Happening @ Michigan https://events.umich.edu/list/rss RSS Feed for Happening @ Michigan Events at the University of Michigan. Bone Marrow Stromal Cells Regulate Functional States of ER+ Breast Cancer Cells (May 25, 2022 1:00pm) https://events.umich.edu/event/94936 94936-21786532@events.umich.edu Event Begins: Wednesday, May 25, 2022 1:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Even with targeted therapies, patients with the most common subtype of breast cancer, estrogen-receptor-positive (ER+) disease, face an ongoing, progressively increasing risk of metastases. ER+ breast cancer predominantly metastasizes to bone marrow (~70% of patients with advanced disease). Current hormone therapies frequently suppress, but fail to eliminate, both proliferating and quiescent breast cancer cells in bone marrow. While drug resistance may arise from cancer-cell intrinsic mechanisms, studies implicate interactions between ER+ breast cancer cells and bone marrow mesenchymal stromal cells (MSCs) as a pivotal cause of resistance to hormone therapies and transitions to CSC states. This dissertation focuses on elucidating targetable mechanisms for MSC-induced increases in cancer cell plasticity and resistance to antiestrogenic therapy.

This work began showing that direct co-culture with MSCs induces resistance to antiestrogenic therapy in ER+ breast cancer cells, in part through increases in intracellular iron. Combining iron chelators or novel lysosomal iron-targeting compounds with clinical antiestrogenic therapy reduced resistance of cancer cells to therapy. Next, we showed that co-culture with MSCs increased oxidative metabolism, intracellular ATP, glucose, and metabolic plasticity in ER+ breast cancer cells treated with antiestrogenic therapy, including under conditions of nutrient stress. We successfully limited metabolic plasticity, heterogeneous treatment responses, and drug resistance by inhibiting monocarboxylate transporters. Finally, we utilized a physiologically-relevant 3D co-culture model with MSCs that successfully recapitulated slow proliferation, signaling, and metabolic profiles of disseminated ER+ breast cancer cells. Simultaneous treatment with inhibitors of Akt and thioredoxin reductase effectively reduced cancer burden versus antiestrogenic therapy in both in vitro and in vivo models. By exploiting adaptations of ER+ breast cancer cells to the stromal microenvironment, we identified multiple clinically-actionable approaches to overcome stromal-mediated drug resistance, paving the way toward more effective treatments against bone marrow metastases.

Date: Wednesday May 25, 2022
Time: 1:00 PM
Zoom: https://umich.zoom.us/j/96774775771
Chair: Dr. Gary Luker

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Presentation Tue, 03 May 2022 08:39:58 -0400 2022-05-25T13:00:00-04:00 2022-05-25T14:00:00-04:00 Off Campus Location Biomedical Engineering Presentation BME PhD Defense
“Genetic regulation of epithelial homeostasis and injury” (June 7, 2022 4:00pm) https://events.umich.edu/event/95318 95318-21789154@events.umich.edu Event Begins: Tuesday, June 7, 2022 4:00pm
Location:
Organized By: Center for Cell Plasticity and Organ Design

The NIH T32 Training Program in Organogenesis trainees are please to present a Special Series, "Building and Rebuilding: Regulation of Cell Signaling in Development and Regeneration," featuring guest speaker, Adam D. Gracz, PhD.

Dr. Gracz is an Assistant Professor of Medicine-Division of Digestive Disease at Emory University.

The talk is entitled, “Genetic regulation of epithelial homeostasis
and injury.”

Trainee Host
Megan Radyk, PhD-Lyssiotis & Shah Labs

For more information email: Organogenesis@umich.edu

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Lecture / Discussion Thu, 26 May 2022 10:58:57 -0400 2022-06-07T16:00:00-04:00 2022-06-07T17:00:00-04:00 Center for Cell Plasticity and Organ Design Lecture / Discussion Gracz flyer
BME PhD Defense: Feiran Li (June 13, 2022 12:00pm) https://events.umich.edu/event/95461 95461-21789961@events.umich.edu Event Begins: Monday, June 13, 2022 12:00pm
Location: North Campus Research Complex Building 520
Organized By: Biomedical Engineering

Cell-based therapies are emerging for Type I diabetes mellitus (T1D), an autoimmune disease characterized by the destruction of insulin producing pancreatic β-cells, as a means to provide long term restoration of glycemic control. The limited supply of donor islets has motivated research into methods for differentiating pancreatic β-cells from renewable pluripotent stem cells such as human pluripotent stem cells (hPSCs). Biomaterial scaffolds maintain the integrity of cell-to-cell and cell-to-matrix connections by avoiding the disruption of the cell niche during handling. This dissertation addresses three key questions with respect to cell therapy and immunomodulation for T1D, including culture system on porous PLG scaffold, functionalized scaffold for improved cell viability and maturation, and immunomodulation with the membrane coated nanoparticles (MCNPs).

Culture on porous biomaterial scaffolds of hPSCs was investigated at multiple stages of differentiation between Stage 0 and 6 for improved differentiation. Scaffolds are biomaterial devices that could provide chemical and physical cues to control the microenvironment and subsequently alter cellular behavior by facilitating cell-cell interactions. The culture of cells on the scaffolds was found to support maturation of SC derived beta cells depending on the stage of seeding. Suspension cultured-pancreatic progenitors seeded onto scaffolds for stage 5 culture (pancreatic endocrine development), demonstrated enhanced expression for many maturation genes compared to cells that remained in suspension culture through the end of stage 6. This study showcased the scaffold culture as a promising platform for maturation that allows cells to develop a niche and may allow for direct transplantation without manipulating cells.

Early engraftment and development of β-cells post transplantation are a major limitation for stem cell derived beta cells due in part to their being immature. The survival and development of hPSC-derived β-cells seeded onto PLG microporous scaffolds were investigated within the initial 2 weeks post transplantation. Early inflammatory events induced by the biomaterial and transplanted cells heavily affected hPSC-derived β-cell engraftment due to the innate immune response. The inflammation includes the production of soluble mediators, inflammatory cytokines and the recruitment of innate cells at the graft site, hindering early graft engraftment and in-vivo hPSC-derived β-cell maturation. The PLG-based biodegradable scaffold chemically linked with a novel form of FasL chimeric with streptavidin, SA-FasL, was applied to create an immunoprivileged transplant site by modulating the local inflammatory microenvironment. The β-cell viability and differentiation were found improved at the SA-FasL induced immunoprivileged site together with a suppressed inflammatory reaction.

Life-long systemic immune suppression due to allogenic graft/cell transplant also limits the translation of cell therapies for T1D. We investigated the design of membrane-coated nanoparticles (MCNPs), with membranes derived from bone marrow-derived dendritic cells and coated onto poly(lactic-co-glycolic acid) (PLGA) nanoparticle cores, to directly interact with both naïve and activated T cells. Mechanistic studies revealed that the developed MCNPs have the capability to communicate with allogenic T cells by modulating the cytokine secretion levels similar to professional antigen presenting cells. Furthermore, the MCNPs can be engineered pre- and post-fabrication for upregulated surface molecules or varied antigen binding and can be functionalized by biotinylation for a wider range of protein loading.

Overall, this dissertation discussed optimization and early immunomodulation of the biomaterial culturing system for hPSC-derived β cells, and development of tunable MCNPs for direct T cell communication.

Date: Monday, June 13, 2022
Time: 12:00 PM
Location: NCRC Building 520 Room 1122 and Zoom (https://umich.zoom.us/j/93840656651)
Chair: Dr. Lonnie Shea

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Lecture / Discussion Tue, 07 Jun 2022 09:22:42 -0400 2022-06-13T12:00:00-04:00 2022-06-13T13:00:00-04:00 North Campus Research Complex Building 520 Biomedical Engineering Lecture / Discussion BME Defense
Understanding and engineering microbes for solving complex problems in biology and medicine (June 16, 2022 3:30pm) https://events.umich.edu/event/95526 95526-21790074@events.umich.edu Event Begins: Thursday, June 16, 2022 3:30pm
Location: Lurie Biomedical Engineering (formerly ATL)
Organized By: Biomedical Engineering

Abstract:

The microbiome represents an exciting frontier in medicine, and early successes in the field have demonstrated the dynamic interactions among individual microbial species and highlighted the crosstalk between microbiota and their hosts at the mucosal interface.  The Li research group in the Department of Bioengineering at Northeastern University focuses on the development of molecular and live cell-based therapeutics, with a major emphasis on harnessing innovative synthetic biology and drug delivery approaches for improving human health in a sustainable manner. In this talk, I will present our work from the past three years in interrogating and manipulating commensal bacteria and probiotics as therapeutic platforms to promote human health.

Bio:

Jiahe Li obtained his PhD in Biomedical Engineering at Cornell University in 2015, where he leveraged synthetic biology approaches and cell biology to engineer bacteria and platelets as platforms for treating metastatic cancer. Later, he pursued his postdoctoral training at the Koch Institute for Integrative Cancer Research at MIT from 2015-2018, where he gained complementary expertise in polymer science and gene delivery. He started a tenure-track faculty position in the Department of Bioengineering at Northeastern University in 2019, and his current research is supported by NIH, DoD, and various biotech companies.

Zoom Link: https://umich.zoom.us/j/97247012805

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Lecture / Discussion Thu, 09 Jun 2022 15:34:33 -0400 2022-06-16T15:30:00-04:00 2022-06-16T16:30:00-04:00 Lurie Biomedical Engineering (formerly ATL) Biomedical Engineering Lecture / Discussion BME Seminar
LHS Collaboratory (June 21, 2022 12:00pm) https://events.umich.edu/event/95245 95245-21789057@events.umich.edu Event Begins: Tuesday, June 21, 2022 12:00pm
Location: Off Campus Location
Organized By: Department of Learning Health Sciences

"Restructuring health systems for learning: Building equity into the Learning Health System"
Learn more about ELSI-LHS (Ethical, Legal, and Social Implications of Learning Health Systems). The session will be moderated by, Jody E. Platt, MPH, PhD, Assistant Professor of Learning Health Sciences.

Speaker:
Lauren A. Taylor, PhD, MDiv, MPH
Assistant Professor
Department of Population Health
Division of Medical Ethics
NYU Grossman School of Medicine

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Lecture / Discussion Wed, 25 May 2022 00:20:49 -0400 2022-06-21T12:00:00-04:00 2022-06-21T13:00:00-04:00 Off Campus Location Department of Learning Health Sciences Lecture / Discussion LHS Collaboratory logo
BioArtography Booth at the Ann Arbor Art Fair (July 21, 2022 10:00am) https://events.umich.edu/event/96071 96071-21791886@events.umich.edu Event Begins: Thursday, July 21, 2022 10:00am
Location:
Organized By: BioArtography

BioArtography will be in South University Booth SU1109 (Between E. Univ. and Church) the Ann Arbor Art Fair! 13 spectacular new images for 2022 will be making their debut!

Every day at the University of Michigan, scientists from many fields work together to study organism development, function and disease. While the goal of these studies is to design new and effective ways to treat disease and provide better understanding of ourselves as well as the world around us, many are also taking the time to share the beauty of their work with others through a program called BioArtography. In the course of research, scientists use special stains to add color to the otherwise transparent tissues. Microscopes then allow detailed observation of the tiny, colorful biological structures revealed in these images. This results in a fascinating combination of art and science that U-M researchers are capturing in pictures taken through microscopes and turning into artworks that would look beautiful on any wall.

The goal of these studies is to design new and effective ways to treat disease and provide better understanding of ourselves as well as the world that surrounds us. Proceeds from the sale of this work help support the training of our next generation of researchers. Past BioArtography sales have raised enough money to send more than 100 graduate students and postdoctoral fellows to scientific conferences, where they can present their work to other scientists and make connections that can help them launch their careers in research and industry.

Throughout the year BioArtography images (a collection of over 250) can be viewed and ordered online at www.bioartography.com

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Exhibition Mon, 18 Jul 2022 12:08:38 -0400 2022-07-21T10:00:00-04:00 2022-07-21T21:00:00-04:00 BioArtography Exhibition BioArtography at the Ann Arbor Art Fair
BioArtography Booth at the Ann Arbor Art Fair (July 22, 2022 10:00am) https://events.umich.edu/event/96071 96071-21791887@events.umich.edu Event Begins: Friday, July 22, 2022 10:00am
Location:
Organized By: BioArtography

BioArtography will be in South University Booth SU1109 (Between E. Univ. and Church) the Ann Arbor Art Fair! 13 spectacular new images for 2022 will be making their debut!

Every day at the University of Michigan, scientists from many fields work together to study organism development, function and disease. While the goal of these studies is to design new and effective ways to treat disease and provide better understanding of ourselves as well as the world around us, many are also taking the time to share the beauty of their work with others through a program called BioArtography. In the course of research, scientists use special stains to add color to the otherwise transparent tissues. Microscopes then allow detailed observation of the tiny, colorful biological structures revealed in these images. This results in a fascinating combination of art and science that U-M researchers are capturing in pictures taken through microscopes and turning into artworks that would look beautiful on any wall.

The goal of these studies is to design new and effective ways to treat disease and provide better understanding of ourselves as well as the world that surrounds us. Proceeds from the sale of this work help support the training of our next generation of researchers. Past BioArtography sales have raised enough money to send more than 100 graduate students and postdoctoral fellows to scientific conferences, where they can present their work to other scientists and make connections that can help them launch their careers in research and industry.

Throughout the year BioArtography images (a collection of over 250) can be viewed and ordered online at www.bioartography.com

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Exhibition Mon, 18 Jul 2022 12:08:38 -0400 2022-07-22T10:00:00-04:00 2022-07-22T21:00:00-04:00 BioArtography Exhibition BioArtography at the Ann Arbor Art Fair
BioArtography Booth at the Ann Arbor Art Fair (July 23, 2022 10:00am) https://events.umich.edu/event/96071 96071-21791888@events.umich.edu Event Begins: Saturday, July 23, 2022 10:00am
Location:
Organized By: BioArtography

BioArtography will be in South University Booth SU1109 (Between E. Univ. and Church) the Ann Arbor Art Fair! 13 spectacular new images for 2022 will be making their debut!

Every day at the University of Michigan, scientists from many fields work together to study organism development, function and disease. While the goal of these studies is to design new and effective ways to treat disease and provide better understanding of ourselves as well as the world around us, many are also taking the time to share the beauty of their work with others through a program called BioArtography. In the course of research, scientists use special stains to add color to the otherwise transparent tissues. Microscopes then allow detailed observation of the tiny, colorful biological structures revealed in these images. This results in a fascinating combination of art and science that U-M researchers are capturing in pictures taken through microscopes and turning into artworks that would look beautiful on any wall.

The goal of these studies is to design new and effective ways to treat disease and provide better understanding of ourselves as well as the world that surrounds us. Proceeds from the sale of this work help support the training of our next generation of researchers. Past BioArtography sales have raised enough money to send more than 100 graduate students and postdoctoral fellows to scientific conferences, where they can present their work to other scientists and make connections that can help them launch their careers in research and industry.

Throughout the year BioArtography images (a collection of over 250) can be viewed and ordered online at www.bioartography.com

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Exhibition Mon, 18 Jul 2022 12:08:38 -0400 2022-07-23T10:00:00-04:00 2022-07-23T20:00:00-04:00 BioArtography Exhibition BioArtography at the Ann Arbor Art Fair
Discovery and Development of Agonist Antibodies for T Cell Receptors (July 29, 2022 10:00am) https://events.umich.edu/event/96254 96254-21792188@events.umich.edu Event Begins: Friday, July 29, 2022 10:00am
Location: Off Campus Location
Organized By: Biomedical Engineering

Agonist antibodies that activate co-stimulatory immune receptors, such as the tumor necrosis factor (TNF) receptors OX40 and CD137, are an important class of emerging therapeutics due to their ability to regulate immune cell activity. Despite their promise, there are no approved agonist antibodies for treating cancer as demonstrated by previous unsuccessful clinical trials. Although multiple factors are responsible for poor clinical efficacy, one major bottleneck is the reliance on FcγR-mediated crosslinking for sufficient receptor activation. This is inherently problematic because FcγR expression varies greatly on different immune cells, leading to a wide range of receptor agonism. Emerging research suggests that antibodies engaging two different epitopes on the same immune receptor mediate receptor superclustering and enable robust antibody agonism without extrinsic Fc crosslinking. However, there are no systematic methods for identifying such biepitopic (also known as biparatopic) agonist antibodies. Therefore, the objective of this research work is to develop facile methods for reliably identifying biepitopic antibodies to activate immune receptors for immunotherapeutic applications.

Biepitopic antibodies have been shown to mediate potent receptor activation for a variety of immune receptors. Traditionally, the generation of these antibodies requires key steps including animal immunization, epitope binning to identify unique antibody pairs, and combining antibody pairs to engineer biepitopic antibodies. While this approach has been used to successfully discover biepitopic antibodies, it suffers from key limitations. Notably, animal immunization and subsequent antibody isolation is an arduous and unpredictable process. Even when successful clones are discovered from these processes, further epitope binning experiments are needed to select antibody pairs to discover potent immune therapeutics. To overcome these limitations, we developed an antibody screening strategy that greatly simplifies the discovery of biepitopic antibodies. Our approach eliminates the need for animal immunization by using existing, off-the-shelf IgG antibodies specific to the target receptor. Next, we perform in vitro selections by blocking the receptor epitope of the existing antibody and conducting subsequent sorts to identify single-chain antibodies with orthogonal binding domains. Thus far, our work has shown that the antibody screening strategy can be used to discover antibodies for a variety of TNF receptors including OX40 and CD137.

Given that receptor clustering of three or more receptors is critical for activating TNF receptors, we first generated biepitopic tetravalent OX40 antibodies by attaching novel single-chain antibodies to the C-termini of the light chain of existing clinical-stage antibodies. These tetravalent biepitopic antibodies showed remarkable T cell proliferation and cytokine secretion for biepitopic antibodies compared to their monoepitopic counterparts. Next, we sought to improve the additional clinical-stage OX40 IgGs engineered as biepitopic antibodies to show the generality of our findings that biepitopic antibodies can mediate superior and FcγR-independent activities. Beyond OX40 IgGs, we also show that biepitopic antibodies can be used to mediate superior T cell proliferation for other TNF receptors including CD137. Looking forward, we anticipate that these research advancements will accelerate the discovery and development of the next generation of immune therapeutics.

Date: Friday, July 29, 2022
Time: 10:00 AM
Zoom: https://umich.zoom.us/j/5163583658
Co-Chairs: Professors Peter Tessier and Lonnie Shea

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Lecture / Discussion Tue, 26 Jul 2022 13:09:39 -0400 2022-07-29T10:00:00-04:00 2022-07-29T11:00:00-04:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Ph.D. Defense
Hierarchical motion modeling of abdominal motions for radiation therapy (August 9, 2022 10:00am) https://events.umich.edu/event/96536 96536-21792631@events.umich.edu Event Begins: Tuesday, August 9, 2022 10:00am
Location: Lurie Biomedical Engineering (formerly ATL)
Organized By: Biomedical Engineering

Abstract:

Human abdominal organs are subject to a variety of physiological forces that superimpose their effects to influence local motion and configuration. Motions include breathing, gastric contraction, and other types of less periodic slow configuration changes. Breathing motion has been extensively studied and well characterized; however, gastric contraction and slow configuration motion have been rarely investigated. By using a golden angle stack-of-star radial sampling magnetic resonance image (MRI) sequence, we constructed a hierarchical motion model that characterizes each of these three motions, as well as their combined effects. Breathing motion is extracted and corrected as the first step, following by reconstruction of gastric motion and slow configuration changes. The model shows non-neglectable geometric displacements raised by all three motion modes. These motions, if not managed properly during radiation therapy, may potentially result in overdose to normal tissue or underdosage to the tumor target. Magnetic resonance guided radiotherapy (MRgRT) systems have been developed which have the technical capability to address these complex motions, but to date their primary applications have been relegated to management of breathing motion. In this dissertation, we proposed a gastric motion prediction framework to allow real-time management of contractile motion during MRgRT taking advantage of the intra-scan stability of gastric contraction motion observed in patients under standard pre-session eating restrictions. The framework was able to achieve submillimeter prediction error with a sufficient future prediction time to overcome the latency introduced by the image sampling reconstruction, motion assessment and treatment interruption or modification on MR-guided linear accelerators. Motions and deformations during radiation treatment present a challenge to precisely and accurately measure the radiation dose delivered to abdominal organs. A dose accumulation tool, developed based on the hierarchical motion model, was built to estimate dose distributions with abdominal motions. The tool demonstrates potential deviations of dose due to motion and shows exceeding of dose constraints in certain cases. It could support offline adaptation or help record delivered dose more accurately than stationary images used for daily patient positioning and/or online adaptation of treatment plans. The motion model is also currently supporting other clinical applications, including providing improved image quality reconstructions from free-breathing scans for improvement of accuracy of perfusion as well as liver functional maps. In the future, the model can be further utilized in other fields including radiology or gastroenterology.  

Room: LBME 2185 / Zoom Link: https://umich.zoom.us/j/93620134849 Meeting ID: 936 2013 4849 Passcode: 268890

Committee Chair(s): Dr. James Balter and Dr. Rojano Kashani

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Lecture / Discussion Fri, 05 Aug 2022 10:05:16 -0400 2022-08-09T10:00:00-04:00 2022-08-09T11:00:00-04:00 Lurie Biomedical Engineering (formerly ATL) Biomedical Engineering Lecture / Discussion BME Defense
Effects of Electric Stimulation on Physiology and Anatomy of the Visual Pathway (August 10, 2022 12:00pm) https://events.umich.edu/event/96539 96539-21792637@events.umich.edu Event Begins: Wednesday, August 10, 2022 12:00pm
Location:
Organized By: Biomedical Engineering

Abstract:
Retinal degenerative diseases that progressively lead to severe blindness impact the affected individual’s quality-of-life. Visual prosthesis technology aims to provide an individual a potential means of obtaining visual information lost to them by blindness. Since the proof-of-concept success in 1968 of a device implanted in a human, visual prostheses have had sustained academic research and commercial interest. However, commercial failure of two retinal prosthesis device has raised concerns for the visual prosthesis field. To learn from this experience, research in this dissertation is aimed at understanding the impact of electric stimulation on the target neural tissue and investigating technology for a visual cortex prosthesis, which can reach a larger patient population (compared to a retinal prosthesis).

My first set of experiments assessed, in an animal model of retinal degeneration, the condition of the brain and its ability to receive artificial vision information. Retinitis Pigmentosa has been proven to impact the human brain. My study investigated the extent to which this was replicated in a rat animal model of a single genetic mutation of Retinitis Pigmentosa. The P23H-1 rat was investigated with electrophysiology and immunohistochemistry to understand the brain’s function and structural condition. The rat brain’s response to light and electric stimulation was investigated, and the change of visually evoked responses and maintenance of electrically evoked responses was observed. Histology images show a relatively stable macrostructure of the blind rat brain.

I also performed retinal and cortical implant procedures to test newly developed visual prosthesis technology to enable investigations into researching neural change occurring from blindness and electric stimulation. A retinal device with Parylene-C as its main component was tested and its feasibility in the small eye of a rat animal model was investigated. The device can survive 4-weeks of implantation and is stable within the eye. In support of the development of a novel cortical visual prosthesis device that fits the need of blind individuals, I used a small animal model first to prove the efficacy and safety of a novel neurostimulation electrode. The device, named StiMote, is in preclinical development. I worked to characterize the full ability of the neural interface, High-Density Carbon Fibers with electrodeposited Platinum-Iridium. The ability of PtIr-HDCF as a recording and stimulation neural interface device was verified using electrochemical measurements before, during, and after a long-duration 7-hour electric stimulation session that simulates a full day of device use.

PtIr-HDCF as a neural interface device was verified by my previous work and its improvement in reducing neuroinflammatory response compared to other microelectrode array archetypes has been previously researched. As a result, PtIr-HDCF can be used as a device to monitor the brain and can better extract the effect of electric stimulation on the brain alone. I recorded neural electrophysiology to verify the rat brain’s sensitivity to stimuli before and after 7-hour stimulation. To supplement the already existing neural implant and electric stimulation inflammation data, Spatial Transcriptomics as a novel method to define electric stimulation safety was performed. Spatial Transcriptomics showed that PtIr-HDCF, when compared to a conventional microwire array, performs better in sustaining neural health by reducing neuroinflammation and eliciting mRNA upregulation of neurotrophic factors.

Findings of this project can be used to better inform future investigations into brain electrophysiology and transcriptomics projects aimed to understand the neural change from blindness and electric stimulation.

Committee Chair(s): Dr. James Weiland

Location: 1501 Auditorium, NCRC Bldg 32 & https://umich.zoom.us/j/91500987159?pwd=RWIvQkZVT2FHZjQ2S1BBS2k0ck1SUT09

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Lecture / Discussion Fri, 05 Aug 2022 10:32:21 -0400 2022-08-10T12:00:00-04:00 2022-08-10T13:00:00-04:00 Biomedical Engineering Lecture / Discussion BME Defense
Instrumentation Grants: S10s? MRIs? Help! (August 26, 2022 12:00pm) https://events.umich.edu/event/96328 96328-21792274@events.umich.edu Event Begins: Friday, August 26, 2022 12:00pm
Location: Off Campus Location
Organized By: OVPR Office of Research Development

Would your research program benefit from an expensive new instrument? Or do you need to upgrade outdated equipment? Would that equipment (that costs more than most houses) change what you can do in your lab? Not sure how to pull together grant applications to get all the new bells and whistles?

Research Development and Proposal Services (RDPS) will host a webinar on applying for major instrumentation grants. We will cover both the NIH S10 and NSF Major Research Instrumentation (MRI) funding mechanisms. Presenters Jill Jividen, PhD, and Rachel Wallace, PhD, will cover application requirements, best practices, common pitfalls, suggested timelines, and more, with plenty of time for questions and discussion.

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Livestream / Virtual Fri, 29 Jul 2022 11:29:11 -0400 2022-08-26T12:00:00-04:00 2022-08-26T13:30:00-04:00 Off Campus Location OVPR Office of Research Development Livestream / Virtual Closeup of microscope
Data-driven Methods for Automated Assessment of Coronary Artery Disease (August 30, 2022 9:00am) https://events.umich.edu/event/97256 97256-21794237@events.umich.edu Event Begins: Tuesday, August 30, 2022 9:00am
Location: Lurie Robert H. Engin. Ctr
Organized By: Biomedical Engineering

Abstract:

The current gold standard for Coronary Artery Disease (CAD) diagnosis is X-ray angiography. Visual estimation can be subjective, therefore semi-automated software tools such as Quantitative Coronary Angiography (QCA) have been developed to quantify disease severity. Alternatively, functional metrics such as Fractional Flow Reserve (FFR) have demonstrated better diagnostic outcomes than anatomical assessment, but they are not widely used due to cost and risk. Ideally, quantitative and functional information could be derived directly from X-ray angiography images without the additional risks, time, and cost associated with performing FFR or QCA.

The goal of this project is to develop automated data-driven approaches for anatomical and functional quantification of disease severity using X-ray angiography images. To this end, we have developed algorithms for 1) automated coronary vessel segmentation, 2) stenosis detection and characterization, 3) 3D reconstruction of coronary anatomy, and 4) image-based flow extraction. These algorithms can be used in conjunction with computational fluid dynamics (CFD) modeling to assess the functional significance of disease.

We first present AngioNet, a neural network for coronary segmentation from X-ray angiography images. Conventional algorithms relying on thresholding or filtering cannot distinguish between the coronary vessels and the catheter used to inject the dye. AngioNet’s key innovation is an Angiographic Processing Network, or APN, which learns the best possible combination of pre-processing filters to improve segmentation performance. AngioNet demonstrates state-of-the-art segmentation accuracy (Dice score = 0.864) and does not segment the catheter in challenging cases where other neural networks fail.

Building upon AngioNet, we developed combination of neural networks and image processing algorithms to automatically localize, segment, and measure stenoses. This pipeline was able to measure stenosis diameter within 0.206±0.155mm or approximately 1 pixel of ground truth measurements from QCA. It is also the first automated pipeline to quantify rather than categorize disease severity.

Although measuring stenosis diameter in 2D images is useful, a more robust approach would be to measure diameters in the 3D coronary anatomy. Another advantage of the 3D coronary anatomy is that it can be used to perform CFD simulations of blood flow and compute functional metrics such as FFR. To this end, we developed a machine learning approach for automated 3D vessel reconstruction from a series of uncalibrated 2D X-ray angiography images. This approach is superior to projective geometry methods for 3D reconstruction due to their semi-automatic nature and reliance on accurate knowledge of input image acquisition angles. Our machine learning approach has demonstrated sub-pixel error in radius reconstruction (0.16±0.07mm) and 1% error in FFR computed in a reconstructed coronary tree.

In addition to the 3D coronary geometry, information about patient-specific flow or pressure is required to perform a hemodynamics simulation and compute FFR. We developed an algorithm that tracks vessel area in sequential frames of a segmented angiography series to estimate relative flow in each branch. We validated the algorithm in the simplest possible case, using a simulation of dye transport under steady flow conditions as the ground truth. On average, the difference in relative flow per branch was 5.15% for a healthy coronary tree and 3.68% in a coronary tree with stenosis.

We finally demonstrated the successes and limitations of the methods developed in this thesis by comparing computational FFR derived using the above algorithms against clinically measured FFR. The error between the calculated and clinically measured FFR was 0.1, corresponding to an 11% error.

Committee Chair(s):
Dr. C. Alberto Figueroa and Dr. Brahmajee K. Nallamothu

Zoom Link: https://umich.zoom.us/j/94364657250, Passcode: 390041 *Registration is required

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Workshop / Seminar Mon, 22 Aug 2022 16:54:04 -0400 2022-08-30T09:00:00-04:00 2022-08-30T10:00:00-04:00 Lurie Robert H. Engin. Ctr Biomedical Engineering Workshop / Seminar BME Defense Announcement
A Novel Bioelastomer Platform with Tailorable Design Parameters for Cartilage Regeneration (August 30, 2022 11:00am) https://events.umich.edu/event/97426 97426-21794553@events.umich.edu Event Begins: Tuesday, August 30, 2022 11:00am
Location: Lurie Biomedical Engineering (formerly ATL)
Organized By: Biomedical Engineering

Abstract:

Articular cartilage has limited ability to self-repair, which often causes focal defects to progress into post traumatic osteoarthritis. Autologous chondrocyte implantation, a process in which chondrocytes are harvested from the patient, expanded in monolayer culture, and injected into the defect site, is one of the most common approaches to treat cartilage defect. However, chondrocyte dedifferentiation during this process reduces their ability to durably restore cartilage function. Chondrocyte-based cartilage tissue engineering offers alternative approaches for cartilage repair to overcome the limitations of current clinical options by developing environments that combines cues from synthetic scaffold and biological factors to enhance chondrocyte function. However, the translation to the clinic has been limited by our incomplete understanding of how scaffold design parameters interact together to control cell function. Therefore, this dissertation focuses on designing a chondrocyte-based biomaterial platform made with a novel elastomeric synthetic scaffold, poly(glycerol dodecanedioate) (PGD), to investigate the combinatory effects of design parameters on chondrocytes behavior in vitro.

First, this thesis evaluates the effects of surface modification of PGD on the shape and extracellular matrix (ECM) production of chondrocyte, both of which are crucial for robust cartilage formation. I investigated two different strategies to generate a biomaterial surface with high cell affinity: 1) coating with various concentration of collagen type I or hyaluronic acid individually or in combination, or 2) altering the surface charge and roughness using various level of alkaline hydrolysis. Our results revealed the combinatorial effects of ligand composition and density or surface charge and roughness on human articular chondrocyte function.

Lastly, I used finite element analysis to determine if the local strain fields that developed inside the pores under load could be tuned to be within the range shown to have an anabolic effect on chondrocyte function. The tensile strains that develop along 31% – 71% pore surfaces inside of porous PGD scaffolds, according to varying pore size and porosity, were at levels shown to stimulate chondrocyte ECM production, indicating that the pore structural parameters could be tuned to optimize cellular-level strain profiles. These results suggest that porous PGD scaffolds have the potential to guide cartilage regeneration.

Overall, this dissertation produces a platform for cartilage tissue engineering using a novel bioelastomer PGD, in which the scaffold design parameters, such as surface modification and cellular strain, can be modified to enhance chondrocyte function.

Committee Chair(s):
Dr. Rhima Coleman

Zoom Link: https://umich.zoom.us/j/91391389305, Passcode: PGD

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Presentation Thu, 25 Aug 2022 11:41:37 -0400 2022-08-30T11:00:00-04:00 2022-08-30T12:00:00-04:00 Lurie Biomedical Engineering (formerly ATL) Biomedical Engineering Presentation BME Ph.D. Defence
Biomaterials and Synthetic Biology for Monitoring Immune Function (September 1, 2022 4:30pm) https://events.umich.edu/event/97432 97432-21794558@events.umich.edu Event Begins: Thursday, September 1, 2022 4:30pm
Location: Electrical Engineering and Computer Science Building
Organized By: Biomedical Engineering

Abstract:
Although the prevalence of autoimmune diseases continues to grow, monitoring these conditions remains a challenge resulting in delayed diagnosis, ineffective treatment, and ultimately increased patient morbidity. The PRecision Immune MicroEnvironments (PRIME) Lab, seeks to address this challenge by combining biomaterials and synthetic biology to create a minimally invasive toolset for monitoring immune responses within tissues. Our work on biomaterial-based immunological niches demonstrates that implantable materials enable the formation of an engineered tissue that can be biopsied to monitor multiple sclerosis (MS). These niches provide insights into the phenotype of immune cells that control disease activity, and can be used to monitor disease dynamics or to gauge the effectiveness of treatment. To move beyond biopsy, we are developing synthetic biology tools that enable detection of specific biomarkers of immune function. I will conclude my talk with a brief discussion of my planned research program that aims to leverage materials, immune engineering, and synthetic biology to build translatable tools for real-time monitoring of tissue immunity.

Bio:
Dr. Aaron Morris is an Assistant Professor in the Department of Biomedical Engineering at the University of Michigan, and runs the PRecision Immune MicroEnvironments Laboratory (PRIME Lab). Dr. Morris completed a B.S. in BME at Georgia Tech, followed by a Ph.D. in BME from Yale University. As a postdoc, Dr. Morris worked with Dr. Lonnie Shea at the University of Michigan to use biomaterials to interrogate the immune system during autoimmunity and with Dr. Joshua Leonard at Northwestern University to build synthetic, modular receptor systems for synthetic biology platforms. Dr. Morris’s work has been supported through a number of mechanisms including the NIH K99/R00, NSF GRFP, NIH T32, Michigan Life Sciences Institute Fellows program, and a Michigan Precision Health grant, and a TED Fellowship (check out his TED talk here if interested).

Zoom:
https://umich.zoom.us/j/91375430500

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Workshop / Seminar Thu, 01 Sep 2022 10:47:54 -0400 2022-09-01T16:30:00-04:00 2022-09-01T17:30:00-04:00 Electrical Engineering and Computer Science Building Biomedical Engineering Workshop / Seminar BME 500 Seminar
From molecules to development: biological timing and patterning (September 8, 2022 4:30pm) https://events.umich.edu/event/97913 97913-21795312@events.umich.edu Event Begins: Thursday, September 8, 2022 4:30pm
Location: Electrical Engineering and Computer Science Building
Organized By: Biomedical Engineering

Abstract:
Organisms from bacteria to humans employ complex biochemical or genetic oscillatory networks, termed biological clocks, to drive a wide variety of cellular and developmental processes for robust timing and patterning. Despite their complexity and diversity, many of these clocks share the same core architectures that are highly conserved from species to species, suggesting an essential role of network structures underlying clock functioning. The Yang lab, bridging biophysics and systems & synthetic biology, has integrated modeling with experiments in minimal cells and live embryos to elucidate universal physical mechanisms underlying the complex processes during development. In this talk, I will focus on our recent efforts in understanding the design and interaction of cellular clocks in cell cycles and embryonic developmental patterns. Computationally, we have identified network motifs, notably incoherent inputs, that universally enhance systems' robust performance. Experimentally, we developed a unique synthetic-cell system in microfluidic droplets to analyze circuits and functions of robustness and tunability. We also established single-cell assays of zebrafish embryos combined with biomechanics to analyze the role of energy and mechanical and biochemical signaling in spatiotemporal patterns.

Bio:
Qiong Yang received a Ph.D. in Physics from MIT in 2009 before joining the Department of Chemical and Systems Biology at Stanford University for postdoctoral research, supported by the Stanford Dean’s Postdoctoral Fellowship and a Damon Runyon Cancer Research Fellowship. She was appointed as an Assistant Professor in Biophysics at the University of Michigan in 2014 and was promoted to Associate Professor in 2022. Her research group is affiliated with the departments of Physics, Applied Physics, BME, Complex Systems, and Computational Medicine & Bioinformatics at UM. She has received awards including NSF CAREER, NIH MIRA, Sloan Fellowship, Elizabeth C. Crosby Award, and Class of 1923 Memorial Teaching Award.​​​​​​​

Zoom:
https://umich.zoom.us/j/91375430500

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Workshop / Seminar Thu, 01 Sep 2022 10:44:42 -0400 2022-09-08T16:30:00-04:00 2022-09-08T17:30:00-04:00 Electrical Engineering and Computer Science Building Biomedical Engineering Workshop / Seminar BME 500 Seminar
What are PRONOUNS - Welcome picnic for international grad students in engineering (September 9, 2022 12:00pm) https://events.umich.edu/event/97217 97217-21794152@events.umich.edu Event Begins: Friday, September 9, 2022 12:00pm
Location:
Organized By: Engineering Education Research

Join us on North Campus to learn PRONOUNS, play activities, win prizes, make new friends and enjoy a free lunch!

Are you ready for the new semester? We prepared a welcome picnic for you. Each participant will receive some swag and a free lunch! By attending this event, you will know more about Pronouns and meet new people. Please come to join us and share the event with your friends.

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Workshop / Seminar Tue, 23 Aug 2022 14:27:40 -0400 2022-09-09T12:00:00-04:00 2022-09-09T13:30:00-04:00 Engineering Education Research Workshop / Seminar Pronoun Event
Science Communication Certificate Program (September 12, 2022 12:00pm) https://events.umich.edu/event/98347 98347-21796523@events.umich.edu Event Begins: Monday, September 12, 2022 12:00pm
Location:
Organized By: Futures in Research, Science, Teaching - FIRST

A science communication program run by the Museum of Natural History and the MCDB department. Create a video based on a past research project/experience to be shared on the Museum's website. Completion of the workshops and final video will earn a science communication certificate.

More details:
https://drive.google.com/file/d/1R0o_bkRGMgPn7L_MVSD_V4b3_j3p8a-Y/view?usp=sharing

Application deadline is Sept. 12th

Please email us with any questions:
SECOND.Contact@umich.edu

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Workshop / Seminar Thu, 08 Sep 2022 17:46:46 -0400 2022-09-12T12:00:00-04:00 2022-09-12T12:00:00-04:00 Futures in Research, Science, Teaching - FIRST Workshop / Seminar SECOND Science Communication
Futures in Research, Science, and Teaching - General meeting (September 13, 2022 4:00pm) https://events.umich.edu/event/96044 96044-21791846@events.umich.edu Event Begins: Tuesday, September 13, 2022 4:00pm
Location:
Organized By: Futures in Research, Science, Teaching - FIRST

General meetings take place every other Tuesday from September 13 to December 6th. Events include:

September 13th: Pathways in Research (Graduate student/Faculty panel)
September 27th: Mixer (food provided)
October 11th: Poster design and presentation
October 25th: Applying to graduate school - application components and essay writing advice
November 8th: Finding paid summer and post-baccalaureate research opportunities
November 22nd: Faculty talk
December 6th: Mixer

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Meeting Mon, 12 Sep 2022 12:26:57 -0400 2022-09-13T16:00:00-04:00 2022-09-13T17:00:00-04:00 Futures in Research, Science, Teaching - FIRST Meeting Event flyer detailing date, time, and location: September 13th at 4 pm, BSB 1010
DCMB / CCMB Weekly Seminar (September 14, 2022 4:00pm) https://events.umich.edu/event/97098 97098-21794444@events.umich.edu Event Begins: Wednesday, September 14, 2022 4:00pm
Location: Palmer Commons
Organized By: DCMB Seminar Series

Talk Title: Deep learning for sequence design with a few data points

Abstract:
Deep learning has begun a renaissance in chemistry and materials. We can devise and fit models to predict molecular properties in a few hours and deploy them in a web browser. We can create novel generative models that were previously PhD theses in an afternoon. In my group, we’re exploring deep learning in peptides. We are focused on two major problems: interpretability and data scarcity. Now that we can make deep learning models to predict any molecular property ad naseum, what can we learn? I will discuss our recent efforts on interpreting deep learning models through symbolic regression and counterfactuals. Data scarcity is a common problem in biochemistry: how can we learn new properties without significant expense of experiments? One method is in judicious choice of experiments, which can be done with active learning. Another approach is self-supervised learning and constraining symmetries, which both try to exploit structure in data. I will cover recent progress in these areas.

Zoom: https://umich-health.zoom.us/j/93929606089?pwd=SHh6R1FOQm8xMThRemdxTEFMWWpVdz09

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Lecture / Discussion Thu, 18 Aug 2022 13:56:14 -0400 2022-09-14T16:00:00-04:00 2022-09-14T17:00:00-04:00 Palmer Commons DCMB Seminar Series Lecture / Discussion
DCM&B Tools and Technology Seminar (September 15, 2022 12:00pm) https://events.umich.edu/event/96847 96847-21793398@events.umich.edu Event Begins: Thursday, September 15, 2022 12:00pm
Location: Palmer Commons
Organized By: DCMB Tools and Technology Seminar

npore is a read realigner which recalculates each read's fine-grained alignment in order to more accurately align ''n-polymers'' such as homopolymers (n=1) and tandem repeats (2 ≤ n ≤ 6). In other words, given an input BAM, it adjusts each read's CIGAR string to more accurately model the most likely sequencing errors and actual variants. Traditional affine gap penalties are context-agnostic, and do not model the higher likelihood of INDELs in low-complexity regions (particularly n-polymers), leading to poor or inconsistent alignments. We find that npore improves pileup concordance across reads and results in slightly better variant calling performance.

Tool Link: https://github.com/TimD1/nPoRe

This presentation will be held in 2036 Palmer Commons. There will also be a remote viewing option via Zoom.

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Presentation Mon, 15 Aug 2022 10:35:55 -0400 2022-09-15T12:00:00-04:00 2022-09-15T13:00:00-04:00 Palmer Commons DCMB Tools and Technology Seminar Presentation
Engineering Operational Transplant Tolerance via Biomaterials (September 15, 2022 4:30pm) https://events.umich.edu/event/97969 97969-21795406@events.umich.edu Event Begins: Thursday, September 15, 2022 4:30pm
Location: Electrical Engineering and Computer Science Building
Organized By: Biomedical Engineering

Abstract:
Organ and cell replacement therapies hold great promise for the treatment of multiple conditions, including autoimmune diseases such as type 1 diabetes. Restoration of endogenous insulin production, via cell delivery, has shown to be clinically successful in lowering complications and improving glucose sensing in patients. Yet, a widespread application has been hampered by the need for chronic immunosuppressive drugs to prevent strong inflammatory and immunological responses to the graft. Engineered materials offer a powerful approach for local, selective targeting of immune functionalities without compromising systemic immune function. In this talk, we will highlight engineered synthetic polymeric materials that can promote tissue integration and induce operational tolerance to cell therapies by generating a multifaced regulatory network.

Bio:
Prof Coronel is a Biological scholar and Assistant Professor of Biomedical Engineering at the University of Michigan. Her lab is centered on engineering biomaterials for perturbing and investigating immunological responses. Dr. Coronel received her BS degree in Biomedical Engineering from the University of Miami, and her Ph.D. in Biomedical Engineering from the University of Florida. She also obtained a certificate in Clinical Translational Research from Emory University Public Health School. She finished her postdoctoral fellowship at the Georgia Institute of Technology. Her work has been funded by JDRF, NIH, and the programmable materials initiative at the University of Michigan.

Zoom:
https://umich.zoom.us/j/91375430500

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Workshop / Seminar Thu, 01 Sep 2022 15:04:37 -0400 2022-09-15T16:30:00-04:00 2022-09-15T17:30:00-04:00 Electrical Engineering and Computer Science Building Biomedical Engineering Workshop / Seminar BME 500 Seminar
CPOD Seminar Talk: Brian Capell, MD, PhD, (UPenn) Chromatin at the nexus of epithelial development, differentiation, and cancer (September 20, 2022 4:00pm) https://events.umich.edu/event/98510 98510-21796732@events.umich.edu Event Begins: Tuesday, September 20, 2022 4:00pm
Location: Off Campus Location
Organized By: Center for Cell Plasticity and Organ Design

Center for Cell Plasticity and Organ Design with UM-Skin Biology and Disease Resource based Center presents:

Brian Capell, MD, PhD
University of Pennsylvania
Chromatin at the nexus of epithelial development, differentiation, and cancer
In-Person: BSRB ABC Seminar Rooms
Zoom Meeting Option ID: 932 944 30678

Faculty Host: Rajesh Rao, MD
Leonard G. Miller Professor of Ophthalmology and Visual Sciences

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Lecture / Discussion Mon, 12 Sep 2022 11:52:11 -0400 2022-09-20T16:00:00-04:00 2022-09-20T17:00:00-04:00 Off Campus Location Center for Cell Plasticity and Organ Design Lecture / Discussion Capell
DCMB Weekly Seminar (September 21, 2022 4:00pm) https://events.umich.edu/event/98815 98815-21797218@events.umich.edu Event Begins: Wednesday, September 21, 2022 4:00pm
Location: Palmer Commons
Organized By: DCMB Seminar Series

Abstract:
The intersect between the life sciences (cells, tissues, organs) and engineered materials (polymers, biomacromolecules, semiconductors) is crucial for a wide range of medical and biotechnological applications. Hence, the precise control of biotic/abiotic interfaces has been one of the main obstacles of past decades. The Lahann Lab designs polymers for a range of different medical applications. In particular, we have developed a class of protein nanoparticles for targeting of glioblastoma. In addition, I will summarize our efforts related to sheet-like 3D organoid systems and will address recent advances with morphologically designed interfaces.

Research Interests:
Designer surfaces, advanced polymers, biomimetic materials, microfluidic devices, engineered microenvironments, nano-scale self-assembly.

Joerg Lahann’s research is broadly related to surface engineering with strong ties to biomedical engineering and nanotechnology. His research on reversibly switching surfaces was featured in an article in Science (J. Lahann, et al., A Reversibly Switching Surface, January 17, 2003, 299, 371-374.) These “smart surfaces” can reversibly switch properties in response to an external stimulus. To demonstrate these findings, a surface design was developed that can be changed from water-attracting to water-repelling with the application of a weak electric field. Designed as a switch, single-layered molecular-level machines are aligned on a surface using self-assembly and then are flipped between defined microscopic states. This type of surface design may offer a new paradigm for interfacial engineering as it amplifies reversible conformational transitions at a molecular level to macroscopic changes in surface properties without altering the chemical identity of the surface.

Joerg has also developed a novel class of polymers with potential for biomimetic and spatially directed surface engineering. This “reactive coating” technology uses chemical vapor deposition (CVD) polymerization to deposit a wide range of chemical signatures on various substrate materials. Its simplicity in providing chemically reactive groups and its applicability to three-dimensional geometries (e.g., for microfluidics) enables the exact tailoring of surface properties and the preparation of biologically relevant microenvironments. Reactive coatings are compatible with soft lithographic processes, allowing for patterning of proteins, DNA, cytokines, and mammalian cells.

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Lecture / Discussion Thu, 15 Sep 2022 11:36:52 -0400 2022-09-21T16:00:00-04:00 2022-09-21T17:00:00-04:00 Palmer Commons DCMB Seminar Series Lecture / Discussion (Protein pattern deposited on a polymer surface, artistic rendering, credit: Bahar Dadfar)
DCM&B Tools and Technology Seminar (September 22, 2022 12:00pm) https://events.umich.edu/event/96848 96848-21793400@events.umich.edu Event Begins: Thursday, September 22, 2022 12:00pm
Location: Palmer Commons
Organized By: DCMB Tools and Technology Seminar

This presentation will be given remotely, with the livestream available for group viewing in 2036 Palmer Commons. There will also be a remote viewing option via Zoom.

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Presentation Mon, 15 Aug 2022 10:42:50 -0400 2022-09-22T12:00:00-04:00 2022-09-22T13:00:00-04:00 Palmer Commons DCMB Tools and Technology Seminar Presentation
LHS Collaboratory (September 22, 2022 12:00pm) https://events.umich.edu/event/96027 96027-21791723@events.umich.edu Event Begins: Thursday, September 22, 2022 12:00pm
Location: Palmer Commons
Organized By: Department of Learning Health Sciences

LHS Collaboratory Kickoff Poster Session Showcasing LHS Work at the University of Michigan

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Lecture / Discussion Tue, 12 Jul 2022 10:55:57 -0400 2022-09-22T12:00:00-04:00 2022-09-22T14:00:00-04:00 Palmer Commons Department of Learning Health Sciences Lecture / Discussion LHS Collaboratory logo
OHS Seminar Series Schedule (September 22, 2022 12:00pm) https://events.umich.edu/event/98131 98131-21795615@events.umich.edu Event Begins: Thursday, September 22, 2022 12:00pm
Location: Dental & W.K. Kellogg Institute
Organized By: Office of Research School of Dentistry

OHS Seminar Series Schedule Fall 2022 - Stay tuned for more updates!

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Presentation Tue, 06 Sep 2022 13:16:28 -0400 2022-09-22T12:00:00-04:00 2022-09-22T13:00:00-04:00 Dental & W.K. Kellogg Institute Office of Research School of Dentistry Presentation OHS Seminar Series Schedule Fall 2022
Postdoc Appreciation Week – Special Presentations (September 22, 2022 12:00pm) https://events.umich.edu/event/98318 98318-21796492@events.umich.edu Event Begins: Thursday, September 22, 2022 12:00pm
Location: Dental & W.K. Kellogg Institute
Organized By: Office of Research School of Dentistry

Felicia Miranda, DDS, MS, PhD
Postdoctoral Fellow
Department of Orthodontics
University of Michigan School of Dentistry
Mentor: Lucia Cevidanes

Amanda Rodriguez, DDS, MS
Research Fellow & PiMA Program Assistant Director
Department of Periodontics and Oral Medicine
University of Michigan School of Dentistry
Mentors: Drs. Hsun-Liang Chan, DDS, MS and
Oliver Kripfgans, PhD

Hiroki Ueharu, Ph.D.
Department of Biologic & Materials Sciences and Prosthodontics, University of Michigan School of Dentistry
Mentor: Dr. Yuji Mishina

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Presentation Thu, 08 Sep 2022 12:20:48 -0400 2022-09-22T12:00:00-04:00 2022-09-22T13:00:00-04:00 Dental & W.K. Kellogg Institute Office of Research School of Dentistry Presentation Postdoc Appreciation Week – Special Presentations
Metabolic Reprogramming of Donor Hearts to Improve Function (September 22, 2022 4:30pm) https://events.umich.edu/event/98895 98895-21797323@events.umich.edu Event Begins: Thursday, September 22, 2022 4:30pm
Location: Electrical Engineering and Computer Science Building
Organized By: Biomedical Engineering

Abstract:
Harmful metabolic processes are well underway during cold preservation of donor hearts. We discovered a method to increase the expression of beneficial enzymes which augment the production of anti-inflammatory metabolites. This leads to lowered oxidative stress, reduced myocardial injury and translates into better cardiac function following transplantation. Future strategies to reduce primary graft dysfunction could involve precise modulation of these cardiac metabolic pathways.

Bio:
Paul Tang is an Assistant Professor of Cardiac Surgery at the University of Michigan-Ann Arbor. His cardiothoracic surgery training was completed at Duke University Medical Center where he also received advanced training in heart transplantation, ventricular assist devices and aortic surgery. He has given talks and published widely on the natural history and surgical outcomes of these diseases. At Yale University, Dr. Tang completed a PhD focused on cardiovascular immunology. Dr. Tang's clinical practice includes surgical treatment of heart failure (i.e. heart transplantation, ventricular assist devices), valvular repair or replacement, and aortic aneurysm surgery. He is an investigator in various national clinical trials for heart failure management, and is a member of professional societies such as The International Society for Heart and Lung Transplantation, Southern Thoracic Surgical Association, American Heart Association, and the Society of Thoracic Surgeons.​​​​​​​

Zoom:
https://umich.zoom.us/j/91375430500

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Workshop / Seminar Fri, 16 Sep 2022 16:19:36 -0400 2022-09-22T16:30:00-04:00 2022-09-22T17:30:00-04:00 Electrical Engineering and Computer Science Building Biomedical Engineering Workshop / Seminar BME 500 Seminar
Predictive analysis and deep learning of functional MRI in Alzheimer's disease (September 26, 2022 10:00am) https://events.umich.edu/event/97916 97916-21795315@events.umich.edu Event Begins: Monday, September 26, 2022 10:00am
Location: Off Campus Location
Organized By: Biomedical Engineering

Abstract:
Alzheimer's disease (AD) and dementia pose a significant burden to individuals and public health. AD is expected to grow in prevalence in the coming decades due to the aging population. Brain atrophy is a major component of AD pathology and can occur before symptoms of cognitive impairment. However, pathological brain atrophy and symptoms of cognitive impairment may be a result of many years of disease impacts. Evidence supports the need for early detection of impacted neurocircuitry to foresee future progression to advanced stages of AD and develop treatments. This dissertation examines predictive modeling and deep learning methods to identify brain-behavior relationships and learn low-dimensional representations of brain activity from MR imaging data. The dissertation and methods are separated into four parts.  

Part one of this work examines multivariate analysis approaches applied to functional connectivity from subjects with an early clinical phenotype of AD, mild cognitive impairment (MCI). A regression framework using partial least squares and feature selection demonstrated significant brain-behavior relationships with measures of cognition and memory. The results also confirm other findings that ecologically relevant task-based connectivity serves as a ``stress-test" for memory-related deficits such as those observed in MCI. This approach elucidated brain regions that may be implicated in MCI and warrant future study (superior temporal gyrus, inferior parietal lobule, and superior frontal gyrus). Part two extends the multivariate analyses studied in part one to an additional brain imaging modality, arterial spin labeling (ASL). Cerebral blood flow (CBF) as measured by ASL demonstrated brain-behavior relationships with composite measures of memory and learning in a cohort along the spectrum of AD, demonstrating that CBF data warrant further investigation as a predictor in this application.

Parts three and four utilize a variational autoencoder (VAE) model, a deep learning approach to encode latent representations that aim to disentangle sources of fMRI signal. A surface-based VAE trained on only healthy controls is shown to be generalizable to patients with known AD pathology. The results maintained individual separation and high input/decoder output spatial reconstruction correlation of r=0.8 across all three groups. Part four extended the surface-based model used in part three to a volumetric fMRI approach. Similarly to the surface-based model, high reconstruction accuracy (NRMSE=0.68) and temporal correlation (r=0.8) between input and decoder output are demonstrated. This approach is more readily applicable to 3D fMRI data as compared to the surface-based model. 

In summary, this work has proposed and developed multivariate and deep learning analysis techniques for brain imaging data in the context of AD with the ultimate goal of improving detection and intervention for early pathological changes in the brain.

Zoom Link: https://umich.zoom.us/meeting/register/tJIpcOigrjIsHtJq_xJ1aboK1T0PdWpTkBP5
*Registration Required

Committee Chair(s):
Dr. Scott J. Peltier and Dr. Douglas C. Noll

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Lecture / Discussion Thu, 01 Sep 2022 11:07:14 -0400 2022-09-26T10:00:00-04:00 2022-09-26T11:00:00-04:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Ph.D. Defense
Evaluation of Phosphate Treatment and Long-Term RUNX2 Suppression On Adult Human MSC Chondrogenesis and Neo-Cartilage Formation (September 26, 2022 3:15pm) https://events.umich.edu/event/99026 99026-21797474@events.umich.edu Event Begins: Monday, September 26, 2022 3:15pm
Location: Lurie Biomedical Engineering (formerly ATL)
Organized By: Biomedical Engineering

Abstract:
Clinical repair strategies for articular cartilage defects are limited by the inability of the tissue to self-repair, often resulting in post-traumatic osteoarthritis (PTOA). PTOA arises from the degradation of structural cartilage extracellular matrix (ECM) proteins responsible for maintaining articular cartilage mechanics, such as aggrecan and collagen. Current cartilage tissue engineering strategies aim to utilize human-derived cells to regenerate cartilage prior to the onset of PTOA. Limited availability of chondrocytes – the primary cell type in articular cartilage – imposes a need for alternatives. Human mesenchymal stem cells (hMSCs) are a promising solution as they can be found in a variety of tissues and can differentiate into MSC-derived chondrocytes (MdChs). However, MSCs are limited by their inability to produce a stable chondrogenic phenotype and deposit and maintain ECM in long-term culture due to maturation, (hypertrophy) where metalloproteinases cleave collagen II and aggrecan. As a result, MSC-derived cartilage regeneration techniques are not yet suitable for clinical use. The central objective of this thesis is to increase cartilage matrix accumulation for more clinically functional cartilage tissue by increasing matrix deposition and stabilizing the chondrogenic phenotype of MSCs.

We investigated two approaches to increase cartilage ECM accumulation and improve MdCh-based cartilage tissue engineering functional outcomes: inorganic phosphate (Pi) treatment and RUNX2 suppression. First, we found that Pi increased cartilage ECM production, but also increased MdCh hypertrophy, while RUNX2 suppression increased stiffness of neo-cartilage tissues long-term. Finally, we showed that combined treatment of Pi and RUNX2 suppression exhibited reduced MdCh hypertrophy but did not significantly increase matrix accumulation. Overall, this dissertation explores methodologies that promote both cartilage matrix accumulation and reduces cartilage matrix loss during long-term culture to better support the use of MdChs in cartilage defect repair strategies.

Zoom Link: https://umich.zoom.us/j/98189564171 Password: cartilage

Committee Chair: Dr. Rhima Coleman

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Lecture / Discussion Mon, 19 Sep 2022 15:31:39 -0400 2022-09-26T15:15:00-04:00 2022-09-26T16:15:00-04:00 Lurie Biomedical Engineering (formerly ATL) Biomedical Engineering Lecture / Discussion BME PhD Defense
Futures in Research, Science, and Teaching - General meeting (September 27, 2022 4:00pm) https://events.umich.edu/event/96044 96044-21791847@events.umich.edu Event Begins: Tuesday, September 27, 2022 4:00pm
Location:
Organized By: Futures in Research, Science, Teaching - FIRST

General meetings take place every other Tuesday from September 13 to December 6th. Events include:

September 13th: Pathways in Research (Graduate student/Faculty panel)
September 27th: Mixer (food provided)
October 11th: Poster design and presentation
October 25th: Applying to graduate school - application components and essay writing advice
November 8th: Finding paid summer and post-baccalaureate research opportunities
November 22nd: Faculty talk
December 6th: Mixer

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Meeting Mon, 12 Sep 2022 12:26:57 -0400 2022-09-27T16:00:00-04:00 2022-09-27T17:00:00-04:00 Futures in Research, Science, Teaching - FIRST Meeting Event flyer detailing date, time, and location: September 13th at 4 pm, BSB 1010
OHS Seminar Series Schedule (September 29, 2022 12:00pm) https://events.umich.edu/event/98131 98131-21795616@events.umich.edu Event Begins: Thursday, September 29, 2022 12:00pm
Location: Dental & W.K. Kellogg Institute
Organized By: Office of Research School of Dentistry

OHS Seminar Series Schedule Fall 2022 - Stay tuned for more updates!

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Presentation Tue, 06 Sep 2022 13:16:28 -0400 2022-09-29T12:00:00-04:00 2022-09-29T13:00:00-04:00 Dental & W.K. Kellogg Institute Office of Research School of Dentistry Presentation OHS Seminar Series Schedule Fall 2022
Re-imagining Ultrasound and Photoacoustic Imaging (September 29, 2022 4:30pm) https://events.umich.edu/event/99202 99202-21797699@events.umich.edu Event Begins: Thursday, September 29, 2022 4:30pm
Location: Electrical Engineering and Computer Science Building
Organized By: Biomedical Engineering

Abstract:
Paradigm shifts in technology are needed for next-generation ultrasound imaging. We introduce novel electrostrictive row-column array technology that promises improved 3D image quality and ultrafast imaging speeds. Moreover, these advances will lead to arrays of unprecedented size and novel form-factors such as endoscopic probes and wearable band-aids that will mitigate operator dependence and lead to longitudinal imaging opportunities. Our technology enables readout from every element of the 2D array using only row and column addressing, and is well-suited to volumetric photoacoustic imaging using pulsed laser excitation to image optical properties of tissues. Novel agents and genetically-encoded reporters will be introduced. Applications to brain imaging, cardiovascular medicine, small animal imaging will be discussed. Furthermore, a new non-contact all optical form of photoacoustic imaging will be discussed with applications to virtual histology of tissues.

Bio:
Roger Zemp earned his PhD from UC Davis in 2004 and after three years of postdoctoral work in the Laboratory of Prof. Lihong Wang, joined the Faculty in the Department of Electrical and Computer Engineering and Biomedical Engineering at the University of Alberta in 2007. He is a recognized international leader in the field of photoacoustic imaging and ultrasound imaging. He has co-founded two startup companies and maintains an active laboratory at the intersection of ultrasound, optics, micro-nano-fabrication, and in vivo imaging. ​​​​​​​

Zoom:
https://umich.zoom.us/j/91375430500

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Workshop / Seminar Thu, 22 Sep 2022 15:39:52 -0400 2022-09-29T16:30:00-04:00 2022-09-29T17:30:00-04:00 Electrical Engineering and Computer Science Building Biomedical Engineering Workshop / Seminar BME 500 Seminar
DCMB / CCMB Weekly Seminar (October 5, 2022 4:00pm) https://events.umich.edu/event/99751 99751-21798643@events.umich.edu Event Begins: Wednesday, October 5, 2022 4:00pm
Location: Palmer Commons
Organized By: DCMB Seminar Series

Abstract:

Accurately predicting the onset of disease is a major challenge in clinical medicine because the genesis of diseases is generally a complex and dynamic process. Wearable sensor technologies provide an unprecedented opportunity to collect physiological data at orders of magnitude higher high time-resolution than conventional clinical practice. This provides unprecedented opportunities for investigating the dynamics of disease processes and may usher in a new era of real-time, personalized medicine. We have proposed the potential of real-time, continuously measured physiological data as a non-invasive, “digital biomarker” approach for detecting the earliest stages in transition to a disease state. In this talk, I will describe an example of our interdisciplinary team’s work on this topic that uses the early detection and possible prediction of febrile (i.e., fever-associated) adverse events in cancer events as an important application.

Clinical Interests
Prostate Cancer, General Oncology, Biomarkers in Oncology
Research Interests
• Biology of circulating, extracellular nucleic acids and translational applications
• Developing next generation approaches for early detection and monitoring of cancer
• Bioinformatics and computational biology, high-throughput sequencing
• New technologies to enable cancer detection and monitoring

https://umich-health.zoom.us/j/93929606089?pwd=SHh6R1FOQm8xMThRemdxTEFMWWpVdz09

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Lecture / Discussion Mon, 03 Oct 2022 15:21:48 -0400 2022-10-05T16:00:00-04:00 2022-10-05T17:00:00-04:00 Palmer Commons DCMB Seminar Series Lecture / Discussion Muneesh Tewari, MD, PhD
DCM&B Tools and Technology Seminar (October 6, 2022 12:00pm) https://events.umich.edu/event/96850 96850-21793401@events.umich.edu Event Begins: Thursday, October 6, 2022 12:00pm
Location: Palmer Commons
Organized By: DCMB Tools and Technology Seminar

This presentation will be held in 2036 Palmer Commons. There will also be a remote viewing option via Zoom.

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Presentation Mon, 29 Aug 2022 13:40:58 -0400 2022-10-06T12:00:00-04:00 2022-10-06T13:00:00-04:00 Palmer Commons DCMB Tools and Technology Seminar Presentation
OHS Seminar Series Schedule (October 6, 2022 12:00pm) https://events.umich.edu/event/98131 98131-21795617@events.umich.edu Event Begins: Thursday, October 6, 2022 12:00pm
Location: Dental & W.K. Kellogg Institute
Organized By: Office of Research School of Dentistry

OHS Seminar Series Schedule Fall 2022 - Stay tuned for more updates!

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Presentation Tue, 06 Sep 2022 13:16:28 -0400 2022-10-06T12:00:00-04:00 2022-10-06T13:00:00-04:00 Dental & W.K. Kellogg Institute Office of Research School of Dentistry Presentation OHS Seminar Series Schedule Fall 2022
Towards a digital lung for medical research and applications (October 6, 2022 4:30pm) https://events.umich.edu/event/99561 99561-21798343@events.umich.edu Event Begins: Thursday, October 6, 2022 4:30pm
Location: Electrical Engineering and Computer Science Building
Organized By: Biomedical Engineering

Abstract:
Respiratory infections and chronic diseases have been among the top causes of death worldwide for decades, killing over 8 million people annually. Current diagnostic methods for respiratory diseases result in late diagnosis and high rates of underdiagnosis. Further, the wide variability in the patient response to treatment challenges population-based therapies. Personalized medicine arises as a promising alternative to standard practice, but it relies on expensive laboratory and testing infrastructure not available worldwide. This motivates the creation of computational models of the human lungs for in silico research and applications.

In this talk, I will present our group's efforts to construct computational models of the lung for medical research and applications. I will review how computer simulations of alveolar structures informed by micro-computed tomography can change our current understanding of the forces acting on the lung extracellular matrix (ECM). Further, I will discuss a class of microstructurally informed models for predicting the lung tissue response and how they can capture mechanical changes in lung mechanics triggered by ECM remodeling. Finally, I will show our current work on creating personalized virtual lungs and how we can use them to simulate the response of patients under respiratory failure that are connected to mechanical ventilation.

Bio:
Daniel E. Hurtado is an associate professor with the School of Engineering at PUC Chile, and a visiting professor at the Institute for Medical Engineering and Science at MIT. He leads the Computational Medicine Group, an interdisciplinary team that focuses on the creation of personalized computational replicas of the human lungs, with applications in the study of mechanical ventilation and early diagnosis of pulmonary diseases. His work also involves the development of wearable respiratory systems to monitor breathing in athletes and hospital patients. 

Prof. Hurtado received his M.S. and Ph.D. degrees from the California Institute of Technology as a Fulbright fellow. His thesis work made him the recipient of the Robert J. Melosh Medal, presented by Duke University. In 2018, the World Economic Forum selected him as one of the 50 most influential young scientists worldwide under 40 years old for his contributions in research and innovation in biomedical engineering. He is also an elected member for the World Council of Biomechanics.

Zoom:
https://umich.zoom.us/j/91375430500

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Workshop / Seminar Thu, 29 Sep 2022 15:17:19 -0400 2022-10-06T16:30:00-04:00 2022-10-06T17:30:00-04:00 Electrical Engineering and Computer Science Building Biomedical Engineering Workshop / Seminar BME 500 Seminar
New AI in Science Postdoctoral Fellowship Program Town Hall Meeting #1 (October 10, 2022 10:00am) https://events.umich.edu/event/99913 99913-21798876@events.umich.edu Event Begins: Monday, October 10, 2022 10:00am
Location: BBB
Organized By: Michigan Institute for Data Science

MIDAS is excited to announce a new AI in Science Postdoctoral Fellowship Program at U-M, which will launch this semester!

Funded by an as-yet-unnamed donor, this campus-wide program, managed by MIDAS, focuses on enabling major research breakthroughs in science and engineering through the adoption of cutting-edge AI methodologies. The program will accept 10 new postdocs each year for the next six years.

On October 10th, we will hold two town hall meetings to introduce the new AI in Science Postdoctoral Fellowship Program at Michigan. The program leadership team will provide details of the program, outline the application process, and answer questions. There will also be networking time so that faculty members interested in being mentors can talk with each other, and potential candidates can connect with faculty mentors.
To support attendees on North and Central campus, we will offer two meetings with identical content:

Meeting #1 (North Campus): Oct. 10, 10am - 12pm, Tishman Lobby, Bob and Betty Beyster Building, 2260 Hayward Street.

Meeting #2 (Central Campus): Oct.10, 12:30pm - 2:30pm, Weiser Hall 10th floor, 500 Church Street.

Sign up to attend a Town Hall session

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Presentation Thu, 06 Oct 2022 11:36:59 -0400 2022-10-10T10:00:00-04:00 2022-10-10T12:00:00-04:00 BBB Michigan Institute for Data Science Presentation Town Hall Meeting
New AI in Science Postdoctoral Fellowship Program Town Hall Meeting #2 (October 10, 2022 12:30pm) https://events.umich.edu/event/99915 99915-21798880@events.umich.edu Event Begins: Monday, October 10, 2022 12:30pm
Location: Weiser Hall
Organized By: Michigan Institute for Data Science

MIDAS is excited to announce a new AI in Science Postdoctoral Fellowship Program at U-M, which will launch this semester!

Funded by an as-yet-unnamed donor, this campus-wide program, managed by MIDAS, focuses on enabling major research breakthroughs in science and engineering through the adoption of cutting-edge AI methodologies. The program will accept 10 new postdocs each year for the next six years.

On October 10th, we will hold two town hall meetings to introduce the new AI in Science Postdoctoral Fellowship Program at Michigan. The program leadership team will provide details of the program, outline the application process, and answer questions. There will also be networking time so that faculty members interested in being mentors can talk with each other, and potential candidates can connect with faculty mentors.
To support attendees on North and Central campus, we will offer two meetings with identical content:

Meeting #1 (North Campus): Oct. 10, 10am - 12pm, Tishman Lobby, Bob and Betty Beyster Building, 2260 Hayward Street.

Meeting #2 (Central Campus): Oct.10, 12:30pm - 2:30pm, Weiser Hall 10th floor, 500 Church Street.

Sign up to attend a Town Hall session

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Presentation Thu, 06 Oct 2022 11:41:41 -0400 2022-10-10T12:30:00-04:00 2022-10-10T14:30:00-04:00 Weiser Hall Michigan Institute for Data Science Presentation Town Hall Meeting
EMERSE Meeting Series (October 11, 2022 1:00pm) https://events.umich.edu/event/98192 98192-21795695@events.umich.edu Event Begins: Tuesday, October 11, 2022 1:00pm
Location: Off Campus Location
Organized By: Department of Learning Health Sciences

Speaker:
Mark Beno, MSM
Executive Director, Cleveland Institute for Computational Biology,
School of Medicine, Case Western Reserve University

The Electronic Medical Record Search Engine (EMERSE) was installed at University Hospitals of Cleveland (UH) in 2021 by the Cleveland Institute for Computational Biology (CICB), a collaboration between Case Western Reserve University (CWRU) and UH.  At present, EMERSE contains indexed medical notes from 2018 through present for over 1.7 million UH patients.  This presentation will discuss the strategies we employed to successfully install EMERSE, the lessons-learned in rolling out EMERSE to research and operational teams, some research success stories since EMERSE adoption, and the additional tools we have developed as add-ons to the EMERSE application that we use internally for tracking EMERSE metrics and plan to share with the broader EMERSE community.

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Lecture / Discussion Tue, 06 Sep 2022 23:35:08 -0400 2022-10-11T13:00:00-04:00 2022-10-11T14:00:00-04:00 Off Campus Location Department of Learning Health Sciences Lecture / Discussion EMERSE logo
CPOD Seminar Talk: Alex Hughes, PhD (UPenn)"Interpreting geometric rules of early kidney formation for synthetic morphogenesis" (October 11, 2022 4:00pm) https://events.umich.edu/event/98601 98601-21796958@events.umich.edu Event Begins: Tuesday, October 11, 2022 4:00pm
Location: Off Campus Location
Organized By: Center for Cell Plasticity and Organ Design

Tuesday, October 11, 2022 4:00 pm
Center for Cell Plasticity and Organ Design presents:

Alex Hughes, PhD
Assistant Professor
Department of Bioengineering
University of Pennsylvania

Seminar entitled: "Interpreting geometric rules of early kidney formation for synthetic morphogenesis"

In-Person: BSRB ABC Seminar Rooms
Zoom Meeting Option ID: 932 944 30678

Faculty Host: Claudia Loebel, MD PhD, Assistant Professor, Materials Science & Engineering

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Lecture / Discussion Mon, 12 Sep 2022 21:04:22 -0400 2022-10-11T16:00:00-04:00 2022-10-11T17:00:00-04:00 Off Campus Location Center for Cell Plasticity and Organ Design Lecture / Discussion Hughes
Futures in Research, Science, and Teaching - General meeting (October 11, 2022 4:00pm) https://events.umich.edu/event/96044 96044-21791848@events.umich.edu Event Begins: Tuesday, October 11, 2022 4:00pm
Location:
Organized By: Futures in Research, Science, Teaching - FIRST

General meetings take place every other Tuesday from September 13 to December 6th. Events include:

September 13th: Pathways in Research (Graduate student/Faculty panel)
September 27th: Mixer (food provided)
October 11th: Poster design and presentation
October 25th: Applying to graduate school - application components and essay writing advice
November 8th: Finding paid summer and post-baccalaureate research opportunities
November 22nd: Faculty talk
December 6th: Mixer

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Meeting Mon, 12 Sep 2022 12:26:57 -0400 2022-10-11T16:00:00-04:00 2022-10-11T17:00:00-04:00 Futures in Research, Science, Teaching - FIRST Meeting Event flyer detailing date, time, and location: September 13th at 4 pm, BSB 1010
Poster Design Workshop (October 11, 2022 4:00pm) https://events.umich.edu/event/99872 99872-21798816@events.umich.edu Event Begins: Tuesday, October 11, 2022 4:00pm
Location: Biological Sciences Building
Organized By: Futures in Research, Science, Teaching - FIRST

A short presentation on STEM poster design, followed by researchers and graduate students sharing personal examples. Topics will included formatting, narrating your research story, and designing a poster that works equally well presented or read on its own.

RSVP: https://forms.gle/DVGvnsSXhtCEBeWy6

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Workshop / Seminar Wed, 05 Oct 2022 13:46:21 -0400 2022-10-11T16:00:00-04:00 2022-10-11T17:00:00-04:00 Biological Sciences Building Futures in Research, Science, Teaching - FIRST Workshop / Seminar FIRST Logo
DCMB / CCMB Weekly Seminar (October 12, 2022 4:00pm) https://events.umich.edu/event/99377 99377-21797973@events.umich.edu Event Begins: Wednesday, October 12, 2022 4:00pm
Location: Palmer Commons
Organized By: DCMB Seminar Series

Abstract:

Our current understanding of how genes are regulated is akin to solving a jigsaw puzzle. Many factors governing gene expression have been identified, and researchers have collected a wide variety of related datasets. However, how these "parts" are pieced together to function as a whole remains unclear. In this talk, I will discuss our research to develop and apply state-of-the-art machine learning methods to genomics datasets to attempt to put together the pieces from the data. I will cover our work using deep learning architecture that captures the data's underlying structure to integrate datasets and connect them to gene expression via the prediction task. We also interpret the prediction results and tie them back to contributing factors to develop potential hypotheses related to gene regulation. I will then move from bulk data to the single-cell data domain and discuss methods to perform unsupervised integration of different types of single-cell experiments. This talk aims to highlight our research direction's potential to reveal the important gene regulatory mechanisms in characterizing cell types and diseases from the collected data.

Bio:

Ritambhara Singh is an Assistant Professor in the Computer Science department and a faculty member of the Center for Computational Molecular Biology at Brown University. Her research lab works at the intersection of machine learning and biology. Prior to joining Brown, Singh was a post-doctoral researcher in the Noble Lab at the University of Washington. She completed her Ph.D. in 2018 from the University of Virginia with Dr. Yanjun Qi as her advisor. Her research has involved developing machine learning algorithms for the analysis of biological data as well as applying deep learning models to novel biological and biomedical applications. She recently received the NHGRI Genomic Innovator Award for developing deep learning methods to integrate and model genomics datasets. URL: https://vivo.brown.edu/display/rsingh47

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Lecture / Discussion Tue, 27 Sep 2022 09:32:07 -0400 2022-10-12T16:00:00-04:00 2022-10-12T17:00:00-04:00 Palmer Commons DCMB Seminar Series Lecture / Discussion Ritambhara Singh, Asst. Professor (Brown University)
DCM&B Tools and Technology Seminar (October 13, 2022 12:00pm) https://events.umich.edu/event/96851 96851-21793402@events.umich.edu Event Begins: Thursday, October 13, 2022 12:00pm
Location: Palmer Commons
Organized By: DCMB Tools and Technology Seminar

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO) in early 2020.

Tool Link: https://github.com/CIDO-ontology/cido

This presentation will be held in 2036 Palmer Commons. There will also be a remote viewing option via Zoom.

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Presentation Mon, 15 Aug 2022 10:49:10 -0400 2022-10-13T12:00:00-04:00 2022-10-13T13:00:00-04:00 Palmer Commons DCMB Tools and Technology Seminar Presentation
OHS Seminar Series Schedule (October 13, 2022 12:00pm) https://events.umich.edu/event/98131 98131-21795618@events.umich.edu Event Begins: Thursday, October 13, 2022 12:00pm
Location: Dental & W.K. Kellogg Institute
Organized By: Office of Research School of Dentistry

OHS Seminar Series Schedule Fall 2022 - Stay tuned for more updates!

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Presentation Tue, 06 Sep 2022 13:16:28 -0400 2022-10-13T12:00:00-04:00 2022-10-13T13:00:00-04:00 Dental & W.K. Kellogg Institute Office of Research School of Dentistry Presentation OHS Seminar Series Schedule Fall 2022
Celebrate Invention (October 13, 2022 1:00pm) https://events.umich.edu/event/98346 98346-21796522@events.umich.edu Event Begins: Thursday, October 13, 2022 1:00pm
Location: Michigan Union
Organized By: Innovation Partnerships

Celebrate University of Michigan inventors and the growing impact of U-M innovations!

Don’t miss this year’s annual Celebrate Invention highlighting demonstrations from promising U-M startups, networking opportunities at the ecosystem fair, panel discussions featuring prominent inventors and alumni, and the presentation of the Distinguished University Innovator of the Year Award.

Thursday, October 13
1:00–6:00pm
Michigan Union, 2nd Floor
530 S. State Street, Ann Arbor, MI 48109

Part of Ann Arbor SPARK's a2Tech360, Celebrate Invention is free and open to the public. Register today at *https://myumi.ch/DJNbM!*

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1:00–3:00pm: Panel Sessions & Ecosystem Fair

3:00–6:00pm: Reception, Rogel Ballroom, Michigan Union, 2nd Floor

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Reception / Open House Thu, 08 Sep 2022 17:06:20 -0400 2022-10-13T13:00:00-04:00 2022-10-13T18:00:00-04:00 Michigan Union Innovation Partnerships Reception / Open House Image of the Celebrate Invention logo on a blue background.
DCMB / CCMB Weekly Seminar (October 19, 2022 4:00pm) https://events.umich.edu/event/99817 99817-21798751@events.umich.edu Event Begins: Wednesday, October 19, 2022 4:00pm
Location: Palmer Commons
Organized By: DCMB Seminar Series

Abstract:
Genome-wide association studies (GWAS) successfully identified more than a hundred genomic regions that contribute to schizophrenia risk. However, extracting biological mechanisms from GWAS is a challenge, because the majority of common risk variants reside in noncoding regions of the genome. In this talk, I will outline how high-resolution 3D maps of chromatin contacts in the human brain permit large-scale annotation of non-coding variants. In particular, I will introduce a novel platform that my lab has developed, Hi-C-coupled MAGMA (H-MAGMA), that annotates GWAS by incorporating chromatin interaction profiles from human brain tissue. While H-MAGMA identified neurobiologically relevant target genes for psychiatric disorders, application of H-MAGMA to schizophrenia GWAS identified thousands of genes to be associated with schizophrenia, necessitating the need for refining variants. To this end, we performed a massively parallel reporter assay (MPRA) on schizophrenia risk variants, from which we detected 440 variants with allelic regulatory activity. Characterization of these functional regulatory variants provided previously unknown regulatory principles of schizophrenia.

Short bio:
Hyejung Won is an Assistant Professor in the Department of Genetics and Neuroscience Center at the University of North Carolina at Chapel Hill. She received her B.S. and Ph.D. in Biology from Korea Advanced Institute of Science and Technology (KAIST), where she conducted research revealing the underlying mechanism of neurodevelopmental conditions using genetically modified mice under the supervision of Dr. Eunjoon Kim. She then joined Dr. Dan Geschwind’s group at UCLA, where she established Hi-C, a genome-wide chromosome conformation capture technology, and generated chromatin interaction profiles from the developing and adult human brain. Her lab leverages the genomics approach to bridge the gap between genetic risk factors and neurobiological mechanisms by mapping genetic variants of unknown function to the genes that they regulate, and identifying how dysfunctional gene regulation contributes to disease pathogenesis. Hyejung is the recipient of the NIH Director’s New Innovator Award, HHMI Gilliam Fellowship, NIH Pathway to Independence Award, and a NARSAD Young Investigator Award. She is also an active participant of the Impact of Genomic Variation on Function (IGVF) and PsychENCODE consortia.

Zoom link: https://umich-health.zoom.us/j/93929606089?pwd=SHh6R1FOQm8xMThRemdxTEFMWWpVdz09

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Lecture / Discussion Tue, 04 Oct 2022 13:40:56 -0400 2022-10-19T16:00:00-04:00 2022-10-19T17:00:00-04:00 Palmer Commons DCMB Seminar Series Lecture / Discussion Hyejung Won, PhD
DCM&B Tools and Technology Seminar (October 20, 2022 12:00pm) https://events.umich.edu/event/96852 96852-21793403@events.umich.edu Event Begins: Thursday, October 20, 2022 12:00pm
Location: Palmer Commons
Organized By: DCMB Tools and Technology Seminar

"Molecular representation has an important implication on biomedical and other chemically related studies, and this talk could serve as a brief introduction to the broad field of representation techniques for molecules like drugs. This talk mainly introduces several widely used molecular representation methods, along with some examples of the implementation and applications for those representation methods."

This presentation will be given remotely, with the livestream available for group viewing in 2036 Palmer Commons. There will also be a remote viewing option via Zoom.

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Presentation Mon, 15 Aug 2022 10:52:38 -0400 2022-10-20T12:00:00-04:00 2022-10-20T13:00:00-04:00 Palmer Commons DCMB Tools and Technology Seminar Presentation
LHS Collaboratory (October 20, 2022 12:00pm) https://events.umich.edu/event/96028 96028-21791725@events.umich.edu Event Begins: Thursday, October 20, 2022 12:00pm
Location: Off Campus Location
Organized By: Department of Learning Health Sciences

Speakers:
Alex John London, PhD
Professor of Ethics and Philosophy
Director of the Center for Ethics and Policy at Carnegie Mellon University
Explainability Is Not the Solution to Structural Challenges to AI in Medicine

Explainability is often treated as a necessary condition for ethical applications of artificial intelligence (AI) in Medicine. In this brief talk I survey some of the structural challenges facing the development and deployment of effective AI systems in health care to illustrate some of the limitations to explainability in addressing these challenges. This talk builds on prior work (London 2019, 2022) to illustrate how ambitions for AI in health care likely require significant changes to key aspects of health systems.

Melissa McCradden, PhD, MHSc
Director of AI in Medicine
The Hospital for Sick Children
On the Inextricability of Explainability from Ethics: Explainable AI does not Ethical AI Make

Explainability is embedded into a plethora of legal, professional, and regulatory guidelines as it is often presumed that an ethical use of AI will require explainable algorithms. There is considerable controversy, however, as to whether post hoc explanations are computationally reliable, their value for decision-making, and the relational implications of their use in shared decision-making. This talk will explore the literature across these domains and argue that while post hoc explainability may be a reasonable technical goal, it should not be offered status as a moral standard by which AI use is judged to be ‘ethical.’

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Livestream / Virtual Sat, 01 Oct 2022 17:10:43 -0400 2022-10-20T12:00:00-04:00 2022-10-20T13:30:00-04:00 Off Campus Location Department of Learning Health Sciences Livestream / Virtual LHS Collaboratory logo
OHS Seminar Series Schedule (October 20, 2022 12:00pm) https://events.umich.edu/event/98131 98131-21795619@events.umich.edu Event Begins: Thursday, October 20, 2022 12:00pm
Location: Dental & W.K. Kellogg Institute
Organized By: Office of Research School of Dentistry

OHS Seminar Series Schedule Fall 2022 - Stay tuned for more updates!

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Presentation Tue, 06 Sep 2022 13:16:28 -0400 2022-10-20T12:00:00-04:00 2022-10-20T13:00:00-04:00 Dental & W.K. Kellogg Institute Office of Research School of Dentistry Presentation OHS Seminar Series Schedule Fall 2022
Rock, Paper, Scissors: The oral microbiome at the intersection of genotypic, anthropogenic and systemic factors (October 20, 2022 12:00pm) https://events.umich.edu/event/99963 99963-21798941@events.umich.edu Event Begins: Thursday, October 20, 2022 12:00pm
Location: Dental & W.K. Kellogg Institute
Organized By: Office of Research School of Dentistry

As a dual-trained periodontist and microbial ecologist, I use my clinical skills and training in ‘-omics’ research to investigate the myriad ways in which the human microbiome can be harnessed to promote health. I firmly believe that oral health and systemic diseases are intricately connected, and that global health can only be achieved when physicians and dentists collaborate to identify at-risk individuals and deliver integrated care.

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Lecture / Discussion Fri, 07 Oct 2022 10:59:44 -0400 2022-10-20T12:00:00-04:00 2022-10-20T13:00:00-04:00 Dental & W.K. Kellogg Institute Office of Research School of Dentistry Lecture / Discussion Purnima Kumar, DDS, PhD
Spinal cord stimulation to restore sensation and reduce phantom limb pain after limb amputation (October 20, 2022 4:30pm) https://events.umich.edu/event/98857 98857-21797273@events.umich.edu Event Begins: Thursday, October 20, 2022 4:30pm
Location: Electrical Engineering and Computer Science Building
Organized By: Biomedical Engineering

Abstract:
Despite important advances in the design of prosthetic devices, loss of a limb causes major challenges that often limit participation in activities of daily living. For people with upper-limb amputation, prosthetic adoption rates remain poor and device control is often unintuitive. Those with lower-limb amputation experience impaired balance control, abnormal gait, and an increased rate of falls. Across both groups, upwards of 85% of people also experience debilitating phantom limb pain. All these problems can be attributed, in part, to the loss of sensory feedback from the limb after amputation. In this talk, I will present our research efforts focused on development of devices to stimulate the spinal cord to restore sensory feedback in people with limb amputation. Using devices that are currently implanted in over 50,000 people every year to treat chronic pain, we have demonstrated that spinal cord stimulation can evoke sensations in the missing limb to improve control of prosthetic limbs and reduce phantom limb pain in people with both upper- and lower-limb amputation.

Bio:
Lee Fisher is an Assistant Professor in the Departments of Physical Medicine & Rehabilitation and Bioengineering at the University of Pittsburgh and Director of Education for the Rehab Neural Engineering Labs. Dr. Fisher received his PhD in Biomedical Engineering from Case Western Reserve University, where his research focused on the use of electrical stimulation to restore standing after spinal cord injury. He was a post-doctoral scholar at the University of Pittsburgh before joining the faculty in 2013. Dr. Fisher was the 2021 recipient of the North American Neuromodulation Society’s Kumar New Investigator Award for his research focused on sensory restoration in people with limb amputation. He is a Senior Member of IEEE and Associate Editor of the IEEE Transactions on Neural Systems and Rehabilitation Engineering and Guest Editor of Frontiers in Pain Research.​​​​​​​

Zoom:
https://umich.zoom.us/j/91375430500

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Workshop / Seminar Fri, 16 Sep 2022 08:52:59 -0400 2022-10-20T16:30:00-04:00 2022-10-20T17:30:00-04:00 Electrical Engineering and Computer Science Building Biomedical Engineering Workshop / Seminar BME 500 Seminar
Telling half a story: A Mixed Methods Approach to Understanding Culturally Relevant Engineering Education in Nigeria and the United States (October 21, 2022 9:00am) https://events.umich.edu/event/99928 99928-21798898@events.umich.edu Event Begins: Friday, October 21, 2022 9:00am
Location: Lurie Robert H. Engin. Ctr
Organized By: Engineering Education Research

In 2021, the United States maintained its reputation as a destination of choice for international students around the globe. More than 80% of them are pursuing advanced degrees in STEM (Institute of International Education, 2021). Unfortunately, many of these international students come in only to experience loneliness, social disconnectedness, and a crisis of identity the longer they stay in their respective programs. The commitment to diversify and attract international students to US institutions must be followed by a clear understanding of what it takes to support these students. Among the myriad of international students that enter the US for higher education every year, I am particularly interested in the experiences of African international students. Is their performance in US higher education exclusively tied to their educational backgrounds or does it stem from a motivation to succeed in a different environment despite the odds? What might we learn about how engineering is taught in their home countries? In this study, I attempt to address these questions by designing a comparative case study using mixed methods, theoretically informed by culturally relevant pedagogy surrounding two contexts. This study poses the question of culture as an integral intrinsic aspect of learning, leveraging a socio-psychological framework to help understand how students receive support from their instructors to excel in engineering. In this presentation, I discuss emerging results of my studies investigating culturally relevant engineering education in Nigeria.

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Workshop / Seminar Fri, 07 Oct 2022 08:17:58 -0400 2022-10-21T09:00:00-04:00 2022-10-21T10:15:00-04:00 Lurie Robert H. Engin. Ctr Engineering Education Research Workshop / Seminar Moses Olayemi
Futures in Research, Science, and Teaching - General meeting (October 25, 2022 4:00pm) https://events.umich.edu/event/96044 96044-21791849@events.umich.edu Event Begins: Tuesday, October 25, 2022 4:00pm
Location:
Organized By: Futures in Research, Science, Teaching - FIRST

General meetings take place every other Tuesday from September 13 to December 6th. Events include:

September 13th: Pathways in Research (Graduate student/Faculty panel)
September 27th: Mixer (food provided)
October 11th: Poster design and presentation
October 25th: Applying to graduate school - application components and essay writing advice
November 8th: Finding paid summer and post-baccalaureate research opportunities
November 22nd: Faculty talk
December 6th: Mixer

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Meeting Mon, 12 Sep 2022 12:26:57 -0400 2022-10-25T16:00:00-04:00 2022-10-25T17:00:00-04:00 Futures in Research, Science, Teaching - FIRST Meeting Event flyer detailing date, time, and location: September 13th at 4 pm, BSB 1010
Writing Personal and Academic Statements (October 25, 2022 4:00pm) https://events.umich.edu/event/100505 100505-21800018@events.umich.edu Event Begins: Tuesday, October 25, 2022 4:00pm
Location: Biological Sciences Building
Organized By: Futures in Research, Science, Teaching - FIRST

Bioscience postdocs and grad students will give a presentation on what to include/avoid and how to frame your story while writing academic and personal statements for research-based grad programs (and others). There will be a chance after for anyone interested in workshopping their statement drafts in small groups.

RSVP: https://forms.gle/43KP9utUYjCknofm8

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Workshop / Seminar Thu, 20 Oct 2022 12:54:49 -0400 2022-10-25T16:00:00-04:00 2022-10-25T17:30:00-04:00 Biological Sciences Building Futures in Research, Science, Teaching - FIRST Workshop / Seminar FIRST Logo
Integrative Systems + Design Open House (October 26, 2022 11:00am) https://events.umich.edu/event/100064 100064-21799047@events.umich.edu Event Begins: Wednesday, October 26, 2022 11:00am
Location: School of Information North
Organized By: Integrative Systems + Design

Join us for the 2022 Integrative Systems + Design (ISD) Open House on Wednesday, October 26 at 11-12:30 PM. You will get to talk with our graduate coordinators, program directors and faculty, as well as current students. This is a great opportunity to visit the University of Michigan’s North Campus where the ISD lives and get to learn more about the opportunities within our six unique graduate degree programs.

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Reception / Open House Tue, 11 Oct 2022 07:31:04 -0400 2022-10-26T11:00:00-04:00 2022-10-26T12:30:00-04:00 School of Information North Integrative Systems + Design Reception / Open House Open House
Graduate Studies in Computational & Data Sciences Information Session (October 26, 2022 1:30pm) https://events.umich.edu/event/100680 100680-21800224@events.umich.edu Event Begins: Wednesday, October 26, 2022 1:30pm
Location: Lurie Robert H. Engin. Ctr
Organized By: Michigan Institute for Computational Discovery and Engineering

The educational programs represented are:
- PhD in Scientific Computing (MICDE)
- Graduate Certificate in Computational Discovery & Engineering (MICDE)
- Graduate Certificate in Computational Neuroscience (MICDE)
- Graduate Certificate in Data Science (MIDAS)

These programs are open to all U-M graduate students with an interest in scientific computing or data science. These methodologies can have a wide range of applications - current and past students have come from a variety of home departments including Aerospace Engineering, Applied Physics, Biostatistics, Biomedical Engineering, Civil & Environmental Engineering, Chemistry, Chemical Engineering, Climate and Space Sciences and Engineering, Computational Medicine and Bioinformatics, Ecology and Evolutionary Biology, Earth and Environmental Sciences, Epidemiology, Health Behavior and Health Education, Health Infrastructures & Learning Systems, Information, Industrial & Operations Engineering, Kinesiology, Linguistics, Macromolecular Science & Engineering, Math, Molecular, Cellular, and Developmental Biology, Mechanical Engineering, Materials Science & Engineering, Naval Architecture & Marine Engineering, Nuclear Engineering & Radiological Sciences, Neuroscience, Pharmaceutical Sciences, Physics, Political Science, Psychology, Environment and Sustainability, Sociology and Statistics.

If you have any questions about these programs or about the information session, please reach out to MICDE (micde-contact@umich.edu) or MIDAS (midas-contact@umich.edu).

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Presentation Tue, 25 Oct 2022 13:46:55 -0400 2022-10-26T13:30:00-04:00 2022-10-26T14:30:00-04:00 Lurie Robert H. Engin. Ctr Michigan Institute for Computational Discovery and Engineering Presentation MICDE/MIDAS Information Session - PhD in Scientific Computing (MICDE) - Graduate Certificate in Computational Discovery & Engineering (MICDE) - Graduate Certificate in Computational Neuroscience (MICDE) - Graduate Certificate in Data Science (MIDAS)
DCM&B Tools and Technology Seminar (October 27, 2022 12:00pm) https://events.umich.edu/event/96867 96867-21793515@events.umich.edu Event Begins: Thursday, October 27, 2022 12:00pm
Location: Palmer Commons
Organized By: DCMB Tools and Technology Seminar

Microbiome data are complex in nature, involving high dimensionality, compositionality, zero inflation, and taxonomic hierarchy. Compositional data reside in a simplex that does not admit the standard Euclidean geometry. Most existing methods rely on transformations that are inadequate or even inappropriate in modeling data with excessive zeros and taxonomic structure. In this talk, I will introduce novel amalgamation-based methods for microbiome compositional data analysis. In particular, we first develop a novel relative-shift regression framework that directly uses compositions as predictors. The new framework provides a paradigm shift for compositional regression and offers a superior biological interpretation. New equi-sparsity and taxonomy-guided regularization methods and an efficient smoothing proximal gradient algorithm are developed to facilitate feature aggregation and dimension reduction in regression. As a result, the framework can automatically identify clinically relevant microbes even if they are important at different taxonomic levels. We also develop a new dimension reduction paradigm for microbiome compositional data based on the amalgamation operation. Our approach aims to aggregate the compositions to a smaller number of principal compositions, guided by the available taxonomic structure, by minimizing a properly measured loss of information. We further demonstrate the efficacy of the new methods on simulations and several real microbiome studies.

Tool Link (Relative Shift): https://github.com/reagan0323/RelativeShift
Tool Link (PAA): https://github.com/LiYanStat/paaPack

This presentation will be given remotely, with the livestream available for group viewing in 2036 Palmer Commons. There will also be a remote viewing option via Zoom.

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Presentation Wed, 26 Oct 2022 08:27:17 -0400 2022-10-27T12:00:00-04:00 2022-10-27T13:00:00-04:00 Palmer Commons DCMB Tools and Technology Seminar Presentation
Immunity at the oral mucosal barrier surface (October 27, 2022 12:00pm) https://events.umich.edu/event/99907 99907-21798867@events.umich.edu Event Begins: Thursday, October 27, 2022 12:00pm
Location: Off Campus Location
Organized By: Office of Research School of Dentistry

My research has been focused on oral mucosal immunity with an emphasis on aberrant inflammatory conditions of
the oral cavity. Over the past decade I have established an independent research program at the NIH aimed at
understanding the molecular and cellular basis of oral immunity in health and in the common inflammatory disease,
periodontitis. In health, the oral immune system maintains a delicate balance with a rich and diverse community of
oral commensals, performing immune surveillance while preventing inflammation. Understanding mechanisms
involved in susceptibility and pathogenesis of periodontitis is not only critical for understanding the disease itself,
but may provide insights into shared mechanisms involved in inflammatory diseases. In periodontitis, the
microbiome is considered a key disease trigger, but it is also well documented that disease occurs and progresses
more rapidly in susceptible individuals. Our studies are focused on host/microbe interactions preserving health and
mediating inflammatory disease in the oral cavity. Ultimately, we aim to define key pathways involved in
susceptibility and progression of aggressive forms of periodontitis with the goal of identifying therapeutic targets.
Our program implements a bench to bedside approach for the study of periodontal immunity and is particularly
focused on the regulation of Th17 immunity in health and periodontitis. Our studies leverage the diverse strengths
of the NIH intramural environment and interrogate mechanisms involved in human oral immunity through the study
of patients with monogenic immune disorders, supplemented by relevant animal models and novel immunologic
techniques for the study of tissue immunity.

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Livestream / Virtual Thu, 06 Oct 2022 10:23:15 -0400 2022-10-27T12:00:00-04:00 2022-10-27T13:00:00-04:00 Off Campus Location Office of Research School of Dentistry Livestream / Virtual Niki M. Moutsopoulos, DDS, PhD Chief, Oral Immunity and Infection Unit National Institute of Dental and Craniofacial Research National Institutes of Health
OHS Seminar Series Schedule (October 27, 2022 12:00pm) https://events.umich.edu/event/98131 98131-21795620@events.umich.edu Event Begins: Thursday, October 27, 2022 12:00pm
Location: Dental & W.K. Kellogg Institute
Organized By: Office of Research School of Dentistry

OHS Seminar Series Schedule Fall 2022 - Stay tuned for more updates!

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Presentation Tue, 06 Sep 2022 13:16:28 -0400 2022-10-27T12:00:00-04:00 2022-10-27T13:00:00-04:00 Dental & W.K. Kellogg Institute Office of Research School of Dentistry Presentation OHS Seminar Series Schedule Fall 2022
Decoding morphogenic instruction in human microphysiological systems (October 27, 2022 4:30pm) https://events.umich.edu/event/100495 100495-21800009@events.umich.edu Event Begins: Thursday, October 27, 2022 4:30pm
Location: Electrical Engineering and Computer Science Building
Organized By: Biomedical Engineering

Abstract:
Tissue structure and function requires coordination between the physical organization of cells and the genetic programs controlling cell phenotype. Our lab investigates how intersections of chemical and mechanical signals at cell adhesive interfaces function across time and length scales to orchestrate 3D tissue morphogenesis and regulatory signaling. To do so, we develop and apply biomimetic human microphysiological culture systems that incorporate 3D organotypic architectures and permit the study of diverse tissue morphogenic processes associated with human development, regeneration, and pathogenesis with high resolution and biological control. Combining these systems with new molecular tools and microscopy-based methods, we have gained new mechanistic insight into diverse tissue morphogenic events ranging from the genesis and progression of human tuberculosis granulomas to the coordinated assembly and maintenance of human microvascular networks. In this talk, I will highlight these recent advances and detail our recent work establishing a previously unappreciated function for Notch receptors that links adhesive and cytoskeletal processes to transcriptional regulation of cell fate.

Bio:
Matt Kutys is an Assistant Professor in the Department of Cell and Tissue Biology at the University of California San Francisco (UCSF) and is faculty in the Helen Diller Family Comprehensive Cancer Center, the Cardiovascular Research Institute, and the UCSF – UC Berkeley Joint Graduate Program in Bioengineering. Dr. Kutys obtained his BS in Bioengineering from Pennsylvania State University working Dr. William Hancock and he received his PhD in Cell and Developmental Biology from the University of North Carolina Chapel Hill and the National Institutes of Health under Dr. Kenneth Yamada. He was a postdoctoral fellow at Boston University under Dr. Christopher Chen before joining UCSF in 2020. Dr. Kutys is the recipient of an NCI Pathway to Independence Award, a UCSF Program for Breakthrough Biomedical Research Award, and is a Shu Chien Early Career Award Lecturer from the Bioengineering Institute of California. ​​​​​​​

Zoom:
https://umich.zoom.us/j/91375430500

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Workshop / Seminar Thu, 20 Oct 2022 11:22:25 -0400 2022-10-27T16:30:00-04:00 2022-10-27T17:30:00-04:00 Electrical Engineering and Computer Science Building Biomedical Engineering Workshop / Seminar BME 500 Seminar
International Symposium and Poster Session (November 2, 2022 10:00am) https://events.umich.edu/event/95320 95320-21789160@events.umich.edu Event Begins: Wednesday, November 2, 2022 10:00am
Location: Off Campus Location
Organized By: Center for Cell Plasticity and Organ Design

Registration Required: https://www.eventbrite.com/e/center-for-cell-plasticity-and-organ-design-symposium-poster-session-tickets-166090175185

VIRTUAL MORNING SESSION
Matthias Hebrok, PhD
Modifying stem cell derived human islet organoids
Professor and Chair
Applied Stem Cell and Organoid Systems Technical University Munich (TUM)

Madeline Lancaster, PhD
Exploring regulators of human brain size determination using cerebral organoids
Research Leader
MRC Laboratory of Molecular Biology

Matthias Lütolf, PhD
Engineering epithelial organoids
Scientific Director, Roche Institute for Translational Bioengineering Professor of Bioengineering
Swiss Federal Institute of Technology

IN-PERSON AFTERNOON SESSION
Kenneth D. Poss, PhD
Regulating tissue regeneration
Professor of Cell Biology
Director of the Duke Regeneration Center Duke University

Sally Temple, PhD
Investigating Tauopathy mechanisms and interventions with 3D brain organoids?
Professor, Department of Biomedical Sciences University at Albany
Scientific Director, Neural Stem Cell Institute

James M. Wells, PhD
Using human pluripotent stem cells to engineer gastrointestinal tissues
Cincinnati Research Foundation Endowed Professor
Chief Scientific Officer, Center for Stem Cell and Organoid Medicine

UM SPEAKERS
Longhua Guo, PhD
From genetics to aging and regeneration in long-lived planarians
Assistant Professor, Molecular and Integrative Physiology
Research Assistant Professor, Institute of Gerontology, Medical School

Claudia Loebel, PhD
Microstructured hydrogels to guide self-assembly and function of lung alveolospheres
Assistant Professor, Materials Science and Engineering
College of Engineering

Daysha Ferrer-Torres, PhD
In vitro Models of the Human Esophagus Reveal Ancestrally Diverse Response to Injury
Research Fellow, Internal Medicine, Medical School
Lab: Jason Spence Laboratory

Charles Zhang
Applying high-content imaging techniques to iPSC-derived liver organoids for studying drug-induced liver injury
Graduate Student, Medicinal Chemistry, College of Pharmacology
Lab: Jonathan Sexton Laboratory


For more information email: Organogenesis@umich.edu

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Conference / Symposium Tue, 25 Oct 2022 23:33:56 -0400 2022-11-02T10:00:00-04:00 2022-11-02T19:00:00-04:00 Off Campus Location Center for Cell Plasticity and Organ Design Conference / Symposium Symposium
Graduate Studies in Computational & Data Sciences Information Session (November 2, 2022 1:30pm) https://events.umich.edu/event/100680 100680-21800225@events.umich.edu Event Begins: Wednesday, November 2, 2022 1:30pm
Location: West Hall
Organized By: Michigan Institute for Computational Discovery and Engineering

The educational programs represented are:
- PhD in Scientific Computing (MICDE)
- Graduate Certificate in Computational Discovery & Engineering (MICDE)
- Graduate Certificate in Computational Neuroscience (MICDE)
- Graduate Certificate in Data Science (MIDAS)

These programs are open to all U-M graduate students with an interest in scientific computing or data science. These methodologies can have a wide range of applications - current and past students have come from a variety of home departments including Aerospace Engineering, Applied Physics, Biostatistics, Biomedical Engineering, Civil & Environmental Engineering, Chemistry, Chemical Engineering, Climate and Space Sciences and Engineering, Computational Medicine and Bioinformatics, Ecology and Evolutionary Biology, Earth and Environmental Sciences, Epidemiology, Health Behavior and Health Education, Health Infrastructures & Learning Systems, Information, Industrial & Operations Engineering, Kinesiology, Linguistics, Macromolecular Science & Engineering, Math, Molecular, Cellular, and Developmental Biology, Mechanical Engineering, Materials Science & Engineering, Naval Architecture & Marine Engineering, Nuclear Engineering & Radiological Sciences, Neuroscience, Pharmaceutical Sciences, Physics, Political Science, Psychology, Environment and Sustainability, Sociology and Statistics.

If you have any questions about these programs or about the information session, please reach out to MICDE (micde-contact@umich.edu) or MIDAS (midas-contact@umich.edu).

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Presentation Tue, 25 Oct 2022 13:46:55 -0400 2022-11-02T13:30:00-04:00 2022-11-02T14:30:00-04:00 West Hall Michigan Institute for Computational Discovery and Engineering Presentation MICDE/MIDAS Information Session - PhD in Scientific Computing (MICDE) - Graduate Certificate in Computational Discovery & Engineering (MICDE) - Graduate Certificate in Computational Neuroscience (MICDE) - Graduate Certificate in Data Science (MIDAS)
Department of Computational Medicine & Bioinformatics -- Weekly Seminar (November 2, 2022 4:00pm) https://events.umich.edu/event/100730 100730-21800294@events.umich.edu Event Begins: Wednesday, November 2, 2022 4:00pm
Location: Palmer Commons
Organized By: DCMB Seminar Series

Abstract:

Graph representation learning leverages knowledge, geometry, and structure to develop powerful machine learning methods. First, I will introduce Shepherd, a graph neural network for personalized diagnosis of patients with rare genetic diseases. Diagnostic delay is pervasive in patients with rare genetic conditions. It can lead to numerous problems, including redundant testing and unnecessary procedures, delays in obtaining disease-appropriate management and therapies, and even irreversible disease progression. Shepherd uses knowledge-guided geometric deep learning to gather information from different parts of a knowledge graph and logically connect a patient's clinical-genomic information to the region in the knowledge graph relevant to diagnosis. Evaluation of patients from the Undiagnosed Diseases Network shows that Shepherd accurately identifies causal disease genes, finds other patients with the same causal gene and disease, and provides interpretable characterizations of novel diseases. Second, I will describe applications of graph neural networks in drug discovery. These are available through Therapeutics Data Commons (https://tdcommons.ai), an initiative to access and evaluate AI capability across therapeutic modalities and stages of drug discovery. The Commons supports the development of machine learning methods, with a strong bent towards developing the foundations for which methods are most suitable for drug discovery and why.

Short Bio:
Marinka Zitnik (https://zitniklab.hms.harvard.edu) is an Assistant Professor at Harvard University with appointments in the Department of Biomedical Informatics, Broad Institute of MIT and Harvard, and Harvard Data Science. Dr. Zitnik has published extensively in top ML venues and leading scientific journals. She has organized conferences and workshops in graph representation learning, drug discovery, and precision medicine at leading conferences (NeurIPS, ICLR, ICML, ISMB, AAAI, WWW), where she is also on the organizing committees. She is an ELLIS Scholar in the European Laboratory for Learning and Intelligent Systems (ELLIS) Society and a member of the Science Working Group at NASA Space Biology. Her research won paper and research awards from the International Society for Computational Biology, Bayer Early Excellence in Science, Amazon Faculty Research, Roche Alliance with Distinguished Scientists, Rising Star Award in Electrical Engineering and Computer Science, and Next Generation in Biomedicine Recognition, being the only young scientist with such recognition in both EECS and Biomedicine. She co-founded Therapeutics Data Commons and also AI for Science community initiative. https://zitniklab.hms.harvard.edu/zitnik-bio170.txt

https://umich-health.zoom.us/j/93929606089?pwd=SHh6R1FOQm8xMThRemdxTEFMWWpVdz09

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Livestream / Virtual Wed, 26 Oct 2022 15:15:31 -0400 2022-11-02T16:00:00-04:00 2022-11-02T17:00:00-04:00 Palmer Commons DCMB Seminar Series Livestream / Virtual Marinka Zitnik, PhD (Assistant Prof. of Biomedical Informatics at HMS)
DCM&B Tools and Technology Seminar (November 3, 2022 12:00pm) https://events.umich.edu/event/96868 96868-21793516@events.umich.edu Event Begins: Thursday, November 3, 2022 12:00pm
Location: Palmer Commons
Organized By: DCMB Tools and Technology Seminar

Single-cell multi-omic datasets, in which multiple molecular modalities are profiled within the same cell, provide a unique opportunity to discover the temporal relationship between epigenome and transcriptome. To realize this potential, we developed MultiVelo, a differential equation model of gene expression that extends the RNA velocity framework to incorporate epigenomic data. MultiVelo uses a probabilistic latent variable model to estimate the switch time and rate parameters of chromatin accessibility and gene expression from single-cell data, providing a quantitative summary of the temporal relationship between epigenomic and transcriptomic changes. Incorporating chromatin accessibility data significantly improves the accuracy of cell fate prediction compared to velocity estimates from RNA only. Fitting MultiVelo on single-cell multi-omic datasets from brain, skin, and blood cells reveals two distinct classes of genes distinguished by whether chromatin closes before or after transcription ceases. Our model also identifies four types of cell states--two states in which epigenome and transcriptome are coupled and two distinct decoupled states. The parameters inferred by MultiVelo quantify the length of time for which genes occupy each of the four states, ranking genes by the degree of coupling between transcriptome and epigenome. Finally, we identify time lags between transcription factor expression and binding site accessibility and between disease-associated SNP accessibility and expression of the linked genes. We provide an open-source Python implementation of MultiVelo on PyPI and GitHub.

Tool Link: https://github.com/welch-lab/MultiVelo

This presentation will be held in 2036 Palmer Commons. There will also be a remote viewing option via Zoom.

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Presentation Mon, 15 Aug 2022 13:23:41 -0400 2022-11-03T12:00:00-04:00 2022-11-03T13:00:00-04:00 Palmer Commons DCMB Tools and Technology Seminar Presentation
OHS Seminar Series Schedule (November 3, 2022 12:00pm) https://events.umich.edu/event/98131 98131-21795621@events.umich.edu Event Begins: Thursday, November 3, 2022 12:00pm
Location: Dental & W.K. Kellogg Institute
Organized By: Office of Research School of Dentistry

OHS Seminar Series Schedule Fall 2022 - Stay tuned for more updates!

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Presentation Tue, 06 Sep 2022 13:16:28 -0400 2022-11-03T12:00:00-04:00 2022-11-03T13:00:00-04:00 Dental & W.K. Kellogg Institute Office of Research School of Dentistry Presentation OHS Seminar Series Schedule Fall 2022
Magnetic Resonance Imaging for Models of Cardiac Performance (November 3, 2022 4:30pm) https://events.umich.edu/event/100777 100777-21800343@events.umich.edu Event Begins: Thursday, November 3, 2022 4:30pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Abstract:
Medical imaging provides several opportunities to collect data for building patient-specific computational models of the heart. These models estimate performance variables that may not be measured directly (e.g., tissue stress and strain, hemodynamics, or electrical activity). Cardiac magnetic resonance imaging (MRI) can acquire time-resolved images that quantitatively encode structure, function, flow, and remodeling. This talk will summarize recent advances on how these MRI data are acquired and fused using computational models to produce microstructurally anchored measures of patient-specific cardiac performance.

Bio:
Daniel Ennis {he/him} is a Professor in the Department of Radiology at Stanford University. As an MRI scientist for nearly twenty-five years, he has worked to develop advanced translational cardiovascular MRI methods for quantitatively assessing structure, function, flow, and remodeling in both adult and pediatric populations. He began his research career as a Ph.D. student in the Department of Biomedical Engineering at Johns Hopkins University during which time he formed an active collaboration with investigators in the Laboratory of Cardiac Energetics at the National Heart, Lung, and Blood Institute (NIH/NHLBI). Thereafter, he joined the Departments of Radiological Sciences and Cardiothoracic Surgery at Stanford University as a postdoc and began to establish an independent research program with an NIH K99/R00 award focused on “Myocardial Structure, Function, and Remodeling in Mitral Regurgitation.” For ten years he led a group of clinicians and scientists at UCLA working to develop and evaluate advanced cardiovascular MRI exams as PI of several NIH funded studies. In 2018 he returned to the Department of Radiology at Stanford University as faculty in the Radiological Sciences Lab to bolster programs in cardiovascular MRI. He is also the Director of Radiology Research for the Veterans Administration Palo Alto Health Care System where he oversees a growing radiology research program.

Zoom:
https://umich.zoom.us/j/91375430500

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Workshop / Seminar Thu, 27 Oct 2022 11:10:03 -0400 2022-11-03T16:30:00-04:00 2022-11-03T17:30:00-04:00 Off Campus Location Biomedical Engineering Workshop / Seminar BME 500 Seminar
EER Prospective Student Open House (November 3, 2022 6:00pm) https://events.umich.edu/event/100092 100092-21799200@events.umich.edu Event Begins: Thursday, November 3, 2022 6:00pm
Location:
Organized By: Engineering Education Research

We are excited to invite all interested students to attend an open house to learn about the UM’s graduate program in Engineering Education Research (EER). UM’s EER program represents a unique, interdisciplinary model: EER Ph.D. students (who enjoy a full funding package) are part of a college-wide program, while several tenure-line EER faculty are embedded within the traditional engineering departments. The integrated nature of the program allows the EER faculty and their research groups to be well-integrated with the traditional engineering disciplines, and it provides students a better opportunity to engage in innovative research and make scholarly contributions to the engineering education community. More information about the program is available at our EER website (https://eer.engin.umich.edu/). We will be hosting a Hybrid Open House on Thursday and Friday, 11/03/22 and 11/04/22. Students from all institutions are invited to attend, whether in-person or by Zoom (a zoom link will be emailed prior to the program). Participants will hear about the EER graduate program, meet faculty and graduate students, tour the beautiful University of Michigan campus, and learn about career opportunities as an UM graduate in this field. For participants who travel within the U.S., a limited number of travel grants are available to offset the costs of traveling to Ann Arbor, so please register soon. Note that we highly encourage applicants to the EER graduate program to have Bachelor’s and Master’s degrees in a traditional engineering discipline. Please register to attend at this open house registration site (tinyurl.com/2022EERUM) and please forward this link to any friends who may be interested. Email us for more information at eerprogram@umich.edu

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Reception / Open House Tue, 11 Oct 2022 15:17:35 -0400 2022-11-03T18:00:00-04:00 2022-11-03T20:00:00-04:00 Engineering Education Research Reception / Open House Engineering Education Research
EER Prospective Student Open House (November 4, 2022 9:00am) https://events.umich.edu/event/100092 100092-21799201@events.umich.edu Event Begins: Friday, November 4, 2022 9:00am
Location: Electrical Engineering and Computer Science Building
Organized By: Engineering Education Research

We are excited to invite all interested students to attend an open house to learn about the UM’s graduate program in Engineering Education Research (EER). UM’s EER program represents a unique, interdisciplinary model: EER Ph.D. students (who enjoy a full funding package) are part of a college-wide program, while several tenure-line EER faculty are embedded within the traditional engineering departments. The integrated nature of the program allows the EER faculty and their research groups to be well-integrated with the traditional engineering disciplines, and it provides students a better opportunity to engage in innovative research and make scholarly contributions to the engineering education community. More information about the program is available at our EER website (https://eer.engin.umich.edu/). We will be hosting a Hybrid Open House on Thursday and Friday, 11/03/22 and 11/04/22. Students from all institutions are invited to attend, whether in-person or by Zoom (a zoom link will be emailed prior to the program). Participants will hear about the EER graduate program, meet faculty and graduate students, tour the beautiful University of Michigan campus, and learn about career opportunities as an UM graduate in this field. For participants who travel within the U.S., a limited number of travel grants are available to offset the costs of traveling to Ann Arbor, so please register soon. Note that we highly encourage applicants to the EER graduate program to have Bachelor’s and Master’s degrees in a traditional engineering discipline. Please register to attend at this open house registration site (tinyurl.com/2022EERUM) and please forward this link to any friends who may be interested. Email us for more information at eerprogram@umich.edu

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Reception / Open House Tue, 11 Oct 2022 15:17:35 -0400 2022-11-04T09:00:00-04:00 2022-11-04T15:00:00-04:00 Electrical Engineering and Computer Science Building Engineering Education Research Reception / Open House Engineering Education Research
LHS Collaboratory (November 8, 2022 12:00pm) https://events.umich.edu/event/96029 96029-21791726@events.umich.edu Event Begins: Tuesday, November 8, 2022 12:00pm
Location: Off Campus Location
Organized By: Department of Learning Health Sciences

LHS Collaboratory November Session

Speaker:

Kadija Ferryman, PhD
Assistant Professor
Johns Hopkins Bloomberg School of Public Health

In this talk, Professor Ferryman will discuss the merits and challenges of conducting health equity reviews of artificial intelligence (AI) tools used in health and medicine. The talk will examine how interdisciplinary approaches from the social sciences, bioethics and humanities, and computational fields can be involved in the development of concepts, methods, frameworks, and guidelines for understanding and governing digital health tools.

Dr. Kadija Ferryman is a cultural anthropologist who studies the social, cultural, and ethical implications of health information technologies. Specifically, her research examines how genomics, digital medical records, artificial intelligence, and other technologies impact racial disparities in health. As a Postdoctoral Scholar at the Data & Society Research Institute in New York, she led the Fairness in Precision Medicine research study, which examines the potential for bias and discrimination in predictive precision medicine.

She earned a BA in Anthropology from Yale University, and a PhD in Anthropology from The New School for Social Research. Before completing her PhD, she was a policy researcher at the Urban Institute where she studied how housing and neighborhoods impact well-being, specifically the effects of public housing redevelopment on children, families, and older adults.

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Livestream / Virtual Thu, 06 Oct 2022 17:39:25 -0400 2022-11-08T12:00:00-05:00 2022-11-08T13:00:00-05:00 Off Campus Location Department of Learning Health Sciences Livestream / Virtual LHS Collaboratory logo
Futures in Research, Science, and Teaching - General meeting (November 8, 2022 4:00pm) https://events.umich.edu/event/96044 96044-21791850@events.umich.edu Event Begins: Tuesday, November 8, 2022 4:00pm
Location:
Organized By: Futures in Research, Science, Teaching - FIRST

General meetings take place every other Tuesday from September 13 to December 6th. Events include:

September 13th: Pathways in Research (Graduate student/Faculty panel)
September 27th: Mixer (food provided)
October 11th: Poster design and presentation
October 25th: Applying to graduate school - application components and essay writing advice
November 8th: Finding paid summer and post-baccalaureate research opportunities
November 22nd: Faculty talk
December 6th: Mixer

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Meeting Mon, 12 Sep 2022 12:26:57 -0400 2022-11-08T16:00:00-05:00 2022-11-08T17:00:00-05:00 Futures in Research, Science, Teaching - FIRST Meeting Event flyer detailing date, time, and location: September 13th at 4 pm, BSB 1010
DCMB / CCMB Seminar (November 9, 2022 4:00pm) https://events.umich.edu/event/101047 101047-21800725@events.umich.edu Event Begins: Wednesday, November 9, 2022 4:00pm
Location: Palmer Commons
Organized By: DCMB Seminar Series

Talk Title:
From variants to functions for coronary artery disease: Systematic Perturb-seq links GWAS loci to disease programs in endothelial cells

Abstract:
Abstract: Genome-wide association studies (GWAS) have discovered >200 associations for coronary artery disease (CAD), each of which could point to genes and pathways that influence disease risk. It is thought that a fraction of these CAD risk loci influences the functions of endothelial cells, and that genes in multiple GWAS loci might act together in certain pathways. Yet, identifying these genes and pathways has proven challenging: each GWAS locus can have 2-20 candidate genes, a gene may participate in one or more pathways in a given cell type, and it remains unclear which genes and pathways would be likely to influence disease risk. I will present our work to address this challenge by developing a Variant-to-Gene-to-Program (V2G2P) framework to study the role of endothelial cells in coronary artery disease, involving building a Variant-to-Gene map with ABC and a Gene-to-Program map with systematic Perturb-seq. Our study nominates new genes that likely influence risk for CAD, identifies convergence of CAD risk loci into certain gene programs in endothelial cells, and demonstrates a generalizable strategy to catalog gene programs to connect disease variants to functions.

Zoom link:
https://umich-health.zoom.us/j/93929606089?pwd=SHh6R1FOQm8xMThRemdxTEFMWWpVdz09

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Livestream / Virtual Thu, 03 Nov 2022 14:17:51 -0400 2022-11-09T16:00:00-05:00 2022-11-09T17:00:00-05:00 Palmer Commons DCMB Seminar Series Livestream / Virtual Jesse Engreitz, PhD (Asst. Prof., Dept. of Genetics, Stanford)
A Neural Control Circuit for Coughing (November 10, 2022 12:00pm) https://events.umich.edu/event/98877 98877-21797292@events.umich.edu Event Begins: Thursday, November 10, 2022 12:00pm
Location: Dental & W.K. Kellogg Institute
Organized By: Office of Research School of Dentistry

A Neural Control Circuit for Coughing
Winner of Dr. Dominic D. Dziewiatkowski Award in 2022

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Lecture / Discussion Fri, 14 Oct 2022 09:24:01 -0400 2022-11-10T12:00:00-05:00 2022-11-10T13:00:00-05:00 Dental & W.K. Kellogg Institute Office of Research School of Dentistry Lecture / Discussion Noam Gannot, Oral Health Sciences PhD Candidate, Li Lab University of Michigan School of Dentistry
DCM&B Tools and Technology Seminar (November 10, 2022 12:00pm) https://events.umich.edu/event/96869 96869-21793517@events.umich.edu Event Begins: Thursday, November 10, 2022 12:00pm
Location: Palmer Commons
Organized By: DCMB Tools and Technology Seminar

Within healthcare, imaging has transformed how we look at and understand diseases of the heart. Magnetic Resonance Imaging (MRI), Computed Tomography (CT) and echocardiography have all provided unique perspectives on the anatomy and function of the heart; yet often the wealth of information these images provide is often ignored. New techniques in image processing and machine learning have opened unique avenues for automating comprehensive analyses of the heart and empowered researchers to dig deeper into the data. Adding biomechanical modeling and simulation, these advances can be further propelled into personalized modeling -- providing tools for understanding disease and predicting treatment response. In this talk we review the tools of imaging, analysis and machine learning, and biomechanical modeling and how they are transforming how we understand the heart.

This presentation will be held in 2036 Palmer Commons. There will also be a remote viewing option via Zoom.

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Presentation Fri, 04 Nov 2022 11:15:36 -0400 2022-11-10T12:00:00-05:00 2022-11-10T13:00:00-05:00 Palmer Commons DCMB Tools and Technology Seminar Presentation
OHS Seminar Series Schedule (November 10, 2022 12:00pm) https://events.umich.edu/event/98131 98131-21795622@events.umich.edu Event Begins: Thursday, November 10, 2022 12:00pm
Location: Dental & W.K. Kellogg Institute
Organized By: Office of Research School of Dentistry

OHS Seminar Series Schedule Fall 2022 - Stay tuned for more updates!

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Presentation Tue, 06 Sep 2022 13:16:28 -0400 2022-11-10T12:00:00-05:00 2022-11-10T13:00:00-05:00 Dental & W.K. Kellogg Institute Office of Research School of Dentistry Presentation OHS Seminar Series Schedule Fall 2022
Predicting and quantifying cardiovascular growth, remodeling, and heterogeneity (November 10, 2022 4:30pm) https://events.umich.edu/event/100779 100779-21800344@events.umich.edu Event Begins: Thursday, November 10, 2022 4:30pm
Location: Electrical Engineering and Computer Science Building
Organized By: Biomedical Engineering

Abstract:
Cardiovascular soft tissues serve critical mechanical functions within the body, but pathologic changes to these tissues alter their material properties causing disruption or reduction in function. This loss can be sudden, such as the rupture of an aortic aneurysm, or it can be gradual, such as ventricular hypertrophy and heart failure. In this talk, I will share strategies for predicting and quantifying the temporal and spatial characteristics of cardiovascular soft tissues. First, I will discuss developing and employing a computational model to predict cardiac growth and remodeling. Second, I will expand on experimental testing and analysis techniques for determining the heterogeneous properties of soft tissues. I will close by discussing future applications of these modeling and analyses techniques.

Bio:
Dr. Colleen Witzenburg is an Assistant Professor in the Biomedical Engineering Department at the University of Wisconsin-Madison. She also has an affiliate appointment in the Mechanical Engineering Department, Department of Pediatrics, and is a member of the Cardiovascular Research Center. Dr. Witzenburg earned BS in Mechanical Engineering from Iowa State University and a PhD in Mechanical Engineering from the University of Minnesota. She then completed postdoctoral research at the University of Virginia. Her lab group, the Cardiovascular Biomechanics Lab (cbl.engr.wisc.edu), has been awarded grants from the American Heart Association, the Children’s Heart Foundation, the National Science Foundation, the Wisconsin Alumni Research Foundation, and the UW Institute for Clinical and Translational Research.

Zoom:
https://umich.zoom.us/j/91375430500

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Workshop / Seminar Thu, 27 Oct 2022 11:40:03 -0400 2022-11-10T16:30:00-05:00 2022-11-10T17:30:00-05:00 Electrical Engineering and Computer Science Building Biomedical Engineering Workshop / Seminar BME 500 Seminar
Evolution, Climate Change and Infectious Disease (November 11, 2022 9:00am) https://events.umich.edu/event/100399 100399-21799706@events.umich.edu Event Begins: Friday, November 11, 2022 9:00am
Location: Rackham Graduate School (Horace H.)
Organized By: MAC-EPID

Guest Speakers:

Aimée Classen (EEB, Professor of Ecology and Evolutionary Biology, Director of the Biological Station, University of Michigan)

Pamela Yeh (Assistant Professor, Ecology and Evolutionary Biology, UCLA)

Jay Graham (Assistant Professor, Environmental Health Sciences, University of California, Berkeley)


Coffee hour directly following talks.
Please register for this free symposium since lunch will be provided. Thank you!

* * * * *

For more information and registration for this FREE event:
www.MAC-EPID.org
Anna Cronenwett, weaverd@umich.edu

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Conference / Symposium Tue, 18 Oct 2022 15:59:50 -0400 2022-11-11T09:00:00-05:00 2022-11-11T15:00:00-05:00 Rackham Graduate School (Horace H.) MAC-EPID Conference / Symposium Flyer for symposium 2022 NOVEMBER 11
Biofabrication Strategies for the Regeneration of Cartilage and Bone (November 14, 2022 12:00pm) https://events.umich.edu/event/100632 100632-21800164@events.umich.edu Event Begins: Monday, November 14, 2022 12:00pm
Location: Dental & W.K. Kellogg Institute
Organized By: Office of Research School of Dentistry

Professor in Biofabrication and Regenerative Medicine
Head of Research, Department of Orthopedics, University Medical Center Utrecht
Department of Clinical Sciences, Faculty of Veterinary Medicine
Regenerative Medicine Center Utrecht, Utrecht, The Netherlands

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Presentation Mon, 24 Oct 2022 12:22:01 -0400 2022-11-14T12:00:00-05:00 2022-11-14T13:00:00-05:00 Dental & W.K. Kellogg Institute Office of Research School of Dentistry Presentation Jos Malda, PhD
DCM&B Tools and Technology Seminar (November 17, 2022 12:00pm) https://events.umich.edu/event/96870 96870-21793518@events.umich.edu Event Begins: Thursday, November 17, 2022 12:00pm
Location: Palmer Commons
Organized By: DCMB Tools and Technology Seminar

This presentation will be held in 2036 Palmer Commons. There will also be a remote viewing option via Zoom.

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Presentation Thu, 13 Oct 2022 08:18:27 -0400 2022-11-17T12:00:00-05:00 2022-11-17T13:00:00-05:00 Palmer Commons DCMB Tools and Technology Seminar Presentation
OHS Seminar Series Schedule (November 17, 2022 12:00pm) https://events.umich.edu/event/98131 98131-21795623@events.umich.edu Event Begins: Thursday, November 17, 2022 12:00pm
Location: Dental & W.K. Kellogg Institute
Organized By: Office of Research School of Dentistry

OHS Seminar Series Schedule Fall 2022 - Stay tuned for more updates!

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Presentation Tue, 06 Sep 2022 13:16:28 -0400 2022-11-17T12:00:00-05:00 2022-11-17T13:00:00-05:00 Dental & W.K. Kellogg Institute Office of Research School of Dentistry Presentation OHS Seminar Series Schedule Fall 2022
Spatial transcriptomics and cell-free nucleic acids to map host-microbe interactions (November 17, 2022 4:30pm) https://events.umich.edu/event/100783 100783-21800348@events.umich.edu Event Begins: Thursday, November 17, 2022 4:30pm
Location: Electrical Engineering and Computer Science Building
Organized By: Biomedical Engineering

Abstract:
Despite the centrality of microbes to human health, we know very little about how microbes interact with each other and their host. This lack of understanding is in large part due to limitations of tools to measure host-microbe interaction. In the first part of this talk, I will present liquid biopsy technologies to profile host-microbe interaction, with applications in the monitoring of COVID-19 and MIS-C. In the second part of this talk, I will share how we have used spatial transcriptomics to study the pathogenesis of viral myocarditis, and I will present a method to create intricate spatial maps of complex microbial communities.

Bio:
Iwijn De Vlaminck is an associate professor of biomedical engineering at Cornell University. Iwijn’s research is focused on the development of precision medicine technologies to monitor and study infectious and immune related disease. His research has led to noninvasive liquid biopsies to diagnose organ transplant rejection, urinary tract infection, blood-borne infection and complications of stem cell transplantation. He developed methods to spatially map the microbiome and the transcriptome. Iwijn’s research was recognized with the NIH New Innovator Award, the Noyce Foundation Assistant Professorship in the Life Sciences, and a Rainin Foundation Synergy Award. He received teaching excellence awards from the College of Engineering in 2017 and 2022. He is a co-founder of Kanvas Biosciences.

Zoom:
https://umich.zoom.us/j/91375430500

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Workshop / Seminar Thu, 27 Oct 2022 14:07:52 -0400 2022-11-17T16:30:00-05:00 2022-11-17T17:30:00-05:00 Electrical Engineering and Computer Science Building Biomedical Engineering Workshop / Seminar BME 500 Seminar
Building the Whole Black Child: Facilitating Engineering with Respect to Culture (November 18, 2022 9:00am) https://events.umich.edu/event/101152 101152-21800879@events.umich.edu Event Begins: Friday, November 18, 2022 9:00am
Location: GG Brown Laboratory
Organized By: Engineering Education Research

Engineering education intentionally excludes and pushes out learners who do not uphold traditional Eurocentric standards for thinking and practice of the profession. Facilitators who uphold such standards gatekeep the discipline and perpetuate the marginalization of racially and ethnically diverse youth when they do not orient the learners’ cultures in their teaching and practices. Oftentimes, to obtain academic and professional achievement, facilitators encourage Black youth seeking entry into the engineering pathway to suppress their culture, linguistic literacy and practice, and history. Given the educational debt that persists in K-12 education for Black American youth, meaningful culturally oriented facilitation is crucial as it often determines whether a learner may persist or perish along their engineering pursuit. Most importantly, the culturally informed engineering facilitator has the power to extract the brilliance and ingenuity that Black youth bring into the engineering classroom. In this talk, I discuss the significance of a culturally centered engineering facilitator on Black American youth’s engineering learning. Founded on asset-focused culturally relevant and sustaining frameworks, I explain how the ethos, beliefs, and training of a multifaceted facilitator influenced engineering learning and practice for Black youth at an interdisciplinary summer camp within an urban creative arts community learning center— Hit Makers Summer Camp. I also detail how culturally relevant and sustaining facilitation guided Black youth to rationalize their place in engineering. Finally, I discuss implications for educational research, teaching, and professional development for engineering educators and initial steps on how the Engineering Education Research community could implement initial policies that maximize cultural prosperity to contribute to diversity, equity, inclusion, and justice in engineering education.

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Workshop / Seminar Tue, 08 Nov 2022 11:53:58 -0500 2022-11-18T09:00:00-05:00 2022-11-18T10:15:00-05:00 GG Brown Laboratory Engineering Education Research Workshop / Seminar Dr. Tikyna Dandridge
Building the Whole Black Child: Facilitating Engineering with Respect to Culture (November 18, 2022 9:00am) https://events.umich.edu/event/101152 101152-21800881@events.umich.edu Event Begins: Friday, November 18, 2022 9:00am
Location: Off Campus Location
Organized By: Engineering Education Research

Engineering education intentionally excludes and pushes out learners who do not uphold traditional Eurocentric standards for thinking and practice of the profession. Facilitators who uphold such standards gatekeep the discipline and perpetuate the marginalization of racially and ethnically diverse youth when they do not orient the learners’ cultures in their teaching and practices. Oftentimes, to obtain academic and professional achievement, facilitators encourage Black youth seeking entry into the engineering pathway to suppress their culture, linguistic literacy and practice, and history. Given the educational debt that persists in K-12 education for Black American youth, meaningful culturally oriented facilitation is crucial as it often determines whether a learner may persist or perish along their engineering pursuit. Most importantly, the culturally informed engineering facilitator has the power to extract the brilliance and ingenuity that Black youth bring into the engineering classroom. In this talk, I discuss the significance of a culturally centered engineering facilitator on Black American youth’s engineering learning. Founded on asset-focused culturally relevant and sustaining frameworks, I explain how the ethos, beliefs, and training of a multifaceted facilitator influenced engineering learning and practice for Black youth at an interdisciplinary summer camp within an urban creative arts community learning center— Hit Makers Summer Camp. I also detail how culturally relevant and sustaining facilitation guided Black youth to rationalize their place in engineering. Finally, I discuss implications for educational research, teaching, and professional development for engineering educators and initial steps on how the Engineering Education Research community could implement initial policies that maximize cultural prosperity to contribute to diversity, equity, inclusion, and justice in engineering education.

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Workshop / Seminar Tue, 08 Nov 2022 11:53:58 -0500 2022-11-18T09:00:00-05:00 2022-11-18T10:15:00-05:00 Off Campus Location Engineering Education Research Workshop / Seminar Dr. Tikyna Dandridge
Engineering Advanced Materials for Neural Regeneration (November 18, 2022 2:30pm) https://events.umich.edu/event/100818 100818-21800387@events.umich.edu Event Begins: Friday, November 18, 2022 2:30pm
Location: Lurie Biomedical Engineering (formerly ATL)
Organized By: Biomedical Engineering

Abstract:
Damage to peripheral nerve and spinal cord tissue can have a devastating impact on the quality of life for individuals suffering from nerve injuries. Our research broadly encompasses analyzing and designing natural-based and electrically conducting biomaterials that can interface with neurons to stimulate and guide nerves to regenerate. This talk will specifically address our work on natural-based biomaterials for both peripheral nerve and spinal cord applications.

To foster peripheral nerve regeneration, we have focused on both “top down” and “bottom up” approaches. For our “top down” approach, we have developed natural acellular tissue grafts created by chemical processing of normal intact nerve tissue to preserve the microarchitecture of the extracellular matrix (ECM) and to eliminate the immune response by removing cell components. This research is the foundation for the Avance Nerve Graft from AxoGen, which is now widely used in clinics for peripheral nerve injuries. In a parallel “bottom up” approach, we have developed advanced hyaluronan-based scaffolds for nerve regeneration applications. Hyaluronic acid (HA; also known as hyaluronan) is a non-sulfated, high molecular weight, glycosaminoglycan found in all mammals; it is a major component of the extracellular matrix in the nervous system and plays a significant role in wound healing and tissue regeneration. Our group has devised novel techniques to process HA into forms for use in peripheral nerve repair applications. For example, we have explored advanced laser-based processes, in situ crystallization, and magnetic particle templating to create microarchitecture within the hyaluronan materials to mimic the native basal lamina of nerve cells and thus to provide physical and chemical guidance features for regenerating axons. These materials have shown promise for supporting peripheral nerve repair after acute transection injury and for promoting regeneration of axons into close proximity of microelectrodes for potential prosthetics applications.

For spinal cord injury (SCI) applications, we have engineered injectable biomaterials for less invasive application in crush injuries, which are the most prominent form of SCI. In this work, we have solubilized decellularized peripheral nerve tissue to create in situ gelling ECM hydrogels. We show that these materials serve as effective therapeutic agents for SCI in rats and are promising delivery agents for cell transplantation applications.

Bio:
Christine E. Schmidt, Ph.D., is the J. Crayton Pruitt Family Professor and Department Chair for the University of Florida Department of Biomedical Engineering. Prior to joining UF in 2013, she was at the University of Texas at Austin in Biomedical Engineering and Chemical Engineering and was one of the founding faculty members of the UT BME Department. 

Dr. Schmidt's research is focused on developing new biomaterials and biomaterial composites (e.g., natural material scaffolds, processed tissues, electronic polymer composites) that can be used to physically guide and stimulate regenerating nerves and the healing of other tissues. Her work is the foundation for the Avance Nerve Repair graft from Axogen and VersaWrap tissue protector from her affiliated start-up company, Alafair Biosciences. Dr. Schmidt has received many major research awards and recognitions, including the Clemson Award for Applied Research from the Society for Biomaterials, induction into the Florida Inventors Hall of Fame, and election to the Florida Academy of Science, Engineering and Medicine of Florida. Dr. Schmidt is a past President for the American Institute for Medical & Biological Engineering (AIMBE). She is a Fellow of AIMBE, the National Academy of Inventors (NAI), the Biomedical Engineering Society (BMES), the American Society for the Advancement of Science (AAAS), the International Academy of Medical and Biological Engineering (IAMBE), and the International Union of Societies for Biomaterials Science and Engineering (FBSE/IUSBSE).

Under Dr. Schmidt’s leadership as Department Chair, UF BME’s undergraduate program first became ABET accredited in Fall 2019 and is now ranked #13 among public BME UG programs (U.S. News & World Report, USNWR). The department’s graduate program is currently ranked #17 among public BME graduate programs by USNWR, climbing more than 20 spots since 2013. Dr. Schmidt has increased the number of women faculty from 2 when she arrived in 2013 to 15 and the number of URM faculty from 1 to 6 (UF BME faculty is now 52% women, 21% URM).

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Lecture / Discussion Wed, 02 Nov 2022 19:59:19 -0400 2022-11-18T14:30:00-05:00 2022-11-18T17:00:00-05:00 Lurie Biomedical Engineering (formerly ATL) Biomedical Engineering Lecture / Discussion Alan J. Hunt Memorial Lecture
Inferring Electromechanical Coupling of the Stomach under Different Gastric States (November 21, 2022 1:00pm) https://events.umich.edu/event/101048 101048-21800727@events.umich.edu Event Begins: Monday, November 21, 2022 1:00pm
Location: Duderstadt Center
Organized By: Biomedical Engineering

Abstract:
A main function of the stomach is to accommodate and break down the ingested food and further push it to the small intestine for nutrient absorption. To carry out this function, gastric smooth muscle cells (SMC) maintain and coordinate their contractions and relaxations across regions of the stomach. The pattern of muscle activity is intrinsically paced by a propagating electrical rhythm initiated by the interstitial cells of Cajal (ICC) and extrinsically regulated by the brain through peripheral nerves innervating the stomach. The ICC-initiated electrical slow wave paces the peristaltic mechanical wave through the active coupling between ICC and SMC (or the electromechanical coupling). The strength of this coupling is up- or down-regulated by the brain through descending vagal nerves, which selectively innervate different types of enteric motor neurons that either excite or inhibit SMC, respectively. The neural control of gastric muscle activity varies across times and conditions to support a wide range of ingestive and digestive processes. In this thesis research, sensors, devices, and signal processing methods were developed for simultaneous recording and real-time analysis of gastric electrical and mechanical activity. Experiments with rats were performed to demonstrate the feasibility of concurrent strain and electrical recordings in both acute and chronic settings. The relationships between the recorded electrical and mechanical activities were evaluated minute-by-minute in terms of their phase, frequency, and amplitude. The electromechanical coupling was stronger and less variable after animals consumed a test meal (or in the fed state) than when the stomach was empty following overnight deprivation of food and drink (or in the fasted state). This finding suggests that the electromechanical coupling may serve as a quantitative biomarker that reports on the real-time neural control of gastric motility, discriminates different gastric states, and by doing so, provides a feedback signal for closed-loop neuromodulation of the stomach. The techniques and findings described in this thesis merit future translational studies to further advance the understanding of gastric physiology and pathophysiology, as well as the diagnosis and treatment of prevailing functional gastrointestinal disorders.

Committee Chair(s):
Dr. Zhongming Liu

Zoom Link: https://umich.zoom.us/j/95286593974
Meeting ID: 952 8659 3974
Passcode: 590590

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Lecture / Discussion Thu, 03 Nov 2022 15:25:04 -0400 2022-11-21T13:00:00-05:00 2022-11-21T14:00:00-05:00 Duderstadt Center Biomedical Engineering Lecture / Discussion Chih Hsuan Tsai
Futures in Research, Science, and Teaching - General meeting (November 22, 2022 4:00pm) https://events.umich.edu/event/96044 96044-21791851@events.umich.edu Event Begins: Tuesday, November 22, 2022 4:00pm
Location:
Organized By: Futures in Research, Science, Teaching - FIRST

General meetings take place every other Tuesday from September 13 to December 6th. Events include:

September 13th: Pathways in Research (Graduate student/Faculty panel)
September 27th: Mixer (food provided)
October 11th: Poster design and presentation
October 25th: Applying to graduate school - application components and essay writing advice
November 8th: Finding paid summer and post-baccalaureate research opportunities
November 22nd: Faculty talk
December 6th: Mixer

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Meeting Mon, 12 Sep 2022 12:26:57 -0400 2022-11-22T16:00:00-05:00 2022-11-22T17:00:00-05:00 Futures in Research, Science, Teaching - FIRST Meeting Event flyer detailing date, time, and location: September 13th at 4 pm, BSB 1010
Professor Career Path (November 22, 2022 4:00pm) https://events.umich.edu/event/101249 101249-21801109@events.umich.edu Event Begins: Tuesday, November 22, 2022 4:00pm
Location: Biological Sciences Building
Organized By: Futures in Research, Science, Teaching - FIRST

This seminar will cover the career path of STEM professors beginning with undergraduate research. Professor Monica Dus of the MCDB department will share her experiences starting in undergrad research, through earning a PhD, working as a post-doctoral researcher, and eventually starting her own research lab at the University of Michigan. Prof. Dus studies nutrigenomics, which looks at how genes interact with our diet to shape neural plasticity and feeding behavior.

RSVP: https://docs.google.com/forms/d/e/1FAIpQLSeJe8DfFZVUeqqguF_u_tNBzZwlU-nj6il4-TkwjVgRXBEfug/viewform?usp=sf_link

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Workshop / Seminar Thu, 17 Nov 2022 14:25:15 -0500 2022-11-22T16:00:00-05:00 2022-11-22T17:00:00-05:00 Biological Sciences Building Futures in Research, Science, Teaching - FIRST Workshop / Seminar FIRST Logo
OHS Seminar Series Schedule (November 24, 2022 12:00pm) https://events.umich.edu/event/98131 98131-21795624@events.umich.edu Event Begins: Thursday, November 24, 2022 12:00pm
Location: Dental & W.K. Kellogg Institute
Organized By: Office of Research School of Dentistry

OHS Seminar Series Schedule Fall 2022 - Stay tuned for more updates!

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Presentation Tue, 06 Sep 2022 13:16:28 -0400 2022-11-24T12:00:00-05:00 2022-11-24T13:00:00-05:00 Dental & W.K. Kellogg Institute Office of Research School of Dentistry Presentation OHS Seminar Series Schedule Fall 2022
DCMB Seminar - Presenter: Luca Pinello (Assoc. Prof. at MGH and HMS) (November 30, 2022 4:00pm) https://events.umich.edu/event/101444 101444-21801349@events.umich.edu Event Begins: Wednesday, November 30, 2022 4:00pm
Location: Palmer Commons
Organized By: DCMB Seminar Series

Abstract:

CRISPR genome editing technologies and single-cell assays have opened new opportunities to study cellular systems and gene regulation at an unprecedented level of detail.

In this talk, I will first present computational methods we have developed to uncover and dissect regulatory elements using CRISPR genome editing technologies. I will also discuss challenges associated with using CRISPR technologies related to designing perturbations and quantifying editing outcomes.

I will then cover our work in modeling data from current single-cell assays, discussing methods to uncover development trajectories, recover RNA-velocity with uncertainty, and create interpretable regulatory maps from multi-omics data using graph embedding techniques.

https://umich-health.zoom.us/j/93929606089?pwd=SHh6R1FOQm8xMThRemdxTEFMWWpVdz09

Short bio:
Luca Pinello is a computational biologist and leader in developing computational methods for functional genomics, genome editing and single cell technologies. He holds a Ph.D. in Mathematics and Computer Science from University of Palermo, Italy. He is currently an Associate Pathologist at Massachusetts General Hospital (MGH) and an Associate Professor of Pathology at Harvard Medical School. He is also part of the MGH Center for Cancer Research and an Associate Member of the BROAD Institute of MIT and Harvard. He has developed several foundational computational tools in the field of genome editing for the design (CRISPRme, CRISPRitz, PrimeDesign), quantification (CRISPResso 1 and 2), and analyses of coding and non-coding tiling screens (CRISPRO, CRISPR-SURF). He was awarded one of the first NIH R35 Genomic Innovator Awards, a prestigious grant supporting highly innovative researchers working on important problems in genomics.

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Lecture / Discussion Thu, 17 Nov 2022 09:07:59 -0500 2022-11-30T16:00:00-05:00 2022-11-30T17:00:00-05:00 Palmer Commons DCMB Seminar Series Lecture / Discussion
DCM&B Tools and Technology Seminar - CANCELED (December 1, 2022 12:00pm) https://events.umich.edu/event/96871 96871-21793519@events.umich.edu Event Begins: Thursday, December 1, 2022 12:00pm
Location: Palmer Commons
Organized By: DCMB Tools and Technology Seminar

Tool Link: https://gkb.dcmb.med.umich.edu/

This presentation will be held in 2036 Palmer Commons. There will also be a remote viewing option via Zoom.

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Presentation Thu, 01 Dec 2022 08:18:15 -0500 2022-12-01T12:00:00-05:00 2022-12-01T13:00:00-05:00 Palmer Commons DCMB Tools and Technology Seminar Presentation
LHS Collaboratory (December 1, 2022 12:00pm) https://events.umich.edu/event/99641 99641-21798493@events.umich.edu Event Begins: Thursday, December 1, 2022 12:00pm
Location: Palmer Commons
Organized By: Department of Learning Health Sciences

"A Double-Edged Sword”: Genetic Data Sharing and Implications for the Learning Health System

Thursday, December 1, 2022

12:00 pm - 1:30 pm ET

Great Lakes Room, Palmer Commons, 4th floor

100 Washtenaw Ave., Ann Arbor, MI

Speaker:
Kayte Spector-Bagdady, JD, MBioethics
Interim Co-Director, Center for Bioethics & Social Sciences in Medicine Assistant Professor, Obstetrics & Gynecology
University of Michigan Medical School

In contrast to the laborious and expensive process of generating genetic datasets de novo, academic genetic researchers are increasingly using large and inexpensive “secondary” research datasets held by government, consortia, and industry for their work. Choosing between different kinds of data providers is about more than just convenience, however, it can also have important implications for the kind of science advanced and to which communities it will generalize. This talk will explore the factors driving researchers to select certain datasets for their work as well as their experiences sharing to, as well as using, shared data resources. As researchers wait for the new National Institutes of Health’s “Policy for Data Management and Sharing” to go into effect in January 2023, this talk will explore who ultimately carries the burden of increasing data sharing requirements

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Lecture / Discussion Tue, 15 Nov 2022 22:30:26 -0500 2022-12-01T12:00:00-05:00 2022-12-01T13:30:00-05:00 Palmer Commons Department of Learning Health Sciences Lecture / Discussion LHS Collaboratory logo
OHS Seminar Series Schedule (December 1, 2022 12:00pm) https://events.umich.edu/event/98131 98131-21795625@events.umich.edu Event Begins: Thursday, December 1, 2022 12:00pm
Location: Dental & W.K. Kellogg Institute
Organized By: Office of Research School of Dentistry

OHS Seminar Series Schedule Fall 2022 - Stay tuned for more updates!

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Presentation Tue, 06 Sep 2022 13:16:28 -0400 2022-12-01T12:00:00-05:00 2022-12-01T13:00:00-05:00 Dental & W.K. Kellogg Institute Office of Research School of Dentistry Presentation OHS Seminar Series Schedule Fall 2022
Jonathan Rubin Collegiate Professorship Ceremony (December 5, 2022 1:30pm) https://events.umich.edu/event/101673 101673-21802211@events.umich.edu Event Begins: Monday, December 5, 2022 1:30pm
Location: Palmer Commons
Organized By: Biomedical Engineering

Mary-Ann Mycek, Ph.D.
Professor of Biomedical Engineering
Interim Department Chair, Biomedical Engineering

cordially invites you to a ceremony
celebrating the installation of

Xueding Wang, Ph.D.
as the
Jonathan Rubin Collegiate Professor of Biomedical Engineering

Monday, December 5, 2022
1:30 p.m. - 2:30 p.m. - Ceremony & Lecture

Palmer Commons
Great Lakes South & Central Rooms (4th Floor)
100 Washtenaw Ave, Ann Arbor, MI 48109

Reception to follow from 2:30 p.m. - 3:30 p.m.

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Ceremony / Service Tue, 29 Nov 2022 13:27:27 -0500 2022-12-05T13:30:00-05:00 2022-12-05T14:30:00-05:00 Palmer Commons Biomedical Engineering Ceremony / Service BME Ceremony
Futures in Research, Science, and Teaching - General meeting (December 6, 2022 4:00pm) https://events.umich.edu/event/96044 96044-21791852@events.umich.edu Event Begins: Tuesday, December 6, 2022 4:00pm
Location:
Organized By: Futures in Research, Science, Teaching - FIRST

General meetings take place every other Tuesday from September 13 to December 6th. Events include:

September 13th: Pathways in Research (Graduate student/Faculty panel)
September 27th: Mixer (food provided)
October 11th: Poster design and presentation
October 25th: Applying to graduate school - application components and essay writing advice
November 8th: Finding paid summer and post-baccalaureate research opportunities
November 22nd: Faculty talk
December 6th: Mixer

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Meeting Mon, 12 Sep 2022 12:26:57 -0400 2022-12-06T16:00:00-05:00 2022-12-06T17:00:00-05:00 Futures in Research, Science, Teaching - FIRST Meeting Event flyer detailing date, time, and location: September 13th at 4 pm, BSB 1010
OHS Seminar Series Schedule (December 8, 2022 12:00pm) https://events.umich.edu/event/98131 98131-21795626@events.umich.edu Event Begins: Thursday, December 8, 2022 12:00pm
Location: Dental & W.K. Kellogg Institute
Organized By: Office of Research School of Dentistry

OHS Seminar Series Schedule Fall 2022 - Stay tuned for more updates!

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Presentation Tue, 06 Sep 2022 13:16:28 -0400 2022-12-08T12:00:00-05:00 2022-12-08T13:00:00-05:00 Dental & W.K. Kellogg Institute Office of Research School of Dentistry Presentation OHS Seminar Series Schedule Fall 2022
Toward an open science ecosystem for neuroimaging (December 8, 2022 4:30pm) https://events.umich.edu/event/101824 101824-21802392@events.umich.edu Event Begins: Thursday, December 8, 2022 4:30pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Abstract:
It is now widely accepted that openness and transparency are keys to improving the reproducibility of scientific research, but many challenges remain to adoption of these practices. I will discuss the growth of an ecosystem for open science within the field of neuroimaging, focusing on platforms for open data sharing and open source tools for reproducible data analysis. I will also discuss the role of the Brain Imaging Data Structure (BIDS), a community standard for data organization, in enabling this open science ecosystem, and will outline the scientific impacts of these resources.
Bio:
Russell A. Poldrack is the Albert Ray Lang Professor in the Department of Psychology, and Director of the Stanford Center for Open and Reproducible Science.  His research uses neuroimaging to understand the brain systems underlying decision making and executive function.  His lab is also engaged in the development of neuroinformatics tools to help improve the reproducibility and transparency of neuroscience, including the Openneuro.org and Neurovault.org data sharing projects and the Cognitive Atlas ontology.​​​​​​​

Zoom:
https://umich.zoom.us/j/91375430500

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Workshop / Seminar Fri, 02 Dec 2022 14:35:11 -0500 2022-12-08T16:30:00-05:00 2022-12-08T17:30:00-05:00 Off Campus Location Biomedical Engineering Workshop / Seminar People in a classroom watching a presentation with the text Biomedical Engineering Seminar Series
Complex Systems Presents the Annual Nobel Symposium (December 9, 2022 10:00am) https://events.umich.edu/event/101838 101838-21802540@events.umich.edu Event Begins: Friday, December 9, 2022 10:00am
Location: Palmer Commons
Organized By: The Center for the Study of Complex Systems

This event will be held at PALMER COMMONS FORUM HALL

Walking Directions: https://palmercommons.umich.edu/article/walking-directions

***THIS WILL BE AN IN PERSON EVENT ONLY***
A limited recording will be available after the event.

During this, 'Nobel Week', join us to learn about the Six Nobel Prizes on the eve of the Laureates receiving their actual awards in Oslo and Helsinki.

Coffee and snacks will be served for both the morning and afternoon sessions.

Registration not required. Free and open to the public.

This popular annual event features six UM faculty experts in each of the six prize fields, each presenting on one of the prizes. Each will present for approximately 35 minutes and then will take some questions. There is a morning session and an afternoon session with a midday break. Come to one talk, come to them all!

SCHEDULE

10:00 AM WELCOME REMARKS
Marisa Eisenberg, Director, Complex Systems

10:05 AM PHYSICS
Speaker: Alex Burgers - Assistant Professor of Electrical Engineering and Computer Science (ECE), and Applied Physics

10:50 AM Chemistry
Speaker: Joerg Lahann - Director of the Biointerfaces Institute. Wolfgang Pauli Collegiate Professor of Chemical Engineering, Materials Science and Engineering, Biomedical Engineering, and Macromolecular Science and Engineering.

11:35 AM Physiology or Medicine
Speaker - Jeff Kidd - Michigan Medicine, Professor of Human Genetics, and Computational Medicine and Bioinformatics

12:20 PM Lunch break 12:20-1:30pm (on own)

1:30 PM Economics
John Leahy - Allen Sinai Professor of Macroeconomics, Department of Economics and Gerald R. Ford School of Public Policy

2:15 PM Literature
Speaker: David Caron - Professor of French and Women’s and Gender Studies.

3:00 PM Peace
Speaker: Geneviève Zubrzycki - Director, Weiser Center for Europe & Eurasia; Center for European Studies; Professor, Sociology

3:45 PM Closing remarks

3:50 PM End

For information on prize winners, and 'Nobel Week' activites, please click the Nobel Prize link below. Other information on the Nobel Prizes can be found on the website nobelprize.org

PUBLIC PARKING - closest is the Forest Avenue Parking Structure at 650 S Forest Ave, Ann Arbor, MI 48104

UM BLUE PARKING - across the road from Weiser Hall at 500 Church Street (and also Forest Avenue Parking Structure)

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Conference / Symposium Fri, 09 Dec 2022 09:03:05 -0500 2022-12-09T10:00:00-05:00 2022-12-09T15:50:00-05:00 Palmer Commons The Center for the Study of Complex Systems Conference / Symposium Nobel poster with illustration of Nobel Prize winners.
Machine Learning-Based Feature Quantification of Clinical High-Frequency Oscillations (December 9, 2022 10:00am) https://events.umich.edu/event/101676 101676-21802214@events.umich.edu Event Begins: Friday, December 9, 2022 10:00am
Location: Lurie Biomedical Engineering (formerly ATL)
Organized By: Biomedical Engineering

Abstract:
The suspense of not knowing when and how a seizure may occur is one of the most exhaustive aspects of an epileptic patient’s life. To address this problem, researchers have been investigating novel biomarkers to gain information about seizure generation and epileptic networks for decades. With modern advancements in recording equipment and computational power, biomarkers that identified from the electrical activity recorded by intracranial electrodes, such as High-Frequency Oscillations (HFOs) have gained traction and are utilized to predict seizure onset zone (SOZ) locations within the brain. However, HFOs are low amplitude waveforms with a time period less than 1 millisecond whose acquisition process can result in noise artifacts. The EEG signals undergo filtering to isolate the HFO events within the 100 – 500 Hz range; a process that can produce false positives due to the occurrence of Gibb’s Phenomenon. Additionally, these filters can also mask the occurrence of artifacts such as head movement and electrical noise. Thus, to address this problem, a machine learning classifier was developed to distinguish events that are clearly artifact from the true HFOs. In this study, logistic regression models were designed to distinguish HFOs naturally occurring in the brain from false positive resulting artifacts amounting to a Positive Predictive Value (PPV) of 84.59%. The correlations of these correctly identified HFOs with inter-patient variability and feature prioritization were also analyzed in a repeated measures study and the significance of each feature was computed. Future directions of this study would follow the estimation of more features from the HFO data to refine the algorithm and improve the precision of identifying true-positive HFO detections. This will heighten the quality of the HFOs being detected in real-time continuous EEG recordings on translation into a clinical environment in the future.

Zoom Link: https://umich.zoom.us/j/96623464149 Meeting ID: 966 2346 4149

Committee Chair(s):
Dr. William Stacey

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Presentation Tue, 29 Nov 2022 14:18:19 -0500 2022-12-09T10:00:00-05:00 2022-12-09T11:00:00-05:00 Lurie Biomedical Engineering (formerly ATL) Biomedical Engineering Presentation BME Master's Defense
Image-guided Transcranial Histotripsy for Brain Tumors (December 14, 2022 11:00am) https://events.umich.edu/event/101679 101679-21802217@events.umich.edu Event Begins: Wednesday, December 14, 2022 11:00am
Location: Lurie Biomedical Engineering (formerly ATL)
Organized By: Biomedical Engineering

Abstract:
The current surgical treatment of malignant brain tumors is invasive and can lead to bleeding and morbid complications. Histotripsy is a noninvasive cavitational ultrasound surgical method that has shown great promise as a noninvasive neurosurgical technology. This dissertation presents image-guided transcranial histotripsy as a potential neurosurgical modality for brain tumors. The first chapter introduces image guidance, brain tumors, the current standard of care, investigative ablation modalities, the mechanism of transcranial histotripsy, and the potential of transcranial histotripsy as a neurosurgical interventional tool. The second chapter discusses the development of a stereotactic transcranial histotripsy targeting system for in vivo murine brain models, The third chapter investigates the magnetic resonance imaging (MRI) analysis and characterization of in vivo features of transcranial histotripsy on murine models. The fourth chapter discusses the first-pass investigation of the blood-brain barrier (BBB) status following transcranial histotripsy in in vivo mice brains. The fifth chapter presents the system error analysis and feasibility of a neuronavigation-guided transcranial histotripsy (NaviTH) system designed for cadaveric models. The final chapter concludes with future work for murine and cadaveric transcranial histotripsy.

Zoom Link: https://umich.zoom.us/j/91504014959
Meeting ID: 915 0401 4959
Password: 0000

Committee Chair(s):
Dr. Zhen Xu

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Lecture / Discussion Tue, 29 Nov 2022 14:31:28 -0500 2022-12-14T11:00:00-05:00 2022-12-14T12:00:00-05:00 Lurie Biomedical Engineering (formerly ATL) Biomedical Engineering Lecture / Discussion BME PhD defense
Computational Hemodynamic Modeling of Pediatric Cardiovascular Diseases (December 16, 2022 10:00am) https://events.umich.edu/event/101921 101921-21802933@events.umich.edu Event Begins: Friday, December 16, 2022 10:00am
Location: Lurie Biomedical Engineering (formerly ATL)
Organized By: Biomedical Engineering

Abstract:
Pediatric cardiovascular disease (CVD) is one of the leading causes of mortality in children. While innovations in pediatric CVD treatment have improved mortality and morbidity, the incidence of residual disease remains high. An increasing level of detail in patients’ diagnostic data has revealed a growing variability in pathology and hemodynamics. Patient-specific hemodynamics are intrinsically linked to the onset and progression of CVD. Therefore, there is a pressing need to improve our understanding of pediatric CVD while considering patient-specific hemodynamics and individualizing treatment plans. 

Computational hemodynamic modeling synergizes patient-specific hemodynamic data with physical and physiological principles to provide a comprehensive description of an individual’s pathology. In this work, computational models are used to study mechanisms contributing to CVD, aid in patient stratification, and aid in surgical planning in three pediatric CVDs: pulmonary arterial hypertension (PAH), renovascular hypertension caused by an abdominal aortic coarctation (AAC), and hypoplastic left heart syndrome (HLHS).

Committee Chair(s):
Dr. David Kohn

Zoom Link: https://umich.zoom.us/j/92042390057
Passcode: modeling

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Presentation Wed, 07 Dec 2022 15:48:17 -0500 2022-12-16T10:00:00-05:00 2022-12-16T11:00:00-05:00 Lurie Biomedical Engineering (formerly ATL) Biomedical Engineering Presentation BME logo on top of a blurred picture of LBME
Resting-State Functional Organization of the Brain in Blindness and Sight Recovery (December 16, 2022 2:00pm) https://events.umich.edu/event/101885 101885-21802611@events.umich.edu Event Begins: Friday, December 16, 2022 2:00pm
Location: North Campus Research Complex Building 10
Organized By: Biomedical Engineering

Abstract:
Reorganization of the human brain after blindness is well-documented, however, subsequent sight restoration can lead to adaptation that is not as well understood. Successful sight restoration therapy must integrate functionally with the visual system for perception to occur. Thus, our study is strongly motivated by the need to understand brain plasticity after regaining vision. In this thesis, I evaluated use of functional magnetic resonance imaging (fMRI) resting-state functional connectivity (rsFC) for vision studies from two angles: 1) from a methodology perspective, I explored the importance of proper data preprocessing on the resulting rsFC outcome, 2) from a neuroscientific perspective, I examined utility of rsFC as a potential metric of blindness and sight restoration.

It has been shown that choice of analysis pipelines can impact the research findings. Therefore, replication studies that aim to reproduce the previously published results are critically necessary. In the first venue of my research, I verified reproducibility of a well-cited published study on ocular blindness using rsFC. By using the original dataset, I utilized another widely used software package to investigate how applying different implementations of the original pipeline or a more rigorous preprocessing stream can alter the outcomes. These alternative workflows changed the distribution of the whole-brain rsFC and functional network densities, reducing the overlap with the original results. Remarkably, the largest rsFC effects appeared to primarily belong to certain connection pairs, irrespective of the pipeline used, likely demonstrating immunity of the larger effects and likely the true results against suboptimal processing. This may highlight the significance of results verification across different computational streams in search of the true findings.

Functional outcome of using Argus II, as the only retinal prosthesis with FDA approval that has been clinically used, can provide an exceptional opportunity to explore brain’s potential for plasticity upon reintroduction of (artificial) vision. Considerable variability in visual performance has been reported across Argus II recipients that remains unexplained. A previous experiment used fMRI to measure tactile-evoked cross-modal responses in visual cortex and reported no significant group-level results between blind and Argus II groups, possibly due to variability in activation baseline across individuals. The rsFC can potentially overcome this issue by providing a more stable metric. Numerous studies have used rsFC to assess cortical reorganization after blindness, nevertheless, it has rarely been utilized to study sight recovery. 

In this study, four resting-state runs from 10 sighted, 10 blind, with severe retinitis pigmentosa, and 7 Argus II subjects were included. The whole-brain ROI-ROI rsFC and some graph theory functional network measures were calculated and compared at the group level. Some quantities decreased after blindness but were not reversed by vision restitution, including visual-visual rsFC, visual-frontal rsFC and some network measures. On the other hand, significant reduction was observed in visual-somatosensory, visual-auditory, visual-motor and visual-association rsFC after blindness that were all returned to the level of sighted individuals in Argus II recipients. These rsFC measures can potentially serve as biomarkers for blindness and sight restoration, in the absence of or as a complement to the behavioral indices.  The proposed metrics can enhance our understanding of variable outcomes among the receivers of sight restorative technologies and enable tracking rehabilitative progress. Future investigation with larger number of test subjects for this rare condition can further unveil the profound ability of our brain to reorganize, following vision restoration.

Committee Chair(s): James Weiland, PhD

Zoom link: https://umich.zoom.us/j/99207257590
Meeting ID: 992 0725 7590
Passcode: 643920

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Presentation Tue, 06 Dec 2022 10:37:24 -0500 2022-12-16T14:00:00-05:00 2022-12-16T15:00:00-05:00 North Campus Research Complex Building 10 Biomedical Engineering Presentation The Biomedical Engineering Logo on a blurred photo of the LBME building at night.
On the in vivo viscoelastic properties of the human lower birth canal during the first stage of labor: secondary analysis of data from the EASE trial (January 11, 2023 10:00am) https://events.umich.edu/event/102845 102845-21805233@events.umich.edu Event Begins: Wednesday, January 11, 2023 10:00am
Location: GG Brown Laboratory
Organized By: Biomedical Engineering

Abstract:
Up to 19% of nulliparous women sustain pelvic muscle injuries while giving vaginal birth. Since these injuries, which are never repaired, can have life-long sequelae including prolapse and incontinence, it seems reasonable to try to prevent them. From a biomechanical perspective, women with unusually stretch-resistant lower birth canals can expect longer labors and a higher risk for muscle and tissue injury. The goals of this dissertation were to (a) quantify the viscoelastic properties of the lower birth canal during the first stage of labor, with special attention to the effects of age and body mass index; (b) identify those at risk for a long second stage of labor, as well as (c) an elevated risk for levator ani injuries. Following an introductory chapter (Chapter 1), we describe the biomechanics of a new device that dilates the lower birth canal (PREP, Materna Medical, LLC., CA) during the first stage of labor, and its use in the ongoing multicenter EASE clinical trial (Chapter 2).

Next, we quantify the normal ranges of lower birth canal resistance to dilation (tension T) in 56 nulliparas during the first stage of labor. We found remarkable variation in birth canal wall tension across all subjects. Specifically, the tension when reaching 55 mm dilation varied 5.5-fold and was 22% greater in older women and correlated strongly with both relaxation during the 5-minute hold and with the maximum tension (r= 0.80, r = 0.59 with p<0.001), thus a reasonable predictor of resistance to lower canal dilation (Chapter 3). The stiffness of the initial 20 s ramp varied 6.8-fold and was 31% higher in older women.

We then demonstrated that the effect of the initial 20 s ramp-and-5 minute hold of PREP insertion on the viscoelastic properties of the lower birth canal can reliably be characterized using a fractional viscoelastic Zener model (FZM). In 61 nullipara, the relative error for the 20 s ramp-and-5 minute hold using the FZM was 8.1 ± 3.6% and provided a relative prediction error in 60 minutes of dilation of 10.0 ± 5.4%. The FZM constant kβ, an analog for the shorter timer constant, was 33% higher in older women (Chapter 4). We then used the fractional Zener viscoelastic constants obtained in Chapter 4 to predict the duration of the second stage of labor and risk for levator ani injury. As labor outcomes are presently unavailable for the PREP subjects due to the ongoing nature of the EASE trial, the model was tested on data from an earlier constant force PILOT dilator study involving 22 healthy women with available labor outcomes. Our prediction model identified both instances of LA injury and predicted 22% of the variation in the second stage of labor duration (Chapter 5). We conclude that the viscoelastic properties of the lower birth canal in the first stage of labor are responsible for nearly a quarter of the variation in second stage duration. When combined with existing obstetric variables, the PREP dilator may prove helpful in the improved management of vaginal delivery.

Zoom Link: https://umich.zoom.us/j/99452208073 Meeting ID: 994 5220 8073 Passcode: 0000

Committee Chair(s): Dr. James Ashton-Miller

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Presentation Thu, 05 Jan 2023 11:07:02 -0500 2023-01-11T10:00:00-05:00 2023-01-11T11:00:00-05:00 GG Brown Laboratory Biomedical Engineering Presentation BME logo over a blurred picture of LBME
Towards defining principles of cell fate plasticity (January 11, 2023 12:00pm) https://events.umich.edu/event/102851 102851-21805240@events.umich.edu Event Begins: Wednesday, January 11, 2023 12:00pm
Location: North Campus Research Complex Building 10
Organized By: Biomedical Engineering

Abstract:
Cell fate plasticity, a cell’s ability to change its identity and function, produces the wide variety of cell types needed to form, maintain, and regenerate all mammalian tissues. All forms of plasticity are tightly regulated to ensure proper tissue function, and when aberrantly activated, can contribute to pathological phenotypes, including impaired tissue repair and tumorigenesis. Understanding how cellular identity is dysregulated during aging, injury, and disease may yield approaches that correct aberrant cell fate transitions with therapeutic applications. This dissertation seeks to characterize the factors that guard cell fate by integrating innovative experimental techniques, including novel cell lines, animal models, and micro-engineered devices, with high-throughput sequencing assays and bioinformatics tools that map molecular information to cellular responses. 

The first three studies provide insights into the mechanisms that preserve the regenerative capacity of muscle stem cells (MuSCs), the resident stem cell population in skeletal muscle. MuSCs lie in a state of mitotic quiescence during homeostasis and activate upon injury to repair damaged tissue while also renewing the quiescent stem cell pool. Over time, MuSCs accumulate intracellular damage that alters metabolic signaling pathways and transcriptional programs supportive of quiescence, blunting the efficient regeneration of skeletal muscle. To further understand how MuSCs acquire dysfunctional molecular programs in old age, we explore the roles of three-dimensional genome organization, an underexplored histone modification (H4K20me1), and a conserved metabolic regulator (Sestrins) in mediating pathological gene expression both at rest and in response to injury. We find that natural aging in MuSCs is accompanied by subtle shifts in global genome architecture and metabolic signaling that are sufficient to induce aberrant regenerative trajectories. 

The fourth and fifth studies describe continuing efforts to develop new models for engineering cell fate. In one study, we identify barriers to cell fate transitions by reprogramming somatic cells such that a specialized cell fate is erased and a new identity is adopted. This process requires spatial remodeling of the epigenetic landscape that is constrained by interactions between peripheral heterochromatin and the protein scaffold that lines the interior of the nucleus. We show that manipulating components of the nuclear scaffold prior to reprogramming alters mechanical properties of the nucleus and peripheral heterochromatin organization, which converge to drive changes in reprogramming dynamics. Finally, we revisit a century-old hypothesis that tumor cells acquire enhanced metastatic potential through fusion with neighboring stromal cells that express pro-metastatic traits such as motility, chemotaxis, and tissue tropism. To investigate this concept, we demonstrate the efficient production of bi-species heterokaryons from human tumor cells and mouse stromal cells in the brain metastatic niche, which allows genetic and metabolic factors to be assigned to their parent cell by species identity. This approach will allow us to identify and inhibit trans-acting factors that promote malignant fate transitions. 

In summary, this thesis provides mechanistic insights into cell fate plasticity in varying health contexts and explores new models for deciphering cell fate regulation.

Committee Chair(s): Dr. Carlos A. Aguilar

Zoom Link: https://umich.zoom.us/meeting/register/tJ0td-2oqDorHNTHn8ikj0vDQx7x7ljfl7uy

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Presentation Thu, 05 Jan 2023 11:44:36 -0500 2023-01-11T12:00:00-05:00 2023-01-11T13:00:00-05:00 North Campus Research Complex Building 10 Biomedical Engineering Presentation BME logo over blurred photo of LBME
DCM&B Tools and Technology Seminar (January 12, 2023 12:00pm) https://events.umich.edu/event/101954 101954-21802987@events.umich.edu Event Begins: Thursday, January 12, 2023 12:00pm
Location: Palmer Commons
Organized By: DCMB Tools and Technology Seminar

Tool link: https://gkb.dcmb.med.umich.edu/

Associated article: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac957/6786196

This presentation will be held in 2036 Palmer Commons. There will also be a remote viewing option via Zoom.

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Presentation Thu, 08 Dec 2022 11:26:15 -0500 2023-01-12T12:00:00-05:00 2023-01-12T13:00:00-05:00 Palmer Commons DCMB Tools and Technology Seminar Presentation
Oral Health Sciences Seminar Series (January 12, 2023 12:00pm) https://events.umich.edu/event/102846 102846-21805235@events.umich.edu Event Begins: Thursday, January 12, 2023 12:00pm
Location: Dental & W.K. Kellogg Institute
Organized By: Office of Research School of Dentistry

Oral Health Sciences Seminar Series Title:
Adverse Childhood Experiences Impact Tooth Emergence and Development

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Workshop / Seminar Fri, 06 Jan 2023 09:28:05 -0500 2023-01-12T12:00:00-05:00 2023-01-12T13:00:00-05:00 Dental & W.K. Kellogg Institute Office of Research School of Dentistry Workshop / Seminar Erin Ealba Bumann, DDS, PhD, MS Assistant Professor Department of Oral and Craniofacial Sciences University of Missouri – Kansas City School of Dentistry
Autonomous Medical Robots Guided by Real-Time 3D Imaging (January 12, 2023 3:30pm) https://events.umich.edu/event/102880 102880-21805277@events.umich.edu Event Begins: Thursday, January 12, 2023 3:30pm
Location: Cooley Building
Organized By: Biomedical Engineering

Abstract:
Medical robots can precisely manipulate tools beyond human capabilities and are thus helpful for surgeries involving delicate tissue interactions. When coupled with live 3D imaging, such robots can independently guide surgical instruments in real time. In practice, however, patients receive only limited benefits from such intraprocedural data streams due to the lack of integration between robots and imaging systems with sufficiently high resolution and framerate. In this seminar, I report on work with medical robots that use optical coherence tomography to guide needle insertions for cornea transplantation, enhance surgeon efficiency with live volumetric guidance, and perform autonomous eye imaging. In addition, I discuss using real-time image feedback to adaptively acquire images that break the framerate-resolution barrier during live 3D imaging.

Bio:
Mark Draelos, MD, PhD, is a surgically-trained physician and engineer who develops novel applications of medical robotics and imaging to improve patient care. After finishing Duke University’s Medical Scientist Training Program where he studied biomedical engineering under Prof. Joseph Izatt, Mark completed an internship in general surgery at Duke University Medical Center. Currently, he is an Assistant Professor of Robotics and Ophthalmology at the University of Michigan, where he directs the Image-Guided Medical Robotics Laboratory. Mark has received K99/R00 support from the National Eye Institute.

Zoom:
https://umich.zoom.us/j/91712262512

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Workshop / Seminar Thu, 05 Jan 2023 13:40:07 -0500 2023-01-12T15:30:00-05:00 2023-01-12T16:30:00-05:00 Cooley Building Biomedical Engineering Workshop / Seminar BME classroom set up for a seminar with guests in the audience.
HHMI Investigator Information Session (January 17, 2023 3:00pm) https://events.umich.edu/event/102240 102240-21803723@events.umich.edu Event Begins: Tuesday, January 17, 2023 3:00pm
Location: Ruthven Administration Building
Organized By: OVPR Office of Research Development

OVPR and Foundation Relations will host an information session for the Howard Hughes Medical Institute (HHMI) Investigator program on January 17, 2023, 3-4:30 pm, in University Hall, Ruthven Administration Building. VPR Rebecca Cunningham will offer opening remarks. Maureen Martin, Executive Director of Foundation Relations, will present an overview of the rigorous HHMI application and interview processes.
The prestigious HHMI Investigator program is offered every three years and provides long-term funding to scientists who push the boundaries of fundamental science. The competition is open to researchers in basic and biomedical sciences, plant biology, evolutionary biology, biophysics, chemical biology, biomedical engineering, and computational biology. Eligible faculty will be tenured or tenure-track, between 5 and 15 years post-training experience, and a PI on one or more active, national, peer-reviewed grants.
Program applications are due to HHMI by 3 pm ET on March 21, 2023.
Register for the information session

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Presentation Wed, 14 Dec 2022 15:03:44 -0500 2023-01-17T15:00:00-05:00 2023-01-17T16:30:00-05:00 Ruthven Administration Building OVPR Office of Research Development Presentation HHMI logo
DCM&B Tools and Technology Seminar (January 19, 2023 12:00pm) https://events.umich.edu/event/101955 101955-21802988@events.umich.edu Event Begins: Thursday, January 19, 2023 12:00pm
Location: Off Campus Location
Organized By: DCMB Tools and Technology Seminar

Modern systems are known to be massive-scale, with a hierarchy of dynamic and unknown topologies. The behavior of these systems can be captured via dynamic graphical models (DGM). An important application of DGMs is in the inference of dynamic gene regulatory networks that may change spatially across different cells and over time in response to different physiological cues. This work aims at developing efficient computational tools for the inference of DGMs that are not only statistically sound, but also adaptive, parallelizable, and implementable in massive scales. Much of the progress in the inference of DGMs with structural constraints is based on the maximum likelihood estimation (MLE) with relaxed regularization, which neither result in ideal statistical properties nor scale to dimensions encountered in realistic settings. This work addresses these challenges by departing from the regularized MLE paradigm and resorting to a new class of constrained and combinatorial optimization that can systematically learn DGMs in near-linear time and memory. For the first time, we can infer instances of DGM with more than 500M variables in less than an hour. We will also show the promise of our method in the context of inferring gene networks underlying oncogenesis, using Glioblastoma as a case study.

This presentation will be held in 2036 Palmer Commons. There will also be a remote viewing option via Zoom.

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Presentation Mon, 19 Dec 2022 17:50:57 -0500 2023-01-19T12:00:00-05:00 2023-01-19T13:00:00-05:00 Off Campus Location DCMB Tools and Technology Seminar Presentation
LHS Collaboratory (January 19, 2023 12:00pm) https://events.umich.edu/event/99642 99642-21798494@events.umich.edu Event Begins: Thursday, January 19, 2023 12:00pm
Location: Off Campus Location
Organized By: Department of Learning Health Sciences

LHS Collaboratory January Session

An interview and discussion with Professor Osagie K. Obasogie, JD, PhD.
Haas Distinguished Chair
Professor of Law and Bioethics, University of California, Berkeley

Interviewers:

Azia Harris-Martin
Health Infrastructures and Learning Systems PhD Student
University of Michigan
Manager of Transformation, Optum PacWest

Salomé Viljoen
Assistant Professor of Law
University of Michigan Law School

Osagie K. Obasogie is the Haas Distinguished Chair and Professor of Law at the University of California, Berkeley School of Law with a joint appointment in the Joint Medical Program and School of Public Health. He received his B.A. in Sociology and Political Science (with distinction in both majors) from Yale University, his J.D. from Columbia Law School where he was a Harlan Fiske Stone Scholar, and his Ph.D. in Sociology from the University of California, Berkeley, where he was a fellow with the National Science Foundation. Obasogie’s scholarly interests include Constitutional law, policing and police use of force, sociology of law, bioethics, race and inequality in law and medicine, and reproductive and genetic technologies.

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Lecture / Discussion Sun, 20 Nov 2022 00:03:28 -0500 2023-01-19T12:00:00-05:00 2023-01-19T13:30:00-05:00 Off Campus Location Department of Learning Health Sciences Lecture / Discussion LHS Collaboratory logo
Multi-Scale Systems Analysis of Metabolic and Mechanical Determinants of Reserve Cardiac Power Output (January 19, 2023 3:30pm) https://events.umich.edu/event/103312 103312-21807011@events.umich.edu Event Begins: Thursday, January 19, 2023 3:30pm
Location: Cooley Building
Organized By: Biomedical Engineering

Abstract:
Exercise capacity, a central factor in determining quality of life in healthy aging as well as cardiovascular disease, is determined by a systems-level interaction of factors that are intrinsic to the heart and myocardium and factors that are extrinsic to the heart. Cardiac intrinsic factors include the metabolic power supply and mechanical pumping power of the myocardium. Extrinsic factors include the capacity of the peripheral vasculature to vasodilate in response to increasing demands of exercising musculature and the autonomic chemo- and baroreflexes. 

     We have developed a whole-heart and whole-body cardiovascular modelling framework to capture and test hypotheses on how specific myocardial, autonomic, and vascular mechanisms determine physiological limitations to cardiac power and output reserve and contribute to diminished left-ventricular power output (LVPO) and exercise intolerance in heart failure. Simulations are driven by a multi-scale model of myocardial metabolism and mechanics. Simulations based on a model parameterization representing a healthy young subject may be used to explore, from a theoretical perspective, if and how myocardial ATP supply can affect myocardial mechanics and power reserve. As an emergent property, the integrated model accurately predicts the oxygen cost of contraction during rest and exercise, yielding the correct quantitative relationship between mechanical power output (in the in vivo whole-body setting) and myocardial mitochondrial oxidative phosphorylation (reflected in myocardial oxygen demand). Simulations also reveal that, under physiological conditions, the myocardial capacity to synthesize ATP at a free energy level needed to drive myocardial mechanics reaches its maximal value at maximal exercise. Thus these theoretical predictions are consistent with the concept that the myocardial energy supply capacity limits physiological cardiac power capacity.

Bio:
Dr. Beard is a Professor in the Department of Molecular and Integrative Physiology and holds affiliate appointments in Biomedical Engineering and Emergency Medicine. His laboratory is focused on systems engineering approaches to understanding the biophysical and biochemical operation of physiological systems. Dr. Beard is the Director of the Virtual Physiological Rat (VPR) project, supported as an NIH National Center for Systems Biology, working to analyze, interpret, simulate, and ultimately predict physiological function in health and disease.

Dr. Beard earned an MS in Applied Mathematics and PhD in Bioengineering in 1997 under the supervision of Dr. James Bassingthwaighte at the University of Washington. After completing his PhD he conducted postdoctoral research at the Courant Institute of New York University, and as a Howard Hughes Medical Institute Postdoctoral Fellow. Before joining the University of Michigan, he was Professor of Physiology at the Medical College of Wisconsin.

Zoom:
https://umich.zoom.us/j/91712262512

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Workshop / Seminar Thu, 12 Jan 2023 11:08:20 -0500 2023-01-19T15:30:00-05:00 2023-01-19T16:30:00-05:00 Cooley Building Biomedical Engineering Workshop / Seminar BME Seminar
Educating Ethical Engineers (January 24, 2023 10:30am) https://events.umich.edu/event/103233 103233-21806517@events.umich.edu Event Begins: Tuesday, January 24, 2023 10:30am
Location: Lurie Robert H. Engin. Ctr
Organized By: Engineering Education Research

In today’s society, the need to graduate engineers who are conscious of their ethical and professional responsibilities is more important than ever. This is especially difficult given the current media environment that publicizes reports of algorithmic bias, drone-based surveillance, and emissions falsification (among other issues) but provides few positive role models for students. While engineering programs have made significant strides to incorporate ethics instruction into the engineering curriculum, there is little evidence about which approaches best prepare students to address the ethical challenges they will face in the workforce. In this session, Dr. Finelli will present research about the state of undergraduate ethics instruction and it’s long term impact, propose a new approach to ethics instruction, and offer two course-based approaches to better educate ethical engineers.

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Workshop / Seminar Wed, 11 Jan 2023 10:25:15 -0500 2023-01-24T10:30:00-05:00 2023-01-24T12:00:00-05:00 Lurie Robert H. Engin. Ctr Engineering Education Research Workshop / Seminar Dr. Cynthia Finelli
Educating Ethical Engineers (January 24, 2023 10:30am) https://events.umich.edu/event/103233 103233-21806518@events.umich.edu Event Begins: Tuesday, January 24, 2023 10:30am
Location: Off Campus Location
Organized By: Engineering Education Research

In today’s society, the need to graduate engineers who are conscious of their ethical and professional responsibilities is more important than ever. This is especially difficult given the current media environment that publicizes reports of algorithmic bias, drone-based surveillance, and emissions falsification (among other issues) but provides few positive role models for students. While engineering programs have made significant strides to incorporate ethics instruction into the engineering curriculum, there is little evidence about which approaches best prepare students to address the ethical challenges they will face in the workforce. In this session, Dr. Finelli will present research about the state of undergraduate ethics instruction and it’s long term impact, propose a new approach to ethics instruction, and offer two course-based approaches to better educate ethical engineers.

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Workshop / Seminar Wed, 11 Jan 2023 10:25:15 -0500 2023-01-24T10:30:00-05:00 2023-01-24T12:00:00-05:00 Off Campus Location Engineering Education Research Workshop / Seminar Dr. Cynthia Finelli
ME Seminar Series (January 24, 2023 4:30pm) https://events.umich.edu/event/103857 103857-21808008@events.umich.edu Event Begins: Tuesday, January 24, 2023 4:30pm
Location: GG Brown Laboratory
Organized By: Mechanical Engineering

Adventures in Cell Herding: Engineering and Control of Multi-agent Cellular Swarms

Presented by
Daniel Cohen
Assistant Professor of Mechanical and Aerospace Engineering
Princeton University

Room 2505 GG Brown
Tuesday, January 24, 2023
4:30 p.m.
ME Seminar Zoom link
Passcode 309714
Add ME Seminar to Google Calendar

Abstract
We are working to accomplish for cells something akin to what a shepherd and sheepdogs bring to flocks of sheep: control over large-scale collective cellular motion. As coordinated cellular motion is foundational to many forms of multicellular life, being able to ‘herd’ or program large-scale cell migration raises exciting possibilities for accelerated healing, tissue engineering, and novel biomaterials. We treat tissues as living, multi-agent systems allowing us to combine approaches from disparate fields—control theory, active matter mechanics, tissue engineering, and materials—both to better understand the rules of cellular crowds and to build new tools to ‘herd’ large-scale cell behaviors. One approach we use is guided self-assembly of tissues, where we establish precise initial conditions and let the tissues develop spontaneously. Here, we combine machine learning, biomechanical modeling, and tissue micropatterning to: characterize the rules of collective migration within tissues of different types; connect cell-cell mechanics to large-scale collective dynamics; and build complex ‘tissue tessellations’ through precise control of healing boundaries between tissues. In contrast to self-assembly, we are also developing tools that allow for true, interactive control of tissue growth and form at the multicellular level. Here, we use a unique bioelectric cue—electrotaxis—to literally program large-scale collective cell migration, enabled by our ‘SCHEEPDOG’ bioreactor. In this case, ionic currents manipulate cellular signaling allowing control of both cell direction and speed, allowing us to: accelerate the ‘healing’ of gap injuries with in vitro tissues; investigate how cell-cell interaction mechanics modulate ‘controllability’; and manipulate the growth of 3D tissues and organoids.

Bio
Daniel Cohen is an Assistant Professor of Mechanical and Aerospace Engineering at Princeton University and a founding member of the new Princeton Bioengineering Institute (PBI). He trained first in Mechanical Engineering at Princeton, followed by a joint Ph.D. in Bioengineering at UC Berkeley/UCSF, the Physiology Course at the MBL at Woods Hole, and as a Life Sciences Research Foundation Fellow at Stanford University. He started his lab at Princeton in 2018, where his work has been awarded an NIH Early Career MIRA award and an NSF CAREER award. His works span dinosaur and organismal mechanics, tissue engineering, biomaterials, and bio-electromechanics. Outside the laboratory, he is heavily engaged in science communication, running both theatrical performances for the public and the yearly, week-long Lab Tales workshop at Princeton to train researchers in the hidden histories and human stories behind modern scientific research.

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Lecture / Discussion Mon, 23 Jan 2023 14:37:17 -0500 2023-01-24T16:30:00-05:00 2023-01-24T17:30:00-05:00 GG Brown Laboratory Mechanical Engineering Lecture / Discussion Dan Cohen, Assistant Professor of Mechanical and Aerospace Engineering at Princeton University, will give a talk on work he is doing to accomplish for cells something akin to what a shepherd and sheepdogs bring to flocks of sheep: control over large-scale collective cellular motion.
DCM&B Tools and Technology Seminar (January 26, 2023 12:00pm) https://events.umich.edu/event/101956 101956-21802989@events.umich.edu Event Begins: Thursday, January 26, 2023 12:00pm
Location: Palmer Commons
Organized By: DCMB Tools and Technology Seminar

Transcriptome-wide association studies (TWAS) and colocalization analysis are complementary integrative genetic association approaches routinely used to identify functional units underlying complex traits in post-genome-wide association study (post-GWAS) analyses. Recent studies suggest that both approaches are individually imperfect, but joint usage can yield robust and powerful inference results. In this talk, we introduce a new statistical framework, INTACT, to perform probabilistic integration of TWAS and colocalization evidence for implicating putative causal genes. This procedure is flexible and can work with a wide range of existing TWAS and colocalization approaches. It has the unique ability to quantify the uncertainty of implicated genes, enabling rigorous control of false-positive discoveries. Taking advantage of this highly-desirable feature, we describe an efficient algorithm, INTACT-GSE, for gene set enrichment analysis based on the integrated TWAS and colocalization analysis results. We examine the proposed computational methods and illustrate their improved performance over the existing approaches through simulation studies. We apply the proposed methods to the GTEx data and a variety of GWAS summary statistics derived from complex and molecular traits. We find empirical evidence that the proposed methods improve and complement existing putative gene implication methods and are advantageous in evaluating and identifying key gene sets and biological pathways. Finally, we present ongoing work that aims to extend INTACT to account for measurements of additional gene products (e.g. protein or isoform levels) in the inference procedure.

Tool link: https://github.com/jokamoto97/INTACT/

This presentation will be held in 2036 Palmer Commons. There will also be a remote viewing option via Zoom.

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Presentation Thu, 08 Dec 2022 11:25:19 -0500 2023-01-26T12:00:00-05:00 2023-01-26T13:00:00-05:00 Palmer Commons DCMB Tools and Technology Seminar Presentation
Oral Heath Sciences Seminar Series (January 26, 2023 1:00pm) https://events.umich.edu/event/103076 103076-21806075@events.umich.edu Event Begins: Thursday, January 26, 2023 1:00pm
Location: Dental & W.K. Kellogg Institute
Organized By: Office of Research School of Dentistry

OHS Seminar Title: "Regulation of Innate Immunity and Wound Healing in the Periodontium"

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Workshop / Seminar Mon, 09 Jan 2023 13:24:17 -0500 2023-01-26T13:00:00-05:00 2023-01-26T14:00:00-05:00 Dental & W.K. Kellogg Institute Office of Research School of Dentistry Workshop / Seminar Dr. Ann Decker, Associate Professor of Internal Medicine, Division of Gastroenterology
The Mechanics of the Vagina: Deformations, Tears, and Contractions (January 26, 2023 3:30pm) https://events.umich.edu/event/103053 103053-21805781@events.umich.edu Event Begins: Thursday, January 26, 2023 3:30pm
Location: Cooley Building
Organized By: Biomedical Engineering

Abstract:
The vagina is a complex fibromuscular organ with walls that are usually collapsed against each other. The same walls can, however, stretch a great deal during important physiological functions such as conception, pregnancy, and delivery. The remarkable deformations of this organ have not been characterized, despite their impact on women’s health. In this talk, I will offer an overview of the research being conducted in my lab to quantify the unique mechanics and complex microstructure of the vagina by combining advanced experimental, theoretical, and computational methods. The vaginal tissue in the rat model was found to experience very large and highly inhomogeneous deformations in both the active (relaxed) and passive (contracted) states. Over time, the vaginal walls deform very quickly when the loads are first applied and more slowly as the same loads are sustained, revealing their inherent viscoelasticity. Even in the presence of tears, the vagina can undergo large deformations with collagen fibers re-orienting to slow the propagation of tears. Higher contractions occur in the proximal (closer to the cervix) region than in the distal (closer to the introitus) region due to the smooth muscle fiber organization. Data-driven reduced-order modeling techniques are being used to construct in silico models of vaginal deformations, with the accuracy of higher-fidelity models and the speed of simplified models. Future research will explore how mechanical and microstructural properties of the vagina are altered in pathological conditions such as sexual dysfunction, maternal trauma, and pelvic organ prolapse.

Bio:
Raffaella De Vita is a professor and associate department head in the Department of Biomedical Engineering and Mechanics at Virginia Tech. She received her Laurea in Mathematics from La Seconda Università degli Study di Napoli, Italy, in 2000 and her M.S. and Ph.D. from University of Pittsburgh in 2003 and 2005, respectively. She is the recipient of the American Society of Biomechanics President’s award, the NSF CAREER award, the PECASE Award, and several awards for research, teaching, and outreach excellence at Virginia Tech. She is a fellow of the ASME and AIMBE. She has served as an associate editor for the Journal of Elasticity since 2020 and as an associate editor for the Journal of Biomedical Engineering from 2017 to 2022. Her research focuses on determining the relationship between the mechanical behavior and the complex structure of biological systems using theoretical, computational, and experimental methods.

Zoom:
https://umich.zoom.us/j/91712262512

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Workshop / Seminar Mon, 09 Jan 2023 11:21:42 -0500 2023-01-26T15:30:00-05:00 2023-01-26T16:30:00-05:00 Cooley Building Biomedical Engineering Workshop / Seminar BME Seminar
Richard A. Auhll Endowed  Professorship Ceremony & Lecture (January 27, 2023 3:00pm) https://events.umich.edu/event/102468 102468-21804084@events.umich.edu Event Begins: Friday, January 27, 2023 3:00pm
Location: Pierpont Commons
Organized By: Biomedical Engineering

On Friday, January 27 at 3:00 p.m., the College of Engineering will honor Professor Xudong (Sherman) Fan for his appointment to an endowed professorship. Please join Professor Fan, Dean Alec D. Gallimore, Robert J. Vlasic Dean of Engineering, and Biomedical Engineering Professor and Interim Chair, Mary-Ann Myeck, for the lecture and ceremony in the East Conference Room of Pierpont Commons, 2101 Bonisteel Blvd, Ann Arbor, MI.

Professor Fan will be installed as the Richard A. Auhll Professor of Engineering and will present a lecture titled “Breath and body odor analysis for precision healthcare: from benchtop to wearable.” A reception will follow in the East Conference room.

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Ceremony / Service Wed, 21 Dec 2022 10:35:33 -0500 2023-01-27T15:00:00-05:00 2023-01-27T17:00:00-05:00 Pierpont Commons Biomedical Engineering Ceremony / Service Biomedical Engineering logo over a blurred image of LBME.
DCM&B Tools and Technology Seminar (February 2, 2023 12:00pm) https://events.umich.edu/event/101957 101957-21802990@events.umich.edu Event Begins: Thursday, February 2, 2023 12:00pm
Location: Palmer Commons
Organized By: DCMB Tools and Technology Seminar

Metagenomics holds potential to improve clinical diagnostics of infectious diseases, but DNA from clinical specimens is often dominated by host-derived sequences. To address this, researchers employ host-depletion methods. Laboratory-based host-depletion methods, however, are costly in terms of time and effort, while computational host-depletion methods rely on memory-intensive reference index databases and struggle to accurately classify noisy sequence data. To solve these challenges, we propose an index-free tool, AMAISE (A Machine Learning Approach to Index-Free Sequence Enrichment). Applied to the task of separating host from microbial reads, AMAISE achieves over 98% accuracy. Applied prior to metagenomic classification, AMAISE results in a 14–18% decrease in memory usage compared to using metagenomic classification alone. Our results show that a reference-independent machine learning approach to host depletion allows for accurate and efficient sequence detection.

Tool Link: https://github.com/MLD3/AMAISE

This presentation will be held in 2036 Palmer Commons. There will also be a remote viewing option via Zoom.

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Presentation Thu, 08 Dec 2022 11:32:43 -0500 2023-02-02T12:00:00-05:00 2023-02-02T13:00:00-05:00 Palmer Commons DCMB Tools and Technology Seminar Presentation
Biomedical Engineering (BME 500) Seminar Series - Kate Wofford, PhD (February 2, 2023 3:30pm) https://events.umich.edu/event/104034 104034-21808299@events.umich.edu Event Begins: Thursday, February 2, 2023 3:30pm
Location: Cooley Building
Organized By: Biomedical Engineering

Abstract:
Traumatic brain injury (TBI) affects millions of individuals annually resulting in disrupted neuronal circuitry, neurological deficits, and neuroinflammation. Resident and peripheral immune cells interact with damaged neurons after TBI and can contribute to chronic neuroinflammation and neuropathology. Dr. Wofford’s research focuses on understanding and controlling neuro-immune interactions as a therapeutic strategy for TBI. In this talk, Dr. Wofford will describe recent experiments investigating neuro-immune interactions in an advanced translational model of TBI and will describe one method to control inflammation at the cellular level.

Bio:
Dr. Kate Wofford trained with Kara Spiller at Drexel University and Kacy Cullen at the University of Pennsylvania for her Ph.D. in Biomedical Engineering where she characterized acute neuroinflammation after brain injury and developed a strategy to reprogram immune cells. Now, Kate is a Postdoctoral Fellow in the lab of Kacy Cullen at the University of Pennsylvania where she uses advanced preclinical models to study behavioral, neuropathological, and immunological consequences of brain injury. Her work has been recognized with receipt of multiple awards including the K99/R00 Career Development Award, F32 National Research Service Award, Koerner Award, Outstanding Scholar in Neuroscience Award, Interdisciplinary Collaboration and Research Excellence Fellowship, Anthony Marmarou Award, Sanjeev Kumar Memorial Award, and the Wan Shih Translational Research Award.

Zoom:
https://umich.zoom.us/j/91712262512

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Workshop / Seminar Wed, 25 Jan 2023 20:41:13 -0500 2023-02-02T15:30:00-05:00 2023-02-02T16:30:00-05:00 Cooley Building Biomedical Engineering Workshop / Seminar BME Seminar Series
Weekly DCMB Seminar with Refreshments (February 8, 2023 4:00pm) https://events.umich.edu/event/103257 103257-21806685@events.umich.edu Event Begins: Wednesday, February 8, 2023 4:00pm
Location: Palmer Commons
Organized By: DCMB Seminar Series

Abstract:

Most disease associated genomic variants have relatively modest effects on target gene expression in reporter or CRISPR perturbation assays. In addition, enhancer disruption in vivo often has surprisingly weak phenotypic consequences. I will present machine learning (ML) methods (gkm-SVM and DNN) which we use to learn the complex transcription factor combinations that control enhancer activity and cell fate. I will then use these methods to develop a quantitative model for enhancer activity which shows that while promoter knockdown has robust effects on target gene expression, individual enhancer knockdown is often weaker and affects temporal transition dynamics, but not the final steady state. This model provides an explanation of the paradox of how enhancer variation can be strongly associated with disease risk while having individually weak effects, by showing in detail how gene regulatory networks control developmentally important and disease relevant cell state transitions and cancer.

https://umich-health.zoom.us/j/93929606089?pwd=SHh6R1FOQm8xMThRemdxTEFMWWpVdz09

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Lecture / Discussion Wed, 11 Jan 2023 15:44:58 -0500 2023-02-08T16:00:00-05:00 2023-02-08T17:00:00-05:00 Palmer Commons DCMB Seminar Series Lecture / Discussion Michael A. Beer, Ph.D., M.A.
DCM&B Tools and Technology Seminar - CANCELED (February 9, 2023 12:00pm) https://events.umich.edu/event/101959 101959-21802991@events.umich.edu Event Begins: Thursday, February 9, 2023 12:00pm
Location: Off Campus Location
Organized By: DCMB Tools and Technology Seminar

Today's Tools and Technology Seminar has been canceled. The originally scheduled presenting has been rescheduled for March 30.

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Presentation Fri, 03 Feb 2023 14:36:18 -0500 2023-02-09T12:00:00-05:00 2023-02-09T13:00:00-05:00 Off Campus Location DCMB Tools and Technology Seminar Presentation
Oral Health Sciences Seminar Series (February 9, 2023 12:00pm) https://events.umich.edu/event/102889 102889-21805297@events.umich.edu Event Begins: Thursday, February 9, 2023 12:00pm
Location: Dental & W.K. Kellogg Institute
Organized By: Office of Research School of Dentistry

Oral Health Sciences Seminar Series Title:
The aging innate immune response: Implications for periodontal disease and bone regeneration

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Workshop / Seminar Fri, 06 Jan 2023 09:14:38 -0500 2023-02-09T12:00:00-05:00 2023-02-09T13:00:00-05:00 Dental & W.K. Kellogg Institute Office of Research School of Dentistry Workshop / Seminar Daniel Clark, DDS, MS, PhD_Assistant Professor Department of Periodontics and Preventive Dentistry_University of Pittsburgh School of Dental Medicine
Bioink Development to Advance 3D Bioprinting (February 9, 2023 3:30pm) https://events.umich.edu/event/104390 104390-21808994@events.umich.edu Event Begins: Thursday, February 9, 2023 3:30pm
Location: Cooley Building
Organized By: Biomedical Engineering

Abstract:
Cardiac tissue engineering has emerged to create living, human, cardiac tissue outside the body as a model system in the near term and as a clinical replacement for diseased or damaged cardiac muscle in the long term. My laboratory seeks to understand the intricate interplay between the extracellular matrix and cardiac cell types in vivo to guide cardiac tissue engineering efforts in vitro. In the course of this seminar I will share our most surprising mechanistic insights and describe how they now guide the development of novel bioink formulations that enable 3D bioprinting of complex cardiac tissues.

Bio:
Brenda Ogle is Professor and Head of Biomedical Engineering, Professor of Pediatrics, and Director of the Stem Cell Institute at the University of Minnesota. Her research team investigates the impact of extracellular matrix proteins on stem cell behavior especially in the context of the cardiovascular system. Insights gleaned over the years established mechanistic links between integrin engagement and the activity of critical transcription factors and most recently led to the development of optimized, extracellular matrix-based bioinks for 3D printing of cardiac muscle mimics featured in Newsweek. The primary strength of her laboratory is the ability to span multiple subdisciplines within both basic science (i.e., stem cell biology, cell-cell fusion, and extracellular matrices) and engineering (cytometry, instrumentation, and 3D printing) fields. Her work received funding from the National Institutes of Health, the National Science Foundation, the Department of Defense, the American Heart Association, the Coulter Foundation, Regenerative Medicine Minnesota, and MnDRIVE. She has partnered on research projects with Becton Dickinson, iCyt, 3M and Medtronic. Professor Ogle is an elected fellow of the American Institute for Medical and Biological Engineering and the Biomedical Engineering Society. She has served as a member of the Board of Directors of the Biomedical Engineering Society, as co-chair of the Women’s Faculty Cabinet, UMN and is recipient of the Mullen-Spector-Truax Women’s Leadership Award.

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Workshop / Seminar Wed, 01 Feb 2023 17:06:54 -0500 2023-02-09T15:30:00-05:00 2023-02-09T16:30:00-05:00 Cooley Building Biomedical Engineering Workshop / Seminar BME Seminar Series
Taking Actions Toward Educational Change in Engineering Education (February 10, 2023 10:30am) https://events.umich.edu/event/104157 104157-21808511@events.umich.edu Event Begins: Friday, February 10, 2023 10:30am
Location: Lurie Robert H. Engin. Ctr
Organized By: Engineering Education Research

As engineering education scholars and engineering educators, many of us pursue educational change and innovation through our research, teaching, service, and leadership activities. In this pursuit, we take intentional and strategic actions towards educational change and innovation goals that matter to us, whether that is reimagining graduate admissions to be a more equitable and inclusive process or redesigning how students are introduced to the ideas of heat and temperature in a foundational engineering course. Our actions towards these goals represent our professional agency towards educational change.

The focus of this talk will be to explore the question of How might we empower and enable faculty to engage in educational change at their institutions? To support this exploration, I will introduce a contextualized theory for professional agency towards educational change that was developed based on a longitudinal and collaborative qualitative study of six early career engineering education scholars. The theory has since been used to examine the actions and experiences of engineering instructional faculty at Hispanic-Serving Institutions. Using both studies as examples, we will consider our own experiences pursuing change efforts through this lens and begin to imagine how we might further promote this type of professional agency within our communities.

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Workshop / Seminar Fri, 27 Jan 2023 12:48:22 -0500 2023-02-10T10:30:00-05:00 2023-02-10T12:00:00-05:00 Lurie Robert H. Engin. Ctr Engineering Education Research Workshop / Seminar Dr. Alexandra Coso Strong
Research Day 2023 (February 16, 2023 10:30am) https://events.umich.edu/event/103074 103074-21806074@events.umich.edu Event Begins: Thursday, February 16, 2023 10:30am
Location: Michigan League
Organized By: Office of Research School of Dentistry

Research Day 02/16/2023

Poster and Exhibit Session 1 (MI League 2nd Floor)
10:30 am - 12:00 pm

Keynote Presentation - Nisha J D'Silva, BDS, MSD, PhD - Donald A Kerr Endowed Collegiate Professor of Oral Pathology, Professor of Dentistry, Department of Oral Medicine/Pathology and Oncology, School of Dentistry and Professor of Pathology, Medical School

1:00 pm - 12:00 pm

Poster and Exhibit Session 2 (MI League 2nd Floor)
2:30 pm - 4:00 pm

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Exhibition Wed, 15 Feb 2023 15:13:57 -0500 2023-02-16T10:30:00-05:00 2023-02-16T16:00:00-05:00 Michigan League Office of Research School of Dentistry Exhibition Research Day 2023
DCM&B Tools and Technology Seminar (February 16, 2023 12:00pm) https://events.umich.edu/event/101960 101960-21802992@events.umich.edu Event Begins: Thursday, February 16, 2023 12:00pm
Location: Palmer Commons
Organized By: DCMB Tools and Technology Seminar

Accurate intraoperative diagnosis is essential for providing safe and effective care during brain tumor surgery. Our standard-of-care diagnostic methods are time, resource, and labor intensive, which restricts access to optimal surgical treatments. To address these limitations, we propose an alternative workflow that combines stimulated Raman histology (SRH), a rapid optical imaging method, with deep learning-based automated interpretation of SRH images for intraoperative brain tumor diagnosis and real-time surgical decision support. Here, we present OpenSRH, the first public dataset of clinical SRH images from 300+ brain tumors patients and 1300+ unique whole slide optical images. OpenSRH contains data from the most common brain tumors diagnoses, full pathologic annotations, whole slide tumor segmentations, raw and processed optical imaging data for end-to-end model development and validation. We provide a framework for patch-based whole slide SRH classification and inference using weak (i.e. patient-level) diagnostic labels. Finally, we benchmark two computer vision tasks: multiclass histologic brain tumor classification and patch-based contrastive representation learning. We hope OpenSRH will facilitate the clinical translation of rapid optical imaging and real-time ML-based surgical decision support in order to improve the access, safety, and efficacy of cancer surgery in the era of precision medicine.

Tool Link: https://opensrh.mlins.org/

This presentation will be held in 2036 Palmer Commons. There will also be a remote viewing option via Zoom.

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Presentation Thu, 08 Dec 2022 11:39:51 -0500 2023-02-16T12:00:00-05:00 2023-02-16T13:00:00-05:00 Palmer Commons DCMB Tools and Technology Seminar Presentation
Biomechanics of the Femoropopliteal Artery in the Lower Limb (February 16, 2023 3:30pm) https://events.umich.edu/event/104391 104391-21808995@events.umich.edu Event Begins: Thursday, February 16, 2023 3:30pm
Location: Cooley Building
Organized By: Biomedical Engineering

Abstract:
Despite years of technological and pharmacological improvements, failure rates remain high for the lower extremity peripheral arterial disease repairs, particularly when the repair devices cross the knee joint. Though much work has been done investigating the pathological processes associated with this failure, the underlying mechanisms remain insufficiently understood. The main arterial segment within the leg, the femoropopliteal artery, appears to be significantly different from other peripheral arteries due to lower blood flow and large deformations experienced during flexion of the limbs. Understanding the magnitude of these deformations in different postures and arterial segments may help improve repair devices through benchtop and computational studies of device-artery interactions. These studies rely on comprehensive assessments of arterial mechanics and structure and call for innovative ways of accounting for patient demographics and risk factors to deliver realistic results. We will summarize our findings related to the quantification of the biomechanical environment of the lower limb arteries, describe their structure and mechanical properties in the context of age and disease, present in vitro and computational frameworks to evaluate device-artery interactions, and introduce a preclinical animal model to assess the performance of new endovascular and open surgical repairs for the lower extremity.​​​​​​​

Bio:
Dr. Kamenskiy earned his Ph.D. in Engineering Mechanics from the University of Nebraska-Lincoln, and started his academic career as an Assistant Professor in the Department of Surgery at the University of Nebraska Medical Center. After advancing through the academic ranks and receiving tenure in Surgery, Dr. Kamenskiy joined the Department of Biomechanics at the University of Nebraska at Omaha, where he currently serves as Department Chair. In his research, Dr. Kamenskiy integrates Biomechanics and Medicine using in vivo, ex vivo, in vitro, and in silico methods. His lab is interested in vascular mechanophysiology, mechanobiology, and aging and closely collaborates with vascular surgeon-scientists who share the goal of developing practical solutions to improve clinical outcomes for vascular disease patients. Dr. Kamenskiy has assembled one of the largest databases of human artery mechanical, structural, and demographic characteristics that includes well over 1,000 specimens 12 to 99 years old. This database is a unique resource for understanding the complex and diverse pathology of human blood vessels. In addition to studying ex vivo arteries, the team of Dr. Kamenskiy also utilizes cell and organ culture systems and large animal models to explore the disease pathways they observe in human tissues. This research is accompanied by designing, modeling, and testing of new vascular and endovascular repair materials and devices for various vascular pathologies and trauma that his team carries out using bench-top, porcine, human cadaver, and clinical experiments.

Zoom:
https://umich.zoom.us/j/91712262512

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Workshop / Seminar Wed, 01 Feb 2023 17:33:02 -0500 2023-02-16T15:30:00-05:00 2023-02-16T16:30:00-05:00 Cooley Building Biomedical Engineering Workshop / Seminar BME Seminar Series
Advancing Environmental Health and Justice: A Call for Assessment and Oversight of Health Care Waste (February 21, 2023 12:00pm) https://events.umich.edu/event/104385 104385-21808988@events.umich.edu Event Begins: Tuesday, February 21, 2023 12:00pm
Location: Off Campus Location
Organized By: Michigan Lifestage Environmental Exposures and Disease Center

ZOOM registration required https://bit.ly/3WuZkDc
Please join us on Zoom (12-12:50 pm) for a Residents & Researchers 'Tuesday Talks at 12' webinar on environment, health and community.

Featuring Panelists: Vincent Martin (V Martin Environmental Justice LLC, Detroit), Omega Wilson (West End Revitalization Assoc., NC) and Denise Patel (NYC human rights and environmental activist). Moderated by Natalie Sampson (University of Michigan, Dearborn).

Recordings of previous webinars in the series can be viewed at https://www.google.com/url?q=https://mleead.umich.edu/Video.php&sa=D&source=calendar&ust=1673977514528131&usg=AOvVaw2wZZ1JKlOsDtcxD7N0jzZL

Organized by the Community Engagement Core (CEC) and the Integrated Health Sciences Core (IHSC) of the Michigan Lifestage Environmental Exposures and Disease Center (M-LEEaD).

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Livestream / Virtual Thu, 02 Feb 2023 10:12:56 -0500 2023-02-21T12:00:00-05:00 2023-02-21T12:50:00-05:00 Off Campus Location Michigan Lifestage Environmental Exposures and Disease Center Livestream / Virtual Residents & Researchers Tuesday Talks
LHS Collaboratory Joint Session with UM School of Dentistry (February 21, 2023 12:00pm) https://events.umich.edu/event/102701 102701-21805007@events.umich.edu Event Begins: Tuesday, February 21, 2023 12:00pm
Location: Off Campus Location
Organized By: Department of Learning Health Sciences

“The Future is Data Analytics: Many Challenges, Many Opportunities”

Keynote Speaker:

Lawrence A. Tabak, DDS, PhD
Director
National Institutes of Health (NIH)

Register in advance via Zoom Webinar: https://umich.zoom.us/webinar/register/WN_GyKMMpgVQHu2ezvxaJfZEA#/registration

12:00 pm-1:15 pm ET (Keynote)

1:30 pm-2:15 pm ET (Breakout rooms)

The keynote presentation (12:00 pm-1:15 pm ET) will be followed by breakout rooms (1:30 pm-2:15 pm ET) on topics presented by the UM faculty and guests.

Opening Remarks:
Laurey McCauley, DDS, MS, PHD

Breakout room #1: Data Integration and Sharing: Opportunities in Entrepreneurship and Research

Wenyuan Shi, PhD
Presentation: Building the Eco-system to Support Disruptive Technologies in Dentistry

Christopher Balaban, DMD, MSC, FACD
Presentation: Entrepreneurship and AI/LHS in Dentistry

Breakout room # 2 Data Integration and Sharing in/out of the Clinic: New Medical and Dental technologies and LHS methods to optimize care

Alexandre F. M. DaSilva, DDS, DMedSc
Presentation: Integrating and Sharing Dental and Medical Data in a Diverse Ecosystem – The Learning Health Systems Perspective

Muhammad F. Walji, PhD
Presentation: BigMouth: Lessons Learned from a Decade of Sharing EHR Data in Dentistry

Breakout room #3: Data Integration and Sharing in Imaging and Pharmacogenetics

Lucia Cevidanes, DDS, MS, PhD
Presentation: Innovations in Multimodal Imaging Data Integration and Sharing

Amy Pasternak, PharmD
Presentation: Integrating Pharmacogenomics into Daily Practice

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Livestream / Virtual Thu, 26 Jan 2023 23:22:37 -0500 2023-02-21T12:00:00-05:00 2023-02-21T14:00:00-05:00 Off Campus Location Department of Learning Health Sciences Livestream / Virtual LHS Collaboratory logo
DCM&B Tools and Technology Seminar (February 23, 2023 12:00pm) https://events.umich.edu/event/101961 101961-21802993@events.umich.edu Event Begins: Thursday, February 23, 2023 12:00pm
Location: Palmer Commons
Organized By: DCMB Tools and Technology Seminar

The analysis of spatially resolved transcriptome enables the understanding of the spatial interactions between the cellular environment and transcriptional regulation. In particular, the characterization of the gene–gene co-expression at distinct spatial locations or cell types in the tissue enables delineation of spatial co-regulatory patterns as opposed to standard differential single gene analyses. To enhance the ability and potential of spatial transcriptomics technologies to drive biological discovery, we develop a statistical framework to detect gene co-expression patterns in a spatially structured tissue consisting of different clusters in the form of cell classes or tissue domains. We develop SpaceX (spatially dependent gene co-expression network), a Bayesian methodology to identify both shared and cluster-specific co-expression network across genes. SpaceX uses an over-dispersed spatial Poisson model coupled with a high-dimensional factor model which is based on a dimension reduction technique for computational efficiency. We show via simulations, accuracy gains in co-expression network estimation and structure by accounting for (increasing) spatial correlation and appropriate noise distributions. In-depth analysis of two spatial transcriptomics datasets in mouse hypothalamus and human breast cancer using SpaceX, detected multiple hub genes which are related to cognitive abilities for the hypothalamus data and multiple cancer genes (e.g. collagen family) from the tumor region for the breast cancer data.

Tool Link: https://satwikach.github.io/SpaceX.github.io/
Tool Link: https://github.com/bayesrx/SpaceX

Associated Article: https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btac645/6731919

Supplementary File: https://bookdown.org/satwik91/SpaceX_supplementary/

This presentation will be held in 2036 Palmer Commons. There will also be a remote viewing option via Zoom.

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Presentation Thu, 08 Dec 2022 11:46:58 -0500 2023-02-23T12:00:00-05:00 2023-02-23T13:00:00-05:00 Palmer Commons DCMB Tools and Technology Seminar Presentation
Oral Health Sciences Seminar Series (February 23, 2023 12:00pm) https://events.umich.edu/event/103551 103551-21807463@events.umich.edu Event Begins: Thursday, February 23, 2023 12:00pm
Location: Dental & W.K. Kellogg Institute
Organized By: Office of Research School of Dentistry

Seminar Title: "The Non-coding Genome: Sequence, Form, and Function"

Sudha Rajderkar, BDS, MS, PhD
Postdoctoral Fellow
Environmental Genomics and Systems Biology
Lawrence Berkeley National Laboratory

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Workshop / Seminar Tue, 17 Jan 2023 15:37:08 -0500 2023-02-23T12:00:00-05:00 2023-02-23T13:00:00-05:00 Dental & W.K. Kellogg Institute Office of Research School of Dentistry Workshop / Seminar Sudha Rajderkar, BDS, MS, PhD _ Postdoctoral Fellow Environmental Genomics and Systems Biology Lawrence Berkeley National Laboratory
Dissecting a post-translational modification code in cardiac reprogramming (February 23, 2023 3:30pm) https://events.umich.edu/event/105100 105100-21810752@events.umich.edu Event Begins: Thursday, February 23, 2023 3:30pm
Location: Cooley Building
Organized By: Biomedical Engineering

Abstract:
Cell fate conversion is associated with extensive epigenetic and post translational modifications (PTMs) and architectural changes of sub-organelles and organelles, yet how these events are interconnected remains unknown. We report here the identification of a phosphorylation code in 14-3-3 binding motifs (PC14-3-3) that greatly stimulates induced cardiomyocyte (iCM) formation from fibroblasts. PC14-3-3 was identified in pivotal functional proteins for iCM reprogramming, including transcription factors and epigenetic factors. Akt1 kinase and PP2A phosphatase were a key writer and eraser of the PC14-3-3 code, respectively. PC14-3-3 activation induces iCM formation with the presence of only Tbx5. In contrast, PC14-3-3 inhibition by mutagenesis or inhibitor-mediated code removal abolished reprogramming. We discovered that key PC14-3-3 embedded factors, such as Hdac4, Mef2c, Nrip1, and Foxo1, formed Hdac4 organized inhibitory nuclear condensates. Notably, PC14-3-3 activation disrupted Hdac4 condensates to promote cardiac gene expression. Our study suggests that sub-organelle dynamics regulated by a post-translational modification code could be a general mechanism for stimulating cell reprogramming and organ regeneration.

Bio:
Dr. Zhong Wang is an Associate Professor of Cardiac Surgery, at the University of Michigan Medical School. The long-term goal of the Wang laboratory is to develop heart therapies to effectively prolong and improve the life of patients with cardiovascular disease. The Wang laboratory has made significant progress in four research directions. One research direction is to define the epigenetic mechanism mediated by ATP-dependent chromatin remodeling in cardiac progenitor specification and differentiation. Direction two is to define essential cross-talks between energy metabolism and epigenetics in heart repair and regeneration. Direction three is to identify epigenetic and post-translational modification mechanism and related molecules in stimulating reprogramming of fibroblasts into cardiomyocytes for heart regeneration. And direction four is to explore novel strategies combining optimal cardiovascular cell types and bioengineering/biomaterials for heart cell therapy.

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Workshop / Seminar Fri, 17 Feb 2023 12:33:28 -0500 2023-02-23T15:30:00-05:00 2023-02-23T16:30:00-05:00 Cooley Building Biomedical Engineering Workshop / Seminar BME Seminar Series
Developing Teacher Empathy – A Journey of Three Engineering Faculty Members Implementing Empathetic Actions in their Classroom (March 7, 2023 10:30am) https://events.umich.edu/event/105424 105424-21811742@events.umich.edu Event Begins: Tuesday, March 7, 2023 10:30am
Location: Duderstadt Center
Organized By: Engineering Education Research

In higher education, teacher empathy is a term that refers to the empathetic skills of teachers and has been researched since the 1980s. Multiple studies in fields such as medicine, nursing and psychology have shown that teacher empathy has reduced teacher burnout, improved teacher satisfaction and student performance. Within engineering education, there is increased research on empathy in recent years, but primarily aimed at introducing and improving empathetic skills of engineering students. There is very little research on teacher empathy within engineering education. In my current study, I explored the potential changes in perception of teacher empathy among three engineering faculty members as they utilized empathetic actions while teaching a second-year engineering course. I also explored the motivations and challenges that could arise in teacher empathy implementation. The outcome of this study could be used by faculty development programs, department heads and university deans to expand the implementation of teacher empathy within a college or university.

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Workshop / Seminar Fri, 24 Feb 2023 12:19:05 -0500 2023-03-07T10:30:00-05:00 2023-03-07T12:00:00-05:00 Duderstadt Center Engineering Education Research Workshop / Seminar Bala Vignesh Sundaram
DCM&B Tools and Technology Seminar (March 9, 2023 12:00pm) https://events.umich.edu/event/101988 101988-21803144@events.umich.edu Event Begins: Thursday, March 9, 2023 12:00pm
Location: Palmer Commons
Organized By: DCMB Tools and Technology Seminar

Tool link: https://pytorch.org/

This presentation will be held in 2036 Palmer Commons. There will also be a remote viewing option via Zoom.

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Presentation Fri, 09 Dec 2022 09:29:56 -0500 2023-03-09T12:00:00-05:00 2023-03-09T13:00:00-05:00 Palmer Commons DCMB Tools and Technology Seminar Presentation
Oral Health Sciences Seminar Series (March 9, 2023 12:00pm) https://events.umich.edu/event/103552 103552-21807464@events.umich.edu Event Begins: Thursday, March 9, 2023 12:00pm
Location: Dental & W.K. Kellogg Institute
Organized By: Office of Research School of Dentistry

Seminar Title: "Determining Sox10-mediated plasticity in irradiated salivary gland cells"

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Workshop / Seminar Tue, 17 Jan 2023 15:54:39 -0500 2023-03-09T12:00:00-05:00 2023-03-09T13:00:00-05:00 Dental & W.K. Kellogg Institute Office of Research School of Dentistry Workshop / Seminar Christina E. Jones _ DDS/Ph.D. Candidate, Lombaert Lab
Vascular-targeted Nanoparticles to Protect the Endothelium from Immune-mediated Injury (March 9, 2023 3:30pm) https://events.umich.edu/event/105816 105816-21812997@events.umich.edu Event Begins: Thursday, March 9, 2023 3:30pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Abstract: In solid organ transplantation, the host immune system acts to reject the transplanted graft. This process is facilitated at the graft endothelial surface, where inflamed endothelial cells (ECs) upregulate adhesion molecules and recruit effector cells of the host immune system. To combat this dysfunctional inflammation locally and with more impact than globally administered therapies, anti-inflammatory agents can be administered directly to the graft endothelium. We have designed a strategy for local and sustained delivery of these agents using molecularly-targeted polymer nanoparticles (NPs) during a period of ex vivo normothermic machine perfusion (EVNMP) of the organ. I will present several approaches for therapeutic delivery using polymeric NPs as well as strategies to direct NPs using molecular targets to the ECs of interest. We have discovered that rapid accumulation of NPs on ECs relies on both the density and accessibility of the potential ligands, and that these parameters can be measured directly in the relevant human vessel setting. The experiments we have conducted within these platforms are being used to develop a high throughput preclinical approach to optimize immune therapy for local and robust treatment in human organ transplant.

Bio: I joined the faculty at Villanova University in the fall of 2022 in the Department of Chemical and Biological Engineering. I am continuing my research into NP-based therapeutic delivery to human vasculature and integrating these strategies with tissue-engineering to create tools for long-term immune modulation. Specifically, materials that provide support for tissue regrowth while temporarily inhibiting inflammation-related injury, thus reducing the burden of chronic inflammation. My work presented here today was done as a Postdoctoral Fellow in Biomedical Engineering at Yale University as part of Dr. W. Mark Saltzman’s research group. In my graduate work, I developed vascular, tissue engineered constructs using a combination of biological and synthetic materials at the University of Maryland with Dr. John Fisher in Bioengineering.

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Workshop / Seminar Mon, 06 Mar 2023 17:21:36 -0500 2023-03-09T15:30:00-05:00 2023-03-09T16:30:00-05:00 Off Campus Location Biomedical Engineering Workshop / Seminar BME Seminar Series
DCM&B Tools and Technology Seminar - CANCELED (March 16, 2023 12:00pm) https://events.umich.edu/event/101989 101989-21803145@events.umich.edu Event Begins: Thursday, March 16, 2023 12:00pm
Location: Off Campus Location
Organized By: DCMB Tools and Technology Seminar

Today's Tools and Technology Seminar has been canceled.

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Presentation Tue, 21 Feb 2023 09:51:11 -0500 2023-03-16T12:00:00-04:00 2023-03-16T13:00:00-04:00 Off Campus Location DCMB Tools and Technology Seminar Presentation
Automated Design to Engineer Organisms: Scaling up Synthetic Biology to Tackle Humanity's Challenges (March 16, 2023 3:30pm) https://events.umich.edu/event/106090 106090-21813703@events.umich.edu Event Begins: Thursday, March 16, 2023 3:30pm
Location: Cooley Building
Organized By: Biomedical Engineering

Automated Design to Engineer Organisms: Scaling up Synthetic Biology to Tackle Humanity's Challenges

Abstract:
Organism engineering is the bedrock of biotechnology from producing high-value products (enzymes, materials, therapeutics) to developing cell therapies. With the latest techniques in DNA synthesis and assembly, it is now possible to construct large genetic systems with (just about) any DNA sequence of interest, enabling one to engineer sophisticated genetic systems inside cells with many genetic parts. Engineered genetic systems can act as sensors, circuits, and actuators to detect environmental states and autonomously act to change them, for example, probiotic bacteria that sense body temperatures to activate the expression of enzymes that treat metabolic diseases. However, it remains highly challenging to build such genetic systems with high-performance behaviors; there are many “tunable knobs” and inter-dependent interactions that create a “curse of dimensionality” with cryptic (unaccounted for) effects. To overcome these challenges, new approaches are needed that parallel the development of a modern engineering discipline centered around organism engineering.

Specifically, we show that it is now possible to rationally engineer genetic systems by combining predictive models of gene expression together with sequence design algorithms. Our models utilize statistical thermodynamics, kinetics, and machine learning to predict how DNA sequence controls transcription rates, translation rates, mRNA decay rates, gene regulation, and more. Leveraging these model predictions, we automate the design of genetic parts and systems (long DNA sequences) using multi-objective optimization to ensure the engineered organisms have the desired specifications (maximizing target functions, while minimizing undesired behaviors). To develop and test these models, we utilize the latest advances in oligopool synthesis, library-based cloning, and next-generation sequencing to carry out thousands of defined experiments per workflow. We illustrate our rational design approach with several recent applications, including engineering genetic systems to sense-and-respond to human biomarker proteins inside cell-free assays for medical diagnostics and engineering genetic systems to sense-and-respond to TNT inside soil systems for countermine detection.

We have also developed an interactive web-based design platform for engineering organisms, which now has over 10000 registered researchers who have designed over 900,000 genetic systems for diverse biotech applications (medical, industrial, agricultural, defense). The platform provides a “no-code” interface to our suite of predictive models & design algorithms, enabling its broad usage by the community. Altogether, these efforts demonstrate that physiochemical models can indeed predict biological functions with sufficient accuracy to automatically design genetic systems with high performance behaviors.

Bio:
Prof. Howard Salis is an Associate Professor in the Biological Engineering, Chemical Engineering, and Biomedical Engineering departments at Penn State University. He is also a member of the Bioinformatics & Genomics and Molecular, Cellular, & Integrative Biosciences graduate programs. Prof. Salis’ expertise is in the design & engineering of genetic systems in microbial organisms for diverse biotech applications (industrial, medical, agricultural, defense). His lab’s mission is to co-develop a new engineering discipline for biology through the development of predictive models & design algorithms that circumvent the need for trial-and-error experimentation. To develop and test these approaches, his lab carries out thousands of defined experiments per workflow utilizing the latest in oligopool synthesis and next-generation sequencing. Prof. Salis has received the DARPA Young Faculty award and the NSF CAREER award for his achievements. He is also the founder of De Novo DNA, which runs a web-based design platform for engineering organisms, used by over 10000 researchers to design over 900000 genetic systems for diverse biotech applications. Prof. Salis earned his B.S. in Chemical Engineering from Rutgers University (2002) and his Ph.D. in Chemical Engineering from the University of Minnesota (2007). He was a postdoc at UCSF with Chris Voigt (2007-2009). He joined Penn State University in 2010.

Zoom:
https://umich.zoom.us/j/91712262512

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Workshop / Seminar Sat, 11 Mar 2023 21:25:37 -0500 2023-03-16T15:30:00-04:00 2023-03-16T16:30:00-04:00 Cooley Building Biomedical Engineering Workshop / Seminar BME Seminar Series
Starting With Self, Then Towards Others: How Students Engage With Empathy in Community-Based Learning (March 21, 2023 10:30am) https://events.umich.edu/event/106180 106180-21813895@events.umich.edu Event Begins: Tuesday, March 21, 2023 10:30am
Location: Lurie Robert H. Engin. Ctr
Organized By: Engineering Education Research

This seminar contributes to a recent movement in engineering education, calling attention to fostering more engineering students to develop social awareness to solve complex problems in the real world. As many engineering problems raised in a community can be related to addressing social issues, community-based learning (CBL) has become a way to educate more empathic engineers. However, there is an ethical consideration in CBL as the outcome of student learning can impact a real-world community partner. Therefore, it is critical to understand how students engage with empathy in CBL to commit to the community’s needs authentically before implementation.

In this seminar, I will share some qualitative findings from my dissertation study focusing on how students shift between the roles of “self” and “others” in the process of engaging with empathy in CBL. I also investigated different types of opportunities to expose students to empathy in CBL, such as structural opportunities (how the CBL activity is organized), social opportunities (how students are guided to work with others), and reflective opportunities (how students think about what they have learned). The seminar concludes with practical recommendations for engineering educators to understand how to support students to engage with empathy in community-based learning contexts.

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Workshop / Seminar Tue, 14 Mar 2023 11:46:25 -0400 2023-03-21T10:30:00-04:00 2023-03-21T12:00:00-04:00 Lurie Robert H. Engin. Ctr Engineering Education Research Workshop / Seminar Dr. Linjue (Jade) Wang
DCMB / CCMB Weekly Seminar Series (March 22, 2023 4:00pm) https://events.umich.edu/event/105990 105990-21813376@events.umich.edu Event Begins: Wednesday, March 22, 2023 4:00pm
Location: Palmer Commons
Organized By: DCMB Seminar Series

Abstract is forthcoming.

Bio:
As the Vice President of R&D - Biologics, Dr. Lakmal Jayasinghe oversees all biological research and development projects at Oxford Nanopore. Lakmal joined ONT in 2006 after finishing his PhD in chemical biology in the University of Oxford. During his PhD in the Hagan Bayley group, Lakmal has studied different nanopores and has gained a wealth of knowledge in engineering nanopores using genetic and chemical approaches. His responsibilities at ONT include improving the readout signal of ONT platforms by upgrading its current nanopore reader and motor, as well as discovering new versions of nanopores, motors and chemistries to suit various ONT applications including protein sequencing. Lakmal also works with many academic collaborators across the world to ensure that Oxford Nanopore uses the best possible biological components and chemistries in its platforms.

https://umich-health.zoom.us/j/93929606089?pwd=SHh6R1FOQm8xMThRemdxTEFMWWpVdz09

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Lecture / Discussion Thu, 09 Mar 2023 09:29:41 -0500 2023-03-22T16:00:00-04:00 2023-03-22T17:00:00-04:00 Palmer Commons DCMB Seminar Series Lecture / Discussion Dr. Lakmal Jayasinghe, VP – R&D Biologics at Oxford Nanopore Technologies plc, UK
DCM&B Tools and Technology Seminar (March 23, 2023 12:00pm) https://events.umich.edu/event/101990 101990-21803146@events.umich.edu Event Begins: Thursday, March 23, 2023 12:00pm
Location: Palmer Commons
Organized By: DCMB Tools and Technology Seminar

Tool link: https://github.com/styvon/TAPE

Associated article: https://doi.org/10.1093/bioinformatics/btac459

This presentation will be given remotely, with the livestream available for group viewing in 2036 Palmer Commons. There will also be a remote viewing option via Zoom.

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Presentation Fri, 09 Dec 2022 09:39:08 -0500 2023-03-23T12:00:00-04:00 2023-03-23T13:00:00-04:00 Palmer Commons DCMB Tools and Technology Seminar Presentation
LHS Collaboratory (March 23, 2023 12:00pm) https://events.umich.edu/event/105035 105035-21810617@events.umich.edu Event Begins: Thursday, March 23, 2023 12:00pm
Location: Off Campus Location
Organized By: Department of Learning Health Sciences

Speaker:
Thomas R. Campion, Jr., Ph.D., FACMI, FAMIA
Chief Research Informatics Officer
Associate Professor of Research in Population Health Sciences
Weill Cornell Medicine

Clinical and translational investigators need patient data, especially from electronic health record (EHR) systems, to conduct research, but optimal approaches are unknown. This talk explores an approach for supporting different types of investigators and study designs by matching investigators with informatics tools and services.

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Lecture / Discussion Wed, 15 Feb 2023 23:51:27 -0500 2023-03-23T12:00:00-04:00 2023-03-23T13:30:00-04:00 Off Campus Location Department of Learning Health Sciences Lecture / Discussion LHS Collaboratory logo
Oral Health Sciences Seminar Series (March 23, 2023 12:00pm) https://events.umich.edu/event/106211 106211-21813928@events.umich.edu Event Begins: Thursday, March 23, 2023 12:00pm
Location: Off Campus Location
Organized By: Office of Research School of Dentistry

Title: "Supporting Translational Genomics and Data Science Research in Dental, Oral, and Craniofacial Biology and Health"

Lu Wang, Ph.D.
Chief of Translational Genomics Research Branch
National Institute of Dental and Craniofacial Research
National Institutes of Health

Via Zoom: https://www.google.com/url?q=https://umich.zoom.us/j/91090112919?pwd%3DL3RQN0JnZE9wZnAycjVJOW1KRGV0UT09&sa=D&source=calendar&ust=1679324173466632&usg=AOvVaw1eiT5nwLbG8ZhbdkPWQO_p

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Workshop / Seminar Wed, 15 Mar 2023 11:01:38 -0400 2023-03-23T12:00:00-04:00 2023-03-23T13:00:00-04:00 Off Campus Location Office of Research School of Dentistry Workshop / Seminar March 23, 2023 Lu Wang, Ph.D.
Exploring Early Origins of Cognitive Decline: The St. Louis Baby Teeth Study (March 23, 2023 3:00pm) https://events.umich.edu/event/106124 106124-21813784@events.umich.edu Event Begins: Thursday, March 23, 2023 3:00pm
Location: Public Health I (Vaughan Building)
Organized By: Michigan Lifestage Environmental Exposures and Disease Center

Please join us in-person for a seminar highlighting environmental research. Marc Weisskopf's research interests mostly come from his background in neurobiology. He is interested in how environmental factors affect the nervous system, as well as the epidemiology of neurologic disorders. Current areas of his work include how environmental exposures relate to:
* Autism Spectrum Disorders (ASD)
* Attention Deficit/Hyperactivity Disorder (ADHD)
* Mental health
* Cognitive function/Alzheimer’s disease (AD)
* Amyotrophic lateral sclerosis (ALS)
Some examples of his current work include exploring how exposure to toxicants (e.g., lead, manganese, and air pollution) affect cognitive function and psychiatric symptoms; how air pollution and other toxicants relate to autism spectrum disorder (ASD); and how toxicant exposures like formaldehyde and lead relate to the development of amyotrophic lateral sclerosis (ALS). In addition, he has a large study in Israel and Denmark to explore the relationship of currently used medications to ALS. He is also very interested in issues of epidemiological methods and causal inferences as they relate to his work.

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Lecture / Discussion Mon, 13 Mar 2023 13:59:45 -0400 2023-03-23T15:00:00-04:00 2023-03-23T16:00:00-04:00 Public Health I (Vaughan Building) Michigan Lifestage Environmental Exposures and Disease Center Lecture / Discussion Marc Weisskopf lecture on early origins of cognitive decline taking place March 23rd at 3pm
Dynamic communication networks between regulatory T cells and mesenchymal stromal cells regulate muscle repair and regeneration (March 23, 2023 3:30pm) https://events.umich.edu/event/106476 106476-21814329@events.umich.edu Event Begins: Thursday, March 23, 2023 3:30pm
Location: Cooley Building
Organized By: Biomedical Engineering

Abstract:

Tissue repair and regeneration require a temporally coordinated immune response to clear affected areas and rebuild tissue architecture. To study the dynamic regulation of muscle repair, we generated a time-resolved single-cell RNA sequencing dataset of regulatory T cells (Tregs) and mesenchymal stromal cells (MSCs) in a mouse model of skeletal muscle injury. We built a computational tool to predict the dynamic cellular communication networks between these cell types and found distinct communication pathways during different phases of repair. Using a combination of in vivo CRISPR and genetic mouse models, we validated these interactions and identified novel communication pathways that regulate tissue regeneration.



Short Bio:

Dr. Andrés Muñoz-Rojas is originally from Mexico City. He has a degree in Bioengineering from the University of Pennsylvania. Andrés got his PhD in Biomedical Engineering at Yale University, where he worked with Dr. Kathryn Miller-Jensen using single-cell secretion and transcription technologies to study macrophage polarization in vitro and in tumor microenvironments. He then joined the lab of Diane Mathis at Harvard Medical School as a Postdoctoral Fellow to study tissue immunology and explore the role of Tregs in regulating tissue function.

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Workshop / Seminar Mon, 20 Mar 2023 13:37:03 -0400 2023-03-23T15:30:00-04:00 2023-03-23T16:30:00-04:00 Cooley Building Biomedical Engineering Workshop / Seminar BME Seminar Series
Integrative Systems + Design (ISD) Open House (March 24, 2023 2:00pm) https://events.umich.edu/event/105246 105246-21811448@events.umich.edu Event Begins: Friday, March 24, 2023 2:00pm
Location: Chrysler Center
Organized By: Integrative Systems + Design

Integrative Systems + Design OPEN HOUSE for Prospective Graduate Students
March 24, 2023
2:00 PM - 3:30 PM
-Learn about our top-ranked interdisciplinary graduate programs
-Browse courses that are available on campus and online
-Explore Sequential Undergraduate/Graduate Study (SUGS), which allows eligible undergrads to double-count certain courses toward an advanced degree

Our six graduate programs include dual degrees, SUGS, master's and doctoral degrees in

-Automotive Engineering (MEng)
-Energy Systems Engineering (MEng)
-Manufacturing Engineering (MEng and DEng)
-Systems Engineering and Design (MEng)
-Global Automotive & Manufacturing Engineering (MEng)
-Design Science (MS and Ph.D.)

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Reception / Open House Tue, 21 Feb 2023 10:38:46 -0500 2023-03-24T14:00:00-04:00 2023-03-24T15:30:00-04:00 Chrysler Center Integrative Systems + Design Reception / Open House Open House
Exploring the Final Frontier (March 27, 2023 5:00pm) https://events.umich.edu/event/106672 106672-21814683@events.umich.edu Event Begins: Monday, March 27, 2023 5:00pm
Location: Chrysler Center
Organized By: Bioastronautics and Life Support Systems

Discover the final frontier and explore the possibilities of space science and bioastronautics with former Chief Scientist of the ISS, Dr. Kathryn Clark. On Monday, March 27th at 5pm, CHRYS220, join BLiSS in welcoming Dr. Clark to North Campus for an engaging presentation on her experience in the field. This is an incredible opportunity to learn about cutting-edge research and technology in space science, and to gain insight into the challenges of living and working in space. Don't miss out on this chance to expand your horizons and engage with one of the leading experts in the field. The presentation will run until 6:30pm, with a Q&A section for students to ask questions and further explore the topic.

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Lecture / Discussion Fri, 24 Mar 2023 13:12:01 -0400 2023-03-27T17:00:00-04:00 2023-03-27T18:30:00-04:00 Chrysler Center Bioastronautics and Life Support Systems Lecture / Discussion Event Poster
DCMB Weekly Seminar (March 29, 2023 4:00pm) https://events.umich.edu/event/106625 106625-21814590@events.umich.edu Event Begins: Wednesday, March 29, 2023 4:00pm
Location: Palmer Commons
Organized By: DCMB Seminar Series

Abstract:
In 1996, Dr. Shilatifard identified the biochemical function of the Mixed Lineage Leukemia (MLL) gene translocation partner for the first time. The translocation partner, a gene called ELL, encodes an elongation factor: a protein that controls when, where and how fast the RNA Polymerase II transcription machinery can “read out” the instructions encoded in our genes. This discovery began a scientific journey to better understand elongation factors and other transcriptional control mechanisms, both in embryonic development and in cancer. Taking you along on this journey, Dr. Shilatifard will describe how he isolated all of the other MLL translocation partners in a “tour de force” application of biochemistry and molecular genetics, resulting in the astounding finding that these seemingly unrelated proteins actually function together within the (now widely known) Super Elongation Complex (SEC). In further research, the SEC emerged as a central factor regulating gene transcription at the elongation stage, and the lab has developed chemical compounds to disrupt or inhibit the Super Elongation Complex that are now in pre-clinical studies for the treatment of cancers caused by transcriptional defects. The story continues with his lab’s current research investigating how elongation factors, chromatin and the epigenome control transcription in human development and disease.

https://umich-health.zoom.us/j/93929606089?pwd=SHh6R1FOQm8xMThRemdxTEFMWWpVdz09

Bio:
Dr. Ali Shilatifard, Chairman and Professor of Biochemistry and Molecular Genetics and Professor of Pediatrics at Northwestern University Feinberg School of Medicine in Chicago, graduated from Kennesaw State University in 1989 with a degree in Chemistry with an emphasis in Organic Chemistry. While at KSU, Shilatifard slept in his car at night for a period in front of the gym and worked all over the campus from bussing tables at the student center, to cooking in the back kitchen, serving as the dispatch for the Kennesaw State College police department, and working as a TA in the Chemistry lab and Math lab to support himself and his education. He was supported by a full academic scholarship by KSU after his first year and graduated in four years. Now, Shilatifard is a renowned biochemist and cancer biologist. He made a seminal contribution to the field of leukemia biology early in his career by identifying the function of a gene translocation in childhood leukemia for the first time. In the 25 years since that discovery, he has dedicated his career to revealing the causes of childhood leukemia and other cancers and to leveraging these findings for the development of new cancer therapies. He currently runs an active research laboratory, heads a large department while he also is the Director of the Simpson Querrey Institute for Epigenetics. Shilatifard has authored over 250 scientific publications and is one of the founding members and is the current Editor of the online publication, Science Advances. He is one of the few scientists in the United States funded by the National Cancer Institute’s Outstanding Investigator Award, and in an effort to inspire young students to consider the STEM fields, he and his wife Laura started the Simpson Querrey Inspire Program.

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Lecture / Discussion Thu, 23 Mar 2023 09:13:22 -0400 2023-03-29T16:00:00-04:00 2023-03-29T17:00:00-04:00 Palmer Commons DCMB Seminar Series Lecture / Discussion Dr. Ali Shilatifard, Northwestern University Feinberg School of Medicine in Chicago
DCM&B Tools and Technology Seminar (March 30, 2023 12:00pm) https://events.umich.edu/event/101991 101991-21803147@events.umich.edu Event Begins: Thursday, March 30, 2023 12:00pm
Location: Off Campus Location
Organized By: DCMB Tools and Technology Seminar

Tool Link: https://github.com/piyuranjan/SNIKT

Associated Article: https://academic.oup.com/bioinformatics/article/38/15/3830/6607583

This presentation will be held in 2036 Palmer Commons. There will also be a remote viewing option via Zoom.

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Presentation Fri, 03 Feb 2023 14:35:14 -0500 2023-03-30T12:00:00-04:00 2023-03-30T13:00:00-04:00 Off Campus Location DCMB Tools and Technology Seminar Presentation
ASC UMAPS Colloquium Series. Inverse Heat Conduction, Cancer, Cultural Repository and Neonatal Health in Africa (March 30, 2023 2:00pm) https://events.umich.edu/event/105437 105437-21811848@events.umich.edu Event Begins: Thursday, March 30, 2023 2:00pm
Location: Weiser Hall
Organized By: African Studies Center

The Winter 2023 UMAPS Research Colloquium Series features the U-M African Presidential Scholars (UMAPS) fellows and their scholarly work. The talks prepared and presented by each visiting scholar are designed to promote dialogue on topics and to share their research with the larger U-M community.

Marissa Balmith (South Africa), “The Role of the estrogen receptor in breast cancer dormancy”
Marissa Balmith is a lecturer in pharmacology at the University of Pretoria, South Africa, and holds a PhD in pharmaceutical chemistry from the University of Kwa-Zulu Natal, South Africa. Her doctoral research focused on silico-molecular modeling and drug design on the Ebola virus, and her interest is in cancer metastasis. At Michigan, Marissa will work on a project titled “Molecular mediators of cancer metastasis,” with Max Wicha (Medical School) as her U-M host.

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Tesfaye Wondyifraw (Ethiopia), “The Newly Discovered Pre-historic Rock Art Paintings along the Valley of the Blue Nile”
Tesfaye Wondyifraw is a senior lecturer in the Department of History and Heritage Management at Debre Markos University, Ethiopia. He holds an MA degree in archeology from Addis Ababa University, Ethiopia. At Michigan, he will work with Brian Stewart (Anthropology, LSA) on a project titled “An Archaeological Study of Buahit Serit: A Newly Discovered Rock Art Site in East Gojjam, Northwestern Ethiopia.” The project will explore and evaluate this site and work toward the conservation of this endangered cultural repository.

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James Orwa (Kenya), “Comparison of machine learning and logistic regression as predictive models for adverse maternal outcomes of deliveries: A hospital-based retrospective study”
James Orwa is a senior instructor of biostatistics at Aga Khan University, Kenya. He received his MSc in biostatistics from Hasselt University, Belgium, and is currently enrolled in a PhD program in public health at Ghent University, Belgium. While at U-M, he will work with Akbar Waljee (Medical School) on a project relating to artificial intelligence/machine learning approaches for the identification of predictors of maternal, neonatal, and child health risks.

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Jean Pierre Ngendahayo (Rwanda), “Estimation of Surface Temperatures from Nonlinear Heat Conduction Models from Quenching Applications”
Jean Pierre Ngendahayo is an assistant lecturer in applied mathematics at the University of Rwanda. He holds MA and BA degrees in mathematics and statistics from the same university, where he is also currently pursuing a PhD. His research centers around mathematical modeling and scientific computing in the areas of epidemiological modeling and so-called “inverse problems.” At U-M, he will work on a project titled “The Solution of Two Dimensional Transient Inverse Heat Conduction Problem,” with U-M host Divakar Viswanath (Mathematics, LSA).


Register in advance at https://myumi.ch/Z37JP

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Lecture / Discussion Fri, 24 Feb 2023 18:19:51 -0500 2023-03-30T14:00:00-04:00 2023-03-30T16:00:00-04:00 Weiser Hall African Studies Center Lecture / Discussion UMAPS Winter 2023 Cohort presentation, group 1
Diagnosing disease on a microchip: Finding nanoscale needles in a nanoscale haystack (March 30, 2023 3:30pm) https://events.umich.edu/event/106711 106711-21814734@events.umich.edu Event Begins: Thursday, March 30, 2023 3:30pm
Location: Cooley Building
Organized By: Biomedical Engineering

Abstract: The transformative growth in microelectronics in the latter half of the 20th century was fueled fundamentally by the ability to miniaturize complex circuits onto chips. The impact of this has been profound– computing is pervasive and portable and communication is instant and global. My research aims to harness this same engineering approach to solve high impact problems in medical diagnostics. To accomplish this goal my lab develops hybrid microchips, where microfluidics are built directly on top of semiconductor chips. In this talk I will focus on recent work at Penn on 'digital asays.' Digital assays — in which ultra-sensitive molecular measurements are made by performing millions of parallel experiments in picoliter droplets — have generated enormous enthusiasm due to their single molecule resolution. These assays have incredible untapped potential for disease diagnostics but are currently confined to laboratory settings due to the instrumentation necessary to generate, control, and measure tens of millions of droplets. To overcome this challenge, we are developing a hybrid microelectronic / microfluidic chip to ‘unlock’ droplet-based assays for mobile use. Our microDroplet Fluorescence Detector (µDFD) takes inspiration from cellular networks, in which phones are identified by their carrier frequency and not their particular location. In collaboration with physicians at The Abramson Cancer Center, we are demonstrating the power of this approach by developing a multiplexed exosome-based diagnostic for the early detection of pancreatic cancer.

Bio: The Issadore lab combines microelectronics, microfluidics, nanomaterials, and machine learning to solve big problems in healthcare. We create miniaturized platforms for the diagnosis of disease, we develop new platforms to manufacture micro and nanomaterials, and we dip our toes into an assortment of other areas where we can leverage our engineering training to improve healthcare. This work requires an interdisciplinary approach in which engineers, scientists, and physicians work together in teams.

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Workshop / Seminar Sat, 25 Mar 2023 18:10:52 -0400 2023-03-30T15:30:00-04:00 2023-03-30T16:30:00-04:00 Cooley Building Biomedical Engineering Workshop / Seminar BME Seminar Series
1,000 Chemicals and their Combined Hormonal Bioactivities in Silicone Wristband Samplers (April 4, 2023 12:00pm) https://events.umich.edu/event/106127 106127-21813787@events.umich.edu Event Begins: Tuesday, April 4, 2023 12:00pm
Location: Off Campus Location
Organized By: Michigan Lifestage Environmental Exposures and Disease Center

*Registration required https://bit.ly/3kXGJCV
Anna Young, MS, PhD is a research associate in the Department of Environmental Health and Associate Director of the Healthy Buildings Program at the Harvard T.H. Chan School of Public Health. Her research focuses on our indoor exposures to complex mixtures of hormone-disrupting chemicals and builds evidence for healthier materials as a strategy to reduce these chemical exposures in buildings. She earned her PhD and MS in Environmental Health from the Harvard Chan School, and she also holds a BA in Computer Science and Environmental Studies from Yale University.

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Lecture / Discussion Mon, 13 Mar 2023 14:19:09 -0400 2023-04-04T12:00:00-04:00 2023-04-04T12:50:00-04:00 Off Campus Location Michigan Lifestage Environmental Exposures and Disease Center Lecture / Discussion Anna Young on chemicals and hormonal bioactivities on April 4, 2034, at 12:00 pm
DCMB Weekly Seminar (April 5, 2023 4:00pm) https://events.umich.edu/event/106871 106871-21814955@events.umich.edu Event Begins: Wednesday, April 5, 2023 4:00pm
Location: Palmer Commons
Organized By: DCMB Seminar Series

ABSTRACT:

Genomic rearrangements, also known as structural variations (SVs), are large scale alterations that changes the DNA structure. They include deletions, duplications, insertions, and other forms that are accompanied by copy number changes as well as inversions, translocations, and other copy-neutral forms. They are an important type of variation, affecting an order of magnitude more base pairs than single nucleotide variations (SNVs) in normal human population. In cancer, several chromosomal translocations have been identified and subsequently became targets of successful treatments. However, the functional impact of genomic rearrangements and their roles in treatment response are largely unexplored. We are developing new computational methods and exploring large scale cancer omics data to infer the mutational mechanisms leading to these alterations, to identify potential disease-driving events, and to study how they affect treatments.

https://umich-health.zoom.us/j/93929606089?pwd=SHh6R1FOQm8xMThRemdxTEFMWWpVdz09

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Livestream / Virtual Tue, 28 Mar 2023 12:21:44 -0400 2023-04-05T16:00:00-04:00 2023-04-05T17:00:00-04:00 Palmer Commons DCMB Seminar Series Livestream / Virtual
DCM&B Tools and Technology Seminar (April 6, 2023 12:00pm) https://events.umich.edu/event/101992 101992-21803148@events.umich.edu Event Begins: Thursday, April 6, 2023 12:00pm
Location: Palmer Commons
Organized By: DCMB Tools and Technology Seminar

This presentation will be held in 2036 Palmer Commons. There will also be a remote viewing option via Zoom.

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Presentation Thu, 23 Mar 2023 17:52:12 -0400 2023-04-06T12:00:00-04:00 2023-04-06T13:00:00-04:00 Palmer Commons DCMB Tools and Technology Seminar Presentation
Oral Health Seminar Series (April 6, 2023 12:00pm) https://events.umich.edu/event/103659 103659-21807611@events.umich.edu Event Begins: Thursday, April 6, 2023 12:00pm
Location: Dental & W.K. Kellogg Institute
Organized By: Office of Research School of Dentistry

Seminar Title: "A cost-effectiveness analysis of population-level dental caries prevention strategies in U.S. children"

Lisa Prosser, Ph.D.
Marilyn Fisher Blanch Research Professor of Pediatrics
Director, Susan B. Meister Child Health Evaluation and Research Center|
Associate Vice President for Research - Health Sciences, Office of the Vice President for Research
Professor, Department of Pediatrics, Medical School
Professor, Department of Health Management and Policy, School of Public Health
University of Michigan

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Workshop / Seminar Thu, 19 Jan 2023 10:13:12 -0500 2023-04-06T12:00:00-04:00 2023-04-06T13:00:00-04:00 Dental & W.K. Kellogg Institute Office of Research School of Dentistry Workshop / Seminar Dr. Prosser, April 6, 2023
Hallucinations and objective assessments of deep learning technologies for medical image formation (April 6, 2023 3:30pm) https://events.umich.edu/event/107076 107076-21815261@events.umich.edu Event Begins: Thursday, April 6, 2023 3:30pm
Location: Cooley Building
Organized By: Biomedical Engineering

Abstract:
A variety of deep learning-based image restoration and reconstruction methods, generically referred to as image formation methods, have been proposed for use with biomedical images. It is widely accepted that the assessment and refinement of biomedical imaging technologies should be performed by objective, i.e., task-based, measures of image quality (IQ). However, the objective evaluation of deep learning-based image formation technologies remains largely lacking, despite the breakneck speed at which they are being developed. As such, there is an ever-growing collection of methods whose utility and trustworthiness remains largely unknown. Moreover, such methods have the capability to ‘hallucinate’ false structures, which is of significant concern in medical imaging applications. In this work, we report studies in which the performance of deep learning-based image restoration methods is objectively assessed. The performance of the ideal observer (IO) and common linear numerical observers are quantified, and detection efficiencies are computed to assess the impact of deep learning image formation methods on signal detection performance. The numerical results indicate that, in the cases considered, the application of a deep image formation network can result in a loss of task-relevant information in the image, despite improvement in traditional computer-vision metrics. We also demonstrate that traditional and objective IQ measures can vary in opposite ways as a function of network depth. These results highlight the need for the objective evaluation of IQ for deep image formation technologies and may suggest future avenues for improving the effectiveness of medical imaging applications. 

Bio:
Dr. Mark Anastasio is the Donald Biggar Willett Professor in Engineering and the Head of the Department of Bioengineering at the University of Illinois at Urbana-Champaign (UIUC). Before joining UIUC in 2019, he was a Professor of Biomedical Engineering at Washington University in St. Louis, where he established one of the nation’s first stand-alone PhD programs in imaging science. Dr. Anastasio’s research accomplishments to the fields of biomedical imaging and image science have been numerous and impactful and his general interests broadly address the computational aspects of image formation, modern imaging science, and applied machine learning. He has conducted research in the fields of diffraction tomography, X-ray phase-contrast imaging, and ultrasound tomography. He one of the world’s leading authorities on photoacoustic computed tomography (PACT) and has made numerous and important contributions to development of PACT for over fifteen years. He has published over 175 peer-reviewed journal papers in leading imaging and optical science journals and was the recipient of a National Science Foundation (NSF) CAREER Award to develop image reconstruction methods. He is a Fellow of the American Institute for Medical and Biological Engineering (AIMBE), the International Academy of Medical and Biological Engineering (IAMBE) and the SPIE. He also served as the Chair of the NIH BMIT-B and EITA Study Sections.

Zoom:
https://umich.zoom.us/j/91712262512

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Workshop / Seminar Fri, 31 Mar 2023 14:53:29 -0400 2023-04-06T15:30:00-04:00 2023-04-06T16:30:00-04:00 Cooley Building Biomedical Engineering Workshop / Seminar BME Seminar Series
DCMB / CCMB Weekly Seminar (April 12, 2023 4:00pm) https://events.umich.edu/event/107182 107182-21815596@events.umich.edu Event Begins: Wednesday, April 12, 2023 4:00pm
Location: Palmer Commons
Organized By: DCMB Seminar Series

Abstract:

From the initial genetic patterning to the assembly of the whole embryo, how ordered structures form has always been a fundamental question in developmental biology. The recent advances in imaging technologies are now providing us with direct visual access to the development of whole organisms in unprecedented detail. However, it is clear that to make the best use of this complex data, we need the help of computer algorithms that can mine it for biologically relevant information, summarize and then visualize it for us. The first project I will present focuses on the mechanisms driving the development of diverse 3D bone morphologies in mice. There, we developed algorithms to analyze micro-CT images to deconstruct the final morphology of each bone into the contributions made by remodeling of mineralized tissue vs. the cartilaginous growth plates. This allowed us to demonstrate the central role of the growth plate in 3D bone morphogenesis in normal and pathological development. The second project aims to understand how different cell activities contribute to large-scale morphogenetic movements. To this end, we generated the first whole embryo single-cell atlas of morphogenetic activity underlying gastrulation in the fruit fly, then used these maps to derive a statistical model associating cell shape changes and rearrangements to body axis elongation.

https://umich-health.zoom.us/j/93929606089?pwd=SHh6R1FOQm8xMThRemdxTEFMWWpVdz09

Areas of Interest:

My lab focuses on understanding how cells organize to form various tissue morphologies during normal and pathological development. We use two model systems to achieve this: the musculoskeletal system in mice and whole embryo development in fruit flies. Our approach centers on the development of cutting-edge bioimage informatics and data science algorithms to analyze the dynamics and the underlying patterns in developing tissues through 3D and 4D (3D+time) fluorescence images.

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Lecture / Discussion Tue, 04 Apr 2023 09:15:53 -0400 2023-04-12T16:00:00-04:00 2023-04-12T17:00:00-04:00 Palmer Commons DCMB Seminar Series Lecture / Discussion
Oral Health Sciences Seminar Series (April 13, 2023 12:00pm) https://events.umich.edu/event/106285 106285-21814023@events.umich.edu Event Begins: Thursday, April 13, 2023 12:00pm
Location: Dental & W.K. Kellogg Institute
Organized By: Office of Research School of Dentistry

Seminar Title: Neurovascular bundle and its regulatory roles on mesenchymal stem cells in tissue homeostasis

Yang Chai, DDS, Ph.D.
University Professor
George and MayLou Boone Chair in Craniofacial Molecular Biology
Director, Center for Craniofacial Molecular Biology
Associate Dean of Research
Ostrow School of Dentistry
University of Southern California

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Workshop / Seminar Fri, 07 Apr 2023 14:28:51 -0400 2023-04-13T12:00:00-04:00 2023-04-13T13:00:00-04:00 Dental & W.K. Kellogg Institute Office of Research School of Dentistry Workshop / Seminar OHS Seminar Dr. Yang Chai April 13, 2023
Tracing molecules through space and time to understand and treat disease (April 13, 2023 3:30pm) https://events.umich.edu/event/107413 107413-21815977@events.umich.edu Event Begins: Thursday, April 13, 2023 3:30pm
Location: Cooley Building
Organized By: Biomedical Engineering

Abstract:
Metabolism is central to virtually all cellular functions and contributes to a range of diseases. A quantitative understanding of how biochemical pathways are dysregulated in the context of diseases such as cancer, metabolic syndrome, and neuropathy is necessary to identify new therapeutic targets. To this end we apply stable isotope tracers, mass spectrometry, and metabolic flux analysis (MFA) to study metabolism in mammalian cells, animal models, and human patients. We are particularly interested in understanding how amino acid and lipid metabolism are coordinated in the context of specific disease states. Serine, glycine and one carbon metabolism is critically important for cell function and health, but the amino acids associated with this pathway are commonly reduced in patients with metabolic syndrome. Here I will detail how we apply MFA and related methods to decipher why serine and glycine are reduced in mouse models of diabetes. At the same time, modulating dietary serine, glycine, and fat impacts lipid metabolism and neuropathy phenotypes in C57BL/6 mice. In turn, supplementation of serine improves sensory function in diabetic animals, suggesting potential therapeutic strategies for treating patients with serine-associated neuropathy. These data provide mechanistic insights into potential drivers diabetes co-morbidities and the role of amino acids in chronic disease. 

Bio:
Christian Metallo is a professor in the Molecular and Cell Biology Laboratory and holds the Daniel and Martina Lewis Chair at the Salk Institute for Biological Studies. He received his BS in chemical engineering from the University of Pennsylvania and his PhD in chemical engineering from the University of Wisconsin-Madison. He completed a postdoctoral fellowship at MIT in chemical engineering studying cancer metabolism before starting his lab in the Bioengineering department at UC San Diego in 2011. He aims to understand how nutrition and metabolism contribute to diseases such as cancer, macular disease and peripheral neuropathy, applying metabolic flux analysis and biochemical engineering approaches to address these questions.

Zoom:
https://umich.zoom.us/j/91712262512

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Workshop / Seminar Sun, 09 Apr 2023 13:05:36 -0400 2023-04-13T15:30:00-04:00 2023-04-13T16:30:00-04:00 Cooley Building Biomedical Engineering Workshop / Seminar BME Seminar Series
"LHS Collaboratory / MIDAS Colloquium: "Implementing AI in Health" (April 17, 2023 8:00am) https://events.umich.edu/event/105462 105462-21811904@events.umich.edu Event Begins: Monday, April 17, 2023 8:00am
Location: Palmer Commons
Organized By: Department of Learning Health Sciences

LHS Collaboratory/MIDAS Colloquium co-presented by the Michigan Institute for Data Science

"Implementing AI in Health"

Monday, April 17, 20023
9:00 AM - 2:30 PM ET

In-person event
Palmer Commons, Great Lakes Room

100 Washtenaw Ave, Ann Arbor, MI 

Speakers:
Barbara A. Barry, PhD
Assistant Professor of Medicine | Collaborative Scientist
Robert D. & Patricia E. Kern Center for the Science of Healthcare Delivery, & Mayo Clinic Alix School of Medicine

Michael J. Kim, MD
Chief of Staff, National Artificial Intelligence Institute
U.S. Department of Veterans Affairs

Lisa S. Lehmann, PhD, MD
Associate Professor of Medicine
Center for Bioethics, Harvard Medical School

Michael Pencina, PhD
Vice Dean for Data Science and Director of Duke AI Health
Duke University School of Medicine

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Lecture / Discussion Sat, 15 Apr 2023 21:40:02 -0400 2023-04-17T08:00:00-04:00 2023-04-17T16:00:00-04:00 Palmer Commons Department of Learning Health Sciences Lecture / Discussion LHS Collaboratory logo
2023 Biomedical Engineering Symposium with Glenn V. Edmonson Lecture (May 4, 2023 10:00am) https://events.umich.edu/event/107592 107592-21816243@events.umich.edu Event Begins: Thursday, May 4, 2023 10:00am
Location: North Campus Research Complex Building 18
Organized By: Biomedical Engineering

The 2023 Biomedical Engineering Symposium with Glenn V. Edmonson Lecture is intended to build the BME community across campus and honor the legacy of the first graduate chair of the Biomedical Engineering program. These events will provide a forum for BME faculty and students campus-wide along with our collaborators to present current research progress and discuss future research opportunities at the interface of engineering and medicine.

Featuring Glenn V. Edmonson Lecture speaker
Naomi Chesler
Chancellor's Inclusive Excellence Professor
Department of Biomedical Engineering University of California, Irvine
Director of the University of California Irvine
Edwards Lifesciences Foundation
Cardiovascular Innovation & Research Center

The events will take place on Thursday, May 4th, from 10:00 AM - 5:00 PM at NCRC, Bldg 18, Dining Hall. Please RSVP by Thursday, April 27th, 2023.

https://forms.gle/9BivDqH4uh4Wvphn9

Questions: Contact bmesymposium2023@umich.edu

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Lecture / Discussion Fri, 14 Apr 2023 09:58:33 -0400 2023-05-04T10:00:00-04:00 2023-05-04T17:00:00-04:00 North Campus Research Complex Building 18 Biomedical Engineering Lecture / Discussion BME Symposium
Regenerative Medicine Biosciences Initiative Grand Challenge (May 23, 2023 12:00pm) https://events.umich.edu/event/107238 107238-21815664@events.umich.edu Event Begins: Tuesday, May 23, 2023 12:00pm
Location: North Campus Recreation Building
Organized By: Regenerative Medicine Biosciences Initiative

Regenerative Medicine Grand Challenge May 23-24, 2023

We wanted to invite you to our second annual Grand Challenge, centered around the new ARPA-H program, with specificity to regenerative medicine and biomaterials!

Biosciences Scientific Research Initiative in Regenerative Medicine Grand Challenge
Tuesday, May 23 (afternoon) and Wednesday, May 24 (morning) NCRC Building 18, Dining Hall

Theme: Regenerative Medicine/Disruptive Biomaterials and ARPA-H.

Goal: Bring together investigators from across campus to explore "needle moving" ideas and connect people to form teams that are competitive for the new ARPA-H funding mechanism.

Agenda:
Day 1
Lunch provided.
Overview of ARPA-H program - Kate Remus (Senior Associate Director & Business Development Group Lead, Innovation Partnerships)

Talks from recent DARPA awardees at UM to demonstrate the types of "needle moving" technologies that get funded and their experiences with this program.

Talks from Regenerative Medicine PIs at UM with technologies that have potential for funding within the ARPA-H themes:
-Health science futures
-Scalable solutions
-Proactive health

Day 2
Breakouts to brainstorm ideas and have teams coalesce around transformative ideas that could be competitive for ARPA-H funding.

Outcome:
For teams ready to submit to ARPA-H, our Biosciences Initiative will help provide guidance. Teams still in need of refining their ideas can submit white papers for potential seed funding.

Please RSVP with the link on this page!

For questions, please email regenerative.medicine@umich.edu.

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Workshop / Seminar Wed, 10 May 2023 11:39:26 -0400 2023-05-23T12:00:00-04:00 2023-05-23T19:30:00-04:00 North Campus Recreation Building Regenerative Medicine Biosciences Initiative Workshop / Seminar Regenerative Medicine Biosciences Initiative Grand Challenge