September 2024 - Bmegradstudents-list

[Bmeroundtable-list] Fall MJIS air handling shutdown
by Gelfand, Johanna K 23 Sep '24

23 Sep '24

Our semi-annual air handling shutdown is scheduled for Tuesday, October 8th. As a reminder: the entire building's air handling system in MJIS will be turned off. ALL chemical hood activity, biosafety cabinet activity, autoclave work and activities in wet labs will need to STOP by 5 PM on Monday, October 7th. Any chemicals stored in the hoods will have to be sealed at that time. Signs will be posted on all hoods to remind users not to use the hoods Monday evening, and removed when the maintenance work is completed and normal operations can resume (some time on Tuesday). Please plan ahead - DO NOT use chemicals in the lab areas that you would normally use in the hoods. Jo Gelfand Intra/Extramural Relations Administrator Purdue University Weldon School of Biomedical Engineering 206 S. Martin Jischke Drive West Lafayette, IN 47907-2032 765-494-2996 jo(a)purdue.edu<mailto:jo@purdue.edu> [cid:image001.jpg@01DB0DA6.DB11F140] -- Bmeroundtable-list mailing list Bmeroundtable-list(a)ecn.purdue.edu https://engineering.purdue.edu/ECN/mailman/listinfo/bmeroundtable-list

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[Bmeroundtable-list] BME 3rd year PhD Seminar Series: Friday 9-27
by Rowen, Elizabeth Pearl 23 Sep '24

23 Sep '24

[cid:image001.jpg@01DB05C3.B4BD0650] BME 3rd Year Seminar Series Friday, September 27th, 2024 1:30 - 2:30 PM EST MJIS 1001 Evaluation links: Himabindu Kovvali: https://purdue.ca1.qualtrics.com/jfe/form/SV_2lPynY9U0mbtWXI<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> Mohammadreza Balouchestani: https://purdue.ca1.qualtrics.com/jfe/form/SV_7OH2BTjlFgBWgRg<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> Evaluation surveys should only be completed after the seminar has taken place, and only by those who attended the seminar. Quantifying the Intercellular Mechanisms of Ebolavirus Transmission using Multi-scale Agent-based Modeling Himabindu Kovvali (Elsje Pienaar, advisor) [cid:image005.jpg@01DB0D9D.11CCC2A0] Abstract: Ebola Virus Disease (EVD) is caused by an Ebolavirus (EBOV) infection and is associated with fatal hemorrhagic fever. It has caused more than 30 outbreaks, some with 100% mortality. There is a gap in our knowledge of the protein-protein and lipid-protein interactions that drive effective viral production, making it challenging to develop therapies. Matrix protein VP40, when expressed independently, can produce virus-like particles (VLPs) with similar size, shape, entry, and cell attachment properties as EBOV virions. The production of VLPs is enhanced when VP40 is co-expressed with NP, nucleoprotein, which forms NP inclusions encapsulated in the VP40 VLP matrix. The production of VLPs has been quantified in individual cells with a subcellular differential equation model. Here, we employ this existing data to develop a multi-scale Agent-based model to represent the VP40-NP system in a population of cells using a Java-based modeling system called Repast Simphony. The model has five agent types: Transfected Kidney cells, IB-free-VLP (no NP inclusions), IB-containing-VLP (with NP inclusions), Healthy Kidney cells, and VLP-entered cells. Kidney cells are assumed to be adherent. VLP's have movement via Brownian motion. VLP agents are budded from Transfected Kidney cells and enter Healthy Kidney cells through contact. We stochastically quantified the number and type of VLPs that enter Healthy Kidney cells in a population of cells. Results suggest that irrespective of the kind of VLP produced, their entry into a healthy cell is defined primarily by the number of VLPs in the environment. The findings provide valuable insights to elucidate how single-cell VP40 and NP interactions propagate across a population of cells to sustain robust viral proliferation. This study introduces a novel framework of multi-scale Agent-based modeling in the context of computational virology. Quantifying Hemodynamic Metrics and Assessing Their Uncertainty in Intracranial Aneurysms with Computational Fluid Dynamics and 4D Flow MRI Mohammadreza Balouchestani (Vitaliy Rayz, advisor) [cid:image006.jpg@01DB0D9D.11CCC2A0] Abstract: Proper risk assessment of the stability of unruptured intracranial aneurysms (IA) is crucial for making treatment decisions. In addition to clinical and morphological factors, hemodynamic forces have been linked to both IA growth and rupture, though their exact role remains unclear. Our work is motivated by the relationship between adverse hemodynamic environments and the growth or rupture of IAs. We propose new metrics to assess the spatiotemporal heterogeneity of the wall shear stress (WSS) vector field, to enable comparison between pre- and post-growth stages of IAs. Spatial autocorrelation of WSS is used to evaluate the heterogeneity of the WSS vector field. Additionally, spatial variation of topological shear is introduced to capture sharp directional changes in the vector field. Post-processing analysis is applied to velocity fields derived from computational fluid dynamics (CFD) simulations. The boundary conditions for CFD models are informed by 4D flow MRI measurements and implemented using Windkessel models. An additional focus of this work is to evaluate the reliability of velocity-based metrics derived from 4D flow MRI, by developing an automated, physic-based method for estimating uncertainty. This method uses a standardized mean of patches (SMP) to estimate velocity error correlations by standardizing background patches, regardless of their signal magnitude. Conservation of mass is employed to infer local variance at each voxel, based on observed errors in the velocity divergence and the estimated correlation matrix. The model is capable of capturing various error sources, such as noise, partial volume effects, image resolution and phase wrapping. It also accounts for error correlations between velocity components, as well as spatial and temporal correlations. The statistical distance of the velocity measurement and the modeled velocity error distribution can be used to assess the reliability of both the velocity measurement and the respective velocity-based metrics. The current model has the potential for inferring the uncertainty and improving the accuracy of gradient-based hemodynamic metrics. 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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Invitation to 'Career Development Counseling Session with Students and Postdocs' – 10/02
by Gelfand, Johanna K 20 Sep '24

20 Sep '24

Dear BME Graduate Students and Postdocs, We are pleased to invite you to a Career Development Counseling Session with Prof. Eric Markvicka from the University of Nebraska-Lincoln, as part of his visit for the Big 10 Exchange Program. The session will take place on October 2nd from 3:30-4:30 pm in MJIS 1096. Prof. Markvicka, a leading researcher in soft materials and robotics, directs the Smart Materials and Robotics Laboratory at UNL. His interdisciplinary work focuses on the development of multifunctional soft materials for wearable electronics and soft robotics, and he has received numerous awards, including the 2024 NSF CAREER award. His seminar will take place in MJIS 1001 from 9:30 to 10:30 am on the same date. Enclosed, please find his bio and abstract for your reference. This session will be particularly beneficial for senior graduate students nearing graduation, offering insights on transitioning from graduate school to postdoctoral or other academic positions. It will cover essential topics like building a competitive CV, effective networking, and preparing for interviews. Postdocs on the academic job market will also gain tailored advice from Prof. Markvicka on applying for faculty positions, crafting strong research and teaching statements, and excelling in job talks, while also engaging in open dialogue and sharing experiences with peers navigating similar career paths. This is a great chance to ask questions, share your concerns, and receive practical guidance from Prof. Markvicka based on his experience in academia and research. We encourage all interested students and postdocs to attend this open session. Thank you. Best regards, Chi Hwan Lee

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[Bmeroundtable-list] MJIS ALERT: EHS/REM
by Gelfand, Johanna K 20 Sep '24

20 Sep '24

EHS contacted us this morning about these hazardous waste containers that were found in our recycling bin. Herrick has already been contacted and it was not any of their labs. Dave Lucas the head of zone 7 has been contacted and confirmed that these are not used by them. It is extremely important that we find out which of our labs placed them in the dumpster asap. Please contact Susan Hardy immediately so we can let EHS know who to contact about this situation. [IMG_2923.PNG] Sent from my iPhone -- Bmeroundtable-list mailing list Bmeroundtable-list(a)ecn.purdue.edu https://engineering.purdue.edu/ECN/mailman/listinfo/bmeroundtable-list

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[Bmeroundtable-list] Today! BME 3rd year PhD Seminar Series: Friday 9-20
by Rowen, Elizabeth Pearl 20 Sep '24

20 Sep '24

[cid:image001.jpg@01DB05C3.B4BD0650] BME 3rd Year Seminar Series Friday, September 20th, 2024 1:30 - 2:30 PM EST MJIS 1001 Evaluation links: Sayeh Jalali Dowlatshahi: https://purdue.ca1.qualtrics.com/jfe/form/SV_9uZc5YCxKVBPVsy<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> Jeffrey Coulter: https://purdue.ca1.qualtrics.com/jfe/form/SV_4UDdcU7Dnqx6CVw<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> Evaluation surveys should only be completed after the seminar has taken place, and only by those who attended the seminar. Quantification and Validation of Cervical Cancer-Associated Protein Biomarkers for Point-of-Care Early Cervical Cancer Detection Sayeh Jalali Dowlatshahi (Jaqueline Linnes, advisor) [cid:image002.jpg@01DB05C3.B4BD0650] Abstract: Cervical cancer is the fourth most common cancer in women and the fourth leading cause of cancer-related deaths among them globally. Current gold-standard cervical cancer screening techniques are expensive and time-consuming, possess low sensitivity or specificity, and require trained personnel and sophisticated instrumentation, limiting their implementation in low-resource settings. Therefore, a low-cost, rapid, sensitive, and specific point-of-care (POC) early-stage cervical cancer diagnostic assay is urgently needed. This research develops a complete workflow for cervical sample collection, processing, testing, and result interpretation, for a POC cervical cancer screening test based on a paper-based lateral flow immunoassay (LFIA). Common cervical samplers were compared to identify the one with optimal cellular recovery. Subsequently, a simplified cell lysis technique using radioimmunoprecipitation assay lysis buffer was developed for specimen processing. The LFIA's target biomarker is topoisomerase II alpha (TOP2A), an enzyme innately involved in DNA replication that tends to be overexpressed in cervical cancer patients. The test's colorimetric labels are 40-nm gold nanoparticles conjugated to mouse anti-TOP2A detector antibody (dAb) molecules. Conjugation efficiency was assessed through commercial quality control dipstick tests and dynamic light scattering. The chosen conjugate was then used with in-house dipstick assays to determine the control line's optimal goat anti-mouse immunoglobulin G antibody concentration. The test line's performance is being evaluated by testing various dAb:protein molar ratios using in-house dipstick tests. Once optimized, all these parameters will be incorporated into the TOP2A LFIA design. The device performance will be evaluated with lysates of clinical cervical swab specimens. Furthermore, the feasibility of multiplexing TOP2A with other known cervical cancer protein biomarkers and machine learning-assisted result interpretation will be investigated. This low-cost rapid test will enable sensitive and specific cervical cancer screening in resource-limited regions, leading to more timely diagnosis and earlier effective treatment. A hybrid discrete-continuum model for simulating multiscale biological systems Jeffery Coulter (Taeyoon Kim/David Umulis, advisors) [cid:image003.jpg@01DB05C3.B4BD0650] Abstract: Biological systems often consist of constituent elements operating at distinct temporal and spatial scales. For example, calcium is a small ion that diffuses quickly throughout the cell and its signaling is known to interact with the actin cytoskeleton to regulate cell-scale morphology and function. It has been suggested that a relationship between calcium and actin is involved in diverse phenomena ranging from fertilization to long-term potentiation. However, due to the differences in length and time scales at which these components operate, attempts to model such systems must make sacrifices regarding information loss or computational effort. Biochemical reactions are often modeled as continuous systems using differential equations while discrete models more accurately capture the dynamics and structure of actin filaments. Here, we present a method that combines discrete and continuum approaches to model filament networks coupled with biochemistry. 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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Fwd: Apply today! Internships and fellowships with DoD through ORISE
by Siemers, Tammy R 19 Sep '24

19 Sep '24

Get Outlook for iOS<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Faka.ms%2F…> ________________________________ From: orisedodrecruiting(a)orise.orau.gov <orisedodrecruiting(a)orise.orau.gov> Sent: Thursday, September 19, 2024 4:51:11 PM To: Siemers, Tammy R <tsiemers(a)purdue.edu> Subject: Apply today! Internships and fellowships with DoD through ORISE ---- External Email: Use caution with attachments, links, or sharing data ---- [https://mcusercontent.com/44959e11342b10cd6967812a8/images/15c0d255-14b2-f1…] The Oak Ridge Institute for Science and Education (ORISE) is accepting applications for paid internship and fellowship opportunities<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Forau.us12…> at the U.S. Department of Defense (DoD). Apply now! Research Development Assessment Internship <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Forau.us12…> Location: Perry, Georgia Degree: Currently pursuing a Bachelor's Degree or Master's Degree Citizenship: U.S. Citizen Environmental Program Support Specialist <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Forau.us12…> Location: Fort Huachuca, Arizona Degree: High School Diploma/GED received within the last 36 months or currently pursuing Citizenship: U.S. Citizen Molecular Biology Support <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Forau.us12…> Location: Fairborn, Ohio Degree: Bachelor's Degree or Master's Degree received within the last 12 months or anticipated to be received by 7/31/2025 Citizenship: U.S. Citizen Bioinformatics Fellowship <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Forau.us12…> Location: Various Degree: Master's Degree received within the last 24 months Citizenship: U.S. Citizen VIEW MORE OPPORTUNITIES WITH DoD<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Forau.us12…> [Facebook]<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Forau.us12…> [Twitter]<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Forau.us12…> [Instagram]<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Forau.us12…> [LinkedIn]<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Forau.us12…> [Website]<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Forau.us12…> --- If you received this mailing from a colleague and would like to receive future mailings directly in your inbox then please send a blank email to: subscribe-dodinternships(a)listserv.orau.org ? ? You received this e-mail due to your institutional or organizational affiliation. If we sent this e-mail to you in error, and you wish not to receive any further e-mails from us, please send a blank email to leave-115788-2862850.884bf76079cfa0dcee4c6597339ce304(a)listserv.orau.org

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[Bmeroundtable-list] FW: department colloquium speaker this Friday
by Gelfand, Johanna K 18 Sep '24

18 Sep '24

From: Wei, Ning <wei307(a)purdue.edu<mailto:wei307@purdue.edu>> Date: Wednesday, September 18, 2024 at 12:57 PM To: Pienaar, Elsje <epienaar(a)purdue.edu<mailto:epienaar@purdue.edu>> Cc: Wei, Ning <wei307(a)purdue.edu<mailto:wei307@purdue.edu>> Subject: department colloquium speaker this Friday Dear Elsje We have a department colloquium speaker, Prof. Qing Nie from UC Irvine. Please see the title and abstract of his talk below. Could you help announce this to the department in case anyone is interested? Thanks! CCAM/Mathematics Colloquium: Qing Nie, UC Irvine - WTHR 320 Friday, Sep 20th 2:30 - 3:30pm Title: Systems Learning of Single Cells Abstract: Cells make fate decisions in response to dynamic environments, and multicellular structures emerge from multiscale interplays among cells and genes in space and time. The recent single-cell genomics technology provides an unprecedented opportunity to profile cells for all their genes. While those measurements provide high-dimensional gene expression profiles for all cells, it requires fixing individual cells that lose many important spatiotemporal information. Is it possible to infer temporal relationships among cells from single or multiple snapshots? How to recover spatial interactions among cells, for example, cell-cell communication? In this talk I will present our newly developed computational tools to study cell fate in the context of single cells as a system. In particular, I will show dynamical models and machine-learning methods, with a focus on inference and analysis of transitional properties of cells and cell-cell communication using both high-dimensional single-cell and spatial transcriptomics, as well as multi-omics data for some cases. Through their applications to various complex systems in development, regeneration, and diseases, we show the discovery power of such methods in addition to identifying areas for further method development for spatiotemporal analysis of single-cell data. Best Ning -- Bmeroundtable-list mailing list Bmeroundtable-list(a)ecn.purdue.edu https://engineering.purdue.edu/ECN/mailman/listinfo/bmeroundtable-list

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[Bmeroundtable-list] Meet BME's 38X38 Award winners!
by Gelfand, Johanna K 18 Sep '24

18 Sep '24

[cid:image002.jpg@01DB082E.7D3BCAF0] Rhonda Jones (she/her/hers) Senior Marketing and Communications Professional Weldon School of Biomedical Engineering O 765.494.3940 | C 765.427.2065 rwjones(a)purdue.edu<mailto:rwjones@purdue.edu> [cid:image001.jpg@01DB082E.710E1DF0] -- Bmeroundtable-list mailing list Bmeroundtable-list(a)ecn.purdue.edu https://engineering.purdue.edu/ECN/mailman/listinfo/bmeroundtable-list

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[Bmeroundtable-list] BME PhD Preliminary Exam announcement for Derrick Dankwa (L. Green, advisor)
by May, Sandra M 18 Sep '24

18 Sep '24

BME PhD Preliminary Exam announcement for Derrick Dankwa (L. Green, advisor) Everyone is invited to attend the public presentation beginning at 11:00 am. Title: An in-silico Study on the Design of a Biological Controller for Regulating Sepsis induced macrophage Paralysis Date: October 2nd, 2024 Time: 11:00 am Location: MRGN 206 or Zoom: https://purdue-edu.zoom.us/j/2977861198<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue-ed…> Committee members: Leopold Green, (chair), Elsje Pienaar, Yoon Yeo, Choi, Jong Hyun Abstract: Macrophages play key roles in both the progression and resolution of inflammation. Their functional plasticity is characterized by polarization into either the pro-inflammatory M1 phenotype or the anti-inflammatory M2 phenotype as well as occupying a position along the continuum between these two extremes. In sepsis, dysregulation of this phenotypic switch (macrophage paralysis) interferes with the proper influx and removal of immune cells, decreasing the efficiency of pathogen clearance and amplifying tissue necrosis. Irrespective of the advancements in understanding the immune response and developing therapeutics to manage the disorder, significant challenges remain in achieving optimal clinical outcomes. Emerging studies suggest modulating macrophage phenotypes and signaling pathways as a novel therapeutic approach to restore immune homeostasis in dysfunctional inflammatory states. In response to this, we propose to inform the design of a novel class of theragnostics that target the dysregulated signaling dynamics to positively regulate the outcomes of the disorder. We will abstract the immune response into the language of mathematical modeling and feedback control,(a mathematical framework traditionally used in engineering to manage dynamic systems) to develop a biologically feasible controller as gene circuits capable of sensing and responding to immune signaling dynamics in real time as a multipronged therapy for sepsis. To achieve this, the following aims would be explored. Aim 1: Design an insilico framework to regulate macrophage paralysis via controlled IL-6 expression. Aim 2: Parameterize and control the spatio-temporal immune cell and signaling dynamics using a lung-on-a-chip system. Overall, our proposed study aims to bridge the gap between theoretical modeling and practical application in the treatment of sepsis. By developing a novel approach that combines advanced mathematical modeling with cutting-edge biotechnology, we seek to inform the design of a novel class of effective therapeutic strategies to combat this serious condition. Our approach has the potential to significantly advance the development of next generation gene and cell-based immunotherapies for inflammatory disorders. -- Bmeroundtable-list mailing list Bmeroundtable-list(a)ecn.purdue.edu https://engineering.purdue.edu/ECN/mailman/listinfo/bmeroundtable-list

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BMES Conference
by Gelfand, Johanna K 16 Sep '24

16 Sep '24

The BMES Conference is quickly approaching, Wednesday, Oct. 23 - Saturday, Oct. 26 in Baltimore. Cindy Holderbaum and I are working diligently to ensure Purdue has a great showing at the conference, but we need your help. 1. Are you attending the conference? Please send a copy of your confirmation to Cindy. 2. We are ordering Purdue BME polo shirts for all attending. Please send your polo shirt size to Cindy by Wednesday, Sept. 25. 3. Will you work the booth twice during the conference for an hour? Please respond to Cindy with your preferred time so we can create a schedule. 4. Are you recruiting? Please complete this Qualtrics<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpurdue.ca…> so we may share your information. We will host a reception on Thursday, from 7 - 10 pm in Poe A&B room. Please plan to be in the reception room around 8 pm as we briefly announce Kevin joining our family. SIZE CHART XS S M L XL 2XL 3XL 4XL 5XL 6XL Chest 32-34 35-37 38-40 41-43 44-46 47-49 50-53 54-57 58-60 61-63 Measure under the arm and around the fullest part of the chest with arms down, keeping tape horizontal. PRODUCT MEASUREMENTS XS S M L XL 2XL 3XL 4XL 5XL 6XL Chest Width 18 3/4 20 1/4 21 3/4 23 1/4 24 3/4 26 1/4 28 1/4 30 1/4 32 1/4 34 1/4 Sleeve Length 17 3/4 18 1/2 19 1/4 20 20 3/4 21 1/4 22 1/4 23 23 3/4 24 1/2 Body Length at Back 28 29 30 31 32 33 33 1/2 34 34 1/2 35 CHEST WIDTH Measured across the chest one inch below armhole when laid flat. SLEEVE LENGTH Start at center of neck and measure down shoulder, down sleeve to hem. BODY LENGTH AT BACK Measured from high point shoulder to finished hem at back. Thank you, Rhonda Jones (she/her/hers) Senior Marketing and Communications Professional Weldon School of Biomedical Engineering O 765.494.3940 | C 765.427.2065 rwjones(a)purdue.edu<mailto:rwjones@purdue.edu> [cid:image001.jpg@01DB0819.A4069120]

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