BME MONDAY ROUNDTABLE

NOVEMBER 7, 2022

Happy Daylight Savings Time! Did you remember to change your clocks yesterday?

 

HEADS NOTE

Hello Weldon School of Biomedical Engineering,

 

We are in full swing of the semester and already starting to gear up for the home stretch.  This week there are a few highlights I want to point out including an RSVP for an AI in ear, nose, and throat meeting with our colleagues at the IU School of Medicine, upcoming Coffee Chat for grad students, and a professional development seminar for postdocs and research associates about time management in the unstructured world of research.  Students, faculty, and postdocs- be sure to take advantage of these offerings and have a great week.

 

UPCOMING IMPORTANT DATES

 

Week of November 7

Mon., Nov. 7: BRAG Meeting for BME postdocs, visiting scientists and research staff, 2:00-3:00 p.m., MJIS 2001. Dr. Tamara Kinzer-Ursem, Associate Professor and Associate Head of Academic Programs in BME will discuss “Time Management in the Unstructured World of Research”. The session will be in the format of a short presentation followed by Q&A, and the speaker has specifically asked us to send suggestions on topics, questions and thoughts ahead of time to best tailor the sessions to us. Please RSVP and email your suggestions to kejendal@purdue.edu. You are of course welcome with spontaneous questions as well! Welcome! Bring a postdoc friend!

Wed., Nov. 9: BME Distinguished Seminar Series, 9:30 a.m., MJIS 1001 and via Zoom. Yen-Yu Ian Shih, Associate Professor and Associate Director for Biomedical Research Imaging Center at the University of North Carolina at Chapel Hill will present “A Silent, Sensitive, Specific, and Artifact-resistant fMRI Technique.”

Wed., Nov. 9:  Frontiers in Biophysics Seminar, 1:30 p.m., MJIS 1001 and via Zoom. Andrei Fokine, Purdue University will present “Structure and assembly of Myoviridae bacteriophages.” Co-sponsored by Structural and Computational Biology & Biophysics (SCBB) in the Department of Biological Sciences and the NIGMS-funded Molecular Biophysics Training Program (MBTP, in partnership with the Departments of Biomedical Engineering, Biochemistry, Physics and Astronomy, Chemistry, and Medicinal Chemistry and Molecular Pharmacology; and the following institutes: PI4D, PCCR, and PIDD. Register in advance for Zoom presentation at: https://purdue.edu/zoom.us/meeting/register/tJUtd-2rrTlqEt28s1D20iZPi-9RRDGj76V5

Wed., Nov. 9: Seminar for Neurotrauma and Diseases, 4:00 p.m. via Zoom. Wen Jiang, Professor of Biological Sciences and Scientific Director of Purdue Cryo-EM Facility will present “Cryo-EM structural characterization of amyloid fibrils in neurodegenerative diseases.” The Seminar for Neurotrauma and Diseases is sponsored by Plexon, a leading neuroscience technology company, and is supported by the Purdue Institute for Integrative Neuroscience and Purdue Institute for Drug Discovery. Join the Center for Paralysis Research and our set of amazing speakers as we explore various facets of neurotrauma and diseases and build a community to make long-lasting impacts on neurotrauma research. Zoom link: https://bit.ly/3QN4YL.

Wed., Nov. 9: Graduate Mentorship Seminar Series: Diversity and Inclusion in Mentorship Relationships, 4:30 p.m., WALC 2051. Learn about how identity and culture are crucial components to recognize in faculty mentor-student advising relationships. Faculty members welcome!

Wed., Nov. 9 – Sat., Nov. 12: The is a go-to conference for underrepresented groups in STEM fields. Scientific or professional development session submissions due July 29.

Thurs., Nov. 10: BME Faculty Coffee Chats for Grad Students, 9:30-10:30  a.m., MJIS 3041. Faculty hosts: Hugh Lee, Taimoor Qazi, Steve Steinhubl. Potential discussion topics: ask me anything/ healthcare, academic jobs/academia, visas/international students

Thurs., Nov. 10:  Seminars in Hearing Research at Purdue, 10:30 a.m., LYLE 1150. Alexander L. Francis, Professor of SLHS will present “RCR Discussion: Practical Considerations for Preregistration in Hearing Science.”

Thurs., Nov. 10:  BMS 692/CPB 697 Graduate Seminar, 3:30 p.m., LYNN 1136. Four graduate students will present their research: Navaporn Sritong, Graduate Student, IBSC will present “Duplex Viral Molecular Assay for Rapid Detection of SARS-CoV-2 and Internal Control Saliva.” Polly Chen, Resident, CPB/ADDL will present “Case Presentation of a Neurologic Sheep.” Tiange Xia, Graduate RA, BMS will present “Examining the Role of the Cortical Amygdala (CoA) in Alcohol Use Disorder (AUD)” and Allegra Stahl, Graduate RA , CPB will present “Attachment Style and Social Fear in Dogs from Commercial Breeding Kennels.” The seminars are hosted by the College of Veterinary Medicine at Purdue.

Fri., Nov. 11: 5th Childhood Diabetes Prevention Symposium, 8:00 a.m. – 3:45 pm MT vi Zoom. The objectives include: (1) Discuss essential components of follow-up and monitoring for children who screen positive for islet autoantibodies (Immune markers, Markers of dysglycemia, Psychological support, Early diabetes education) (2) Review the status of general population screening programs world-wide, and (3) Address new challenges. The registration is free but mandatory for in-person or webinar participation. Click to register:  https://redcap.ucdenver.edu/surveys/?s=WFPKALWFWFXTNNL3

 

Upcoming important deadlines and info.

Mon., Nov. 14: RSVP Deadline for IUSOM Fall Otolaryngology Workshop. Workshop is entitled “AI Topics in Medicine and Otolaryngology, and will be held Wednesday, Nov. 30 from 9 a.m. to 2 p.m. in Fesler Hall, Indianapolis. RSVP to Ashley Claxton (aclaxto@iu.edu)

Wed., Nov. 16: BME PhD Preliminary Exam Announcement for Alexis Hoerter (E. Pienaar, advisor), 11:00 a.m., MJIS 2001 and via Zoom. Research Title: Agent Based Models Characterizing In Vitro M. Tuberculosis Granuloma Dynamics: Host-Immune Status Determinants and HIV Coinfection Mechanisms

Wed., Nov. 16:  Frontiers in Biophysics Seminar Series, 1:30 p.m., MJIS 1001 and via Zoom. Hong Li, Florida State University will present “Small changes, big impact: Roles of chemical medications in gene editing and protein synthesis enzymes.” Register in advance at https://purdue.edu.zoom.us/meeting/register/UUtd-2rrTlqEt28s1D20iZPi-9RRDGj76V5  Seminar series is co-sponsored by Structural and Computational Biology & Biophysics (SCBB) and the NIGMS-funded Molecular Biophysics Training Program (MBTP) in partnership with the Departments of Biomedical Engineering, Biochemistry, Physics and Astronomy, Chemistry, and Medicinal Chemistry and Molecular Pharmacology; and the following Institutes: PI4D, PCCR, and PIDD.

Thurs., Nov. 24 and Fri., Nov. 25: Thanksgiving Holiday. No classes, all university offices and buildings closed.

Tues., Nov. 29: BRAG Meeting for BME postdocs, visiting scientists and research staff, 2:00-3:00 p.m., MJIS 2001. Dr. Elsje Pienaar, Assistant Professor in BME will discuss “Strategies and challenges in learning about DEI”. The session will be in the format of a short presentation followed by Q&A, and the speaker has specifically asked us to send suggestions on topics, questions and thoughts ahead of time to best tailor the sessions to us. Please RSVP and email your suggestions to kejendal@purdue.edu. You are of course welcome with spontaneous questions as well! Welcome! Bring a postdoc friend!

Thurs., Dec. 8: BME Faculty Coffee Chats for Grad Students, 2:00-3:00 p.m., MJIS 2041. Faculty host: Deva Chan. Potential discussion topics: AMA work-life, teaching & diversity statements, time management

Thurs., Dec. 15 The BME Senior Design Expo will be from 3:30 - 5:30pm in MJIS 1097, 1001, and Atrium. There will be 24 projects presented followed by awards ceremony. Stay tuned for additional details.

Fri., Dec. 23 through Mon., Jan. 2: Winter Recess. No classes, all university offices and buildings closed. Purdue will reopen Tuesday, January 3.

 

PROTECT PURDUE

https://protect.purdue.edu/updates/fall-2022-what-you-need-to-know/

 

Committee Updates

 

Academic Programs Update

 

For all course instructors:

As the semester winds down, it’s time to make plans now for how you will approach providing final exam testing accommodations for students who have disability accommodation. Many instructors will plan to provide these accommodations themselves. That is great and often the best approach. However, some may want the DRC’s Accommodated Testing staff to administer their final for these students. In these cases, it is important to be aware of three critical deadlines: 

 

 

If these deadlines are met, DRC Testing will make every effort to administer the instructor’s exam.

 

One last consideration: While DRC Testing does everything it can to work with instructors, they cannot promise to administer the instructor’s exams at the same time that their class is taking it in all cases. Instructors who are able to be flexible with the date and time for their final exam increase the likelihood that DRC Testing will be able to support them.

 

Please feel free to connect with the Director of the DRC, Randall Ward, ward176@purdue.edu, as needed.

 

Undergraduate Programs Update

 

The BME Senior Design Expo will be Thursday, December 15 from 3:30 - 5:30pm in MJIS 1097, 1001 and Atrium. There will be 24 projects presented followed by awards ceremony. Stay tuned for additional details.

 

Graduate Office Update

 

BME Coffee Chats

We are once again hosting are faculty coffee chats for grad students.  Remember, we need attendance for this event to be successful so get these on your calendars today😊.

 

These coffee chats will attempt to accomplish some priorities that have been shared with us by you:  

  1. First year students—what a great opportunity to find out more about other labs and find potential mentors for your qual committee.
  2. Grad student professional development—to learn/ask/chat about topics of interest to the student either about research or other topics.
  3. Increase faculty involvement with graduate students outside of their own lab.
  4. Help build community between grad students.

 

Here are the dates and faculty for fall:

November

Date:  November 10th

Time: 9:30 am-10:30 am

Location: MJIS 3041

Faculty hosts: Hugh Lee, Taimoor Qazi, Steve Steinhubl

Potential discussion topics: ask me anything/healthcare, academic jobs/academia, visas/international students

 

December:

Date:  December 8th

Time: 2:00 pm-3:00 pm

Location: MJIS 2041

Faculty host: Deva Chan

Potential discussion topics: AMA work-life, teaching & diversity statements, time management

 

Please plan to participate in as many as your schedule will allow.  There will be free snacks and drinks included.

 

Graduate Admissions Update

 

Fall 2022 (Fall 2023 Admit Term) BME Graduate Admissions

DateDATE

Activity

Now

Research Areas create a plan and potentially agree on dates to meet ranking deadlines.

December 19th—All Fellowship Nominations Due

Nov 10

Virtual Recruiting Faculty Research Presentations (3-5:30 pm presentations)

Dec 1

Complete applications due for priority admission and funding consideration

Dec 2

Prescreening of eligibility of Purdue Doctoral and George Washington Carver sent to faculty

Dec 2

Spreadsheet and applications posted to Engineering Intranet for Research Area and faculty review

Dec 19

DUE: All Fellowship Nominations and Additional Invite Lists

Dec 20

Grad office to process admission for all fellowship-nominated applicants to the Purdue Graduate School and any additional applicants you would like to admit from the open house invitation list.

Dec 20

Tammy to send invitations to invited students to participate in our virtual open house.

Jan 3

Deadline for students to respond to Open House RSVP (hotels released today).

Jan 26

Agendas for all invited students due from faculty to Tammy and sent to student.

Feb 2-4

Weldon School Visitation Days (Hybrid)

Feb 8

Last chance for Research Areas / Faculty to remove students from fellowship consideration

Feb 10

Fellowship offers announced and complete rankings list made available to BME faculty; BME Graduate Office will notify students by email (offer letters distributed as soon as signed by BME Head and COE Dean)

Mar 10

DUE: All Master’s students to be decisioned as either admit, deny or hold

Mar 31

Due: All PhD students to be decisioned as either admit, deny or hold

April 15

Graduate applicant acceptance deadline

 

Research Area Update

 

The NIH OITE is pleased to offer the RAISING A RESILIENT SCIENTIST series for faculty, staff scientists, and administrators who mentor students and postdoctoral fellows in the biomedical, behavioral, and social sciences. A variety of topics will be covered with a specific focus on communication and shared problem-solving to help trainees deal with the inevitable setbacks experienced in high knowledge environments. The goal of the Raising a Resilient Scientist series is to promote the mental health and well-being of the academic research community by supporting faculty and administrators to develop self-management, relationship-management, and mentoring skills. There will be five units in the series and start on November 9th, 2022; each unit will consist of a 75-minute lecture followed by a 1-hour facilitated discussion with peers.

Previous participants found participation very valuable, and the tools presented practical and actionable. Here is what those who participated in series have to say:

  1. “Informative workshop that I think all faculty should be required to attend. Making this a requirement for mentoring teams for fellowship and training grants would be a great approach! They need to be invested in mentoring and training, as much as training fellows.”
  2. “Thank you! I've done a lot of mentoring workshops/training but feel like this one is already taking things to another level.”
  3. “This course needs to be offered again and again, such an important resource in any academic curriculum.”

 

There is no charge for participation, but advanced registration is required. For more information, and to register, please visit our webpage.  Participation in the entire series is recommended but is not required. Please do not hesitate to email us if you have any questions. 

 

Dr. Sharon L. Milgram

(she/her/hers)

Director, NIH Office of Intramural Training & Education

NIH Office of the Director

www.training.nih.gov 

 

Resources, attachments, further information

 

BME Distinguished Seminar Series, Wed., Nov. 9, 9:30 a.m., MJIS 1001 and via Zoom. Yen-Yu Ian Shih, Associate Professor and Associate Director for Biomedical Research Imaging Center at the University of North Carolina at Chapel Hill will present “A Silent, Sensitive, Specific, and Artifact-resistant fMRI Technique.”

Abstract: Gradient-recalled echo (GRE)–based echo planar imaging (EPI) has been the gold standard functional magnetic resonance imaging (fMRI) technique for nearly three decades due to its ability to rapidly acquire whole brain volumes with MR T2* sensitivity to blood oxygenation — a well-known surrogate marker for brain activity. This immensely utilized technique, however, suffers from high acoustic noise, ghosting and motion artifacts, magnetic field inhomogeneity–related artifacts, low sensitivity compared to other neuroimaging modalities, and poor spatial specificity. An fMRI sampling technique that addresses these problems has the potential to change day-to-day fMRI practices. Aptly, imaging sequences with “zero” acquisition delay and minimal increment of gradients are insensitive to problems stated above and have the potential to provide superior spatial specificity and sensitivity compared to GRE-EPI-fMRI. To explore the utility of a hard-pulse-based zero-echo-time (ZTE) based sequence for fMRI, we modeled ZTE contrast mechanisms, improved its sequence design for fMRI, and examined parameters that may augment ZTE-fMRI sensitivity. We hope the results brought by these efforts to make positive influences to fMRI methods using short acquisition delay.

Bio: Dr. Shih earned both his Bachelor’s and PhD degrees from National Yan Ming University in Taiwan. His lab focuses on understanding the mechanisms by which fMRI signal and functional networks are generated. The expertise of his lab builds on knowledge about magnetic resonance, cerebral hemodynamics, and neuroengineering with proven technical skills in developing MR sequences and implementing novel brain recording/manipulating tools in high magnetic fields, including electrophysiology, fiber photometry, fast-scan cyclic voltammetry, optogenetics, chemogenetics, and electrical microstimulation. Since 2019, his lab has devoted significant effort in improving short acquisition delay methods for fMRI, initially in a form of a zero echo time (ZTE) sequence in rodents which won the Bruker MRI Award in ISMRM 2020.

~BME Faculty Host: Dr. Uzay Emir ~

Zoom link: https://purdue-edu.zoom.us/j/7731446991?pwd=RHdkZTVnRkxTM3J3dnRvY1VLWTlYUT09

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

 

Seminars in Hearing Research at Purdue, Thurs., Nov. 10,  10:30 a.m., LYLE 1150. Alexander L. Francis, Professor of SLHS will present “RCR Discussion: Practical Considerations for Preregistration in Hearing Science.”

Abstract: In this presentation I will introduce “preregistration” within the broader context of open science practices. I will follow the example set by Brown & Strand (2022) (https://psyarxiv.com/f52gj/) and structure my talk around a demonstration of the process of preregistering using a study my lab group is designing to replicate previous research on the effects of wearing hearing aids on postural sway in older adults. Participants are encouraged to take a look at the Brown & Strand article beforehand, and bring a laptop to follow along to pre-register their own projects.

Zoom link for remote attendees: https://purdue-edu.zoom.us/j/4326340458 Meeting ID: 432 634 0458

The working schedule is available here: https://purdue.edu/TPAN/hearing/shrp_schedule

The titles and abstracts of the talks will be added here: https://purdue.edu/TPAN/hearing/shrp_abstracts

 

5th Childhood Diabetes Prevention Symposium, Fri., Nov. 11, 8:00 a.m. – 3:45 pm MT vi Zoom. The objectives include: (1) Discuss essential components of follow-up and monitoring for children who screen positive for islet autoantibodies (Immune markers, Markers of dysglycemia, Psychological support, Early diabetes education) (2) Review the status of general population screening programs world-wide, and (3) Address new challenges. The registration is free but mandatory for in-person or webinar participation. Click to register: https://redcap.ucdenver.edu/surveys/?s=WFPKALWFWFXTNNL3  While this meeting is open to everybody, we ask you to register by providing your name, email address and affiliation.

Upon registration, you will receive email with a Zoom invitation including link to the webinar. This symposium features 18 short presentations, followed by Q&A sessions with expert panelists. The program is attached. All presentations will be recorded and available at the Barbara Davis Center website.  

 

RSVP Deadline for IUSOM Fall Otolaryngology Workshop Mon., Nov. 14.  Workshop is entitled “AI Topics in Medicine and Otolaryngology, and will be held Wednesday, Nov. 30 from 9 a.m. to 2 p.m. in Fesler Hall, Suite 400, 1130 W. Michigan Street, Indianapolis. RSVP to Ashley Claxton (aclaxto@iu.edu). The Department of Otolaryngology—Head and Neck Surgery at IU School of Medicine and the Department of Biomedical Engineering at Purdue University are hosting a joint workshop to understand current challenges and opportunities in the application of artificial intelligence and machine learning (AI/ML) to clinical medicine. The purpose of this workshop is to bring together experts in ML/AI engineering, biomedical research, and clinical applications, to understand to the current state of the field and identify specific plans to address existing needs, barriers, and goals for development and implementation in the otolaryngology field. As otolaryngology—head and neck surgery is a specialty with both medical and surgical aspects, with a high degree of technology familiarity and utilization, identified themes are expected to be broadly applicable to medicine and surgery in general. The format for the workshop will be short talks followed by ample time for discussion and networking. Our workshop planning committee has identified you as valued faculty member in this space and would like to invite you to participate. We sincerely hope you can attend. 

 

BME PhD Preliminary Exam Announcement for Alexis Hoerter (E. Pienaar, advisor), Wed., Nov. 16, 11:00 a.m., MJIS 2001 and via Zoom. Research Title: Agent Based Models Characterizing In Vitro M. Tuberculosis Granuloma Dynamics: Host-Immune Status Determinants and HIV Coinfection Mechanisms.

Zoom link: https://purdue-edu.zoom.us/j/95200759998?pwd=ZG1PMDh6eG9jWGFqWWptM0RuNkVhUT09 

Thesis Committee: Dr. Elsje Pienaar - Major Professor, Dr. Larry S. Schlesinger, Dr. Alexandria Volkening, Dr. Qing Deng 

Abstract:  Tuberculosis (TB) is the 2nd most deadly infectious disease behind Covid-19 with ~10 million new cases and ~1.5 million deaths worldwide in 2020. TB infection is associated with a wide spectrum of outcomes ranging from complete elimination of bacteria, to bacterial containment in asymptomatic clinical states [latent TB infection (LTBI)], to high bacterial replication in active disease with severe clinical symptoms. How individuals move throughout this spectrum is still being uncovered; however, the host immune status is a strong determinant of infection progression. The risk of active TB is ~10% in individuals with LTBI and 15-21 times higher in those coinfected with human immunodeficiency virus-1 (HIV). The hallmark of TB infection is the formation of granulomas – unique microenvironments orchestrated by the immune response to contain Mycobacterium tuberculosis (Mtb) and localize host-pathogen interactions. Granulomas are the main site of infection and driver of disease progression, but studying intra-granuloma dynamics of human Mtb infection in vivo is challenging. In vitro Mtb granulomas using human donor cells have shown how the host immune status (LTBI vs Mtb-naïve) as well as coinfection with HIV can have critical and distinct impacts on the formation of granulomas. However, identifying mechanisms behind these differences using experimental data alone is a formidable task. Here, we present a complementary approach using an agent-based model of these in vitro granulomas to help elucidate differences between LTBI and naïve host cell responses as well as mechanisms of coinfection with HIV. Coupling computational modeling with experimental efforts could accelerate new treatment discoveries.

 

Attachments

 

BDC Symposium Program