weekend with a record 9 graduation ceremonies. I wanted to find some time on Monday to gather information and do reflections. To many of us, last Friday and the past weekend has been a memorable one. To the faculty, isn't it one of the most rewarding things in your career to hood your students, which signifies the completion of their long and often frustrating journey of PhD research. I proudly hooded two of my PhD students on Sunday evening. At the Armory and the Elliot Hall of Music, I saw Sherry, Craig, Joseph, Vitaliy, Luis, and Elsje (I apologize if I missed anyone). I saw a number of our students on stage receiving their well-deserved diplomas. Congratulations to the major professors and the recent PhD alumni. We've all made it together finally! Yay! Professor Kathleen Howell, the Hsu Lo Distinguished Professor of Aeronautics and Astronautics in the College of Engineering at Purdue University was the Guest Speaker of the Ninth Division (for doctoral and master's degree recipients). In her speech, she quoted President John Kennedy's famous saying from his "We Choose the Moon" speech: "We choose to go to the moon in this decade and do the other things, not because they are easy, but because they are hard." Many research projects in biomedicine are what JFK referred to as "the other things". Our finest faculty and PhD students are doing those things, exactly because they are hard. So proud of you all. Congratulations on your accomplishments. Particularly to those recent PhD alumni, this may be the last Roundtable email you read. I wish you the best of luck in your future. Continue to choose great things in biomedicine to do because they are hard. Last weekend, it was also a memorable weekend for our graduating seniors. They will never forget the four years' education in one of the finest schools at one of the finest engineering colleges. Kudos to our faculty and graduate student mentors. You are a big reason they are who they are now, with your teaching and mentoring as someone introducing to them the wonderful profession of biomedical engineering, and more importantly, someone who was set as their role model for the past four years and the many years to come. On Saturday morning, the department hosted the graduates and their parents at a Commencement Reception here in the MJIS Atrium. I was unable to attend it. Tami, as an attendee, wrote the following: To honor our Weldon School graduates, we held our annual Senior Dinner and BME Commencement Reception this past week. Over 150 new alumni and their families joined in the celebrations. These students have successfully navigated some of the most challenging years in recent history (COVID, economic downturns, changing education landscape). We applaud them for their hard work and thank them for their contributions to the Weldon School over the years. All the best to our recent Graduates! I attended the graduation ceremony for our graduating seniors last Friday afternoon (Second Division). It was an exciting experience shaking so many hands with them (definitely record-setting in the number of handshakes in one day). I was particularly taken by the commencement speech given by our President Chiang on artificial intelligence, besides getting the laughs out of it (e.g., he joked about the speech was not written by ChatGPT. The AI version of the speech if asking ChatGPT, would read like a B- high school essay, a grammatically correct synthesis with little specificity, originality or humor). His speech called on all Boilermakers to lead in "sharpening the ability to doubt, debate and dissent" in world of AI. I thought a lot about it over the weekend. I could not find a better area than human health where we really need great ability to doubt, debate and dissent what AI will give us. And our school undoubtedly should be the frontrunner in enhancing such ability. How would a physician really trust AI in assisting their decision making? How would an aging-in-place elderly adult really benefit from an AI-enabled digital companion? How would an AI-enabled analytics module, when deployed by a healthcare organization, be made sure to not widen health disparities while driving up the organization's revenue? How we can ensure ethical, privacy-preserving ways to collect data from human when the AI is just thirsting for more and more data? Important MJIS Alerts Starting Tuesday, May 16th (NOTE new date!), Martin Jischke Drive will be CLOSED to all traffic. The university will be performing infrastructure repairs in the area. The street will be closed to traffic for most, if not all of the summer. When the street reopens, bike lanes will replace the on-street parking, although we do not currently have details/confirmation on the entire process yet. Stay tuned for additional details. Wednesday, May 17th and Thursday, May 18th: MJIS passenger elevator will be DOWN both days for much-needed repairs. Analog stairwells will still be fully functional. Week of May 22: Exterior washing of windows in MJIS will take place this week. If you feel like you're being watched, look out your windows to see if there is someone there. We don't know specifically what days they will be working on MJIS, but it will be this week. There will be lifts moving around the building, so please be aware and be careful. REMINDER: Purdue University is a NON-SMOKING campus. You are not permitted to smoke/vape in or around MJIS. There is a smoking area on the other side of Martin Jischke Drive, near the police station. Remember that the air intakes for the entire building are located externally. If you smoke on the sidewalk outside of MJIS, it is drawn into and distributed throughout the building! Don't do it! Here is a map of all the smoking areas on campus: https://www.purdue.edu/smokefree/Smoking_map.pdf The closest to MJIS is labeled "4" UPCOMING IMPORTANT DATES Week of May 15 Wed., May 17: BME Summer Seminar Series, 9:30 a.m., via Zoom. The BME Summer Seminar Series will run from May 17th - August 9th. The first week's speakers will be Ruhi Sharmin and Brendan Ball. Full schedule is attached. Fri., May 19: BME PhD Preliminary Exam Announcement for Shulan Xiao (K. Jayant, advisor), Everyone is invited to attend the presentation beginning at 11:00 a.m. in MJIS 2001 and via Zoom. Title: The Biophysical Basis of Sensory Feature Binding in Cortical Pyramidal Neurons. Upcoming Opportunity for Fun! Do you play a band instrument? Purdue Bands and Orchestras has just opened registration for the 2023 Purdue University Summer Band! This ensemble is open to all area musicians that are high school age and up. Participation in Purdue's Summer Band is FREE to all. We plan to begin rehearsals on Tuesday, June 20, and rehearse on Tuesday and Thursday afternoons from 4:00-5:30 PM in Hagle Hall, Room 178. Our concert will be held on Thursday, July 20, 6:30 PM at Columbian Park Memorial Island Amphitheater immediately prior to a performance by the Lafayette Citizens' Band. Register Here: https://docs.google.com/forms/d/e/1FAIpQLSd8v47EEuzyl070XPk4QyH0fIBflpdLywlC... Upcoming important deadlines and info. Tues., May 23: BME PhD Defense Announcement for Mrugesh Krishna Parasa (Dr. Kevin Solomon, advisor). Everyone is invited to attend the public presentation beginning at 3:00 PM via Zoom. Title of the Thesis Research: Programmable Control of Protein Activity via Formation of Biomolecular Condensates in Bacteria. Thurs., May 25: Application Deadline for Trailblazers in Engineering workshop, to be held on the Purdue campus July 25-26. Trailblazers in Engineering (TBE) is a multi-day workshop focused on preparing future outstanding engineering scholars for future engineering faculty careers who are also committed to increase the success of underrepresented communities of engineers. Trailblazers in Engineering Fellows are selected not only for their outstanding scholarly achievements but also for their potential impact in expanding representation and diversity in engineering. See attached flyer for application instructions. Tues., May 30: C.R.A.S.E. (Civilian Response to Active Shooter Events) training is available through the Purdue University Police Department. Contact Sarah Clark (sclark32@purdue.edu<mailto:sclark32@purdue.edu>) to sign up for your 9:30, 1:30 or 5:30 session. All faculty and staff are encouraged to attend. For additional information see: https://www.purdue.edu/newsroom/purduetoday/releases/2023/Q2/pupd-to-offer-f... Committee Updates Graduate Office Update Dear BME Faculty, Weldon BME PhD students performing research in one of these areas - cardiovascular devices, implantable biomaterials design, drug-delivery systems, or biochemical sensors - are eligible for nomination for the Ronald W. Dollens Scholarship. For the nomination, we will need from you a short description (less than 250 words) of an outstanding, current graduate student in your lab who is excelling in research performance and service to the department. In your description, please mention/include the following: * Student's year in the PhD program (1st year, 2nd year, etc.) * Brief description of outstanding research performance * Brief description of service to the department * Mention of recent awards, presentations made at conferences, papers authored, etc., that you think help describe the student's contributions * Student's CV Please send the nomination to tsiemers@purdue.edu<mailto:tsiemers@purdue.edu> by Sunday, May 21st. The Ronald W. Dollens Scholarships in Life Sciences will be awarded based on academic merit to two deserving graduate students in the Weldon School of Biomedical Engineering who meet the criteria and are selected. The scholarship award is $5,000 with half being awarded in the Fall 2023 semester and half in the Spring 2024 semester. If you have any questions, please don't hesitate to reach out. New Course for Fall 2023: BME 69500 Pediatric Medical Devices (CRN 14011). Details below. Research Update To safeguard our valuable work and bolster Weldon's standing, it is important that we exercise caution with predatory journals and "hidden" predatory journals. We are collaborating with the Purdue library to organize a session. Stay tuned. https://www.science.org/content/article/fast-growing-open-access-journals-st... https://retractionwatch.com/2023/03/21/nearly-20-hindawi-journals-delisted-f... Participants needed for a Motor Function Study, "Development of a Diagnostic System for Assessment of Motor Impairment," IRB# IRB-2022-1299. See below for details. Resources and further information BME PhD Defense Announcement for Xiao Liu (E. Pienaar, advisor). Everyone is invited to attend the public presentation on Mon., May 15, beginning at 1:00 PM in MJIS 2001. Title: A Deep Understanding of Ebola Virus VLP Assembly: Ode-based Modeling Approach. Thesis Committee members: Elsje Pienaar, Nan Kong, Leopold Green, Robert Stahelin Abstract: EBOV infection remains to be a challenge to human health by its high mortality rate. There are only two antibody-based therapy approved today, and the mortality rate is still high. This can be partially due to the fact that study on EBOV is strictly limited to BSL-4 labs, which hinders our understanding of the pathogen. We also lack a systematical and quantitative view of EBOV infection. Mathematical modeling has been used to assist biological and medical studies for a long time, as it has the advantage of integrating data and providing quantitative insight to a biosystem. In our study, we build the primary ODE-based model of EBOV at subcellular level step by step. Through our computation al study, we propose that PS can directly influence the oligomerization process of VP40 filaments and the budding process of VLPs. Also, the oligomerization of VP40 filaments may also follow the nucleation-elongation process. We conduct in-silico simulation to evaluate the efficiency of fendiline in treating EBOV. We find that while in general, fendiline can decrease VLP production, there can be fendiline-induced VLP production at certain time points due to slow filament growth rate or fast VLP budding rate. Also, fendiline is relatively more effective when applied in the budding stage. Moreover, it can be extra efficient when applied with VLP budding step targeted treatment. Finally, we integrate nucleoprotein (NP) into our model. We predict that NP increase VLP production through impacting filament oligomerization and VLP budding steps. Also, dual-effect of NP on VLP production may exist, as too high NP/VP40 production ratio can inversely decrease VLP production. From the aspect of protein expression time, we find that a bit earlier NP production than VP40 production is beneficial for both IB-containing VLPs production and prevention in energy waste on empty VLPs. Overall, we have built a solid foundation towards mathematical EBOV model and demonstrated its ability in assisting experimental EBOV studies. BME Summer Seminar Series, Wed., May 17, 9:30 a.m., via Zoom. The BME Summer Seminar Series will run from May 17th - August 9th. The first week's speakers will be Ruhi Sharmin and Brendan Ball. Ruhi Sharmin (Pavlos Vlachos, advisor): Spectro-temporal Feature Generation Method for Atrial Fibrillation Detection in ECGs Abstract: This work presents a framework for extracting a novel set of features from Lead II ECGs and using these features to detect atrial fibrillation. Our method pre-processes the signal using a denoising step, identification of the QRS complexes, and beat segmentation. Subsequently, we use a series of signal processing methods including proper orthogonal decomposition (POD), the continuous wavelet transform (CWT), discrete cosine transform (DCT) and the standard cross correlation to extract a total of 48 signal features. The extracted features are classified into four groups: correlation (C), morphology (M), Discrete cosine transform (D), and entropy (E). In general, these features represent novel and robust ways to characterize and assess key aspects of arrhythmias, such as beat-to-beat variability and the presence of fibrillatory waves. Subsequently, we use the feature set to train a machine learning based ECG classifier using XGBoost (eXtreme Gradient Boosting). For designing, training, and testing of our method, we used the 2017 PhysioNet Challenge dataset which annotates ECGs into categories of 'Normal', 'Atrial Fibrillation', 'Other', and 'Noisy'. For this purpose, first, we took an exhaustive grid search approach for hyper-parameter optimization of the classifier algorithm. Second, a k-fold cross-validation was used for creating k-unique subsets from the original undivided dataset for enhanced generalization of our model. Third, we partitioned each subset into different 80-20 train-test splits for building the model. The drop in the weighted average of the F1 scores of our proposed model from the training to the testing phase was only 3% whereas it was ~10% for prior works. This proves that our model is free from overfit and more generalized towards ECG dataset. On the other hand, mean F1-scores on the test dataset were 84% and 94% for the Normal and AFib categories, respectively. Moreover, the F1-score of AFib at 94% showed significant improvement (~10%) over established methods (82%~85%), while also using significantly fewer total features comparably. This demonstrates that our novel feature XGBoost arrythmia classifier can differentiate AFib and normal sinus rhythm from other arrhythmias in Lead II ECGs effectively. Moreover, by using a smaller feature set, our method is adaptable for real-time arrhythmia detection and is effective even for short (<10 beat) ECGs. Evaluation link Ruhi Sharmin: https://purdue.ca1.qualtrics.com/jfe/form/SV_eIZzuVuHE8dCC2i Brendan Ball (Doug Brubaker, advisor) ; Profiling Neuron Cytokine Expression Stimulated from Metabolites Associated with Alzheimer's Disease & Type 2 Diabetes Abstract: Alzheimer's disease (AD) is the most common form of dementia that leads to memory loss, behavioral changes, and decline of cognitive function. In the United States, more than six million people are living with AD. Of this population, 81% of people with AD also reported to have impaired glucose levels or type 2 diabetes (T2D), a metabolic disease that affects blood sugar regulation. While there is a connection between T2D and AD, the biological pathway and mechanism in which T2D exacerbates AD progression is not well-understood. A literature review revealed nine candidate metabolites that are upregulated in the presence of people with T2D, AD, or both. We compared metabolites associated with neuroprotective or neurodegenerative properties, which include lauric acid, asparagine, fructose, arachidonic acid, aminoadipic acid, sorbitol, retinol, tryptophan, and niacinamide. The nine metabolites associated with the potential development of AD or T2D were used to individually stimulate cultures of primary neurons collected from embryonic CD1 mice. After neuronal stimulation, the cell media was sampled and analyzed using a Luminex assay. Our findings indicate that cytokines involved in the JAK/STAT and chemokine receptor pathways may be involved in T2D or AD development. Specifically, we have found that cytokines including MCP-1, MIP-1alpha, and RANTES are consistently active across all metabolite stimulations, despite associations to different disease groups. These cytokines may serve an important role in AD and T2D progression. Improving our understanding of the relationship between AD and T2D will enable further studies that utilize biosystems for the development of potential treatments. Evaluation link Brendan Ball: https://purdue.ca1.qualtrics.com/jfe/form/SV_doH4Ktq6v86aBZs *Join Zoom Meeting https://purdue-edu.zoom.us/j/98811885943?pwd=Nll1MlE3TTYyOHZJL3hIYlpGSXhUUT0... Meeting ID: 988 1188 5943, Passcode: biomedical BME PhD Preliminary Exam Announcement for Shulan Xiao (K. Jayant, advisor), Fri., May 19. Everyone is invited to attend the presentation beginning at 11:00 a.m. in MJIS 2001 and via Zoom. Title: The Biophysical Basis of Sensory Feature Binding in Cortical Pyramidal Neurons. Advisory committee: Krishna Jayant, Chair; Alexander A. Chubykin; Edward L. Bartlett; Fang Huang; Scott R. Pluta Abstract: Feature binding is critical for sensory perception and pattern classification. In cortical layer 2/3 and layer 5 pyramidal neurons (L2/3 and L5 PNs) feedforward inputs synapse onto basal dendritic arbors in distinct spatio-temporal patterns. How these distributed inputs integrate, multiplex, and dictate unique output codes, however, remains poorly mapped. Furthermore, it remains unclear how specific input sequences learn over time to aid pattern classification and whether this plasticity and integration is shaped by top-down feedback. To address these outstanding challenges, I have designed and implemented a new microscope capable of stimulating synapses via 3D transmitter uncaging while simultaneously recording the electrical input-output transformation. Using this platform across in vitro acute slice preparations, I propose to unravel the biophysics of multibranch dendritic integration and feature classification under quiescent and in vivo like states in L5 pyramidal neurons - the primary output layer of the cortex. Here, my aims are focused on dissecting mechanisms that underlie multiplexing across basal dendrites, plasticity mechanisms that assist efficient feature classification, and the role of top-down modulation in shaping basal dendritic integration. I propose innovative methods including two-photon holographic uncaging, dynamic clamp, computational modeling, and in vivo two-photon calcium imaging to test and validate my hypotheses. Successful completion of my aims will lead to a new understanding of how dendritic nonlinearities facilitate efficient feature classification amidst noisy backgrounds in individual L5 PNs, including different subtypes. The outcome of this finding is not only poised to improve our understanding of neural signal processing but could bolster the design of future biologically inspired artificial intelligence-based neuromorphic systems. Zoom link: https://purdue-edu.zoom.us/j/9146700686 BME PhD Defense Announcement for Mrugesh Krishna Parasa (Dr. Kevin Solomon, advisor). Everyone is invited to attend the public presentation on Tues., May 23, beginning at 3:00 PM via Zoom. Title of the Thesis Research: Programmable Control of Protein Activity via Formation of Biomolecular Condensates in Bacteria. Thesis Committee members: Dr. Kevin Solomon, Dr. Tamara Kinzer-Ursem, Dr. David Thompson, Dr. Leopold Green Abstract: Biomolecular condensates or membraneless organelles are phase separated proteins and/or other biomolecules that are ubiquitous in eukaryotic cells. While these condensates may be liquid with exchange and diffusion of their components with the rest of the cell (e.g. cytoplasm), they locally concentrate their constituent biomolecules altering their interactions in normal cellular processes. Here, we exploit this phenomenon via reversible coacervate formation to control the activity of cellular proteins in E. coli. To induce liquid-liquid phase separation, we fuse proteins to elastin-like polypeptides (ELP) that reversibly aggregate in response to increases in temperature and/or changes in intracellular pH. In so doing, we sequester their fusion partners from the cytoplasm, limiting their ability to participate in cytoplasmic reactions. We have demonstrated this concept in vivo with enzymes and transcription factors for switchable control of protein activity with temperature. For example, I-SceI mediated cleavage of a host genome can be inhibited by increasing the cultivation temperature, creating a simple temperature-sensitive kill switch; accidental release will lower the culture temperature leading to cell death. Similarly, coupled transcription factors exhibit a 2-fold increase in transcription in response to temperature. More importantly, the threshold for coacervate formation and control of protein activity may be tuned through appropriate design of the ELP fusion partner. Our results introduce a simple yet effective, rapid and tunable approach to control protein activity via induction of coacervate formation that may form a powerful new tool for synthetic biology. Zoom link: https://purdue-edu.zoom.us/j/99880181010 Participants Needed for Research Study: (Aditya Shanghavi is a graduate student in Biomedical Engineering at Purdue.) I am currently working on a research project under the direction of my advisor, Dr Anne Sereno. We are inviting you to participate in a brief arm movement study. We are specifically looking for participants aged 45-85 with no history of neurological diseases who are fluent in English and have adequate hearing (with or without amplification) to process verbal instruction and adequate vision to see the computer screen. Participants should be able to perform simple upper arm motions without experiencing major pain or discomfort. We will use non-invasive motion sensors on a wristband to collect arm motion signals during normal and simulated abnormal movements (after viewing short videos) as well as an eye tracker to collect eye motion signals during a prosaccade-antisaccade task. This study's goal is to develop algorithms to detect latencies and amplitudes of movements and to quantify the sensitivity, reliability, and accuracy of the sensors and these algorithms to differentiate normal versus simulated abnormal movements. The study should take no more than 60 minutes and it will be conducted in PSYCH 3125. We will highly appreciate you taking time out of your busy schedule and will compensate you $15 for your help in our research study in addition to our heartfelt gratitude. This study is conducted in accordance with IRB # IRB-2022-1299. If you have more questions regarding this study, please contact Aditya Shanghavi at ashangha@purdue.edu<mailto:ashangha@purdue.edu>. New Course for Fall 2023: BME 69500 Pediatric Medical Devices (CRN 14011). Fall 2023, 3.0 credit hours Wednesdays 11:30-2:20 in MJIS 1083 (in person attendance only) Prerequisite: BME Graduate Standing Course Description: The unique medical needs of pediatric patients in the context of current and emerging clinical technologies are presented in this novel course. Anatomical, physiological, and pathophysiological underpinnings of diseases in infants and children are studied. Unique aspects of pediatric device design, regulation, and translation, including clinical studies and ethical considerations, are explored. Numerous clinical sub specialties such as cardiology, surgery, nephrology, pulmonology, and gastroenterology are examined in terms of technology adoption and remaining clinical needs. Future directions in device development and emerging trends in patient care are considered throughout. Weekly Course Topics: August 23 Pediatrics Introduction August 30 Neonatology Introduction September 6 Pediatric Device Design and Development I September 13 Pediatric Device Design and Development II September 20 Pediatric Device Regulation September 27 Pediatric Clinical Studies October 4 Pediatric Cardiology October 18 Pediatric Cardiovascular Surgery October 25 Pediatric Nephrology November 1 Pediatric Pulmonology November 8 Pediatric Wound Healing November 15 Pediatric Gastroenterology November 29 Ethical Considerations in Pediatrics December 6 Future Directions and Trends Primary Instructor: George Wodicka, MJIS 3036, wodicka@purdue.edu Numerous experts from the Indiana University School of Medicine Department of Pediatrics, Riley Hospital for Children, and Cook Medical, Inc. will actively participate. Attachments 2023ClimateSurveyFlyer_Emailing.pdf Summer Seminar Flyer 2023 -- Bmeroundtable-list mailing list Bmeroundtable-list@ecn.purdue.edu https://engineering.purdue.edu/ECN/mailman/listinfo/bmeroundtable-list
