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/1FAIpQLSd8v47EEuzyl070XPk4QyH0fIBflpdLywlCfrGKLKZTtr4Stw/viewform
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)
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-free-active-threat-training-on-may-30.html
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
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.
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=Nll1MlE3TTYyOHZJL3hIYlpGSXhUUT09
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.
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