Happening @ Michigan https://events.umich.edu/list/rss RSS Feed for Happening @ Michigan Events at the University of Michigan. RNA Seminar featuring: Elena Conti, Max Planck Institute of Biochemistry (January 25, 2021 9:00am) https://events.umich.edu/event/75826 75826-19613920@events.umich.edu Event Begins: Monday, January 25, 2021 9:00am
Location: Off Campus Location
Organized By: Center for RNA Biomedicine

KEYWORDS: molecular mechanisms, RNA, ribosome, biochemistry, cryo-EM, X-ray crystallography

ABSTRACT: All RNAs in eukaryotic cells are eventually degraded. The RNA exosome is a conserved macromolecular machine that degrades a vast number and variety of RNAs. Exosome-mediated RNA degradation leads to the complete elimination of nuclear and cytoplasmic transcripts in turnover and quality control pathways, and to the partial trimming of RNA precursors in nuclear processing pathways. How the exosome combines specificity and versatility to either eliminate or process RNAs has been a long-standing question.

ZOOM REGISTRATION REQUIRED: https://umich.zoom.us/webinar/register/WN_IjnWw1UcRkW8zcDeuAM2tQ

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Lecture / Discussion Mon, 04 Jan 2021 10:08:44 -0500 2021-01-25T09:00:00-05:00 2021-01-25T10:00:00-05:00 Off Campus Location Center for RNA Biomedicine Lecture / Discussion Elena Conti, Max Planck Institute of Biochemistry
Bioethics Discussion: Population Control (January 26, 2021 7:00pm) https://events.umich.edu/event/58835 58835-14563727@events.umich.edu Event Begins: Tuesday, January 26, 2021 7:00pm
Location: Lurie Biomedical Engineering
Organized By: The Bioethics Discussion Group

A discussion on limiting ourselves.

Join us at: https://umich.zoom.us/j/99926126455.

A few readings to consider:
––Population Control Policies and Fertility Convergence
––Contraception and its ethical considerations
––Must Growth Doom the Planet?
––The Population Control Holocaust

For more information and/or to receive a copy of the readings visit http://belmont.bme.umich.edu/bioethics-discussion-group/discussions/054-population-control/.

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The masses will not be controlled at the blog: https://belmont.bme.umich.edu/incidental-art/

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Lecture / Discussion Fri, 08 Jan 2021 09:42:14 -0500 2021-01-26T19:00:00-05:00 2021-01-26T20:30:00-05:00 Lurie Biomedical Engineering The Bioethics Discussion Group Lecture / Discussion Population Control
Supporting the Integration of Numerical Computation in Physics Education (January 27, 2021 3:30pm) https://events.umich.edu/event/80602 80602-20761740@events.umich.edu Event Begins: Wednesday, January 27, 2021 3:30pm
Location: Off Campus Location
Organized By: Engineering Education Research

Computation has revolutionized how modern science is done. Modern scientists use computational techniques to reduce mountains of data, to simulate impossible experiments, and to develop intuition about the behavior of complex systems. Much of the research completed by modern scientists would be impossible without the use of computation. And yet, while computation is a crucial tool of practicing scientists, most modern science curricula do not reflect its importance and utility. In this talk, I will discuss the urgent need to construct such curricula and present research that investigates the challenges at a variety of scales from the large (institutional structures) to the small (student understanding of a concept). I will discuss how the results of this research can be leveraged to facilitate the computational revolution in science education. This research will help us understand and develop institutional incentives, effective teaching practices, evidence-based course activities, and valid assessment tools. This work has been supported by Michigan State University’s CREATE for STEM Institute, the National Science Foundation, the Norwegian Agency for Quality Assurance in Education (NOKUT), the Norwegian Research Council, and the Thon Foundation.

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Lecture / Discussion Mon, 11 Jan 2021 12:45:09 -0500 2021-01-27T15:30:00-05:00 2021-01-27T16:30:00-05:00 Off Campus Location Engineering Education Research Lecture / Discussion Danny Caballero
Department of Computational Medicine & Bioinformatics Seminar (January 27, 2021 4:00pm) https://events.umich.edu/event/80722 80722-20777538@events.umich.edu Event Begins: Wednesday, January 27, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract: Massively parallel single-cell and single-nucleus RNA sequencing (sc/snRNA-seq) has opened the way to systematic tissue atlases in health and disease, but as the scale of data generation is growing, so is the need for computational pipelines for scaled analysis. We developed Cumulus, the first comprehensive cloud-based framework, to address the big data challenge arising from sc/snRNA-seq analysis. Cumulus combines the power of cloud computing with improvements in algorithm and implementation to achieve high scalability, low cost, user-friendliness and integrated support for a comprehensive set of features. We benchmark Cumulus on the Human Cell Atlas Census of Immune Cells dataset of bone marrow cells and show that it substantially improves efficiency over conventional frameworks, while maintaining or improving the quality of results, enabling large-scale studies.

In recent years, biologists have found that sc/snRNA-seq alone is not enough to reveal the full picture of how cells function and coordinate with each other in a complex tissue. They begin to couple sc/snRNA-seq with other common data modalities, such as single-cell ATAC-seq (scATAC-seq), single-cell Immune Repertoire sequencing (scIR-seq), spatial transcriptomics and mass cytometry. This data coupling is called single-cell multimodal omics. As it is becoming a new common practice, new analysis needs emerge along with two major computational challenges: big data challenge and integration challenge. The big data challenge requires us to develop scalable computational infrastructure and algorithms to deal with the ever-growing large datasets produced from the community. The integration challenge requires us to design new algorithms to enable holistic integration of heterogeneous data from different modalities. In the last part of my talk, I will discuss my team’s efforts and plans to develop Cumulus as an integrated data analysis framework for scaled single-cell multimodal omics.

Single-cell multimodal omics has the potential to provide a more comprehensive characterization of complex multicellular systems than the sum of its parts. As the datasets produced from the community keep growing substantially, the enhanced Cumulus will continue playing an important role in the effort to build atlases of complex tissues and organs at higher cellular resolution, and in leveraging them to understand the human body in health and disease.

Short bio: Dr. Bo Li is an assistant professor of medicine at Harvard Medical School, the director of Bioinformatics and Computational Biology at Center for Immunology Inflammatory Diseases, Massachusetts General Hospital, and an associate member of the Broad Institute of MIT and Harvard. His research focuses on large-scale single-cell and single-nucleus genomics data analysis. He received his Ph.D. in computer science from UW-Madison and completed two postdoctoral trainings with Dr. Lior Pachter at UC Berkeley and Dr. Aviv Regev at Broad Institute. He is best known for developing RSEM, an impactful RNA-seq transcript quantification software. RSEM is cited 9,384 times (Google Scholar) and adopted by several big consortia such as TCGA, ENCODE, GTEx and TOPMed.

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

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Livestream / Virtual Wed, 13 Jan 2021 14:32:34 -0500 2021-01-27T16:00:00-05:00 2021-01-27T17:00:00-05:00 Off Campus Location DCMB Seminar Series Livestream / Virtual Bo Li, PhD (Assistant Professor at Harvard Medical School in Boston, MA)
DCM&B Tools and Technology Seminar (January 28, 2021 12:00pm) https://events.umich.edu/event/79924 79924-20515557@events.umich.edu Event Begins: Thursday, January 28, 2021 12:00pm
Location: Off Campus Location
Organized By: DCMB Tools and Technology Seminar

Contact-map of a protein sequence dictates the global topology of structural fold. Accurate prediction of the contact-map is thus essential to protein 3D structure prediction, which is particularly useful for the protein sequences that do not have close homology templates in the Protein Data Bank.

In this talk, we present a new method, ResPRE, to predict residue-level protein contacts using inverse covariance matrix (or precision matrix) of multiple sequence alignments (MSAs) through deep residual convolutional neural network training. Detailed data analyses show that the major advantage of ResPRE lies at the utilization of precision matrix that helps rule out transitional noises of contact-maps compared with the previously used covariance matrix. Meanwhile, the residual network with parallel shortcut layer connections increases the learning ability of deep neural network training. It was also found that appropriate collection of MSAs can further improve the accuracy of final contact-map predictions.

Tool Link: https://zhanglab.ccmb.med.umich.edu/ResPRE

URL for remote viewing: https://umich-health.zoom.us/j/94886745590?pwd=LzhLU243K2ZhbXNzU1BJRHQ5V25BZz09

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Livestream / Virtual Fri, 11 Dec 2020 08:30:40 -0500 2021-01-28T12:00:00-05:00 2021-01-28T13:00:00-05:00 Off Campus Location DCMB Tools and Technology Seminar Livestream / Virtual
BME 500 Seminar: Aaron Morris, Ph.D. (January 28, 2021 4:00pm) https://events.umich.edu/event/81261 81261-20879893@events.umich.edu Event Begins: Thursday, January 28, 2021 4:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

NOTICE: This event will be held via Zoom. The link will be posted below.
https://umich.zoom.us/j/94405051853

Seminar Abstract:

My research program, the Precision Immune Microenvironment (PIM) Lab, will create a minimally invasive toolset for monitoring immune responses within tissues. In my research seminar I will begin by briefly discussing the work I performed with Dr. Themis Kyriakides as a PhD student at Yale - strategies to manipulate the early stages of the foreign body response (FBR) to implanted materials. I will next discuss my work as a postdoctoral fellow at the University of Michigan with Dr. Lonnie Shea. I focus on harnessing the chronic phase of the FBR, as a tool to monitor the immune system. I use biomaterial-based immunological niches to provide insights into the phenotype of innate immune cells that control disease activity. Cells harvested from these niches exhibit differential gene expression sufficient to monitor disease dynamics and to gauge the effectiveness of treatment. I will then discuss work developing sensors for secreted proteins to non-invasively measure protein expression in vivo via luminescence and FRET. I will conclude my talk with a brief discussion of my planned research
program that aims to leverage my materials and immune engineering experience to harness bio-responsive materials as translatable tools for real-time monitoring of tissue immunity.

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Lecture / Discussion Tue, 26 Jan 2021 12:39:22 -0500 2021-01-28T16:00:00-05:00 2021-01-28T17:00:00-05:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Logo
Timothy Jugovic (Chemistry) and Jacqueline Larouche (Biomedical Engineering) (January 28, 2021 4:00pm) https://events.umich.edu/event/81189 81189-20871998@events.umich.edu Event Begins: Thursday, January 28, 2021 4:00pm
Location: Off Campus Location
Organized By: Michigan Institute for Computational Discovery and Engineering

Timothy Jugovic: Timothy "Raz" Jugovic is a 3rd year PhD candidate in Physical chemistry conducting research on relativistic quantum mechanics in the lab of Dr. Paul Zimmerman. Raz previously earned a Master's in chemistry from ISU with research focus on crown ether synthesis. Today he will be talking on the computation of Spin-Orbit coupling in large molecules.

Talk Title and Abstract: "Effective Calculation of Spin-Orbit Coupling in Large Molecules" | Spin-Orbit coupling (SOC) is a relativistic quantum effect resulting from the coupling of electron spin (m{s}) with orbital angular momentum (l) that can play a role in intersystem crossings. Many large molecule catalysts behavior depend on these complex spin interactions that are prohibitively expensive to calculate using traditional methods. An additional complication in heavy atoms, present in many catalysts, is electron correlation which is separately calculated and similarly expensive. Development of cheap and accurate methods of determining relativistic and correlation effects in large molecules is an area of intense computational research. Proposed is a new combinatory computational method called RAS-SF-SOC (Restricted Active Space Spin Flip Spin Orbit Coupling). This method can effectively determine correlation and relativistic effects in large molecules containing many heavy atoms in reasonable computational time.

Jacqueline Larouche: Jacqueline is a third year PhD candidate in Dr. Carlos Aguilar's lab. Her research focuses on elucidating and correcting inter-cellular communication networks in skeletal muscle that are disrupted as a result of severe trauma or aging.

Talk Title and Abstract: "Single cell deconstruction of murine volumetric muscle loss reveals natural killer cell and neutrophil imbalances prevent muscle stem cell mediated regeneration" | Volumetric muscle loss (VML) overwhelms the innate regenerative capacity of mammalian skeletal muscle (SkM), leading to numerous disabilities and reduced quality of life. Immune cells are critical responders to muscle injury and guide muscle stem cell (MuSC) mediated myogenic repair. However, how immune cell infiltration and inter-cellular communication networks are altered following VML to drive pathological outcomes remains unclear. Thus, we sought to characterize the cellular and molecular mechanisms driving fibrotic degeneration of SkM after VML by comparing the healing trajectories between muscle loss injuries that regenerate to those that result in fibrosis. Using single-cell RNA sequencing (scRNA-Seq), lineage-tracing mouse models, in vitro assays, histological analysis, cell transplants, and in vivo small molecule inhibition, we elucidate new cellular and molecular players post VML. We observed that degenerative VML injuries result in persistent infiltration of inflammatory neutrophils. Cytolytic natural killer (NK) cells were also observed to accumulate in degenerative defects and interact with neutrophils via secretion of chemokine receptor type 1 (CCR1) ligands. Intramuscular NK cell transplants significantly reduced neutrophil abundance and enhanced healing rates, while systemic delivery of a CCR1 inhibitor exacerbated neutrophil accumulation. As a consequence of exacerbated neutrophils in degenerative injuries, we observed reductions in MuSC myogenic capacity. The reductions in regenerative potential of MuSCs were also impacted by overexpression of transforming growth factor beta 1 (TGF1) and local inhibition of TGF1 signaling reduced neutrophil populations and improved tissue morphology. Together, these findings enhance our understanding of immune cell-stem cell communication dynamics governing muscle healing outcomes. This work provides a valuable resource for further exploration into mechanisms driving VML-induced fibrosis and may help elucidate drivers of fibrosis and chronic inflammation in other pathologies.

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Workshop / Seminar Mon, 25 Jan 2021 13:24:50 -0500 2021-01-28T16:00:00-05:00 2021-01-28T17:00:00-05:00 Off Campus Location Michigan Institute for Computational Discovery and Engineering Workshop / Seminar T. Jugovic and J. Larouche
RNA Seminar featuring: Jeff Twiss, MD, PhD, SmartState Chair in Childhood Neurotherapeutics, Professor of Biological Sciences, University of South Carolina (February 1, 2021 4:00pm) https://events.umich.edu/event/75813 75813-19608028@events.umich.edu Event Begins: Monday, February 1, 2021 4:00pm
Location: Off Campus Location
Organized By: Center for RNA Biomedicine

REGISTRATION REQUIRED: https://umich.zoom.us/webinar/register/WN_Rss4i-7WTwyf8m8ogCPXEQ

Abstract: Neurons are extremely polarized cells with axonal and dendritic processes extending 100 to 1000 fold longer or more than the cell body diameter. Our lab has been interested in how axons grow to such great distances and how they respond to injury. mRNAs are transported into axons, with their localized translation providing the axon with autonomy to respond to different stimuli by modifying their local proteome. Transport, translation, and stability of axonal mRNAs is driven by interactions with RNA binding proteins and different signaling cascades. I will focus on recent work that gives insight into how specificity of these mechanisms is driven for different cohorts of axonal mRNAs.

Keywords - Neuron, Axon, RNA transport, Translational regulation

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Lecture / Discussion Fri, 15 Jan 2021 14:13:00 -0500 2021-02-01T16:00:00-05:00 2021-02-01T17:00:00-05:00 Off Campus Location Center for RNA Biomedicine Lecture / Discussion Jeff Twiss, University of South Carolina
CCMB / DCMB Weekly Seminar Series (February 3, 2021 4:00pm) https://events.umich.edu/event/81571 81571-20927558@events.umich.edu Event Begins: Wednesday, February 3, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract:
Understanding intra-tumour heterogeneity (ITH), in particular identifying the presence of subclonal populations of cancer cells that may respond differently to treatments, is key to support precision medicine approaches. Capturing ITH from genomic measures raises however a number of computational challenges. In this talk I will present CloneSig, a method to infer ITH from "bulk" genomic data, in particular whole-exome sequencing data, and capture changes in mutational processes active in different subclones. I will then discuss the promises of single-cell genomics and some challenges it raises, in particular to transform raw count data into useful representations, integrate heterogeneous modalities, and learn gene regulation.

Short bio: Jean-Philippe Vert has been a research scientist at Google Brain in Paris and adjunct researcher at PSL University Mines ParisTech since 2018. He graduated from Ecole Polytechnique and holds a PhD in mathematics from Paris University. He was research professor and the founding director of the Centre for Computational Biology at Mines ParisTech from 2006 to 2018, team leader at the Curie Institute on computational biology of cancer (2008-2018), visiting scholar at UC Berkeley (2015-2016), and professor at the department of mathematics of Ecole normale supérieure in Paris (2016-2018).
His research interest concerns the development of statistical and machine learning methods, particularly to model complex, high-dimensional and structured data, with an application focus on computational biology, genomics and precision medicine. His recent contributions include new methods to embed structured data such as strings, graphs or permutations to vector spaces, regularization techniques to learn from limited amounts of data, and computationally efficient techniques for pattern detection and feature selection.
He is also working on several medical applications in cancer research, including quantifying and modeling cancer heterogeneity, predicting response to therapy, and modeling the genome and epigenome of cancer cells at the single-cell level.

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

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Livestream / Virtual Mon, 01 Feb 2021 14:12:04 -0500 2021-02-03T16:00:00-05:00 2021-02-03T17:00:00-05:00 Off Campus Location DCMB Seminar Series Livestream / Virtual Jean-Philippe Vert, PhD (Research Scientist at Google Brain in Paris, Adjunct Researcher at PSL University Mines ParisTech)
DCM&B Tools and Technology Seminar (February 4, 2021 12:00pm) https://events.umich.edu/event/79914 79914-20515545@events.umich.edu Event Begins: Thursday, February 4, 2021 12:00pm
Location: Off Campus Location
Organized By: DCMB Tools and Technology Seminar

URL for remote viewing: https://umich-health.zoom.us/j/94886745590?pwd=LzhLU243K2ZhbXNzU1BJRHQ5V25BZz09

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Livestream / Virtual Fri, 11 Dec 2020 08:00:22 -0500 2021-02-04T12:00:00-05:00 2021-02-04T13:00:00-05:00 Off Campus Location DCMB Tools and Technology Seminar Livestream / Virtual
Oral Health Sciences Semianr (February 4, 2021 12:00pm) https://events.umich.edu/event/81685 81685-20943434@events.umich.edu Event Begins: Thursday, February 4, 2021 12:00pm
Location: Off Campus Location
Organized By: Office of Research School of Dentistry

YUYING XIE, PhD
Assistant Professor,
Department of Computational Mathematics, Science and Engineering; Department of Statistics and Probability
Michigan State University

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Presentation Wed, 03 Feb 2021 12:08:29 -0500 2021-02-04T12:00:00-05:00 2021-02-04T13:00:00-05:00 Off Campus Location Office of Research School of Dentistry Presentation Yuying Xie
BME 500 Seminar: Maria Coronel (February 4, 2021 4:00pm) https://events.umich.edu/event/81382 81382-20889813@events.umich.edu Event Begins: Thursday, February 4, 2021 4:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

BME Faculty Candidate
Maria Coronel, Ph.D.
Georgia Institute of Technology

Seminar Abstract:
Two major challenges to the translation of cellular-based tissue-engineered therapies are the lack of adequate oxygen support post-implantation and the need for systemic immunosuppression to halt the strong inflammatory and immunological response of the host. As such, strategies that aim at addressing oxygen demand, and local immunological responses can be highly beneficial in the translation of these therapies. In this seminar, I will focus on two biomaterial strategies to create a more favorable transplant niche for pancreatic islet transplantation. The first half will describe an in-situ oxygen-releasing biomaterial fabricated through the incorporation of solid peroxides in a silicone polymer. The implementation of this localized, controlled and sustained oxygen-generator mitigates the activation of detrimental hypoxia-induced pathways in islets and enhances the potency of extrahepatic 3D islet- loaded devices in a diabetic animal model. In the second part, I will focus on engineering synthetic biomaterials for the delivery of immunomodulatory signals for transplant acceptance. Biomaterial carriers fabricated with polyethylene glycol microgels are used to deliver immunomodulatory signals to regulate the local microenvironment and prevent allograft rejection in a clinically relevant pre-clinical transplant model. The use of synthetic materials as an off-the-shelf platform, without the need for manipulating the biological cell product, improves the clinical translatability of this engineered approach. Designing safer, responsive biomaterials to boost the delivery of targeted therapeutics will significantly reinvigorate interventional cell-based tissue-engineered therapies.

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Lecture / Discussion Fri, 29 Jan 2021 17:14:27 -0500 2021-02-04T16:00:00-05:00 2021-02-04T17:00:00-05:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Logo
Bioethics Discussion: Sex (February 9, 2021 7:00pm) https://events.umich.edu/event/58836 58836-14563728@events.umich.edu Event Begins: Tuesday, February 9, 2021 7:00pm
Location: Lurie Biomedical Engineering
Organized By: The Bioethics Discussion Group

A discussion on what we do.

Join us at: https://umich.zoom.us/j/99926126455.

A few readings to consider:
––Sex Differences in Institutional Support for Junior Biomedical Researchers
––Sex as an important biological variable in biomedical research
––Deciding on Gender in Children with Intersex Conditions: Considerations and Controversies
––The Use of Sex Robots: A Bioethical Issue

For more information and/or to receive a copy of the readings visit http://belmont.bme.umich.edu/bioethics-discussion-group/discussions/055-sex/.

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Not going to make a sex joke. We're above that here. All the same, please come to the blog: https://belmont.bme.umich.edu/incidental-art/

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Lecture / Discussion Fri, 08 Jan 2021 09:42:03 -0500 2021-02-09T19:00:00-05:00 2021-02-09T20:30:00-05:00 Lurie Biomedical Engineering The Bioethics Discussion Group Lecture / Discussion Sex
CCMB / DCMB Weekly Seminar (February 10, 2021 4:00pm) https://events.umich.edu/event/81413 81413-20893777@events.umich.edu Event Begins: Wednesday, February 10, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract: The increasing omics data and advanced AI technology present a great opportunity for novel biomarker-driven cancer therapies. My talk will cover two parts. First, I will introduce DrBioRight, a natural language-oriented and AI-driven analytic platform for omic data analysis. This platform allows users to perform analysis directly through human languages and it improves the performance through adaptive learning. Armed with NLP and AI technologies, this analytic will maximize the utility of omics data and lead to a new paradigm for biomedical research. Second, I will discuss our recent work on enhancer RNAs. We show that the eRNAs provide explanatory power for cancer phenotypes beyond that provided by mRNA expression through resolving intratumoral heterogeneity with enhancer cell-type specificity. Our study provides a high-resolution map of eRNA loci through which enhancer activities can be quantified by RNA-seq, enabling a broad range of biomedical investigations.

Bio: Dr. Liang is a Barnhart Family Distinguished Professor in Targeted Therapies and the Deputy Chair of Department of Bioinformatics and Computational Biology at the University of Texas MD Anderson Cancer Center. He is also a professor in the Department of Systems Biology. He received his B.S. in chemistry from Peking University (China) in 2001 and Ph.D. in quantitative and computational biology from Princeton University (NJ, USA) in 2006. Dr. Liang then finished his postdoctoral training in evolutionary and computational genomics at the University of Chicago. He joined MD Anderson Cancer Center as Assistant Professor and started his own group in 2009.
At MD Anderson, Dr. Liang’s group focuses on bioinformatics tool development, integrated cancer genomic analysis, regulatory RNA regulation/modification, and cancer systems biology. His systematic studies on enhancer regulation, RNA editing, functional proteomics, sex effects, and driver mutations in cancer have generated profound impacts on the biomedical research community and attracted wide attention such as The Wall Street Journal and Newsweek. The bioinformatics tools his group developed (such as TCPA, TANRIC, FASMIC, DrBioRight) collectively have >110,000 active users worldwide. Since 2010, he has published >140 papers total citation >25,000 times), including 41 corresponding-author papers in top journals such as Cell, Cancer Cell, Nature Genetics, Nature Biotechnology, and Nature Methods.
Dr. Liang has taken leadership roles in large cancer consortium projects, including chair of The Cancer Genome Atlas (TCGA) PanCanAtlas working groups, one co-leader of International Cancer Genome Consortium (ICGC) Pan-Cancer Whole Genome Analysis Project, and one co-chair of NCI Genomic Data Commons (GDC) QC working group. He won several awards including MD Anderson R. Lee Clark Fellow Award (2014), the University of Texas System STARS Award (2015), MD Anderson Faculty Scholar Award (2018), and AACR Team Science Award (2020). He is an elected Fellow of American Association for the Advancement of Science (AAAS).

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

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Livestream / Virtual Thu, 28 Jan 2021 11:33:05 -0500 2021-02-10T16:00:00-05:00 2021-02-10T17:00:00-05:00 Off Campus Location DCMB Seminar Series Livestream / Virtual Han Liang, PhD Professor and Deputy Chair, Department of Bioinformatics and Computational Biology Professor, Department of Systems Biology Barnhart Family Distinguished Professor in Targeted Therapies The University of Texas MD Anderson Cancer Center
DCM&B Tools and Technology Seminar (February 11, 2021 12:00pm) https://events.umich.edu/event/79915 79915-20515548@events.umich.edu Event Begins: Thursday, February 11, 2021 12:00pm
Location: Off Campus Location
Organized By: DCMB Tools and Technology Seminar

Tool Link: https://micv.works

URL for Remote viewing: https://umich-health.zoom.us/j/94886745590?pwd=LzhLU243K2ZhbXNzU1BJRHQ5V25BZz09

(Disclosure: Nigel Michki is the founder and CEO of MiOmics Inc. (MI, USA))

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Livestream / Virtual Fri, 11 Dec 2020 08:01:07 -0500 2021-02-11T12:00:00-05:00 2021-02-11T13:00:00-05:00 Off Campus Location DCMB Tools and Technology Seminar Livestream / Virtual
Oral Health Sciences Seminar Series (February 11, 2021 12:00pm) https://events.umich.edu/event/81688 81688-20943436@events.umich.edu Event Begins: Thursday, February 11, 2021 12:00pm
Location: Off Campus Location
Organized By: Office of Research School of Dentistry

Lola Eniola-Adefeso, Ph.D.
University Diversity and Social Transformation Professor of Chemical Engineering
Vice-Chair for Graduate Studies in Chemical Engineering
Professor of Biomedical Engineering
Professor of Macromolecular Science and Engineering
Miller Faculty Scholar
Director, Cell Adhesion and Drug Delivery Lab
Associate Director, NIH Cellular Biotechnology Training Grant
University of Michigan

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Presentation Mon, 31 Jan 2022 10:25:38 -0500 2021-02-11T12:00:00-05:00 2021-02-11T13:00:00-05:00 Off Campus Location Office of Research School of Dentistry Presentation Lola Eniola-Adefeso, Ph.D.
RNA Seminar featuring: Karla Neugebauer, Yale University School of Medicine (February 15, 2021 4:00pm) https://events.umich.edu/event/78295 78295-20004839@events.umich.edu Event Begins: Monday, February 15, 2021 4:00pm
Location: Off Campus Location
Organized By: Center for RNA Biomedicine

ZOOM REGISTRATION REQUIRED: https://umich.zoom.us/webinar/register/WN_aZggyZ0yQcSPcJrsHloXjQ

ABSTRACT: My lab is interested in the coordination between transcription, RNA processing and nuclear organization that governs gene expression. We have established experimental systems in budding yeast, zebrafish embryos, and mammalian tissue culture cells to explore transcription and splicing regulation in a variety of biological contexts and with a diversity of tools, from imaging to genome-wide approaches. Our observations have provided novel insights into transcription and splicing mechanisms as well as principles of cellular organization that facilitate efficient gene expression. In this talk, I will be discussing rapid co-transcriptional splicing during erythropoiesis and how Cajal bodies assemble to ensure a steady supply of spliceosomal components.

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Lecture / Discussion Tue, 02 Feb 2021 16:32:41 -0500 2021-02-15T16:00:00-05:00 2021-02-15T17:00:00-05:00 Off Campus Location Center for RNA Biomedicine Lecture / Discussion Prof. Karla Neugebauer, Ph.D.
Improving the Evidence to Practice Gap through Innovation in Health Science Education (February 17, 2021 3:00pm) https://events.umich.edu/event/81403 81403-20893762@events.umich.edu Event Begins: Wednesday, February 17, 2021 3:00pm
Location: Off Campus Location
Organized By: RISE (Research. Innovation. Scholarship. Education.)

Please join us on Wednesday, February 17, 2021, 3:00 - 4:00 PM for a discussion on Improving the Evidence to Practice Gap through Innovation in Health Science Education.

Register for the event via Eventbrite: https://www.eventbrite.com/e/rise-virtual-talking-circle-tickets-130006826919

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Workshop / Seminar Thu, 28 Jan 2021 06:37:46 -0500 2021-02-17T15:00:00-05:00 2021-02-17T16:00:00-05:00 Off Campus Location RISE (Research. Innovation. Scholarship. Education.) Workshop / Seminar RISE Virtual Talking Circle
An Honest Conversation: Diversity and Inclusion in Engineering (February 17, 2021 3:30pm) https://events.umich.edu/event/81702 81702-20943454@events.umich.edu Event Begins: Wednesday, February 17, 2021 3:30pm
Location: Off Campus Location
Organized By: Engineering Education Research

In 2020, we witnessed several examples of social injustice and social unrest. As human beings and engineers, we must decide how we want to respond to what happened and how we want to move forward. Calls to improve our approach to diversity, equity, and inclusion (DEI) have coincided with the call to update our overall engineering curriculum. Over the years, several initiatives have been launched to address such issues, which primarily attempt to address perceived inadequacies in underrepresented students. However, scarce efforts have been developed to address the engineering culture that has limited the full participation of women and people of color in engineering. Furthermore, few of us in engineering have the knowledge, skills, or ability to productively engage with issues leading to the marginalization and social unrest. Rarely do we dare to apply our problem-solving or critical thinking approaches to how to educate or improving DEI. As a result, the goal of this talk is to provide engineers with language to have an honest conversation about our individual and collective response to the inequity in engineering and realign our actions to improve engineering education. This impactful workshop will provide definitions and practical examples of key DEI concepts in engineering based on holistic interdisciplinary research.

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Lecture / Discussion Thu, 04 Feb 2021 08:44:52 -0500 2021-02-17T15:30:00-05:00 2021-02-17T16:30:00-05:00 Off Campus Location Engineering Education Research Lecture / Discussion Dr. Kelly Cross
Special Joint Seminar between our Department and the Genome Science Training Program (February 17, 2021 4:00pm) https://events.umich.edu/event/80415 80415-20719669@events.umich.edu Event Begins: Wednesday, February 17, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract: The human genome sequence folds in three dimensions (3D) into a rich variety of locus-specific contact patterns. Despite growing appreciation for the importance of 3D genome folding in evolution and disease, we lack models for relating mutations in genome sequences to changes in genome structure and function. Towards that goal, we discovered that the organization of gene regulatory domains within chromosomes and the specific sequences that sit at boundaries between domains are under strong negative selection in the human population and over primate evolution. Motivated by this signature of functional importance, we developed a deep convolutional neural network, called Akita, that accurately predicts genome folding from DNA sequence alone. Representations learned by Akita underscore the importance of the structural protein CTCF but also reveal a complex grammar beyond CTCF binding sites that underlies genome folding. Akita enabled rapid in silico predictions for effects of sequence mutagenesis on the 3D genome, including differences in genome folding across species and in disease cohorts, which we are validating with CRISPR-edited genomes. This prediction-first strategy exemplifies my vision for a more proactive, rather than reactive, role for data science in biomedical research.

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

Short bio: Dr. Katherine S. Pollard is Director of the Gladstone Institute of Data Science & Biotechnology, Investigator at the Chan Zuckerberg Biohub, Professor in the Department of Epidemiology & Biostatistics and Bioinformatics Graduate Program at UCSF. Her lab develops statistical models and open source bioinformatics software for the analysis of massive genomic datasets. Previously, Dr. Pollard was an assistant professor in the University of California, Davis Genome Center and Department of Statistics. She earned her PhD in Biostatistics from the University of California, Berkeley and was a comparative genomics postdoctoral fellow at the University of California, Santa Cruz. She was awarded the Thomas J. Watson Fellowship, the Sloan Research Fellowship, and the Alumna of the Year from UC Berkeley. She is a Fellow of the International Society for Computational Biology and of the California Academy of Sciences.

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Livestream / Virtual Wed, 06 Jan 2021 09:24:05 -0500 2021-02-17T16:00:00-05:00 2021-02-17T17:00:00-05:00 Off Campus Location DCMB Seminar Series Livestream / Virtual Katherine S. Pollard, PhD (Director, Gladstone Institute of Data Science & Biotechnology; Professor, UCSF; Investigator, Chan Zuckerberg Biohub)
DCM&B Tools and Technology Seminar (February 18, 2021 12:00pm) https://events.umich.edu/event/79916 79916-20515549@events.umich.edu Event Begins: Thursday, February 18, 2021 12:00pm
Location: Off Campus Location
Organized By: DCMB Tools and Technology Seminar

Tool Link: https://github.com/hhabra/metabCombiner

URL for remote viewing: https://umich-health.zoom.us/j/94886745590?pwd=LzhLU243K2ZhbXNzU1BJRHQ5V25BZz09

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Livestream / Virtual Wed, 20 Jan 2021 11:08:42 -0500 2021-02-18T12:00:00-05:00 2021-02-18T13:00:00-05:00 Off Campus Location DCMB Tools and Technology Seminar Livestream / Virtual
Powering through Uncertainty (February 18, 2021 1:00pm) https://events.umich.edu/event/80885 80885-20816994@events.umich.edu Event Begins: Thursday, February 18, 2021 1:00pm
Location: Off Campus Location
Organized By: Office of Research School of Dentistry

Platform Architect, Intel & Founder, Timouns

Dr. Simon is a biomedical engineer, author and inventor who graduated from the University of Michigan Biomedical Engineering PhD program and was a School of Dentistry T32-TEAM Training Grant trainee. Her keynote seminar titled "Powering through Uncertainty" will encourage and inspire our students, faculty and staff as we strive to meet our mission of advancing health through education, service, research and discovery.

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Livestream / Virtual Mon, 18 Jan 2021 14:05:48 -0500 2021-02-18T13:00:00-05:00 2021-02-18T14:00:00-05:00 Off Campus Location Office of Research School of Dentistry Livestream / Virtual Keynote Speaker, Arlyne Simon
BME 500 Seminar: Adam Glaser (February 18, 2021 4:00pm) https://events.umich.edu/event/81384 81384-20889815@events.umich.edu Event Begins: Thursday, February 18, 2021 4:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Seminar Abstract:

New developments in microscopy, tissue clearing, and fluorescent labeling are enabling unprecedented access to the structural and molecular contents of biological tissues. These technologies are now opening new doors in scientific research and shedding light on the critical factors which underpin complex disease processes. In this presentation, I will present my recent work in these areas, with a focus on applications to cancer at both the clinical and preclinical level.

ZOOM LINK: https://umich.zoom.us/j/94405051853

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Lecture / Discussion Sat, 13 Feb 2021 20:04:17 -0500 2021-02-18T16:00:00-05:00 2021-02-18T17:00:00-05:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Logo
LHS Collaboratory- February session (February 23, 2021 12:00pm) https://events.umich.edu/event/81035 81035-20838675@events.umich.edu Event Begins: Tuesday, February 23, 2021 12:00pm
Location: Off Campus Location
Organized By: Department of Learning Health Sciences

The keynote presentation (12:00 pm-1:15 pm ET) will be followed by breakout sessions (1:15 pm-2:15 pm ET) on topics presented by the UM faculty and guests.
Zoom links to the individual breakout sessions are listed below.

Keynote speaker: Dr. Bernardo Mariano, Jr.
Topic: Digital Transformation in Healthcare for a Diverse World
Director of Digital Health & Innovation
Chief Information Officer (CIO)
World Health Organization (WHO)

Remarks:
Laurie McCauley, DDS, MS, PhD
Dean, William K and Mary Anne Najjar Professor of Periodontics
University of Michigan School of Dentistry


Breakout sessions from 1:15 pm-2:15 pm (ET)

Breakout Session #1 LHS and Pain
Zoom link: https://umich.zoom.us/j/99190944947

Topic: Integrating Diverse Health Ecosystems for
Optimal Pain Treatment, Education and Research
Alex F. DaSilva, DDS, DMedSc
University of Michigan School of Dentistry

Perspective: Data De‐Identification and Clinical Decision Support
Ivo Dinov, Ph.D.
Department of Health Behavior and Biological Sciences
University of Michigan


Breakout Session #2 LHS and Caries Risk
Zoom link: https://umich.zoom.us/j/97070468943

Topic: Caries Risk Prediction Models
Margherita Fontana, DDS, PhD
University of Michigan School of Dentistry

Perspective: LHS and Evidence-based Clinical Practice
Alonso Carrasco-Labra, DDS, MSc, PhD
Department of Evidence Synthesis and Translation Research
American Dental Association

Breakout Session #3 LHS and Opioids
Zoom link: https://umich.zoom.us/j/96029888703


Topic: Iteratively Learning about Dental Opioid Prescribing
Romesh Nalliah, BDS, MHCM
University of Michigan School of Dentistry

Perspective: Precision Health in Opioid Management
Chad Brummett, M.D.
University of Michigan Department of Anesthesiology

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Lecture / Discussion Thu, 21 Jan 2021 09:43:32 -0500 2021-02-23T12:00:00-05:00 2021-02-23T14:15:00-05:00 Off Campus Location Department of Learning Health Sciences Lecture / Discussion LHS Collaboratory Logo
Bioethics Discussion: Artificial Life (February 23, 2021 7:00pm) https://events.umich.edu/event/58837 58837-14563729@events.umich.edu Event Begins: Tuesday, February 23, 2021 7:00pm
Location: Off Campus Location
Organized By: The Bioethics Discussion Group

A discussion on new forms.

Join us at: https://umich.zoom.us/j/99926126455.

A few readings to consider:
––Is the creation of artificial life morally significant?
––Why Do We Need Artificial Life?
––Artificial Life
––The Bioethicist Who Cried “Synthetic Biology”: An Analysis of the Function of Bioterrorism Predictions in Bioethics

For more information and/or to receive a copy of the readings visit http://belmont.bme.umich.edu/bioethics-discussion-group/discussions/056-artificial-life/.

––
Life finds a way over to the blog: https://belmont.bme.umich.edu/incidental-art/

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Lecture / Discussion Fri, 08 Jan 2021 09:41:49 -0500 2021-02-23T19:00:00-05:00 2021-02-23T20:30:00-05:00 Off Campus Location The Bioethics Discussion Group Lecture / Discussion Artificial Life
CCMB / DCMB Weekly Seminar (February 24, 2021 4:00pm) https://events.umich.edu/event/82197 82197-21052530@events.umich.edu Event Begins: Wednesday, February 24, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract: COVID Moonshot is an international consortium aiming to discover patent-free oral antiviral against SARS-CoV-2, targeting the main protease. Operating under an open science ethos, we make all data and structures publicly available, and crowdsource molecule designs from the community. In less than a year, we went from fragment hits to nanomolar leads in biochemical and antiviral assays. In my talk, I will discuss Moonshot’s journey towards orally bioavailable, non-covalent, and non-peptidomimetic Mpro inhibitors. I will discuss how machine learning technologies have accelerated our design-make-test cycle, and the learnings we gleaned from this large-scale prospective use of algorithms.

Bio: Dr. Alpha Lee is a Group Leader in the Department of Physics, University of Cambridge. His research focuses on developing machine learning technologies that close the design-make-test cycle for small molecule drug discovery and materials discovery. He is interested in how physical and chemical insights can be integrated into the design of interpretable algorithms. Before joining Cambridge, Dr. Lee was a Fulbright Scholar at Harvard and obtained his PhD from the University of Oxford.

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

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Livestream / Virtual Wed, 17 Feb 2021 13:18:31 -0500 2021-02-24T16:00:00-05:00 2021-02-24T17:00:00-05:00 Off Campus Location DCMB Seminar Series Livestream / Virtual
DCM&B Tools and Technology Seminar (February 25, 2021 12:00pm) https://events.umich.edu/event/79917 79917-20515550@events.umich.edu Event Begins: Thursday, February 25, 2021 12:00pm
Location: Off Campus Location
Organized By: DCMB Tools and Technology Seminar

URL for remote viewing: https://umich-health.zoom.us/j/94886745590?pwd=LzhLU243K2ZhbXNzU1BJRHQ5V25BZz09

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Livestream / Virtual Fri, 22 Jan 2021 12:31:37 -0500 2021-02-25T12:00:00-05:00 2021-02-25T13:00:00-05:00 Off Campus Location DCMB Tools and Technology Seminar Livestream / Virtual
BME 500 Seminar: Jorge Marchand (February 25, 2021 4:00pm) https://events.umich.edu/event/81385 81385-20889816@events.umich.edu Event Begins: Thursday, February 25, 2021 4:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Seminar Abstract:

In living organisms, translation of genetic information by the ribosome transforms
the information embedded in DNA into actuating components, namely proteins. Though life itself is incredibly diverse at the macroscopic level, at the molecular level, all of life uses the same set of machinery for translation - 20 standard amino acid building blocks (with minor exceptions), transfer RNAs (tRNA), and ribosomes. The convergence and association of these interdependent biomolecules is neatly captured in a table known as the ‘standard genetic code’. Even after billions of years of genetic drift, the ‘standard genetic code’ has been largely refractory to change. In this talk, I will be discussing strategies and methods for building organisms that can make and use non-standard amino acids to make proteins with enhanced or expanded function.

ZOOM LINK: https://umich.zoom.us/j/94405051853

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Lecture / Discussion Sun, 21 Feb 2021 22:07:28 -0500 2021-02-25T16:00:00-05:00 2021-02-25T17:00:00-05:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Logo
RNA Seminar featuring: Melissa Moore, Moderna Therapeutics (March 3, 2021 4:00pm) https://events.umich.edu/event/81265 81265-20879904@events.umich.edu Event Begins: Wednesday, March 3, 2021 4:00pm
Location: Off Campus Location
Organized By: Center for RNA Biomedicine

**Please register here for March 3rd seminar: https://umich.zoom.us/webinar/register/WN_l0kt_NjpRh-f33LJj7KGpA

Dr. Moore will address scientists and non-scientists, and will take live questions.

In her role as Chief Scientific Officer, Platform Research, Dr. Melissa Moore is responsible for leading mRNA biology, delivery and computation science research at Moderna. She joined Moderna in 2016 from the University of Massachusetts Medical School, where she served as Professor of Biochemistry & Molecular Pharmacology, Eleanor Eustis Farrington Chair in Cancer Research and a long-time Investigator at the Howard Hughes Medical Institute (HHMI). Dr. Moore was also a founding Co-Director of the RNA Therapeutics Institute (RTI) at UMassMed, and was instrumental in creating the Massachusetts Therapeutic and Entrepreneurship Realization initiative (MassTERi), a faculty-led program intended to facilitate the translation of UMMS discoveries into drugs, products, technologies and companies. Dr. Moore is an elected member of the National Academy of Sciences (2017) and a Fellow of the American Academy of Arts and Sciences (2019).

Dr. Moore holds a B.S. in Chemistry and Biology from the College of William and Mary, and a Ph.D. in Biological Chemistry from MIT, where she specialized in enzymology under Prof. Christopher T. Walsh. She began working on RNA metabolism during her postdoctoral training with Phillip A. Sharp at MIT. During her 23 years as a faculty member, first at Brandeis and then at UMassMed, her research encompassed a broad array of topics related to the roles of RNA and RNA-protein (RNP) complexes in gene expression, and touched on many human diseases including cancer, neurodegeneration, and preeclampsia.

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Lecture / Discussion Wed, 10 Feb 2021 19:47:49 -0500 2021-03-03T16:00:00-05:00 2021-03-03T17:00:00-05:00 Off Campus Location Center for RNA Biomedicine Lecture / Discussion Melissa Moore, Ph.D., Moderna Therapeutics
DCM&B Tools and Technology Seminar (March 4, 2021 12:00pm) https://events.umich.edu/event/79918 79918-20515551@events.umich.edu Event Begins: Thursday, March 4, 2021 12:00pm
Location: Off Campus Location
Organized By: DCMB Tools and Technology Seminar

Tool link: https://github.com/rdcrawford/cognac

URL for remote viewing: https://umich-health.zoom.us/j/94886745590?pwd=LzhLU243K2ZhbXNzU1BJRHQ5V25BZz09

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Livestream / Virtual Fri, 19 Feb 2021 14:34:43 -0500 2021-03-04T12:00:00-05:00 2021-03-04T13:00:00-05:00 Off Campus Location DCMB Tools and Technology Seminar Livestream / Virtual
BME 500 Seminar: Danielle Bassett (March 4, 2021 4:00pm) https://events.umich.edu/event/81388 81388-20889818@events.umich.edu Event Begins: Thursday, March 4, 2021 4:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

TBD

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Lecture / Discussion Wed, 27 Jan 2021 21:05:02 -0500 2021-03-04T16:00:00-05:00 2021-03-04T17:00:00-05:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Logo
BME 500 Seminar: Sasha Cai Lesher-Perez (March 4, 2021 4:00pm) https://events.umich.edu/event/81387 81387-20889817@events.umich.edu Event Begins: Thursday, March 4, 2021 4:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Efforts to close the gap between in vitro to in vivo model systems have produced technologies that more effectively evaluate spatial, structural, and mechanical control mechanisms. However, existing in vitro models lack temporal regulation that captures the controlled, rhythmic processes that often occur in biological phenomena. A major contributor to this tech-bio mismatch is the difficulty to easily and sustainably scale our ability to apply timed oscillations, representative of biorhythms, in vitro. Developing technologies that are simpler and more adoptable for users, while ensuring higher throughput, have the potential to shift the way in which we establish cell cultures with a dynamic biorhythmic baseline.

In this talk, I will cover how my previous work in different technology platforms will be leveraged to establish next generation cell and tissue culture platforms that enable biomolecule timed oscillations in more complex microenvironments. First, I will discuss the development of microfluidic self-regulating circuits as a tool to produce modular chemical profiles on-chip at different timescales. Second, I will describe microparticle building blocks for the generation of customizable porous scaffolds that are porous, and consequently perfusable, enabling our ability to apply biomolecule timed oscillations through liquid flow to 3D scaffolds. Finally, I will describe my proposed research on establishing biorhythms in vitro and how these in vitro model systems will enable my research group to begin studying how stress within our lives lead to specific disease priming mechanisms.

ZOOM LINK: https://umich.zoom.us/j/94405051853

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Lecture / Discussion Fri, 26 Feb 2021 16:50:20 -0500 2021-03-04T16:00:00-05:00 2021-03-04T17:00:00-05:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Logo
Bioethics Discussion: Infection (March 9, 2021 7:00pm) https://events.umich.edu/event/58838 58838-14563730@events.umich.edu Event Begins: Tuesday, March 9, 2021 7:00pm
Location: Off Campus Location
Organized By: The Bioethics Discussion Group

A discussion spreading to others.

Join us at: https://umich.zoom.us/j/99926126455.

A few readings to consider:
––Evidence and Effectiveness in Decision-Making for Quarantine
––The 1918 Influenza Pandemic: Insights for the 21st Century
––From SARS to Ebola: Legal and Ethical Considerations for Modern Quarantine
––Responding to the COVID-19 pandemic: Ethical considerations for conducting controlled human infection studies

For more information and/or to receive a copy of the readings visit http://belmont.bme.umich.edu/bioethics-discussion-group/discussions/057-infection/.

––
Feel free to stop by the website, not even the blog is viral: https://belmont.bme.umich.edu/incidental-art/

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Lecture / Discussion Fri, 08 Jan 2021 09:40:23 -0500 2021-03-09T19:00:00-05:00 2021-03-09T20:30:00-05:00 Off Campus Location The Bioethics Discussion Group Lecture / Discussion Infection
Motivation and Identity as Signals of Systemic Problems in Engineering Education (March 10, 2021 3:30pm) https://events.umich.edu/event/82513 82513-21114065@events.umich.edu Event Begins: Wednesday, March 10, 2021 3:30pm
Location: Off Campus Location
Organized By: Engineering Education Research

There is a well-documented history of systemic engineering education problems ranging from a persistently chilly climate to a burgeoning mental health crisis. Outcomes of these problems include but are not limited to increased attrition, decreased learning, and reduced engineering innovation resulting from a homogenous engineering population. While these measures provide concrete evidence of systemic problems, they do not provide clear targets for change or an early warning system of how systemic problems influence students before crucial decision points.

To address the limitations of existing engineering education outcome measures, measures of how students internalize engineering experiences are needed. Students' motivations for engineering tasks and identifications as engineers can fill this gap as they are contextually responsive and connected to educational outcomes such as deep learning, student retention, and task persistence. Additionally, students' educational experiences directly influence their motivations and identities.

Informed by specific theories of motivation and identity (future time perspective and engineering role identity, respectively), this presentation describes how students' motivations and identities are shaped by their engineering education experiences and shape engineering education cultures. Specifically, I will discuss the homogenization of undergraduates' motivations and identities; the connections between motivation and identity and experiences of discrimination and bias; and the identity and motivationally undermining experiences of engineering graduate students. I will conclude by discussing actionable steps to shift engineering education defaults to foster students' motivations and identities.

Biographical Sketch: Dr. Adam Kirn is an Associate Professor of Engineering Education in the Department of Electrical and Biomedical Engineering at the University of Nevada, Reno. His research focuses on the ways students' motivations and identities shape and are shaped by their engineering education experiences. The results of this work seek to implement evidence-based practices to create educational defaults that foster student success and thriving. Adam has a B.S. in Biomedical Engineering from Rose-Hulman Institute of Technology, an M.S. in Bioengineer, and a Ph.D. in Engineering and Science Education from Clemson University.

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Lecture / Discussion Thu, 25 Feb 2021 09:26:14 -0500 2021-03-10T15:30:00-05:00 2021-03-10T16:30:00-05:00 Off Campus Location Engineering Education Research Lecture / Discussion Dr. Adam Kirn
CCMB / DCMB Weekly Seminar Series (March 10, 2021 4:00pm) https://events.umich.edu/event/82479 82479-21108092@events.umich.edu Event Begins: Wednesday, March 10, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract: Single-cell technologies have transformed biomedical research in the last few years. With single-cell sequencing, we can now simultaneously measure thousands of genomics features in a large number of cells, which provides an ultrahigh resolution phenotypic map for each individual. However, single-cell protocols are complex. Even with the most sensitive platforms, the data are often sparse and noisy. Recent development of single-cell multi-omics and spatial transcriptomics technologies further imposed additional challenges on data integration. In this talk, I will present several machine learning methods that my group recently developed for single-cell and spatial transcriptomics data analysis. I will discuss methods for simultaneous denoising, clustering and batch effect correction, single-cell multi-omics data integration, identification of spatially variable genes, generation of super-resolution gene expression, and inference of cell type distribution in spatial transcriptomics. I will illustrate our methods by showing results from ongoing collaborations on cardiometabolic disease and applications to brain and cancer data.
* * *
Biography: Dr. Li’s research interests include statistical genetics and genomics, bioinformatics, and computational biology. The central theme of her current research is to use statistical and computational approaches to understand cellular heterogeneity in human-disease-relevant tissues, to characterize gene expression diversity across cell types, to study the patterns of cell state transition and crosstalk of various cells using data generated from single-cell and spatial transcriptomics studies, and to translate these findings to the clinics. In addition to methods development, Dr. Li is also interested in collaborating with researchers seeking to identify complex disease susceptibility genes and acting cell types. She is Director of Biostatistics for the Gene Therapy Program at Penn, where she advises biostatistics and bioinformatics analysis for various gene therapy studies. She is also Chair of the Graduate Program in Biostatistics. Dr. Li actively serves in the scientific community. She served as a regular member for the NIH Genomics, Computational Biology and Technology (GCAT) study section for 6 years, and the NHGRI Center for Inherited Disease Research (CIDR) for 3 years. She is an Associate Editor of Annals of Applied Statistics, Statistics in Biosciences, PLOS Computational Biology, and Human Genetics and Genomics Advances. She is an elected member of the International Statistical Institute and a Fellow of the American Statistical Association.

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

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Livestream / Virtual Wed, 24 Feb 2021 12:57:46 -0500 2021-03-10T16:00:00-05:00 2021-03-10T17:00:00-05:00 Off Campus Location DCMB Seminar Series Livestream / Virtual
DCM&B Tools and Technology Seminar (March 11, 2021 12:00pm) https://events.umich.edu/event/79919 79919-20515552@events.umich.edu Event Begins: Thursday, March 11, 2021 12:00pm
Location: Off Campus Location
Organized By: DCMB Tools and Technology Seminar

Genomic and epigenomic features are captured at a genome-wide level by using high-throughput sequencing technologies. Peak calling is one of the first essential steps in analyzing these features by delineating regions such as open chromatin regions and transcription factor binding sites. Our original peak calling software, F-Seq, has been widely used and shown to be the most sensitive and accurate peak caller for DNase I hypersensitive sites sequencing (DNase-seq) data. However, F-Seq lacks support for user-input control dataset nor reporting test statistics, limiting its ability to capture systematic and experimental biases and accurately estimate background distributions. Here we present an improved version, F-Seq2, which combined the power of kernel density estimation and a dynamic “continuous” Poisson distribution to robustly account for local biases and solve ties when ranking candidate peaks. In F-score and motif distance analysis, we demonstrated the superior performance of F-Seq2 than other competing peak callers used by the ENCODE Consortium on simulated and real ATAC-seq and ChIP-seq datasets. The output of F-Seq2 is suitable for irreproducible discovery rate (IDR) analysis as the test statistics calculated for individual candidate summit and ties are robustly solved.

Tool Link: https://github.com/Boyle-Lab/F-Seq2

URL for remote viewing: https://umich-health.zoom.us/j/94886745590?pwd=LzhLU243K2ZhbXNzU1BJRHQ5V25BZz09

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Livestream / Virtual Fri, 11 Dec 2020 08:08:59 -0500 2021-03-11T12:00:00-05:00 2021-03-11T13:00:00-05:00 Off Campus Location DCMB Tools and Technology Seminar Livestream / Virtual
BME 500 Seminar: George Christ (March 11, 2021 4:00pm) https://events.umich.edu/event/81389 81389-20889819@events.umich.edu Event Begins: Thursday, March 11, 2021 4:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Despite the well-documented capability of skeletal muscle to repair, regenerate, and remodel following injury, there remain a multitude of diseases, disorders, and traumatic injuries that result in irrecoverable loss of muscle structure and function. For example, volumetric muscle loss (VML) injuries are characterized by a degree of composite muscle tissue loss so severe, that it exceeds the native ability of the muscle to repair, thereby resulting in permanent cosmetic and functional deficits to the limbs, neck, or face. These injuries significantly impact both the civilian and military populations. Current treatment for VML injury involves surgical muscle transfer, although these procedures are often associated with both poor engraftment and donor site morbidity, as well as incomplete cosmesis and functional recovery. Not surprisingly, this unmet medical need has stimulated research efforts to develop new technologies for treatment of VML injuries. Recent attention has focused on development of tissue engineering (TE)/regenerative medicine (RM) technologies to provide more effective treatment options for large scale muscle injuries. A variety of preclinical approaches have been tried that include implantation of synthetic and/or natural extracellular matrices/scaffolds/constructs at the site of VML injury, both with and without a cellular component. Extant data indicate that the inclusion of a cellular component generally leads to a greater degree of functional improvement. Consistent with these preclinical results, recent clinical studies for treatment of VML injury, solely with implanted decellularized extracellular matrix scaffolds, have provided evidence for modest functional recovery but with little de novo muscle tissue regeneration at the injury site. More recently, bio-printed tissue engineered constructs and their potential applications to treatment of VML injury have been reported in the literature. While these initial clinical and preclinical observations are encouraging for the TE/RM paradigm, full structural and functional recovery has yet to be achieved, and thus, there remains significant room for therapeutic advancement. To this end, I will describe our highly collaborative efforts to boost development and evaluation of a range of implantable regenerative therapeutics (biomaterials and tissue engineered constructs) in biologically relevant animal models. The overall goal is to increase the efficiency of clinical translation of TE/RM technologies capable of more complete functional recovery following repair of VML injury.

ZOOM LINK: https://umich.zoom.us/j/94405051853

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Lecture / Discussion Mon, 08 Mar 2021 11:13:19 -0500 2021-03-11T16:00:00-05:00 2021-03-11T17:00:00-05:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Logo
RNA Seminar featuring: James Nuñez, HHMI Hanna Gray Fellow, University of California, San Francisco (March 15, 2021 4:00pm) https://events.umich.edu/event/81286 81286-20881887@events.umich.edu Event Begins: Monday, March 15, 2021 4:00pm
Location: Off Campus Location
Organized By: Center for RNA Biomedicine

REGISTRATION REQUIRED: https://umich.zoom.us/webinar/register/WN_f8wC8rrJQzuhYzTEXoW69Q


ABSTRACT
General approaches for heritably altering gene expression would enable many discovery and therapeutic efforts. I will present CRISPRoff— a programmable epigenetic memory writer consisting of a single dead Cas9 fusion protein that establishes DNA methylation and repressive histone modifications to turn off transcription. Transient CRISPRoff expression initiates highly specific DNA methylation and gene repression that is maintained through cell division and differentiation of stem cells to neurons. Pairing CRISPRoff with genome-wide screens and analysis of chromatin marks enabled us to explore the rules for heritable silencing. We identify sgRNAs capable of silencing the large majority of genes including those lacking canonical CpG islands (CGIs) and reveal a wide targeting window extending beyond annotated CGIs. Our finding that targeted DNA methylation outside of CGIs leads to memorized gene silencing expands the canonical model of methylation-based silencing and broadly enables diverse applications including genome-wide screens, multiplexed cell engineering, enhancer silencing, and mechanistic exploration of epigenetic inheritance.

KEYWORDS: CRISPR, transcription, epigenetics
Flyer in PDF: https://rna.umich.edu/wp-content/uploads/2021/02/Seminar-Flyer-03152021-Nunez.pdf

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Lecture / Discussion Thu, 18 Feb 2021 09:21:31 -0500 2021-03-15T16:00:00-04:00 2021-03-15T17:00:00-04:00 Off Campus Location Center for RNA Biomedicine Lecture / Discussion James Nunez, Ph.D. UCSF
Innovations in Global Maternal Healthcare Delivery (March 15, 2021 5:00pm) https://events.umich.edu/event/82932 82932-21225228@events.umich.edu Event Begins: Monday, March 15, 2021 5:00pm
Location: Off Campus Location
Organized By: Center for the History of Medicine

Hi UMMS!

NextGen Med and the Society for the History and Philosophy of Medicine are excited to co-host an educational discussion on Monday, March 15th from 5-6PM via Zoom! Please join us for a talk and Q&A, "How Philanthropy Can Catalyze Innovation in Global Public Health: Maternal, Newborn, and Child Health Focuses in the Gates Foundation," with Program Officer Mrs. Anisha Gururaj.

Anisha Gururaj is a Program Officer at the Bill & Melinda Gates Foundation, in the Maternal Newborn Child Health, Discovery & Tools team, where she develops strategy and manages an investment portfolio focused on developing and delivering novel technologies, like digital health, AI, and connected diagnostics, to transform maternal and newborn health across sub-Saharan Africa and South Asia. Previously, she has worked for a wide variety of technology and public health-focused organizations, ranging from the Baltimore city health department to med device startups and large manufacturing companies. She has a B.S. in Chemical-Biological Engineering from MIT and a dual MSc in Global Governance & Diplomacy and Women's Health Sciences from the University of Oxford where she studied as a Rhodes Scholar.

Zoom link here: https://umich.zoom.us/j/93942689324
Meeting ID: 939 4268 9324

Hope to see you there!

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Livestream / Virtual Thu, 11 Mar 2021 12:50:14 -0500 2021-03-15T17:00:00-04:00 2021-03-15T18:15:00-04:00 Off Campus Location Center for the History of Medicine Livestream / Virtual
TSCA @ 5 Years: Opportunities to Act with Foresight (March 16, 2021 7:00pm) https://events.umich.edu/event/82485 82485-21108121@events.umich.edu Event Begins: Tuesday, March 16, 2021 7:00pm
Location: Off Campus Location
Organized By: Michigan Lifestage Environmental Exposures and Disease Center

The University of Michigan M-LEEaD Center is co-sponsoring an event to mark the 5-year anniversary of the bipartisan legislation called the Frank R. Lautenberg Chemical Safety for the 21st Century Act. This reform law was designed to modernize U.S. industrial chemical policy to promote health, but has it lived up to its promise?

Public understanding is limited regarding how exposures to toxic chemicals affect health and how they might be regulated. Unlike pharmaceuticals, industrial and commercial chemicals are rarely tested for safety before they reach the U.S. market. The 1976 TSCA has been widely acknowledged to be a weak and ineffective law, and widespread exposures and harms continue. In the U.S., everyone is exposed to industrial and toxic chemicals, dozens and probably hundreds – well before birth. The amount of chemicals manufactured and imported continues to grow – it is trillions of pounds – and these chemicals remain largely unregulated. At the same time, we have seen an increase in chronic diseases, such as diabetes, autism, and infertility. Not everyone is equally at risk, and a higher burden of disease falls on low wealth communities and communities of color. These health disparities in exposures and health effects are illustrated and exacerbated by COVID.

The amended TSCA gave the U.S. Environmental Protection Agency new requirements and authorities. The public health impact points to the need for the U.S. EPA to fully use its new powers to evaluate all risks from hazardous chemicals and set policies which protect health and are accountable to high-risk communities. Preventive actions are urgently needed.

Watch “THE FOREVER CHEMICALS” documentary (2019, 26 min) at Great Lakes Now then join the March 16 forum. https://www.greatlakesnow.org/fc
“The Forever Chemicals” is an Emmy-winning examination of the impact of PFAS contamination in west Michigan
communities.

LEARN MORE AT OUR LIVE VIRTUAL PANEL DISCUSSION (registration required) on March 16 with Sandra Svoboda, “The Forever Chemicals” co-producer and Great Lakes Now Program Director; Tracey Woodruff, PhD, MPH, Professor, Ob/Gyn, Reproductive Sciences, University of CA-San Francisco; and Justin Onwenu, Environmental Justice Organizer, Sierra Club. Moderated by Patricia Koman, MPP, PhD, Research Investigator, Environmental Health Sciences, University of Michigan with Welcoming remarks from Gilbert S. Omenn, MD, PhD, the Harold T Shapiro Distinguished University Professor of Medicine (also Professor of Computational Medicine & Bioinformatics; Internal Medicine; Human Genetics; and Public Health, Univ of Mich).

REGISTER HERE https://bit.ly/37I2JaU

SPONSORED BY the Michigan Center on Lifestage Environmental Exposures and Disease (M-LEEaD) • U-M Environmental Health Sciences • Detroit Public Television • Wayne State CURES Center • U-M Sustainable Living Experience • UROP (U-M Undergraduate Research Opportunity Program) • UMIHSA (U-M Industrial Hygiene Students Association) • EHSA (Environmental Health Student Association) • American Chemical Society Outreach Organization • U-M Health Policy Student Association • Ecology Center • Michigan Environmental Justice Coalition • UCSF Program for Reproductive Health and the Environment • UCSF EaRTH Center

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Conference / Symposium Wed, 03 Mar 2021 12:57:09 -0500 2021-03-16T19:00:00-04:00 2021-03-16T20:30:00-04:00 Off Campus Location Michigan Lifestage Environmental Exposures and Disease Center Conference / Symposium March 16 Panel Discussion: TSCA @ 5 Years
CCMB / DCMB Weekly Seminar Series featuring Sriram Chandrasekaran (Assistant Professor, Biomedical Engineering) (March 17, 2021 4:00pm) https://events.umich.edu/event/82825 82825-21179592@events.umich.edu Event Begins: Wednesday, March 17, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract: Drug combinations have the potential to greatly expand our pharmacopeia while reducing both cost and drug resistance. Yet the current drug-discovery approach is unable to screen the astronomical number of possible combinations in different cell types and does not account for the complex environment inside the body. We have developed AI tools - INDIGO and MAGENTA - that predict the efficacy of drug combinations based on the properties of the drugs, the pathogen, and the infection environment. We are also using modeling to identify drugs that work in synergy with the host immune system. Using INDIGO and MAGENTA, we have identified highly synergistic combinations of repurposed drugs to treat drug resistant infections including Tuberculosis, the deadliest bacterial infection. INDIGO also accurately predicts the outcome of past clinical trials of drug combinations. Our ultimate goal is to create a personalized approach to treat infections using AI.
* * *
Biography: Chandrasekaran received his bachelor’s degree in Biotechnology from Anna University in 2008, and a PhD in Biophysics from the University of Illinois at Urbana-Champaign in 2013. He worked at Harvard University and MIT as a Harvard Junior Fellow between 2013 and 2016 and became an Assistant Professor at UM in 2017. His lab develops systems biology algorithms for drug discovery. Computer models from his lab like INDIGO and MAGENTA are being used to design effective therapies against drug resistant pathogens. His lab also develops systems biology algorithms to understand metabolic regulation. The approaches that they have created (PROM, ASTRIX, DFA, EGEM and GEMINI) perform complementary functions in modeling of metabolic and regulatory networks. Chandrasekaran’s research has been published in Cell, Genome Biology, mBio, and PNAS. For his work, Chandrasekaran previously received the 2013 Harvard Junior Fellowship, the 2011 Howard Hughes Medical Institute (HHMI) International Predoctoral Fellowship, the 2014 William Milton Fund award, 2018 UM Precision Health Investigator Award, and the 2018 Distinguished Young Investigator Award from the AICHE COBRA society.


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

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Livestream / Virtual Fri, 05 Mar 2021 14:44:14 -0500 2021-03-17T16:00:00-04:00 2021-03-17T17:00:00-04:00 Off Campus Location DCMB Seminar Series Livestream / Virtual Sriram Chandrasekaran, PhD (Assistant Professor, Biomedical Engineering)
DCM&B Tools and Technology Seminar (March 18, 2021 12:00pm) https://events.umich.edu/event/79920 79920-20515553@events.umich.edu Event Begins: Thursday, March 18, 2021 12:00pm
Location: Off Campus Location
Organized By: DCMB Tools and Technology Seminar

Tool Link: WIZARD: https://github.com/ML4LHS/wizard
Tool Link: Clinspacy: https://github.com/ML4LHS/clinspacy
Tool Link: Runway: https://github.com/ML4LHS/runway

URL for remote viewing: https://umich-health.zoom.us/j/94886745590?pwd=LzhLU243K2ZhbXNzU1BJRHQ5V25BZz09

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Livestream / Virtual Fri, 11 Dec 2020 08:11:56 -0500 2021-03-18T12:00:00-04:00 2021-03-18T13:00:00-04:00 Off Campus Location DCMB Tools and Technology Seminar Livestream / Virtual
What Should Education Innovation at Michigan Medicine Be Known For? (March 18, 2021 12:00pm) https://events.umich.edu/event/82425 82425-21098206@events.umich.edu Event Begins: Thursday, March 18, 2021 12:00pm
Location: Off Campus Location
Organized By: RISE (Research. Innovation. Scholarship. Education.)

Please join us for our next Virtual Talking Circle on March 18 at 12:00 pm, where we will discuss how to construct a more cohesive direction for education innovation at our institution. What problems should we be focusing on? Where should we as an “innovation system” invest?

RISE will be working across our entire community to construct such a vision, a process suggested by previous Virtual Talking Circles, the RISE Advisory Council, and education leaders in the biomedical sciences, as well as undergraduate, graduate, and continuing medical education. A specific proposal will be presented for reflection and feedback by attendees, and we invite all of you to attend and provide input into this conversation.

Please also invite your colleagues who may be interested. See you then!

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Workshop / Seminar Tue, 23 Feb 2021 07:25:35 -0500 2021-03-18T12:00:00-04:00 2021-03-18T13:00:00-04:00 Off Campus Location RISE (Research. Innovation. Scholarship. Education.) Workshop / Seminar RISE Virtual Talking Circle
BME 500 Seminar: Daniel Rueckert (March 18, 2021 4:00pm) https://events.umich.edu/event/81390 81390-20889820@events.umich.edu Event Begins: Thursday, March 18, 2021 4:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Zoom Link: https://cwru.zoom.us/webinar/register/WN_tmHJ7ArQRyO01NN6SfYYtg

Hosted by Dr. Frederick Epstein

Seminar Abstract:
The talk will focus on the use of deep learning techniques for the discovery and quantification of clinically useful information from medical images. The talk will describe how deep learning can be used for the reconstruction of medical images from undersampled data, image super-resolution, image segmentation and image classification. It will also show the clinical utility of applications of deep learning for the interpretation of medical images in applications such as brain tumour segmentation, cardiac image analysis and applications in neonatal and fetal imaging. Finally, it will be discussed how deep learning may change the future of medical imaging. https://openbme.org/

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Lecture / Discussion Mon, 15 Mar 2021 14:07:10 -0400 2021-03-18T16:00:00-04:00 2021-03-18T17:00:00-04:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Logo
"Coming together in challenging times: Multicellular assembly in engineered microenvironments" (March 23, 2021 4:00pm) https://events.umich.edu/event/83016 83016-21243198@events.umich.edu Event Begins: Tuesday, March 23, 2021 4:00pm
Location: Off Campus Location
Organized By: Center for Cell Plasticity and Organ Design

The Center for Cell Plasticity and Organ Design, alongside the Department of Biomedical Engineering, is proud to present a seminar with guest speaker Brendon M. Baker, PhD.

Dr. Baker is an Assistant Professor of Biomedical Engineering at the University of Michigan.

The talk is entitled, "Coming together in challenging times: Multicellular assembly in engineered microenvironments"

Faculty Host: Ariella Shikanov, PhD, Associate Professor of Biomedical Engineering

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Lecture / Discussion Wed, 17 Mar 2021 15:35:19 -0400 2021-03-23T16:00:00-04:00 2021-03-23T17:00:00-04:00 Off Campus Location Center for Cell Plasticity and Organ Design Lecture / Discussion Flyer for the Event
Bioethics Discussion: Accidents (March 23, 2021 7:00pm) https://events.umich.edu/event/58839 58839-14563731@events.umich.edu Event Begins: Tuesday, March 23, 2021 7:00pm
Location: Off Campus Location
Organized By: The Bioethics Discussion Group

A discussion we were not meant to have.

Join us at: https://umich.zoom.us/j/99926126455.

A few readings to consider:
––Defining Failure: The Language, Meaning and Ethics of Medical Error
––Taking the blame: appropriate responses to medical error
––Medical Error and Moral Luck
––When AIs Outperform Doctors: Confronting the Challenges of a Tort-Induced Over-Reliance on Machine Learning

For more information and/or to receive a copy of the readings visit http://belmont.bme.umich.edu/bioethics-discussion-group/discussions/058-accidents/.

––
By accident, by choice, or not at all, the three ways of arriving somewhere, such as the blog: https://belmont.bme.umich.edu/incidental-art/

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Lecture / Discussion Fri, 08 Jan 2021 09:39:36 -0500 2021-03-23T19:00:00-04:00 2021-03-23T20:30:00-04:00 Off Campus Location The Bioethics Discussion Group Lecture / Discussion Accidents
Concussion Prevention: A Multi-Disciplinary Approach (March 24, 2021 11:30am) https://events.umich.edu/event/83111 83111-21272914@events.umich.edu Event Begins: Wednesday, March 24, 2021 11:30am
Location: Off Campus Location
Organized By: U-M Office of Research

Please join the Michigan Exercise & Sport Science Initiative and the University of Michigan Concussion Center on Wednesday, March 24, 2021, at 11:30am for a panel discussion focusing on concussion prevention. You will learn concussion prevention methods from experts in athlete conditioning, equipment manufacturing, and sports policy at the state, national, and international levels.

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Lecture / Discussion Wed, 17 Mar 2021 10:43:41 -0400 2021-03-24T11:30:00-04:00 2021-03-24T12:30:00-04:00 Off Campus Location U-M Office of Research Lecture / Discussion Concussion
Community Cultural Wealth, Program Evaluation, and ASEE CDEI, Oh My! (March 24, 2021 3:30pm) https://events.umich.edu/event/83003 83003-21235293@events.umich.edu Event Begins: Wednesday, March 24, 2021 3:30pm
Location: Off Campus Location
Organized By: Engineering Education Research

As a sociologist who has been working in STEM and Engineering Education for 18 years, and who isn’t on the tenure track, Liz will share a little bit about a few different areas (Research, Evaluation, and Service) that she has focused on in her career.  Assets-based frameworks for understanding student experience are receiving more and more visibility these days and Liz’s work has used critical race theory Community Cultural Wealth (Samuelson & Litzler, JEE 2016) to understand the ways minoritized engineering undergraduates deployed their cultural assets to persist in engineering. She is also now working on further Community Cultural Wealth research with her colleagues on the PNW-LSAMP project.  She will also talk about using her social science research skills to conduct high quality program evaluation of projects focused on improving DEI in STEM.  Finally, she’ll share about the work of the ASEE Commission on Diversity, Equity, and Inclusion, of which she is the current chair. CDEI is a great resource for the community and also a wonderful opportunity to develop new connections with colleagues while providing important service to the engineering education field.

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Lecture / Discussion Fri, 12 Mar 2021 14:42:39 -0500 2021-03-24T15:30:00-04:00 2021-03-24T16:30:00-04:00 Off Campus Location Engineering Education Research Lecture / Discussion Dr. Elizabeth Litzler
CCMB / DCMB Weekly Seminar Series Featuring Duncan K. Ralph (Fred Hutchinson Cancer Research Center) (March 24, 2021 4:00pm) https://events.umich.edu/event/82733 82733-21169592@events.umich.edu Event Begins: Wednesday, March 24, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract: Antibodies are an integral part of the adaptive immune response, and are a critical component of both vaccine-induced and naturally-acquired immunity. The development of deep sequencing approaches in recent years has allowed us to sample a significant fraction of the diverse repertoire of B cell receptor sequences from which antibodies are made. These sequences encode a wealth of information on the somatic rearrangement and evolutionary processes that determine the contours of our antibody repertoires, and thus our ability to respond appropriately to pathogens and vaccines. Extracting this information, however, requires a careful inference approach across several different analysis steps. I will describe the computational approaches that we have taken to solving these problems, which constitute the partis software package, and describe their application in several projects, including HIV and Dengue data.

* * *

Biography: Duncan attended the University of California at Santa Cruz for his undergraduate studies in physics, completing his thesis on energy transport in condensed matter theory in 2005. He completed his PhD at the Massachusetts Institute of Technology in 2014, working on the Large Hadron Collider at the European particle physics laboratory (CERN). His thesis described the observation of Higgs boson decays to four leptons. Since 2014, he has worked in Frederick Matsen’s lab at the Fred Hutchinson Cancer Research Center, first as a postdoctoral researcher and more recently as a staff scientist, writing new computational methods for the analysis of B cell receptor deep sequencing data.

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

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Livestream / Virtual Thu, 04 Mar 2021 11:20:24 -0500 2021-03-24T16:00:00-04:00 2021-03-24T17:00:00-04:00 Off Campus Location DCMB Seminar Series Livestream / Virtual
5th Annual RNA Symposium, "Processing RNA" (March 25, 2021 11:00am) https://events.umich.edu/event/80161 80161-20572609@events.umich.edu Event Begins: Thursday, March 25, 2021 11:00am
Location: Off Campus Location
Organized By: Center for RNA Biomedicine

FOR MORE DETAILS & ABSTRACTS VISIT: https://rna.umich.edu/2021-symposium/

Thursday, March 25, 2021
11:00 / Welcome
11:05 / KEYNOTE 1: Tracy Johnson, UCLA, “RNA Splicing, Chromatin Modification, and the Coordinated Control of Gene expression”
12:00 / Short break
12:10 / KEYNOTE 2: Kevin Weeks, UNC, “Structure-Based Discovery of New Functions in Large RNAs”
1:05 / Data Blitz: Cathy Smith, Daniel Peltier, Yan Zhang
1:35 / KEYNOTE 3: Feng Zhang, MIT, “Exploration of Biological Diversity to Discover Novel Molecular Technologies”
2:30 / Close Day 1

Friday, March 26, 2021
11:00 / Welcome
11:05 / KEYNOTE 4: Brenda Bass, University of Utah, “Distinguishing self and non-self dsRNA in vertebrates and invertebrates”
12:00 / Short break
12:10 / KEYNOTE 5: Christopher Lima, Sloan-Kettering Institute, “Mechanisms that target RNA for destruction”
1:05 / Data Blitz: Meredith Purchal, Adrien Chauvier, Shannon Wright
1:35 / Panel discussion with keynote speakers
2:30 / Close Day 2

Liveblogging by MiSciWriters! https://misciwriters.com/

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Lecture / Discussion Tue, 23 Mar 2021 15:03:26 -0400 2021-03-25T11:00:00-04:00 2021-03-25T14:30:00-04:00 Off Campus Location Center for RNA Biomedicine Lecture / Discussion 5th Annual RNA Symposium
DCM&B Tools and Technology Seminar (March 25, 2021 12:00pm) https://events.umich.edu/event/82051 82051-21012687@events.umich.edu Event Begins: Thursday, March 25, 2021 12:00pm
Location: Off Campus Location
Organized By: DCMB Tools and Technology Seminar

URL for remote viewing: https://umich-health.zoom.us/j/94886745590?pwd=LzhLU243K2ZhbXNzU1BJRHQ5V25BZz09

(please note that this session will not be recorded)

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Workshop / Seminar Tue, 23 Mar 2021 17:42:45 -0400 2021-03-25T12:00:00-04:00 2021-03-25T13:00:00-04:00 Off Campus Location DCMB Tools and Technology Seminar Workshop / Seminar
LHS Collaboratory March Session (March 25, 2021 12:00pm) https://events.umich.edu/event/82008 82008-21006745@events.umich.edu Event Begins: Thursday, March 25, 2021 12:00pm
Location: Off Campus Location
Organized By: Department of Learning Health Sciences

Speakers Stefan Boes, PhD and Sarah Mantwill, PhD from the university of Lucerne will discuss the Swiss Learning Health System.

Promoting and supporting uptake of evidence and evidence-informed decision-making in health-systems related policy and practice is a challenge. In Switzerland, the need to address this matter has been increasingly emphasized by different actors in the health system. In particular, the lack of comprehensive coordination efforts in the field of health services research, and subsequent knowledge translation activities, has been stressed. In response, the Swiss Learning Health System (SLHS) was established as a nationwide project in 2017, currently involving 10 academic partner institutions. One of the overarching objectives of the SLHS is to bridge research, policy, and practice by providing an infrastructure that supports learning cycles by: continuously identifying issues relevant to the Swiss health system, systemizing relevant evidence, presenting potential courses of action, and revising and reshaping responses. Key features of learning cycles in the SLHS include the development of policy/evidence briefs that serve as a basis for stakeholder dialogues with actors from research, policy and practice. Issues that are identified to be further pursued are monitored for potential implementation and eventually evaluated to inform new learning cycles and to support continuous learning within the system.

Dr. Boes and Dr. Mantwill will provide an overview of the SLHS and its key features, as well as its capacity building efforts to train young researchers in the field of learning health systems, and the development of a centralized metadata repository in support of creating a sufficient large evidence basis to support learning cycles in the Swiss health system. Further, they will discuss lessons learned from the past and the newest developments of the SLHS in light of a second funding phase supported by the Swiss government.

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Livestream / Virtual Thu, 25 Feb 2021 23:57:27 -0500 2021-03-25T12:00:00-04:00 2021-03-25T13:30:00-04:00 Off Campus Location Department of Learning Health Sciences Livestream / Virtual LHS Collaboratory Logo
BME 500 Seminar: Warren L. Grayson (March 25, 2021 4:00pm) https://events.umich.edu/event/81391 81391-20889821@events.umich.edu Event Begins: Thursday, March 25, 2021 4:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Tissue engineering provides a viable means of regenerating bone and skeletal muscle tissues following injuries that lead to large volumetric defects. Our lab has developed advanced biomaterial and stem cell-based approaches to promote functional recovery following volumetric muscle loss and critical-sized craniofacial bone injuries. This presentation will focus on three areas of ongoing research: (1) I will present our lab’s efforts to regenerate vascularized and innervated skeletal muscle in mice including our recent studies using human pluripotent stem cells. (2) Recently, our group completed a study focused on designing biomaterials to guide bone regeneration in situ in minipigs using intraoperative protocols for combining autologous stem cells with 3D-printed scaffolds. (3) Understanding the interaction between vascular cells and osteoprogenitors is critical for developing effective treatment methods. I will describe recent studies in which we developed a quantitative imaging platform for characterizing the spatial relationships between cell populations in the native murine calvarium. https://openbme.org/

ZOOM LINK TO REGISTER: https://cwru.zoom.us/webinar/register/WN_Kgyl3yf4TcKvlk9xNKluhA

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Lecture / Discussion Sun, 21 Mar 2021 17:46:23 -0400 2021-03-25T16:00:00-04:00 2021-03-25T17:00:00-04:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Logo
5th Annual RNA Symposium, "Processing RNA" (March 26, 2021 11:00am) https://events.umich.edu/event/80161 80161-20572610@events.umich.edu Event Begins: Friday, March 26, 2021 11:00am
Location: Off Campus Location
Organized By: Center for RNA Biomedicine

FOR MORE DETAILS & ABSTRACTS VISIT: https://rna.umich.edu/2021-symposium/

Thursday, March 25, 2021
11:00 / Welcome
11:05 / KEYNOTE 1: Tracy Johnson, UCLA, “RNA Splicing, Chromatin Modification, and the Coordinated Control of Gene expression”
12:00 / Short break
12:10 / KEYNOTE 2: Kevin Weeks, UNC, “Structure-Based Discovery of New Functions in Large RNAs”
1:05 / Data Blitz: Cathy Smith, Daniel Peltier, Yan Zhang
1:35 / KEYNOTE 3: Feng Zhang, MIT, “Exploration of Biological Diversity to Discover Novel Molecular Technologies”
2:30 / Close Day 1

Friday, March 26, 2021
11:00 / Welcome
11:05 / KEYNOTE 4: Brenda Bass, University of Utah, “Distinguishing self and non-self dsRNA in vertebrates and invertebrates”
12:00 / Short break
12:10 / KEYNOTE 5: Christopher Lima, Sloan-Kettering Institute, “Mechanisms that target RNA for destruction”
1:05 / Data Blitz: Meredith Purchal, Adrien Chauvier, Shannon Wright
1:35 / Panel discussion with keynote speakers
2:30 / Close Day 2

Liveblogging by MiSciWriters! https://misciwriters.com/

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Lecture / Discussion Tue, 23 Mar 2021 15:03:26 -0400 2021-03-26T11:00:00-04:00 2021-03-26T14:30:00-04:00 Off Campus Location Center for RNA Biomedicine Lecture / Discussion 5th Annual RNA Symposium
CCMB / DCMB Weekly Seminar (March 31, 2021 4:00pm) https://events.umich.edu/event/83395 83395-21369780@events.umich.edu Event Begins: Wednesday, March 31, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract:

Large, deeply phenotyped cohorts are reshaping the world of environmental epidemiology. Two such “big data” resources that are reshaping how we understand environmental health are electronic health records and human cohorts with genome-wide molecular phenotyping. Each provides a unique perspective that is moving the field closer towards “personalized” insights into environmental health risks. Here I will talk about a series of studies which utilize electronic health records and molecularly phenotyped cohorts to investigate vulnerable populations, gene-environment interactions, and epigenetic biomarkers of environmental sensitivity. Together these studies are helping us to understand environmental health risks in a new light.

Short bio:

Dr. Cavin Ward-Caviness is a Principal Investigator in the Public Health and Integrated Toxicology Division of the US Environmental Protection Agency. With a background in computational biology and environmental epidemiology, Dr. Ward-Caviness seeks to understand the environmental factors which influence health in vulnerable populations and the molecular mechanisms that influence environmental health risks. The Ward-Caviness lab uses a variety of “big data” approaches, and Dr. Ward-Caviness is the PI of the EPA CARES research resource, which allows researchers to study environmental health effects in vulnerable patient populations, e.g. individuals with heart failure, using large electronic health record databases. Dr. Ward-Caviness is also interested in how epigenetics and metabolomics can serve as an early indicator of adverse health effects from chemical and social environmental exposures and in particular how molecular biomarkers can give us insight into how the environment may accelerate the aging process and thus contribute to chronic disease. By integrating molecular and clinical data, Dr. Ward-Caviness seeks to understand environmental health as a way to advance personalized medicine and reduce health disparities.

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

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Livestream / Virtual Mon, 29 Mar 2021 15:15:11 -0400 2021-03-31T16:00:00-04:00 2021-03-31T17:00:00-04:00 Off Campus Location DCMB Seminar Series Livestream / Virtual
DCM&B Tools and Technology Seminar (April 1, 2021 12:00pm) https://events.umich.edu/event/79922 79922-20515555@events.umich.edu Event Begins: Thursday, April 1, 2021 12:00pm
Location: Off Campus Location
Organized By: DCMB Tools and Technology Seminar

Many protein function databases are built on automated or semi-automated curations and can contain various annotation errors. The correction of such misannotations is critical to improving the accuracy and reliability of the databases. We proposed a new approach to detect potentially incorrect Gene Ontology (GO) annotations by comparing the ratio of annotation rates (RAR) for the same GO term across different taxonomic groups, where those with a relatively low RAR usually correspond to incorrect annotations. As an illustration, we applied the approach to 20 commonly studied species in two recent UniProt-GOA releases and identified 250 potential misannotations in the 2018-11-6 release, where only 25% of them were corrected in the 2019-6-3 release. Importantly, 56% of the misannotations are “Inferred from Biological aspect of Ancestor (IBA)”, i.e. reviewed computational annotations based on phylogenetic analysis. This is in contrast to previous observations that attributed misannotations mainly to “Inferred from Sequence or structural Similarity (ISS)”, probably reflecting an error source shift due to the new developments of function annotation databases. The results demonstrated a simple but efficient misannotation detection approach that is useful for developing taxonomic constraints in large-scale comparative protein function studies.

Tool Link: https://zhanglab.ccmb.med.umich.edu/RAR

URL for remote viewing: https://umich-health.zoom.us/j/94886745590?pwd=LzhLU243K2ZhbXNzU1BJRHQ5V25BZz09

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Livestream / Virtual Fri, 11 Dec 2020 08:17:31 -0500 2021-04-01T12:00:00-04:00 2021-04-01T13:00:00-04:00 Off Campus Location DCMB Tools and Technology Seminar Livestream / Virtual
BME 500 Seminar: Tim Downing (April 1, 2021 4:00pm) https://events.umich.edu/event/81392 81392-20889822@events.umich.edu Event Begins: Thursday, April 1, 2021 4:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

https://openbme.org/

ZOOM LINK TO REGISTER: https://cwru.zoom.us/webinar/register/WN_iY_PMZevQwWRYkMyK7ifzA

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Lecture / Discussion Fri, 26 Mar 2021 14:01:59 -0400 2021-04-01T16:00:00-04:00 2021-04-01T17:00:00-04:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Logo
BME Seminar: Synthetic Genome Engineering for Cell and Tissue Engineering (April 1, 2021 4:00pm) https://events.umich.edu/event/80692 80692-20783435@events.umich.edu Event Begins: Thursday, April 1, 2021 4:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Title: Synthetic Genome Regulation for Cell and Tissue Engineering

Abstract: Molecular heterogeneity is emerging as a critical feature of multicellular life. While single-cell analyses have revealed the existence of cell-to-cell variation in the levels and activities of the molecules responsible for gene regulation, the source of such variation is still poorly understood. The Downing Lab studies how genome replication contributes to epigenetic heterogeneity across stem cell populations. We recently developed a new sequencing method (Repli-Bisulfite Sequencing) that enables analysis of DNA methylation within newly replicated strands of DNA over time. Using this method, we discovered that much of the methylation heterogeneity observed within human embryonic stem cells (hESCs) is temporal in nature and associated with DNA replication. Here, we employ bioinformatic analyses to explore how properties of post-replication DNA methylation dynamics relate to well-established features of the genome and the broader chromatin landscape. Our findings reveal that unique patterns of methylome replication associate with distal regulatory regions throughout the genome, enrich for cytosine residues dynamically methylated across cell types, and coincide with the location of stem cell-specific transcription factor binding and chromatin architectures. We also find correlations between sub-cell cycle kinetics in DNA methylation and the divergence of bulk methylation patterns observed during multiple cell generations and natural aging. Taken together, our studies suggest that (epi)genome replication may act as an important source of (temporal) regulatory variation in hESCs while, simultaneously, conferring susceptibility to epigenetic drift throughout the human lifespan. Our lab is also interested in understanding how the chemical and biophysical microenvironment influences adult cell behavior and phenotype through epigenetic gene regulatory mechanisms. We hope to use this information in the design of next-generation biomaterials. The second part of this presentation will describe how focal adhesions and cell-mediated forces contribute to inefficiencies observed during the acquisition of stemness from somatic cell states.



Biography: Tim Downing has been on the faculty at UC Irvine since 2016 and holds a primary appointment in the Department of Biomedical Engineering. He also holds a courtesy appointment in the Department of Microbiology & Molecular Genetics. Tim received his B.S. in Chemical Engineering in 2008 from Northwestern University and Ph.D. in Bioengineering from UC Berkeley in 2013 under the mentorship of Dr. Song Li. As a Ford Foundation and UNCF/Merck Fellow, Tim completed his postdoctoral training in stem cell epigenomics with Dr. Alexander Meissner at Harvard University and the Broad Institute (Cambridge, Massachusetts). The Downing Lab focuses on understanding gene regulation during tissue development, regeneration, and disease progression. Building on this information, the lab also aims to develop molecular tools and biomaterials to synthetically regulate the epigenome for better control over cell fate and behavior. Tim is a 2019 NIH (DP2) New Innovator Award recipient and a 2020 recipient of the “Rising Star” Award from the Cellular and Molecular Bioengineering (CMBE) Special Interest Group within the Biomedical Engineering Society (BMES).

Zoom Registration Link: https://cwru.zoom.us/webinar/register/WN_iY_PMZevQwWRYkMyK7ifzA

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Workshop / Seminar Thu, 25 Mar 2021 13:09:17 -0400 2021-04-01T16:00:00-04:00 2021-04-01T17:00:00-04:00 Off Campus Location Biomedical Engineering Workshop / Seminar Dr. Timothy L. Downing, UC Irvine
RNA Seminar featuring: Natoya Peart, PhD, University of Pennsylvania (April 5, 2021 4:00pm) https://events.umich.edu/event/81288 81288-20881888@events.umich.edu Event Begins: Monday, April 5, 2021 4:00pm
Location: Off Campus Location
Organized By: Center for RNA Biomedicine

Registration required: https://umich.zoom.us/webinar/register/WN_0lUfePb0Qdac-cQZDpeiEQ


KEYWORDS: Alternative splicing, RNAMap, Esrp1

ABSTRACT: Coordinated regulation of alternative splicing is essential to the establishment of cell identity. The Epithelial Splicing Regulatory Proteins (Esrps), ESRP1 and ESRP2, are highly conserved paralogous proteins required for organogenesis of multiple organ systems and compromised function of Esrps contributes to human diseases and pathologies. Esrps are robustly expressed in the epithelial cells of the epidermis, large and small intestines, salivary glands, stomach, and a variety of other tissues, where they are vital in promoting an epithelial splicing network. Although ESRP1 and ESRP2 share partial functional redundancy, ESRP1 appears to play a larger role in regulating gene expression.
Using a combination of enhanced immunoprecipitation coupled with high throughput sequencing (eCLIP) in the epithelial cells of mouse epidermis and RNA sequencing analysis of alterations in splicing and total gene expression that result from epidermal ablation of Esrp1 and Esrp2 we generate a map of Esrp1 binding to RNA. We show that ESRP1 regulates splicing primarily through direct binding in a position-dependent manner to either promote exon inclusion or skipping. In particular, we show that Esrp1 binding upstream of or withing alternatively spliced exons suppresses exon inclusion, whilst binding downstream of the non-constitutive exon promotes exon inclusion. In addition, we identified widespread binding of ESRP1 in 3’ and 5’ untranslated regions (UTRs) of genes enriched for epithelial cell function suggesting that it directly regulates post-transcriptional gene expression steps in addition to splicing.


If you are having difficulties registering, please contact Martina Jerant at mjerant@umich.edu

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Lecture / Discussion Mon, 08 Mar 2021 12:23:08 -0500 2021-04-05T16:00:00-04:00 2021-04-05T17:00:00-04:00 Off Campus Location Center for RNA Biomedicine Lecture / Discussion Natoya Peart, PhD, University of Pennsylvania
Bioethics Discussion: Virtual Reality (April 6, 2021 7:00pm) https://events.umich.edu/event/58840 58840-14563732@events.umich.edu Event Begins: Tuesday, April 6, 2021 7:00pm
Location: Lurie Biomedical Engineering
Organized By: The Bioethics Discussion Group

A discussion like any other?

Join us at: https://umich.zoom.us/j/99926126455.

A few reading to consider:
––Internet-Delivered Health Interventions That Work: Systematic Review of Meta-Analyses and Evaluation of Website Availability
––Ethics of Virtual Reality in Medical Education and Licensure
––Wearables and the medical revolution
––Creating Bioethics Distance Learning Through Virtual Reality

For more information and/or to receive a copy of the readings visit http://belmont.bme.umich.edu/bioethics-discussion-group/discussions/059-virtual-reality/.

––
A decently maintained virtual reality may be found on the blog: https://belmont.bme.umich.edu/incidental-art/

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Lecture / Discussion Fri, 08 Jan 2021 09:39:24 -0500 2021-04-06T19:00:00-04:00 2021-04-06T20:30:00-04:00 Lurie Biomedical Engineering The Bioethics Discussion Group Lecture / Discussion Virtual Reality
CCMB / DCMB Weekly Seminar Series (April 7, 2021 4:00pm) https://events.umich.edu/event/83241 83241-21320453@events.umich.edu Event Begins: Wednesday, April 7, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract: More than 3,000 new Marine recruits were studied prospectively during their initial Marine-mandated two-week quarantine and their subsequent basic training at Parris Island. The COVID Health Action Response for Marines (CHARM) studied completed 20,000 study visits and obtained more than 70,000 biosamples including pre- to post- SARS-CoV-2 infections in more than 1000 recruits. Serological, transcriptomic, and epigenetic analyses identify the response signature to SARS-CoV-2 infection in these largely asymptomatic young adults. Phylogenetic analysis and modeling provide insight into epidemiology and guidance for public health measures.

* * *

Specialty: Neurology

Research Topics: Addiction, Apoptosis/Cell Death, Basal Ganglia, Bioinformatics, Brain, Cellular Immunity, Cerebral Cortex, Mathematical and Computational Biology, Multiple Sclerosis, Neuro-degeneration/protection, Receptors, Reproductive Biology, Signal Transduction, Theoretical Biology, Vaccine Development, Viruses and Virology

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

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Livestream / Virtual Tue, 23 Mar 2021 11:23:58 -0400 2021-04-07T16:00:00-04:00 2021-04-07T17:00:00-04:00 Off Campus Location DCMB Seminar Series Livestream / Virtual
Coded Bias - Free Film Screening (April 8, 2021 12:01am) https://events.umich.edu/event/83579 83579-21430617@events.umich.edu Event Begins: Thursday, April 8, 2021 12:01am
Location: Off Campus Location
Organized By: Information Assurance

The U-M Dissonance Event Series invites you to watch a free, on-demand screening of the documentary film Coded Bias. Watch Coded Bias on-demand anytime between Thursday, April 8, through Wednesday, April 14.

Visit the Dissonance events page to learn more, watch the trailer and receive the passcode you will need to access Coded Bias and watch the film for free.

https://safecomputing.umich.edu/events/dissonance/coded-bias-free-movie-viewing

Please also join us over Zoom on Thursday, April 15 at 4 p.m. EST for an "At the Movies" style panel discussion of the film Coded Bias. A panel of U-M experts will exchange views on the challenges presented by technologies that reflect the systemic biases in American society.

Links to the panel discussion can be found on the same event link above and on Happenings at Michigan on Thursday, April 15.

Access to Coded Bias and the panel discussion are brought to you by the Dissonance Event Series, ITS Information Assurance, the U-M School of Information, and the Law School’s Privacy and Technology Law Association.

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Film Screening Fri, 09 Apr 2021 14:43:58 -0400 2021-04-08T00:01:00-04:00 2021-04-08T23:59:00-04:00 Off Campus Location Information Assurance Film Screening Dissonance Event Series: Free Screening of the Film Coded Bias
DCM&B Tools and Technology Seminar (April 8, 2021 12:00pm) https://events.umich.edu/event/79923 79923-20515556@events.umich.edu Event Begins: Thursday, April 8, 2021 12:00pm
Location: Off Campus Location
Organized By: DCMB Tools and Technology Seminar

URL for remote viewing: https://umich-health.zoom.us/j/94886745590?pwd=LzhLU243K2ZhbXNzU1BJRHQ5V25BZz09

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Livestream / Virtual Fri, 11 Dec 2020 08:19:03 -0500 2021-04-08T12:00:00-04:00 2021-04-08T13:00:00-04:00 Off Campus Location DCMB Tools and Technology Seminar Livestream / Virtual
BME 500 Seminar: James Collins (April 8, 2021 4:00pm) https://events.umich.edu/event/81393 81393-20889823@events.umich.edu Event Begins: Thursday, April 8, 2021 4:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

James Collins, Ph.D.
Massachusetts Institute of Technology

https://openbme.org/

ZOOM LINK TO REGISTER: https://cwru.zoom.us/webinar/register/WN_MSUiecgNTLyXR5bM8HSnR

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Lecture / Discussion Fri, 02 Apr 2021 15:01:39 -0400 2021-04-08T16:00:00-04:00 2021-04-08T17:00:00-04:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Logo
Coded Bias - Free Film Screening (April 9, 2021 12:01am) https://events.umich.edu/event/83579 83579-21430618@events.umich.edu Event Begins: Friday, April 9, 2021 12:01am
Location: Off Campus Location
Organized By: Information Assurance

The U-M Dissonance Event Series invites you to watch a free, on-demand screening of the documentary film Coded Bias. Watch Coded Bias on-demand anytime between Thursday, April 8, through Wednesday, April 14.

Visit the Dissonance events page to learn more, watch the trailer and receive the passcode you will need to access Coded Bias and watch the film for free.

https://safecomputing.umich.edu/events/dissonance/coded-bias-free-movie-viewing

Please also join us over Zoom on Thursday, April 15 at 4 p.m. EST for an "At the Movies" style panel discussion of the film Coded Bias. A panel of U-M experts will exchange views on the challenges presented by technologies that reflect the systemic biases in American society.

Links to the panel discussion can be found on the same event link above and on Happenings at Michigan on Thursday, April 15.

Access to Coded Bias and the panel discussion are brought to you by the Dissonance Event Series, ITS Information Assurance, the U-M School of Information, and the Law School’s Privacy and Technology Law Association.

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Film Screening Fri, 09 Apr 2021 14:43:58 -0400 2021-04-09T00:01:00-04:00 2021-04-09T23:59:00-04:00 Off Campus Location Information Assurance Film Screening Dissonance Event Series: Free Screening of the Film Coded Bias
Coded Bias - Free Film Screening (April 10, 2021 12:01am) https://events.umich.edu/event/83579 83579-21430619@events.umich.edu Event Begins: Saturday, April 10, 2021 12:01am
Location: Off Campus Location
Organized By: Information Assurance

The U-M Dissonance Event Series invites you to watch a free, on-demand screening of the documentary film Coded Bias. Watch Coded Bias on-demand anytime between Thursday, April 8, through Wednesday, April 14.

Visit the Dissonance events page to learn more, watch the trailer and receive the passcode you will need to access Coded Bias and watch the film for free.

https://safecomputing.umich.edu/events/dissonance/coded-bias-free-movie-viewing

Please also join us over Zoom on Thursday, April 15 at 4 p.m. EST for an "At the Movies" style panel discussion of the film Coded Bias. A panel of U-M experts will exchange views on the challenges presented by technologies that reflect the systemic biases in American society.

Links to the panel discussion can be found on the same event link above and on Happenings at Michigan on Thursday, April 15.

Access to Coded Bias and the panel discussion are brought to you by the Dissonance Event Series, ITS Information Assurance, the U-M School of Information, and the Law School’s Privacy and Technology Law Association.

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Film Screening Fri, 09 Apr 2021 14:43:58 -0400 2021-04-10T00:01:00-04:00 2021-04-10T23:59:00-04:00 Off Campus Location Information Assurance Film Screening Dissonance Event Series: Free Screening of the Film Coded Bias
Coded Bias - Free Film Screening (April 11, 2021 12:01am) https://events.umich.edu/event/83579 83579-21430620@events.umich.edu Event Begins: Sunday, April 11, 2021 12:01am
Location: Off Campus Location
Organized By: Information Assurance

The U-M Dissonance Event Series invites you to watch a free, on-demand screening of the documentary film Coded Bias. Watch Coded Bias on-demand anytime between Thursday, April 8, through Wednesday, April 14.

Visit the Dissonance events page to learn more, watch the trailer and receive the passcode you will need to access Coded Bias and watch the film for free.

https://safecomputing.umich.edu/events/dissonance/coded-bias-free-movie-viewing

Please also join us over Zoom on Thursday, April 15 at 4 p.m. EST for an "At the Movies" style panel discussion of the film Coded Bias. A panel of U-M experts will exchange views on the challenges presented by technologies that reflect the systemic biases in American society.

Links to the panel discussion can be found on the same event link above and on Happenings at Michigan on Thursday, April 15.

Access to Coded Bias and the panel discussion are brought to you by the Dissonance Event Series, ITS Information Assurance, the U-M School of Information, and the Law School’s Privacy and Technology Law Association.

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Film Screening Fri, 09 Apr 2021 14:43:58 -0400 2021-04-11T00:01:00-04:00 2021-04-11T23:59:00-04:00 Off Campus Location Information Assurance Film Screening Dissonance Event Series: Free Screening of the Film Coded Bias
Coded Bias - Free Film Screening (April 12, 2021 12:01am) https://events.umich.edu/event/83579 83579-21430621@events.umich.edu Event Begins: Monday, April 12, 2021 12:01am
Location: Off Campus Location
Organized By: Information Assurance

The U-M Dissonance Event Series invites you to watch a free, on-demand screening of the documentary film Coded Bias. Watch Coded Bias on-demand anytime between Thursday, April 8, through Wednesday, April 14.

Visit the Dissonance events page to learn more, watch the trailer and receive the passcode you will need to access Coded Bias and watch the film for free.

https://safecomputing.umich.edu/events/dissonance/coded-bias-free-movie-viewing

Please also join us over Zoom on Thursday, April 15 at 4 p.m. EST for an "At the Movies" style panel discussion of the film Coded Bias. A panel of U-M experts will exchange views on the challenges presented by technologies that reflect the systemic biases in American society.

Links to the panel discussion can be found on the same event link above and on Happenings at Michigan on Thursday, April 15.

Access to Coded Bias and the panel discussion are brought to you by the Dissonance Event Series, ITS Information Assurance, the U-M School of Information, and the Law School’s Privacy and Technology Law Association.

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Film Screening Fri, 09 Apr 2021 14:43:58 -0400 2021-04-12T00:01:00-04:00 2021-04-12T23:59:00-04:00 Off Campus Location Information Assurance Film Screening Dissonance Event Series: Free Screening of the Film Coded Bias
Coded Bias - Free Film Screening (April 13, 2021 12:01am) https://events.umich.edu/event/83579 83579-21430622@events.umich.edu Event Begins: Tuesday, April 13, 2021 12:01am
Location: Off Campus Location
Organized By: Information Assurance

The U-M Dissonance Event Series invites you to watch a free, on-demand screening of the documentary film Coded Bias. Watch Coded Bias on-demand anytime between Thursday, April 8, through Wednesday, April 14.

Visit the Dissonance events page to learn more, watch the trailer and receive the passcode you will need to access Coded Bias and watch the film for free.

https://safecomputing.umich.edu/events/dissonance/coded-bias-free-movie-viewing

Please also join us over Zoom on Thursday, April 15 at 4 p.m. EST for an "At the Movies" style panel discussion of the film Coded Bias. A panel of U-M experts will exchange views on the challenges presented by technologies that reflect the systemic biases in American society.

Links to the panel discussion can be found on the same event link above and on Happenings at Michigan on Thursday, April 15.

Access to Coded Bias and the panel discussion are brought to you by the Dissonance Event Series, ITS Information Assurance, the U-M School of Information, and the Law School’s Privacy and Technology Law Association.

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Film Screening Fri, 09 Apr 2021 14:43:58 -0400 2021-04-13T00:01:00-04:00 2021-04-13T23:59:00-04:00 Off Campus Location Information Assurance Film Screening Dissonance Event Series: Free Screening of the Film Coded Bias
Coded Bias - Free Film Screening (April 14, 2021 12:01am) https://events.umich.edu/event/83579 83579-21430623@events.umich.edu Event Begins: Wednesday, April 14, 2021 12:01am
Location: Off Campus Location
Organized By: Information Assurance

The U-M Dissonance Event Series invites you to watch a free, on-demand screening of the documentary film Coded Bias. Watch Coded Bias on-demand anytime between Thursday, April 8, through Wednesday, April 14.

Visit the Dissonance events page to learn more, watch the trailer and receive the passcode you will need to access Coded Bias and watch the film for free.

https://safecomputing.umich.edu/events/dissonance/coded-bias-free-movie-viewing

Please also join us over Zoom on Thursday, April 15 at 4 p.m. EST for an "At the Movies" style panel discussion of the film Coded Bias. A panel of U-M experts will exchange views on the challenges presented by technologies that reflect the systemic biases in American society.

Links to the panel discussion can be found on the same event link above and on Happenings at Michigan on Thursday, April 15.

Access to Coded Bias and the panel discussion are brought to you by the Dissonance Event Series, ITS Information Assurance, the U-M School of Information, and the Law School’s Privacy and Technology Law Association.

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Film Screening Fri, 09 Apr 2021 14:43:58 -0400 2021-04-14T00:01:00-04:00 2021-04-14T23:59:00-04:00 Off Campus Location Information Assurance Film Screening Dissonance Event Series: Free Screening of the Film Coded Bias
Can Education Innovation at Michigan Medicine Benefit from Being More Cohesive? (April 14, 2021 12:00pm) https://events.umich.edu/event/83220 83220-21314487@events.umich.edu Event Begins: Wednesday, April 14, 2021 12:00pm
Location: Off Campus Location
Organized By: RISE (Research. Innovation. Scholarship. Education.)

RISE invites you attend the Virtual Talking Circle (VTC) to contribute your input in co-creating a cohesive pathway for education innovation across health science education at Michigan Medicine.  We invite you to attend and provide your input into this conversation.

Please invite your colleagues who may also be interested. See you then!

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Workshop / Seminar Wed, 24 Mar 2021 14:31:47 -0400 2021-04-14T12:00:00-04:00 2021-04-14T13:00:00-04:00 Off Campus Location RISE (Research. Innovation. Scholarship. Education.) Workshop / Seminar RISE Virtual Talking Circle
Assessing the Progress of Diversity, Equity, and Inclusion Initiatives in the College of Engineering: Student Perceptions of the Climate at the University of Michigan (April 14, 2021 3:30pm) https://events.umich.edu/event/83292 83292-21367800@events.umich.edu Event Begins: Wednesday, April 14, 2021 3:30pm
Location: Off Campus Location
Organized By: Engineering Education Research

The University of Michigan College of Engineering is nearing the end of its five-year strategic plan to improve the climate on campus with regards to Diversity, Equity, and Inclusion (DEI). As part of that plan, focus groups were held with students across every department and program in the College of Engineering, to gather qualitative data that can serve as metrics to consider how the DEI strategic plan is progressing. Over thirty focus groups were held with more than 220 undergraduate and graduate students across the College in the 2019-2020 and 2020-2021 academic years. Students were asked about various elements of their perception of DEI, including factors that impacted their sense of inclusion, if they had been treated differently based on their identity, and their perceptions of the College and their department with regards to diversity. The data collected in these focus groups illuminates the nuance and complexity of the engineering student experience, and how that experience, and their perceptions of DEI in the College, can vary based on their identities and home department.

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Lecture / Discussion Mon, 29 Mar 2021 10:00:26 -0400 2021-04-14T15:30:00-04:00 2021-04-14T16:30:00-04:00 Off Campus Location Engineering Education Research Lecture / Discussion Dr. Laura Hirshfield
CCMB / DCMB Weekly Seminar (April 14, 2021 4:00pm) https://events.umich.edu/event/83595 83595-21436485@events.umich.edu Event Begins: Wednesday, April 14, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract:
My lab's research involves the development and application of systems biology approaches—combining computation, machine learning, quantitative modeling, and experiments—to study the immune system in health and disease. Recent technological and computational advances allow comprehensive interrogation of multiple modalities (e.g., proteins, mRNAs, immune receptor sequences) in single cell resolution in the human population. Here I will highlight our work in the analysis human and single cell variations along the axes of early immune development, vaccination, and COVID-19. If time permits, I will also discuss the integration of tissue imaging, machine learning, and multiscale dynamical modeling of immune cell interactions to investigate the homeostatic regulation of autoreactive T cells.

* * *

Biography: Dr. Tsang is a senior investigator in the NIH Intramural Research Program and leads a laboratory focusing on systems and quantitative immunology at the National Institute of Allergy and Infectious Diseases (NIAID). He also co-directs the Trans-NIH Center for Human Immunology (CHI) and leads its research program in systems human immunology. Dr. Tsang trained in computer engineering and computer science at the University of Waterloo and received his Ph.D. in biophysics from Harvard University. Dr. Tsang has worked as a software engineer and pursued systems biology research in both academia and industry including Rosetta Inpharmatics, Caprion Proteomics, MIT, and Merck Research Laboratories. Dr. Tsang has won several awards for his research, including NIAID Merit Awards for the development of a data reuse and crowdsourcing platform OMiCC and for leading a system biology study of human immune variability and influenza vaccination, which was selected as a top NIAID Research Advances of 2014. He currently serves as the founding chief editor of systems immunology for Frontiers in Immunology. He has served as a scientific advisor for a number of programs and organizations including ImmPort (the clinical and molecular data repository for NIAID), the Committee on Precision Medicine for the World Allergy Organization, the NIAID Modeling Immunity for Biodefense Program, the Allen Institute, the Immuno-Epidemiology Program at the National Cancer Institute, and the Human Vaccines Project.

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

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Livestream / Virtual Wed, 07 Apr 2021 08:59:05 -0400 2021-04-14T16:00:00-04:00 2021-04-14T17:00:00-04:00 Off Campus Location DCMB Seminar Series Livestream / Virtual
BME 500 Seminar: Kelly J. Cross (April 15, 2021 4:00pm) https://events.umich.edu/event/81394 81394-20889824@events.umich.edu Event Begins: Thursday, April 15, 2021 4:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Join us for a virtual seminar series on topics related to race and science, technology, engineering and math (STEM) education. https://happenings.wustl.edu/event/an_honest_conversation_about_inequity_in_engineering#.YG9vT-hKhPY

Details:
DATE: Thursday, April 15, 2021
TIME: 4:00-5:00 PM
ZOOM LINK TO REGISTER: https://wustl.zoom.us/webinar/register/WN_NvH4qVTSRx2uSXbdW-eXNA

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Lecture / Discussion Wed, 14 Apr 2021 14:13:34 -0400 2021-04-15T16:00:00-04:00 2021-04-15T17:00:00-04:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Logo
Coded Bias "At the Movies" Panel Discussion (April 15, 2021 4:00pm) https://events.umich.edu/event/83580 83580-21430624@events.umich.edu Event Begins: Thursday, April 15, 2021 4:00pm
Location: Off Campus Location
Organized By: Information Assurance

Join a panel of U-M experts over Zoom for an "At the Movies" style discussion of the film Coded Bias. The panelists will exchange views on the challenges presented by technologies that reflect the systemic biases in American society. Panelists include:
- Nazanin Andalibi, assistant professor of information, School of Information; assistant professor of Digital Studies Institute, College of Literature, Science, and the Arts (LSA)
- Mingyan Liu, Peter and Evelyn Fuss Chair of Electrical and Computer Engineering, Electrical Engineering and Computer Science (EECS)
- Nicholson Price, professor of law, Law School
- Grace Trinidad (moderator), Ethics, Legal, and Social Implications (ELSI) postdoctoral fellow, School of Public Health

AVAILABLE PRIOR TO THE DISCUSSION
To be better informed prior to the Coded Bias panel discussion, be sure to take time to watch a free screening of the film between April 8 and April 14. More information is available at https://safecomputing.umich.edu/events/dissonance/coded-bias-free-movie-viewing

Access to Coded Bias and the panel discussion are brought to you by the Dissonance Event Series, ITS Information Assurance, the U-M School of Information, and the Law School’s Privacy and Technology Law Association.

Add the panel discussion to your Google Calendar: https://calendar.google.com/calendar/u/0/r/eventedit/copy/MWZjMnFtNmw0MzN2MDk0cmRyaHQ4b3VpMTggdW1pY2guZWR1X2ZkczI0Z2V2cGE0MnY5NTc2bG5wZTJjbWxrQGc

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Lecture / Discussion Fri, 09 Apr 2021 14:43:13 -0400 2021-04-15T16:00:00-04:00 2021-04-15T17:00:00-04:00 Off Campus Location Information Assurance Lecture / Discussion Dissonance Event Series: Panel Discussion on the film Coded Bias
BME Master's Defense: Fatimah Alkaabi (April 16, 2021 12:00pm) https://events.umich.edu/event/83558 83558-21424731@events.umich.edu Event Begins: Friday, April 16, 2021 12:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

The central auditory system consists of the brain nuclei that transmit peripheral auditory nerve input to the auditory cortex for hearing perception. Damage to the auditory end organ, the cochlea, can result in hearing loss that drives the central auditory system to disarray causing disorders such as hyperacusis and tinnitus. These disorders can negatively affect patients’ quality of life. Tinnitus sufferers generally describe their tinnitus as a narrowband of sound that occurs in quiet, while hyperacusis sufferers express an exaggerated perception of sound level or intensity. These two disorders are often grouped together because tinnitus sufferers tend to report symptoms of hyperacusis and vice versa. However, hyperacusis and tinnitus do not always co-occur, suggesting that they have different neural origins. To study these conditions, researchers have induced cochlear damage in animal models, followed by behavioral and electrophysiological assessments. However, no study has adequately distinguished hyperacusis from tinnitus in individual animals. In this thesis, I detail the development of a novel hyperacusis and tinnitus assessment paradigm for individual animals using the pinna reflex combined with auditory brainstem responses (ABR). In the first chapter, I detail several enhancements to a computer system that ensures accurate sound presentation concurrently with capture of pinna reflex video data, as well as streamlines the subsequent data analysis. In the second chapter, the ABR, an evoked potential reflecting the summed electrical activity of cells in the auditory brainstem pathway, was assessed. Several studies suggest that ABR-wave characteristics might provide evidence of hyperacusis. ABRs were evoked using conventional and novel sound stimuli. They were then examined to look for possible indications of hyperacusis in noise overexposed guinea pigs. The present findings are discussed with several suggestions for future hyperacusis assessments.



Date: Friday, April 16, 2021

Time: 12:00 PM

Zoom: https://umich.zoom.us/j/91698183229

Chair: Dr. Susan Shore

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Lecture / Discussion Mon, 05 Apr 2021 23:04:39 -0400 2021-04-16T12:00:00-04:00 2021-04-16T13:00:00-04:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Logo
RNA Seminar featuring: Jailson (Jay) Brito Querido, Ph.D. MRC Laboratory of Molecular Biology, Cambridge, UK (April 19, 2021 4:00pm) https://events.umich.edu/event/81408 81408-20893767@events.umich.edu Event Begins: Monday, April 19, 2021 4:00pm
Location: Off Campus Location
Organized By: Center for RNA Biomedicine

REGISTRATION REQUIRED: https://umich.zoom.us/webinar/register/WN_78YYOhIhTbOBy2_JSdM7Wg

ABSTRACT: A key step in translational initiation is the recruitment of the 43S pre-initiation complex (43S PIC) by the cap-binding complex (eIF4F) at the 5´ end of mRNA. Eukaryotic initiation factors eIF1, eIF1A, eIF3, eIF5, and the ternary complex (TC) of eIF2–GTP–tRNAiMet bind to the 40S ribosomal subunit to form the 43S PIC. Once assembled, the 43S PIC is recruited to the cap-binding complex eIF4F at the 5´end of mRNA to form a 48S initiation complex (48S). The 48S then scans along the mRNA to locate a start codon. To understand the mechanisms involved, we determined the structure of a reconstituted human 48S using cryo-electron microscopy. The structure reveals insights into early events of translation initiation complex assembly. It reveals how eIF4F interacts with subunits of the eIF3 structural core near the mRNA exit channel in the 43S. The location of eIF4F is consistent with a slotting model of mRNA recruitment and suggests a “blind-region” that would preclude recognition of start sites upstream of the location of the P site at the point of recruitment.

KEYWORDS: mRNA, ribosome, eIF4F, eIF4A, translation

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Lecture / Discussion Tue, 13 Apr 2021 12:58:40 -0400 2021-04-19T16:00:00-04:00 2021-04-19T17:00:00-04:00 Off Campus Location Center for RNA Biomedicine Lecture / Discussion Jailson (Jay) Brito Querido, Ph.D.
Bioethics Discussion: Abdication (April 20, 2021 7:00pm) https://events.umich.edu/event/58841 58841-14563735@events.umich.edu Event Begins: Tuesday, April 20, 2021 7:00pm
Location: Lurie Biomedical Engineering
Organized By: The Bioethics Discussion Group

A discussion on our renunciation.

Join us at: https://umich.zoom.us/j/99926126455

A few readings to consider:
––The Idea of Legitimate Authority in the Practice of Medicine
––Decentralization of health care systems and health outcomes: Evidence from a natural experiment
––Vox Populi or Abdication of Responsibility?: The Influence of the Irish Citizens’ Assembly on the Public Discourse Regarding Abortion, 2016-2019
––Lifeboat Ethics: The Case Against Helping the Poor
For more information and/or to receive a copy of the readings visit http://belmont.bme.umich.edu/bioethics-discussion-group/discussions/060-abdication/.

––
Before you give up, consider the blog: https://belmont.bme.umich.edu/incidental-art/

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Lecture / Discussion Fri, 08 Jan 2021 09:38:57 -0500 2021-04-20T19:00:00-04:00 2021-04-20T20:30:00-04:00 Lurie Biomedical Engineering The Bioethics Discussion Group Lecture / Discussion Abdication
Master's Defense: Annie Taylor (April 21, 2021 10:30am) https://events.umich.edu/event/83750 83750-21485477@events.umich.edu Event Begins: Wednesday, April 21, 2021 10:30am
Location: Off Campus Location
Organized By: Biomedical Engineering

Dopamine regulates motor performance and learning. Current models suggest that dopamine signals reward-prediction errors and/or movement vigor. These functions have been assessed predominantly using simple behavioral tasks. The role of dopamine in dexterous skill, however, is unknown. This question is important to understanding motor disorders such as Parkinson's Disease. Here we describe an experimental model to interrogate the role of dopamine release during learning and performance of dexterous skill. Fluorescent sensors dLight1.1 and GCaMP are used to monitor dopamine and calcium activity in the striatum and substantia nigra pars compacta (SNc) in rats performing skilled reaching tasks. Preliminary experiments have successfully recorded reward-associated signals in both striatum and SNc. Adaptations to the recording setup to facilitate long-term recording in larger rodents are described. These results demonstrate the viability of fiber photometry for measuring dopamine-related activity during skilled reaching tasks.



Date: Wednesday April 21, 2021

Time: 10:30 AM

Zoom: https://umich.zoom.us/j/96449273959

Chair: Dr. Dan Leventhal

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Lecture / Discussion Tue, 13 Apr 2021 15:34:29 -0400 2021-04-21T10:30:00-04:00 2021-04-21T11:30:00-04:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Logo
Special Joint Seminar between DCMB, Mathematics, MIDAS, and Smale Institute (April 22, 2021 1:00pm) https://events.umich.edu/event/83615 83615-21491327@events.umich.edu Event Begins: Thursday, April 22, 2021 1:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract:

The quest to understand consciousness, once the purview of philosophers and theologians, is now actively pursued by scientists of many stripes. This talk looks at consciousness from the perspective of theoretical computer science. It formalizes the Global Workspace Theory (GWT) originated by cognitive neuroscientist Bernard Baars and further developed by him, Stanislas Dehaene, and others. Our major contribution lies in the precise formal definition of a Conscious Turing Machine (CTM), also called a Conscious AI. We define the CTM in the spirit of Alan Turing’s simple yet powerful definition of a computer, the Turing Machine (TM). We are not looking for a complex model of the brain nor of cognition but for a simple model of (the admittedly complex concept of) consciousness. After formally defining CTM, we give a formal definition of consciousness in CTM. We then suggest why the CTM has the feeling of consciousness. The reasonableness of the definitions and explanations can be judged by how well they agree with commonly accepted intuitive concepts of human consciousness, the range of related concepts that the model explains easily and naturally, and the extent of its agreement with scientific evidence.

https://umich.zoom.us/j/95135773568

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Livestream / Virtual Wed, 14 Apr 2021 10:17:45 -0400 2021-04-22T13:00:00-04:00 2021-04-22T14:00:00-04:00 Off Campus Location DCMB Seminar Series Livestream / Virtual
Implantable Neural Interfaces for Direct Control of Hand Prostheses (April 27, 2021 10:00am) https://events.umich.edu/event/83793 83793-21530358@events.umich.edu Event Begins: Tuesday, April 27, 2021 10:00am
Location: Off Campus Location
Organized By: Michigan Robotics

State of the art robotic hands can mimic many functions of the human hand. These devices are a capable of actuating individual finger and multi-joint movements while providing adequate gripping force for daily activities. However, for patients with spinal cord injuries or amputations, there are few options to control these functions seamlessly or intuitively. A common barrier to restoring hand function to both populations is a lack of high-fidelity control signals. Non-invasive electrophysiological techniques record global summations of activity and lack the spatial or temporal resolution to extract or “decode” precise movement commands. The ability to decode finger movements from the motor system would allow patients to directly control hand functions and provide intuitive and scalable prosthetic solutions. This thesis investigates the capabilities of implantable devices to provide finger-specific commands for prosthetic hands. We adapt existing reasoning algorithms to two different sensing technologies.

The first is intracortical electrode arrays implanted into primary motor cortex of two non-human primates. Both subjects controlled a virtual hand with a regression algorithm that decoded their brain activity into finger kinematics. Performance was evaluated with a single degree of freedom target matching task. A state-of-the-art re-calibration approach improved performance, measured as bit rate, by an average of 33.1%. Notably, decoding performance was not dependent on subjects moving their intact hands. In future research, this approach can improve grasp precision for patients with spinal cord injuries.

The second sensing technology is intramuscular electrodes implanted into residual muscles and Regenerative Peripheral Nerve Interfaces of two patients with transradial amputations. Both participants used a high-speed pattern recognition system to switch between 10 individual finger and wrist postures in a virtual environment with an average success rate of 94.7% and a trial latency of 255 ms. When the set was reduced to five grasp postures, average metrics improved to 100% success and 135 ms latency. These results are a significant improvement over state-of-the-art systems that use surface electromyography as inputs. Furthermore, grasp performance remained reliable across arm positions and both participants used this controller to complete a functional assessment with robotic prostheses.
For a more dexterous solution, we combined the high-speed pattern recognition system with a regression algorithm that enabled simultaneous position control of both the index finger and middle-ring-small finger group. Both patients used this system to complete a virtual two degree of freedom target matching task with throughputs of 1.79 and 1.15 bits per second each. The controllers in this study used only four and five differentiated inputs, which can feasibly be processed with portable or implantable hardware.

These results demonstrate that implantable systems can provide patients with fluid and precise control of hand prostheses, eliminating the need to use movement substitutions and triggers to cycle through grip modes. However, clinically translatable implantable electronics need to be developed to realize the potential of these sensing and reasoning approaches. Further advancement of this technology will likely increase the utility and demand of robotic prostheses.

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Livestream / Virtual Mon, 19 Apr 2021 13:55:31 -0400 2021-04-27T10:00:00-04:00 2021-04-27T12:00:00-04:00 Off Campus Location Michigan Robotics Livestream / Virtual prosthetic hand stacks block
Master's Defense: Ivo Cerda (April 30, 2021 10:00am) https://events.umich.edu/event/83915 83915-21612995@events.umich.edu Event Begins: Friday, April 30, 2021 10:00am
Location: Off Campus Location
Organized By: Biomedical Engineering

Co-registering, chronic, and naturalistic assessments of the electrophysiological and behavioral features of the murine stress response can teach us how stress-behaviors are mechanistically driven by electrophysiological activity in neural circuits, how those relationships change over the course of the multi-week developing response to chronic ongoing stress, and how these changes ultimately contribute to the pathogenesis and progression of major depressive disorder and other psychiatric conditions. However, the long duration and multiplexed nature of the murine stress response have long been barriers to achieving such understandings. To address the need for technology that better captures the time progression of the murine stress response, we engineered the first-ever chronic recording system capable of gathering both behavioral and electrophysiological data in a naturalistic environment for freely-moving mice. Building from previous unpublished work at our lab, we first developed 16 units of a novel photointerrupter-based, Arduino-controlled digital phenotyping system capable of simultaneously recording 50+ behavioral metrics at a sub-second resolution continuously for weeks at a time. Subsequently, with the goal of assisting the concurrent exploration of brain mechanisms and behavior, we engineered a scaffold and cabling structure to support an ultra low-resistance commutator that allows chronic, multi-region brain electrophysiological recordings and integrated it into our digital behavioral phenotyping system. Our novel co-recording system is now fully operational and, along with allowing chronic electrophysiological recordings, supports measures of eating, drinking, food and sugary drink preference (a measure of anhedonia), locomotor activity, sleep, and actigraphy, all the while using 24/7 video tracking to allow detailed classification of behaviors at sub-second resolution. The system is also compatible with standard assessments in the field, including daily weight and fur checks. To demonstrate the duration of its co-recording capabilities, we implanted a cohort of mice with electrodes in three brain regions involved in the murine stress response – olfactory bulb, dorsal hippocampus, and medial prefrontal cortex – and recorded for five weeks. This is the first system to ever produce highly dense behavioral and electrophysiological data simultaneously and continuously over such a period of time.


Details:
DATE: Friday, April 30, 2021
TIME: 10:00 am - 12:00 pm
LOCATION: Zoom https://umich.zoom.us/j/93571968494)
Chair Committee: Brendon Watson, Tim Bruns, Cindy Chestek

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Lecture / Discussion Thu, 29 Apr 2021 20:12:17 -0400 2021-04-30T10:00:00-04:00 2021-04-30T12:00:00-04:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Logo
BME Commencement 2021 (May 1, 2021 3:30pm) https://events.umich.edu/event/83890 83890-21595415@events.umich.edu Event Begins: Saturday, May 1, 2021 3:30pm
Location: Off Campus Location
Organized By: Biomedical Engineering

PLEASE MAKE SURE TO RSVP WITH THE LINK!

BME COMMENCEMENT CEREMONY
SATURDAY, MAY 1, 2021 | 3:30 PM EDT


COMMENCEMENT CEREMONY
ZOOM @ (3:30 PM)

AFTER PARTY
Spatial Chat @ (~4:30 PM)
(AFTER THE CEREMONY)

PROGRAM
Welcome & Introduction | Lonnie Shea Ph.D.
Program Chair Remarks | Rachael Schmedlen, Ph.D., Jan Stegemann, Ph.D., & Tim Bruns, Ph.D.
Program Coordinator Remarks | Rachel Patterson & Maria Steele
Alumni Welcome and Congratulations | Scott Merz, Richard Youngblood, & Xiaotian Tan
Student Addresses | Dipra Debnath, Ivo Woldarsky, & Katy Norman
Announcing the Graduates | Melissa Wrobel Ph.D., Brendon Baker, Ph.D., James Weiland, Ph.D., & Tim Bruns, Ph.D.
Confirmation of Degrees | Lonnie Shea, Ph.D.
Congratulations and Closing | Lonnie Shea, Ph.D.
Virtual socializing & After Party | Come congratulate and socialize with your fellow graduates, families, professors, and friends following the BME Commencement Ceremony.

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Ceremony / Service Tue, 27 Apr 2021 15:09:45 -0400 2021-05-01T15:30:00-04:00 Off Campus Location Biomedical Engineering Ceremony / Service BME Logo
RNA Seminar featuring: Olivia Rissland, University of Colorado School of Medicine (May 3, 2021 4:00pm) https://events.umich.edu/event/81302 81302-20881902@events.umich.edu Event Begins: Monday, May 3, 2021 4:00pm
Location: Off Campus Location
Organized By: Center for RNA Biomedicine

Registration Required: https://umich.zoom.us/webinar/register/WN_vA9zYS5nSEenf8Zmt1f-qA


ABSTRACT: The maternal-to-zygotic transition (MZT) is a conserved step in animal development, where control is passed from the maternal to the zygotic genome. Although the MZT is typically considered from its impact on the transcriptome, we previously found that three maternally deposited Drosophila RNA binding proteins (ME31B, Trailer Hitch [TRAL], and Cup) are also cleared during the MZT by unknown mechanisms. Here, we show that these proteins are degraded by the ubiquitin-proteasome system. Marie Kondo, an E2 conjugating enzyme, and the E3 CTLH ligase are required for the destruction of ME31B, TRAL, and Cup. Structure modeling of the Drosophila CTLH complex suggests that substrate recognition is different than orthologous complexes. Despite occurring hours earlier, egg activation mediates clearance of these proteins through the Pan Gu kinase, which stimulates translation of Kondo mRNA. Clearance of the maternal protein dowry thus appears to be a coordinated, but as-yet underappreciated, aspect of the MZT.

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Lecture / Discussion Fri, 02 Apr 2021 16:07:11 -0400 2021-05-03T16:00:00-04:00 2021-05-03T17:00:00-04:00 Off Campus Location Center for RNA Biomedicine Lecture / Discussion Olivia Rissland, Ph.D.
PhD Defense: Jonas Schollenberger (May 4, 2021 3:00pm) https://events.umich.edu/event/83855 83855-21555868@events.umich.edu Event Begins: Tuesday, May 4, 2021 3:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Cerebrovascular occlusive disease (CVOD) is a major risk factor for ischemic stroke and is characterized by the presence of stenosis in the arteries supplying the brain. The cerebral vasculature has an innate ability to compensate for flow reductions, caused by the presence of CVOD, through a network of collateral pathways in the circle of Willis (CoW). However, flow compensation is highly patient-specific and dependent on the cerebral vasculature anatomy, availability of collateral pathways, degree of stenosis and, the condition of the cerebral microcirculation and its autoregulatory response. Unfortunately, clinically available imaging tools only provide limited information on flow compensation and the underlying cerebral hemodynamics. Given the complexity of the cerebral vasculature, better tools are necessary to characterize cerebral hemodynamics and guide the risk assessment of ischemic stroke.



Image-based computational fluid dynamics (CFD) provides a powerful tool for non-invasively analyzing cerebral hemodynamics with high spatial and temporal resolutions. However, CFD modeling of cerebral hemodynamics is challenging due to the need for patient-specific data to calibrate outflow boundary conditions in the brain. In this thesis, we explore a novel strategy to quantitatively characterize cerebral hemodynamics using CFD in combination with tissue perfusion from arterial spin labeling (ASL) MRI.



Firstly, we quantified territorial perfusion in the cerebral circulation through implementing and optimizing a vessel-selective arterial spin labeling (VS-ASL) sequence. VS-ASL is generally limited by its low labeling efficiency causing poor signal-to-noise ratio. We investigated the effects of off‐resonance, pulsatility, and vessel movement, and evaluated methods to maximize labeling efficiency and overall image quality. We found that an off-resonance calibration scan in combination with cardiac-triggering significantly improved labeling efficiency and image quality. Vessel movement during the MRI protocol occurred in the majority of study subjects and needs to be accounted for to maximize labeling efficiency.



Secondly, we developed a strategy to calibrate patient-specific CFD models of cerebral blood flow. The calibration consisted of estimating the total inflow to the CoW from PC-MRI and the flow splits in the CoW from non-selective ASL perfusion images. The outflow boundary conditions were iteratively tuned to match the estimated flow splits, and the ASL-calibrated CFD model was then validated against territorial perfusion maps from VS-ASL by calculating the blood supply to each cerebral territory using Lagrangian particle tracking (LPT). We found an overall good match in a small group of subjects; particularly, the flow compensation between hemispheres was captured well by the calibrated CFD models.



Thirdly, we investigated the impact of two outflow boundary condition strategies, an ASL-based and allometric-based calibration, on cerebral hemodynamics. The ASL-based calibrated CFD analysis captured the flow compensation between hemispheres as measured with VS-ASL and lead to an approximately symmetrical flow distribution in the CoW. In contrast, the allometric-based calibrated CFD analysis was unable to capture the collateral flow compensation, which resulted in large differences in flow between hemispheres.



Finally, the clinical feasibility and capabilities of our proposed CFD analysis was demonstrated in two CVOD patients. The CFD analysis showed significant differences in cerebral hemodynamics between the patients despite similar degrees of stenosis severity, highlighting the importance of a patient-specific assessment. Comparison of pre-operative and post-operative hemodynamics in one patient resulted in only minor changes following revascularization despite severe carotid stenosis. We demonstrated that our CFD analysis can provide detailed and quantitative information about hemodynamic impact of carotid stenosis and collateral flow compensation in the circle of Willis.


Date: Tuesday, May 4, 2021

Time: 3:00 PM

Zoom: https://umich.zoom.us/j/93059726229 (Zoom link requires prior registration)

Co-Chairs: Dr. C. Alberto Figueroa and Dr. Luis Hernandez-Garcia

For Assistance or Questions
um-bme@umich.edu

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Lecture / Discussion Thu, 22 Apr 2021 13:33:46 -0400 2021-05-04T15:00:00-04:00 2021-05-04T16:00:00-04:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Logo
PhD Defense: Elissa Welle (May 7, 2021 10:00am) https://events.umich.edu/event/83883 83883-21587612@events.umich.edu Event Begins: Friday, May 7, 2021 10:00am
Location: Off Campus Location
Organized By: Biomedical Engineering

Neural interfaces create a connection between neural structures in the body and external electronic devices. Brain-machine interfaces and bioelectric medicine therapies rely on the seamless integration of neural interfaces with the brain, nerves, or spinal cord. However, conventional neural interfaces cannot meet the demands of high channel count, signal fidelity, and signal longevity that these applications require.



In this thesis we characterized the damage resulting from conventional Utah arrays after multiple years of implantation in the cortex of a non-human primate. The neuron density around the electrode shanks was compared to the neuron density of nearby healthy tissue, finding a 73% loss in density around the electrodes. The explanted arrays were imaged and characterized for forms of electrode surface inconsistency. Coating cracks, tip breakage, and parylene cracks were the most common inconsistency. A significantly higher number of tip breakage and coating crack occurrences were found on the edges of the arrays as compared to the middle. In this work, we made clear the need for a minimally damaging alternative to the Utah electrode array.



Neural interfaces composed of carbon fiber electrodes, with a diameter of 6.8 microns, could enable a more seamless integration with the body. Previous work resulted in an array of individuated carbon fiber electrodes that could record reliably high signal-to-noise ratio neural signals from the brain for several months. However, the carbon fiber arrays were limited by only 30% of the electrodes recording neural signals, despite inducing very minimal inflammation. Additionally, it was relatively unknown if carbon fibers would make suitable long-term peripheral neural interfaces. Here, we illustrate the potential of carbon fiber electrodes to meet the needs of a variety of neural applications.



First, we optimized state-of-the-art carbon fiber electrodes to reliably record single unit electrophysiology from the brain. By analyzing the previous manufacturing process, the cause of the low recording yield of the carbon fiber arrays was identified as the consistency of the electrode tip. A novel laser cutting technique was developed to produce a consistent carbon fiber tip geometry, resulting in a near tripling of recording yield of high amplitude chronic neural signals. The longevity of the carbon fiber arrays was also addressed. The conventional polymer coating was compared against platinum iridium coating and an oxygen plasma treatment, both of which outperformed the polymer coating. In this work, we customized carbon fiber electrodes for reliable, long-term neural recording.



Secondly, we translated the carbon fiber technology from the brain to the periphery in an architecture appropriate for chronic implantation. The insertion of carbon fibers into the stiffer structures in the periphery is enabled by sharpening the carbon fibers. The sharpening process combines a butane flame to sharpen the fibers with a water bath to protect the base of the array. Sharpened carbon fibers recorded electrophysiology from the rat vagus nerve and feline dorsal root ganglia, both structures being important targets for bioelectric medicine therapies. The durability of carbon fibers was also displayed when partially embedded carbon fibers in medical-grade silicone withstood thousands of repeated bends without fracture. This work showed that carbon fibers have the electrical and structural properties necessary for chronic application.



Overall, this work highlights the vast potential of carbon fiber electrodes. Through this thesis, future brain-machine interfaces and bioelectric medicine therapies may utilize sub-cellular electrodes such as carbon fibers in medical applications.



Date: Friday, May 7, 2021

Time: 10:00 AM

Zoom: https://umich.zoom.us/j/95839545566 (Zoom link requires prior registration)

Chair: Dr. Cynthia Chestek

For Assistance or Questions
um-bme@umich.edu

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Lecture / Discussion Mon, 26 Apr 2021 17:03:39 -0400 2021-05-07T10:00:00-04:00 2021-05-07T11:00:00-04:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Logo
2021 BME Symposium (May 10, 2021 12:00pm) https://events.umich.edu/event/82858 82858-21203302@events.umich.edu Event Begins: Monday, May 10, 2021 12:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

To register please see:
https://myumi.ch/r8GzZ

The 2021 BME symposium will showcase our work in the areas of Imaging, Neural Engineering, Regenerative Medicine, and Precision Health. The event will take place over two days in the afternoons of Monday, May 10, 12:00 PM - 5:00 PM, and Tuesday, May 11, 12:00 PM - 5:00 PM. Each afternoon will include faculty talks, mini student dissertations, a panel discussion, and student poster sessions.

The goal of this event is to bring together faculty and students affiliated with BME from all parts of campus as a step toward building the BME community and celebrating accomplishments through difficult times while having an eye toward the future.

Please sign up and join us!

2021 U-M BME Symposium



May 10, 2021: 12:00 PM - 5:00 PM


Imaging at UM

May 10, 2021 - 12:00pm - 1:30pm
Location: Virtual/Zoom
Livestream Available (Visible After Registration)

Moderator: Doug Noll
12:00 - 12:15 - Zhongming Liu, “Preclinical MRI of brain-gut interactions”
12:15 - 12:30 - Nicole Seiberlich, “Translating Quantitative MRI to the Clinic”
12:30 - 12:45 - Yannis Paulus, “Multimodal Photoacoustic Microscopy, OCT, and Fluorescence Molecular and Cellular Imaging of the Retina”
12:45 - 1:05 - Student Dissertations
1:05 - 1:30 - Panel Discussion - “The Future of Imaging Research at Michigan” - Vikas Gulani, Jeff Fessler, Cheri Deng, Zhen Xu, Xueding Wang


Neural Engineering at UM

May 10, 2021 - 2:00pm - 3:30pm
Location: Virtual/Zoom
Livestream Available (Visible After Registration)

Moderator: Jim Weiland
2:00 - 2:15 - Kamran Diba, TBD
2:15 - 2:30 - Scott Lempka, TBD
2:30 - 2:45 - Deanna Gates, TBD
2:45 - 3:05 - Student Dissertations
3:05 - 3.30 - Panel Discussion - “The Science Fiction Future of Neural Engineering” - Cindy Chestek, Parag Patil, Tim Bruns, Bill Stacey


Poster Session: Imaging & Neural Engineering

May 10, 2021 - 4:00pm - 5:00pm
Location: Virtual/Spatial Chat

This poster session will give BME students a chance to present and discuss their research in the areas of Imaging and Neural Engineering.


May 11, 2021: 12:00 PM - 5:00 PM


Regenerative Medicine at UM

May 11, 2021 - 12:00pm - 1:30pm
Location: Virtual/Zoom
Livestream Available (Visible After Registration)

Moderator: Lonnie Shea
12:00 - 12:15 - Carlos Aguilar, ”Understanding & Re-Writing Stem Cell Programs to Live Forever.”
12:15 - 12:30 - Idse Heemskerk, “Predicting cell fate from signaling history in human pluripotent stem cells”
12:30 - 12:45 - Ariella Shikanov, TBD
12:45 - 1:05 - Student Dissertations
1:05 - 1:30 - Panel Discussion - "Grand Challenges in Regenerative Medicine" - Dave Kohn


Precision Health at UM

May 11, 2021 - 2:00pm - 3:30pm
Location: Virtual/Zoom
Livestream Available (Visible After Registration)

Moderator: TBD
2:00 - 2:15 - Sriram Chandrasekharan, TBD
2:15 - 2: 30 - James Moon, TBD
2:30 - 2:45 - Deepak Nagrath, TBD
2:45 - 3:05 - Student Dissertations
3:05 - 3:30 - Panel Discussion - "Hope or Hype for Treating Diseases" - James Moon, Sriram Chandrasekharan, Deepak Nagrath



Poster Session: Regenerative Medicine & Precision Health


May 11, 2021 - 4:00pm - 5:00pm
Location: Virtual/Spatial Chat


This poster session will give BME students a chance to present and discuss their research in the areas of Regenerative Medicine and Precision Health.

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Conference / Symposium Thu, 22 Apr 2021 13:38:37 -0400 2021-05-10T12:00:00-04:00 2021-05-10T17:00:00-04:00 Off Campus Location Biomedical Engineering Conference / Symposium BME Logo
2021 BME Symposium (May 11, 2021 12:00pm) https://events.umich.edu/event/82858 82858-21555869@events.umich.edu Event Begins: Tuesday, May 11, 2021 12:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

To register please see:
https://myumi.ch/r8GzZ

The 2021 BME symposium will showcase our work in the areas of Imaging, Neural Engineering, Regenerative Medicine, and Precision Health. The event will take place over two days in the afternoons of Monday, May 10, 12:00 PM - 5:00 PM, and Tuesday, May 11, 12:00 PM - 5:00 PM. Each afternoon will include faculty talks, mini student dissertations, a panel discussion, and student poster sessions.

The goal of this event is to bring together faculty and students affiliated with BME from all parts of campus as a step toward building the BME community and celebrating accomplishments through difficult times while having an eye toward the future.

Please sign up and join us!

2021 U-M BME Symposium



May 10, 2021: 12:00 PM - 5:00 PM


Imaging at UM

May 10, 2021 - 12:00pm - 1:30pm
Location: Virtual/Zoom
Livestream Available (Visible After Registration)

Moderator: Doug Noll
12:00 - 12:15 - Zhongming Liu, “Preclinical MRI of brain-gut interactions”
12:15 - 12:30 - Nicole Seiberlich, “Translating Quantitative MRI to the Clinic”
12:30 - 12:45 - Yannis Paulus, “Multimodal Photoacoustic Microscopy, OCT, and Fluorescence Molecular and Cellular Imaging of the Retina”
12:45 - 1:05 - Student Dissertations
1:05 - 1:30 - Panel Discussion - “The Future of Imaging Research at Michigan” - Vikas Gulani, Jeff Fessler, Cheri Deng, Zhen Xu, Xueding Wang


Neural Engineering at UM

May 10, 2021 - 2:00pm - 3:30pm
Location: Virtual/Zoom
Livestream Available (Visible After Registration)

Moderator: Jim Weiland
2:00 - 2:15 - Kamran Diba, TBD
2:15 - 2:30 - Scott Lempka, TBD
2:30 - 2:45 - Deanna Gates, TBD
2:45 - 3:05 - Student Dissertations
3:05 - 3.30 - Panel Discussion - “The Science Fiction Future of Neural Engineering” - Cindy Chestek, Parag Patil, Tim Bruns, Bill Stacey


Poster Session: Imaging & Neural Engineering

May 10, 2021 - 4:00pm - 5:00pm
Location: Virtual/Spatial Chat

This poster session will give BME students a chance to present and discuss their research in the areas of Imaging and Neural Engineering.


May 11, 2021: 12:00 PM - 5:00 PM


Regenerative Medicine at UM

May 11, 2021 - 12:00pm - 1:30pm
Location: Virtual/Zoom
Livestream Available (Visible After Registration)

Moderator: Lonnie Shea
12:00 - 12:15 - Carlos Aguilar, ”Understanding & Re-Writing Stem Cell Programs to Live Forever.”
12:15 - 12:30 - Idse Heemskerk, “Predicting cell fate from signaling history in human pluripotent stem cells”
12:30 - 12:45 - Ariella Shikanov, TBD
12:45 - 1:05 - Student Dissertations
1:05 - 1:30 - Panel Discussion - "Grand Challenges in Regenerative Medicine" - Dave Kohn


Precision Health at UM

May 11, 2021 - 2:00pm - 3:30pm
Location: Virtual/Zoom
Livestream Available (Visible After Registration)

Moderator: TBD
2:00 - 2:15 - Sriram Chandrasekharan, TBD
2:15 - 2: 30 - James Moon, TBD
2:30 - 2:45 - Deepak Nagrath, TBD
2:45 - 3:05 - Student Dissertations
3:05 - 3:30 - Panel Discussion - "Hope or Hype for Treating Diseases" - James Moon, Sriram Chandrasekharan, Deepak Nagrath



Poster Session: Regenerative Medicine & Precision Health


May 11, 2021 - 4:00pm - 5:00pm
Location: Virtual/Spatial Chat


This poster session will give BME students a chance to present and discuss their research in the areas of Regenerative Medicine and Precision Health.

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Conference / Symposium Thu, 22 Apr 2021 13:38:37 -0400 2021-05-11T12:00:00-04:00 2021-05-11T17:00:00-04:00 Off Campus Location Biomedical Engineering Conference / Symposium BME Logo
Connecting Education Innovation to Activism (May 12, 2021 12:00pm) https://events.umich.edu/event/83807 83807-21538170@events.umich.edu Event Begins: Wednesday, May 12, 2021 12:00pm
Location: Off Campus Location
Organized By: RISE (Research. Innovation. Scholarship. Education.)

R.I.S.E., the Center for Academic Innovation, and the Center for Research on Learning & Teaching (CRLT) invite you to join a Virtual Talking Circle (VTC) to discuss unique connections between education innovation & activism.

This collaboration across the University will serve as a first step in building a community interested in designing and promoting education innovation to improve society.

Anyone interested in education innovation and/or social justice and activism is invited!  We want to learn who is already doing this important work and identify potential collaborations across the University.

Please join us on Wednesday, May 12, 2021 from 12:00 - 1:00 PM

Register via Eventbrite

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Workshop / Seminar Tue, 20 Apr 2021 06:37:52 -0400 2021-05-12T12:00:00-04:00 2021-05-12T13:00:00-04:00 Off Campus Location RISE (Research. Innovation. Scholarship. Education.) Workshop / Seminar RISE Virtual Talking Circle
RNA Seminar featuring: Thomas Martinez, Salk Institute for Biological Studies (May 17, 2021 4:00pm) https://events.umich.edu/event/81303 81303-20881903@events.umich.edu Event Begins: Monday, May 17, 2021 4:00pm
Location: Off Campus Location
Organized By: Center for RNA Biomedicine

Registration Required: https://umich.zoom.us/webinar/register/WN_90RkcQTGQZa7ifQ8kbSdNQ

KEYOWORDS: microprotein, smORF, ribosome profiling

ABSTRACT: Functional protein-coding small open reading frames (smORFs) are emerging as an important class of genes. Several smORF-encoded microproteins have been characterized and implicated in a variety of critical processes, including regulation of mRNA decay, DNA repair, and muscle formation. Thus, rigorous and comprehensive annotation of protein-coding smORFs is critical to our understanding of basic biology and physiology, as well as disease. We recently developed an improved workflow that integrates de novo transcriptome assembly and ribosome profiling to overcome obstacles with previous methods to more confidently annotate thousands of novel smORFs across multiple human cell lines, including hundreds encoded on putative non-coding RNAs. Over 1,500 smORFs are found in two or more cell lines, and ~40% lack a canonical AUG start codon. Evolutionary conservation analyses suggest that hundreds of smORF-encoded microproteins are likely functional. We also find that smORF-derived peptides are detectable on human leukocyte antigen complexes, positioning smORFs as a source of novel antigens. The annotation of protein-coding smORFs radically alters the current view of the human genome’s coding capacity and will provide a rich pool of unexplored, functional human genes.

BIO: Thomas received his B.S. in Biological Engineering from MIT and trained in Prof. JoAnne Stubbe’s laboratory, where he studied the mechanism of ribonucleotide reductase. He then recieved his Ph.D. in Biochemistry & Molecular Biophysics from Caltech as an NIH NRSA predoctoral fellow under the mentorship of Prof. Peter Dervan. His thesis work focused primarily on characterizing the effects of DNA binding pyrrole-imidazole polyamides on DNA replication in prostate cancer cells. Thomas is currently an NIH NRSA postdoctoral fellow in Prof. Alan Saghatelian’s laboratory, where he has developed an integrative platform combining ribosome profiling and de novo transcriptome assembly to discover functional smORF encoded microproteins in the human genome.

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Lecture / Discussion Wed, 14 Apr 2021 12:39:54 -0400 2021-05-17T16:00:00-04:00 2021-05-17T17:00:00-04:00 Off Campus Location Center for RNA Biomedicine Lecture / Discussion Thomas Martinez, Salk Institute for Biological Studies
Precision Health Webinar (May 25, 2021 1:00pm) https://events.umich.edu/event/83924 83924-21617135@events.umich.edu Event Begins: Tuesday, May 25, 2021 1:00pm
Location: Off Campus Location
Organized By: Precision Health

Precision Health at the University of Michigan (U-M) invites you to engage with two outstanding Scholars who have been funded by Precision Health to develop their research.
Arun Subramaniyan, BE, MS (graduate student, College of Engineering): “Hardware-accelerated systems for next-generation sequencing analysis”

Alyse Krausz, BS, MS (graduate student research assistant, Biomedical Engineering): “A Point-of-Care Microfluidic System for Traumatic Brain Injury Diagnosis and Prognosis”

You'll hear more about their work and how they used Precision Health resources in these innovative projects.

**Please register to attend. We will send a link to the virtual presentation a few days in advance. We hope you'll join us!**

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Livestream / Virtual Tue, 04 May 2021 13:45:53 -0400 2021-05-25T13:00:00-04:00 2021-05-25T14:00:00-04:00 Off Campus Location Precision Health Livestream / Virtual May 2021 PH Webinar
PhD Defense: Edward Peter Washabaugh IV (May 27, 2021 10:00am) https://events.umich.edu/event/84050 84050-21619709@events.umich.edu Event Begins: Thursday, May 27, 2021 10:00am
Location: Off Campus Location
Organized By: Biomedical Engineering

Injuries to the neuromusculoskeletal systems often result in muscle weakness, abnormal coordination strategies, and gait impairments. Functional resistance training during walking—where a patient walks while a device increases loading on the leg—is an emerging approach to combat these symptoms. While simple passive devices (i.e., ankle weights and resistance bands) can be applied for this training, rehabilitation robots have more potential upside because they can be controlled to treat multiple gait abnormalities and can be monitored by clinicians. However, the cost of conventional robotic devices limits their use in the clinical or home setting. Hence, in this dissertation, we designed, developed, and tested passive and semi-passive wearable exoskeleton devices as a low-cost solution for providing controllable/configurable functional resistance training during walking.


We developed and tested two passive exoskeleton devices for providing resistance to walking and tested their effects on able-bodied participants and stroke survivors. First, we created a patented device that used a passive magnetic brake to provide a viscous (i.e., velocity-dependent) resistance to the knee. The resistive properties of the device could be placed under computer control (i.e., made semi-passive) to control resistance in real-time. Next, we created a passive exoskeleton that provided an elastic (i.e., position-dependent) resistance. While not controllable, this device was highly configurable. Meaning it could be used to provide resistance to joint flexion, extension, or to both (i.e., bidirectionally). Human subjects testing with these devices indicated they increased lower-extremity joint moments, powers, and muscle activation during training. Training also resulted in significant aftereffects—a potential indicator of therapeutic effectiveness—once the resistance was removed. A separate experiment indicated that individuals often kinematically slack (i.e., reduce joint excursions to minimize effort) when resistance is added to the limb. We also found that providing visual feedback of joint angles during training significantly increased muscle activation and kinematic aftereffects (i.e., reduced slacking).


With passive devices, the type of passive element used largely dictates the muscle groups, types of muscle contraction, joint actions, and the phases of gait when a device is able to apply resistance. To examine this issue, we compared the training effects of viscous and elastic devices that provided bidirectional resistance to the knee during gait. Additionally, we compared training with viscous resistances at the hip and knee joints. While the resistance type and targeted joint altered moments, powers, and muscle activation patterns, these methods did not differ in their ability to produce aftereffects, alter neural excitability, or induce fatigue in the leg muscles. While this may indicate that the resistance type does not have a large effect on functional resistance training during walking, it is possible that an extended training with these devices could produce a different result.


Lastly, we used musculoskeletal modeling in OpenSim to directly compare several strategies that have been used to provide functional resistance training to gait in the clinic or laboratory setting. We found that devices differed in their ability to alter gait parameters during walking. Hence, these findings could help clinicians when selecting a resistive strategy for their patients, or engineers when designing new devices or control schemes.



Date: Thursday, May 27, 2021

Time: 10:00 AM

Zoom: https://umich.zoom.us/meeting/register/tJIufumrrDgtHd3z5Jg3Y_BG4ZC70OPrjTjk (Zoom link requires prior registration)

Chair: Dr. Chandramouli Krishnan

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Lecture / Discussion Fri, 14 May 2021 13:49:26 -0400 2021-05-27T10:00:00-04:00 2021-05-27T11:00:00-04:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Logo
PhD Defense: William Y. Wang (June 4, 2021 12:30pm) https://events.umich.edu/event/84102 84102-21620248@events.umich.edu Event Begins: Friday, June 4, 2021 12:30pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Mechanoreciprocity in cell migration is an emerging concept describing the dynamic, bi-directional interactions between migrating cells and the surrounding extracellular matrix (ECM) they negotiate. Migrating cells not only sense and adapt to biochemical and biophysical ECM cues, but also, exert forces, deposit matrix, and secrete chemokines, matrix metalloproteinases, and matrix crosslinking enzymes that dynamically alter the same ECM properties known to regulate cell migration. Due to limitations in standard cell migration assays, how matrix properties influence cell migration and in turn, how cells influence matrix properties, has previously been studied as separate processes. However, observations from development, wound healing, and a variety of disease processes highlight the interdependency and iterative relationship between cell migration and ECM. An improved understanding of the underlying mechanisms that orchestrate the coevolution of migrating cells and ECM will aid in tissue engineering and regenerative medicine efforts to guide repair fibroblasts to regenerate wound beds, direct collective endothelial cell migration to vascularize ischemic or engineered tissue grafts and confine otherwise metastatic cancer cells to the primary tumor. Thus, the focus of this dissertation is to design biomimetic microsystems that afford investigation of cell migration mechanoreciprocity with a focus on fibroblasts, endothelial cells, and cancer cells.



First, this thesis investigated how single mesenchymal cells (fibroblasts and cancer cells) migrate in fibrous stromal tissue settings, such as in trans-stromal cancer cell migration during metastasis. To model fibrous stromal tissue, 3D fiber networks were electrospun over microfabricated wells to define ECM mechanics. Independently tuning alignment and stiffness of these matrices resulted in two phenotypically distinct cell migration modes. In contrast to stiff matrices where cells migrated continuously in a traditional mesenchymal fashion, cells in deformable matrices stretched matrix fibers to store elastic energy; subsequent adhesion failure triggered sudden matrix recoil and rapid cell translocation (termed slingshot migration). Across a variety of cell types, traction force measurements revealed a relationship between cell contractility and the matrix stiffness where slingshot migration mode occurred optimally.



Next, this thesis describes how microenvironmental cues influence collective endothelial cell migration during sprouting angiogenesis towards the design of pro-angiogenic biomaterials. This work employed a multiplexed angiogenesis-on-a-chip platform to assess the chemokine-directed 3D invasion of endothelial cells from a lumenized parent vessel into user-defined ECM. By tuning soluble and physical cues of the ECM, this work identified how 1) functional angiogenesis requires microenvironmental cues that balance cell invasion speed and proliferation; 2) dynamic interactions between sprout stalk cells and ECM regulates neovessel lumenization; and 3) imbuing microporosity within synthetic hydrogels can enhance endothelial cell invasion and angiogenic sprout lumenization.



Lastly, this thesis investigated how fibrous matrix cues activate quiescent vessel-lining endothelial cells into invasive tip cells in the context of fibrosis. Composite hydrogels (electrospun fiber segments suspended within 3D ECM) were integrated with the angiogenesis-on-a-chip platform. These studies establish that heightened matrix fiber density destabilizes cell-cell adherens junctions, reduces endothelium barrier function, and promotes the invasion of endothelial tip cells. Performing transcriptomic and secretomic analyses on fiber-induced tip endothelial cells revealed that fibrous ECM cues promote a fibrosis propagating phenotype.



Overall, the work presented in this dissertation integrates tunable biomaterials with microfabricated devices to investigate cell migration mechanoreciprocity of single mesenchymal cell migration, the collective migration of endothelial cells during angiogenesis, and endothelial-mesenchymal transition of quiescent endothelial cells into a fibrosis propagating cell phenotype.



Date: Friday, June 4, 2021

Time: 12:30 PM

Zoom: https://umich.zoom.us/meeting/register/tJcsf-uhpj4vGtyM7x-td2VV39BzqmF_zoob (Zoom link requires prior registration)

Chair: Dr. Brendon Baker

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Lecture / Discussion Mon, 24 May 2021 14:17:02 -0400 2021-06-04T12:30:00-04:00 2021-06-04T13:30:00-04:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Logo
Getting Engaged in Campus Education Innovation Activities (June 9, 2021 12:00pm) https://events.umich.edu/event/84084 84084-21619928@events.umich.edu Event Begins: Wednesday, June 9, 2021 12:00pm
Location: Off Campus Location
Organized By: RISE (Research. Innovation. Scholarship. Education.)

Our next Virtual Talking Circle (VTC) will feature representatives from several units on campus that are leading the way in cultivating education innovation: The Center for Academic Innovation (CAI), Fast Forward Medical Innovation (FFMI), and the International Mixed Reality Grand Rounds.

Join us on Wednesday, June 9, 2021 from 12:00 - 1:00 PM to learn more about these units and how you can get involved in their education innovation activities. We hope you will also share other education innovation resources available to faculty, staff and learners.

All are welcome!

Register via Zoom at: https://umich.zoom.us/webinar/register/WN_xVYKDuaYSXa6AevHutqXBA

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Workshop / Seminar Thu, 20 May 2021 06:44:41 -0400 2021-06-09T12:00:00-04:00 2021-06-09T13:00:00-04:00 Off Campus Location RISE (Research. Innovation. Scholarship. Education.) Workshop / Seminar RISE Virtual Talking Circle
RNA Innovation Seminar featuring Rising Scholars: Khan & McMillan (June 14, 2021 4:00pm) https://events.umich.edu/event/83934 83934-21619166@events.umich.edu Event Begins: Monday, June 14, 2021 4:00pm
Location: Off Campus Location
Organized By: Center for RNA Biomedicine

Registration Required: https://umich.zoom.us/webinar/register/WN_uLz-ONHVQPuRINMYUNvBJQ

“CCR5 as a model to examine reporter assays in evaluating translational phenomena”
Yousuf Khan
Knight-Hennessy Scholar
Stanford University

KEYWORDS: dual luciferase, frameshifting, recoding, CCR5
ABSTRACT: During the decoding of a subset of mRNAs, a proportion of ribosomes productively shift to the −1 reading frame at specific slippage-prone sites in a phenomenon known as programmed −1 ribosomal frameshifting (−1 PRF) to generate a frameshifted, C-terminally unique protein. The first experimentally verified occurrence of functionally utilized non-retroelement derived −1 PRF in humans has been reported in the mRNA encoding the immune-functioning C-C chemokine receptor 5 (CCR5). Here, we show that frameshifting does not occur during CCR5 decoding. Apart from its importance in understanding expression of a gene relevant to cancer, an HIV-1 receptor (and the associated claimed rationale for generating the first humans derived from genetically modified embryos), the findings imply that caution is appropriate in assessing results from translational reporter assays.

~and~

“Intersection between RNA methylation and TDP43-mediated toxicity in ALS”
Michael McMillan
Ph.D. candidate
Cellular and Molecular Biology
University of Michigan

KEYWORDS: TDP43, m6A, ALS, RNA stability
ABSTRACT: Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease resulting in the death of upper and lower motor neurons. ALS has no known cure and limited therapeutic options, and the underlying pathological mechanisms remain unclear. Despite considerable variability in clinical presentation, over 95% of ALS cases exhibit cytoplasmic inclusions of the RNA binding protein TDP43. Emerging evidence suggests that TDP43 is crucial for RNA stability, and that dysregulation of RNA homeostasis may contribute to ALS pathogenesis.
Methylation of RNA at the 6th position nitrogen (N6-methyladenosine methylation, or m6A) by methyltransferases (writers) or removal of methyl groups by demethylases (erasers) has dramatic effects on RNA stability and translation mediated by a family of RNA biding proteins that recognize methylated RNA (readers). m6A writers and erasers specifically localize to nuclear speckles, membraneless nuclear organelles rich in RNA binding proteins and splicing factors, including TDP43. Together with our data showing that TDP43 regulates RNA stability, these observations suggest that TDP43 may destabilize m6A modified RNA. Here, we show that methylated RNA co-purified with TDP43 from cultured cells via RNA immunoprecipitation, and abrogation of methylation sites disrupted TDP43 binding, suggesting that TDP43 recognizes m6A modified RNA in cellulo. We also noted profound and widespread hypermethylation of coding and non-coding transcripts in ALS spinal cord, many overlapping with confirmed TDP43 target transcripts. Consistent with a central role for m6A modification in TDP43-mediated toxicity, we identified several factors operating within the m6A pathway that enhance or suppress the toxicity of TDP43 in rodent primary cortical neurons via a single-cell CRISPR/Cas9 candidate-based screen. Genetic knockout of the established m6A reader YTHDF2 rescued TDP43 toxicity in primary neurons, and YTHDF2 was also upregulated in ALS postmortem sections. Together, these data imply a fundamental link between m6A RNA modifications and ALS pathogenesis, potentially mediated by TDP43-dependent RNA destabilization.

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Lecture / Discussion Tue, 18 May 2021 14:31:45 -0400 2021-06-14T16:00:00-04:00 2021-06-14T17:00:00-04:00 Off Campus Location Center for RNA Biomedicine Lecture / Discussion Yousuf Khan (Stanford) & Mike McMillan (U-M)
Precision Health Graduate Certificate Program - Information Session (June 17, 2021 1:00pm) https://events.umich.edu/event/84199 84199-21620752@events.umich.edu Event Begins: Thursday, June 17, 2021 1:00pm
Location: Off Campus Location
Organized By: Department of Learning Health Sciences

Plan to attend this information session to learn more about the growing field of precision health which seeks to tailor health care for individuals via a multidisciplinary, data-driven approach.

The new U-M Precision Health Graduate Certificate Program has arrived to educate current and future practitioners and researchers in this emerging field so they can become better equipped to customize patient care.

**Only 12 credits of graduate coursework required
**Great opportunity for graduate students to design their own plan
**Network with other precision health students and faculty at seminars and professional development workshops
**Mentoring with faculty

The certificate is open to all graduate students enrolled at U-M. Application deadline is August 1.

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Other Thu, 03 Jun 2021 10:50:45 -0400 2021-06-17T13:00:00-04:00 2021-06-17T13:30:00-04:00 Off Campus Location Department of Learning Health Sciences Other learners and researchers in lab, classroom and research settings
UM Single Cell Spatial Analysis Program (SCSAP) Kickoff Symposium (June 22, 2021 1:00pm) https://events.umich.edu/event/84222 84222-21620781@events.umich.edu Event Begins: Tuesday, June 22, 2021 1:00pm
Location: Off Campus Location
Organized By: Single Cell Spatial Analysis Program (SCSAP)

The UM BSI SINGLE CELL SPATIAL ANALYSIS PROGRAM KICK OFF SYMPOSIUM

Featuring Keynote Speaker Tzumin Lee, M.D. PhD.
Presenting: Linking single-cell genomics with single-cell genetics.

Date: June 22nd
Time: 1:00 pm -4:30 PM EST
Location: Zoom Webinar
Register at: https://umich.zoom.us/webinar/register/WN_Zax2iT5TReGILR_sQmIZ3w

Additional Mini-talks on: Spatial Transcriptomics, Single Cell RNA-Seq, CyTOF, Multispectral Imaging, Seq-SCOPE, Rare Cell Isolation.

Speakers:
Roger Cone, Ph.D. Evan Keller, Ph.D.
Thomas Wilson, M.D., Ph.D. Jun Li, Ph.D.
Tim Frankel, M.D. Sue Hammoud, Ph.D.
Jun Hee Lee, Ph.D. Olivia Koues, Ph.D.
Sunitha Nagrath, Ph.D. Justin Colacino, Ph.D.
Arvind Rao, Ph.D. Max S. Wicha, M.D.
Patricia Schnepp, Ph.D.

Find us at https://singlecellspatialanalysis.umich.edu
Questions/Comments please contact us at singlecellspatialanalysis@umich.edu

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Workshop / Seminar Fri, 04 Jun 2021 13:26:44 -0400 2021-06-22T13:00:00-04:00 2021-06-22T16:30:00-04:00 Off Campus Location Single Cell Spatial Analysis Program (SCSAP) Workshop / Seminar Dr. Tzumin Lee
PhD Defense: Jiayue Cao (June 23, 2021 3:00pm) https://events.umich.edu/event/84287 84287-21621035@events.umich.edu Event Begins: Wednesday, June 23, 2021 3:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

The stomach and brain interact closely with each other. Their interactions are central to digestive functions and the “gut feeling”. The neural pathways that mediate the stomach-brain interactions include the vagus nerve and the thoracic nerve. Through these nerves, the stomach can relay neural signals to a number of brain regions that span a central gastric network. This gastric network allows the brain to monitor and regulate gastric physiology and allows the stomach to influence emotion and cognition. Impairment of this gastric network may lead to both gastric and neurological disorders, e.g., anxiety, gastroparesis, functional dyspepsia, and obesity. However, the structural constituents and functional roles of the central gastric network remain unclear. In my dissertation research, I leveraged complementary techniques to characterize the central gastric network in rats across a wide range of scales and different gastric states. In animal experiments, I used functional magnetic resonance imaging (fMRI) to map brain activity synchronized with gastric electrical activity and to map brain activations induced by electrical stimulation applied to the cervical vagus or its afferent terminals on the stomach. I also used neurophysiology to characterize gastric neurons in brainstem in response to gastric electrical stimulation. Results from my studies suggest that 1) gastric neurons in the brainstem are selective to the orientation of muscle activity relayed through intramuscular arrays, 2) the central gastric network is intrinsically coupled to gastric slow waves and their amplitude fluctuations primarily via vagal signaling, 3) selective stimulation of the vagus can evoke widespread and fast brain responses and alter functional connectivity within and beyond the central gastric network. My dissertation research contributes to the foundation of mapping and characterizing the central and peripheral mechanisms of gastric interoception and sheds new light on where and how to stimulate the peripheral nerves to modulate stomach-brain interactions.



Date: Wednesday, June 23, 2021

Time: 3:00 PM

Zoom: https://umich.zoom.us/j/2757414653

Chair: Dr. Zhongming Liu

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Lecture / Discussion Tue, 15 Jun 2021 23:04:33 -0400 2021-06-23T15:00:00-04:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Logo
PhD Defense: Eric Charles Hobson (June 24, 2021 10:30am) https://events.umich.edu/event/84237 84237-21620794@events.umich.edu Event Begins: Thursday, June 24, 2021 10:30am
Location: Off Campus Location
Organized By: Biomedical Engineering

Mechanical testing of viscoelastic biomaterials is of critical importance in biomedical engineering, enabling basic research into the role of the extracellular matrix, investigatory and diagnostic testing of tissues and biofluids, and the development and characterization of tissue engineered therapeutics. Conventional material testing approaches used for soft biomaterials generally require force application through direct contact with a sample, leading to potential contamination and damage, and thereby limiting these approaches to end-point measurements. To overcome these limitations, we have developed a new measurement technique, Resonant Acoustic Rheometry (RAR), which enables high-throughput, quantitative, and non-contact viscoelastic characterization of biomaterials, soft tissues, and biological fluids.



RAR uses ultrasonic pulses to both generate microscale perturbations and measure the resulting resonant oscillations at the surface of soft materials using standard labware. Resonant oscillatory properties obtained from the frequency spectra of the surface oscillations, including the resonant frequency and the damping coefficient, are used to quantify material properties such as shear modulus, shear viscosity, and surface tension in both viscoelastic solids and liquids.



We developed a prototype RAR system and tested it on a range of soft biomaterials, with shear moduli ranging from under 100 Pa to over 50 kPa, including fibrin, gelatin, and polyethylene glycol (PEG). Shear moduli measured using RAR were validated both computationally using finite element analysis and experimentally using conventional shear rheometry, with excellent linear correlation in measured elasticity between techniques (R2 > 0.95). By performing parallel RAR experiments using microwells of different sizes, we verified that resonant oscillatory behaviors could be used to quantify the intrinsic viscoelastic properties of a material. We also demonstrated the rapid, non-contact monitoring of changes in material properties over a variety of temporal scales, ranging from processes occurring on the order of milliseconds to those occurring over hours and days. High temporal resolution RAR measurements, with sampling intervals as low as 0.2 seconds, were used to characterize the gelation process. Characteristic features of the resonant surface waves during phase transition were applied to identify the gel point for various hydrogels. High sample throughput was demonstrated by performing longitudinal RAR testing to explore the impact of hydrogel polymer and crosslinker concentration on both reaction kinetics and final mechanical properties in full factorial experiments consisting of over 15,000 unique measurements. We were able to identify individual effects of design parameters as well as interactions that led to unexpected mechanical properties, demonstrating the importance of combinatorial methods and high-throughput mechanical characterization in material design.



These studies demonstrate that RAR can rapidly and accurately assess the mechanical properties of soft viscoelastic biomaterials. The measurements generated are analogous to those produced using conventional mechanical testing, and RAR is further capable of longitudinal viscoelastic studies over time. RAR applies automation in both data collection and analysis, allowing high throughput measurement of an array of samples without contact or the need for manual intervention. Furthermore, RAR uses standard microwell plates, which simplifies sample preparation and handling. The viscoelastic properties of soft biomaterials are relevant in a wide range of applications, including for clinical diagnostic assays and the development of hydrogel materials for regenerative medicine. RAR represents a fast, accurate, and cost-effective method for materials characterization in these applications.



June 24 - 10:30 AM

Zoom: https://umich.zoom.us/meeting/register/tJcsd-iurTosGdNn_gR-FbOCe5TUR09Y58WV

Co-Chairs: Dr. Cheri Deng and Dr. Jan Stegmann

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Lecture / Discussion Tue, 22 Jun 2021 16:37:33 -0400 2021-06-24T10:30:00-04:00 2021-06-24T11:30:00-04:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Logo
LHS Collaboratory-Summer Workshop (June 24, 2021 1:00pm) https://events.umich.edu/event/83809 83809-21538171@events.umich.edu Event Begins: Thursday, June 24, 2021 1:00pm
Location: Off Campus Location
Organized By: Department of Learning Health Sciences

This virtual workshop will review the basic concepts behind Learning Health Systems including the learning cycle, infrastructure, and learning communities.  Participants will engage in a collaborative activity to design a learning cycle.

Registration for this virtual event is limited-
please register early!

Charles P. Friedman

Department Chair of Learning Health Sciences
Josiah Macy Jr. Professor of Medical Education
Professor of Information
Professor of Public Health
University of Michigan

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Workshop / Seminar Tue, 20 Apr 2021 10:17:48 -0400 2021-06-24T13:00:00-04:00 2021-06-24T16:00:00-04:00 Off Campus Location Department of Learning Health Sciences Workshop / Seminar LHS Collaboratory logo
BME Master's Defense: Spencer Morris (June 28, 2021 10:00am) https://events.umich.edu/event/84342 84342-21623372@events.umich.edu Event Begins: Monday, June 28, 2021 10:00am
Location: Off Campus Location
Organized By: Biomedical Engineering

Acquiring accurate measurements for blood flow is a clinically relevant problem of interest. Three-dimensional color flow with partial volume correction (PVC) is a relatively new method for measuring blood flow that accounts for beams located partially outside of the blood vessel. Recent work has shown that the relationship between color flow power and partially perfused voxels is nonlinear. This work investigates the statistics of color power measurements in simulated plug flow to help explain this nonlinear behavior. Data was acquired using Field II simulations in which a 3.75 MHz mechanically swept linear array obtained RF data of blood moving through a vessel. Blood in the vessel exhibited plug flow, and tissue backscatter was set to 40 dB below blood. The statistics of color power at each point in the processing chain were analyzed using histograms, established results in ultrasound statistics, and derived probability density functions (pdfs). For locations completely inside the beam, power before additional processing showed exponential behavior, whereas the square root of power, i.e., amplitude, was Rician distributed. After implementing the Kasai algorithm, the power values could be estimated with a gamma distribution with a shape parameter of 2.21. Kasai powers corresponding to tissue could also be fitted with a gamma distribution, albeit with a shape parameter close to 1, indicating close to exponential behavior. Kasai powers for partial volume data were intermediate between the tissue and blood data. A method for estimating partial volume weight from the skewness and kurtosis of samples taken from the same location is also discussed.

Date: Monday, June 28, 2021
Time: 10:00 AM
Zoom: https://umich.zoom.us/j/97162930417
Chair: Dr. Oliver Kripfgans

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Presentation Tue, 22 Jun 2021 11:48:21 -0400 2021-06-28T10:00:00-04:00 2021-06-28T11:00:00-04:00 Off Campus Location Biomedical Engineering Presentation BME Event
PhD Defense: Hans Zander (July 9, 2021 9:00am) https://events.umich.edu/event/84346 84346-21623406@events.umich.edu Event Begins: Friday, July 9, 2021 9:00am
Location: Off Campus Location
Organized By: Biomedical Engineering

Spinal cord stimulation (SCS) is a neuromodulation technique that applies electrical stimulation to the spinal cord to alter neural activity or processing. While SCS has historically been used as a last resort therapy for chronic pain management, novel applications and technologies have recently been developed that either increase the efficacy of treatment for chronic pain or drive neural activity to produce muscular activity/movement following a paralyzing spinal cord injury (SCI). Despite these recent innovations, there remain fundamental questions concerning the neural recruitment underlying these efficacious results. This work evaluated the neural activity and mechanisms for two novel SCS applications: closed-loop spinal cord stimulation for pain management, and ventral, high frequency spinal cord stimulation (HF-SCS) for inspiratory muscle activation following a SCI.

To evaluate neural activity, I developed computational models of SCS. Models consisted of 3 components: a finite element model (FEM) of the spinal cord to predict voltages during stimulation, biophysical neuron models, and algorithms to apply time-dependent extracellular voltages to the neuron models and simulate their response. While this cutting-edge modeling methodology could be used to predict neural activity following stimulation, it was unclear how common anatomical or technical model simplifications affected neural predictions. Therefore, the initial goal of this work was to evaluate how modeling assumptions influence neural behavior.

My initial work identified how several relevant anatomical and technical factors influence model predictions of neural activity. To evaluate these factors, I designed an FEM of a T9 thoracic spine with an implanted electrode. Then, I sequentially removed details from the model and quantified the changes in neural predictions. I identified several factors with profound (>30%) impacts on neural thresholds, including overall model impedance (for voltage-controlled stimulation), the presence of a detailed vertebral column, and dura mater conductivity. I also identified several factors that could safely be ignored in future models. This work will be invaluable as a guide for future model development.

Next, I developed a canine model to evaluate T2 ventral HF-SCS for inspiratory muscle activation. I designed and positioned two neuron models hypothesized to lead to inspiratory behavior: ventrolateral funiculus fibers (VLF) leading to diaphragm activation and inspiratory intercostal motoneurons. With this model, I predicted robust VLF and T2-T5 motoneuron recruitment within the physiologic range of stimulation. Additionally, I designed two stimulation leads that maximize inspiratory neuron recruitment. The finalized leads were evaluated via in vivo experiments, which found excellent agreement with the model. This work builds our mechanistic understanding of this novel therapy, improves its implementation, and aids in future translational efforts towards human subjects.

Finally, I developed a computational model to evaluate closed-loop stimulation for chronic pain. This work characterized the neural origins of the evoked compound action potential (ECAP), the controlling biomarker of closed-loop stimulation. I modified my modeling methodology to predict ECAPs generated during low thoracic dorsal stimulation in humans, which matched with experimental measurements. This modeling work showed that ECAP properties depend on activation of a narrow range of neuron diameters and quantified how anatomical and stimulation factors (CSF thickness, stimulation configuration, lead position, pulse width) influence ECAP morphology, timing, and neural recruitment. These results improve our mechanistic understanding of closed-loop stimulation and may lead to expanded clinical utility as well as better validation of future SCS computational models.

Date: Friday, July 9, 2021

Time: 9:00 AM EDT

Zoom: https://umich.zoom.us/j/96847307388

Chair: Dr. Scott Lempka

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Lecture / Discussion Tue, 22 Jun 2021 16:45:26 -0400 2021-07-09T09:00:00-04:00 2021-07-09T10:00:00-04:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Logo
BME Ph.D. Defense: Michael Bregenzer (July 21, 2021 9:00am) https://events.umich.edu/event/84438 84438-21623984@events.umich.edu Event Begins: Wednesday, July 21, 2021 9:00am
Location: Off Campus Location
Organized By: Biomedical Engineering

High grade serous ovarian cancer (HGSOC) is the deadliest gynecological malignancy. Despite successful first line therapies, most patients relapse and develop more chemoresistant disease. This recurrence and development of chemoresistance is attributed to a rare population of tumor cells, termed cancer stem cells (CSCs), which are more chemoresistant, have the capacity to self-renew, and can repopulate the entire tumor. Research has shown that CSCs are maintained by the non-cancer cells in the tumor microenvironment (TME), such as mesenchymal stem cells (MSCs), endothelial cells (ECs), and immune cells. Furthermore, the role of non-cancer cells in clinical outcomes and chemoresistance has been highlighted by recent evidence showing that classification of HGSOC molecular subtypes, which have variable clinical prognoses, are influenced by the presence of non-cancer cells in the tumor. However, it is currently unclear exactly how CSCs and the nuanced cell composition of the TME work together to promote chemoresistance. Current models used to study these phenomena either suffer from a lack of cellular complexity in the case of many in vitro models or impractical experimental constraints such as long latency periods and poor control over cell composition in patient-derived xenografts. To better understand the role of CSCs and the TME cells in chemoresistance, practical in vitro model systems that more closely represent in vivo processes and microenvironments are needed. We hypothesize that the development of these in vitro model systems will contribute novel insights into TME-mediated CSC regulation and the development of chemoresistance in HGSOC.

In aim 1 we examined the emergence of chemoresistance in the context of CSCs by developing a 3D in vitro serial passaging model system that allows for long term culture of patient-derived tumor cells with periodic evaluation of stemness and chemoresistance. Using this model system, we demonstrated increased proliferation, expression of CSC markers, tumorigenicity, and chemoresistance over the course of long-term passaging, reflective of emerging chemoresistance in vivo. Furthermore, this system enabled us to define a malignant gene expression signature that is associated with chemoresistance, tumorigenicity, and stemness and to evaluate patient-specific chemoresistance development following treatment. Finally, we demonstrated the translational value of this model system by showing that Metformin treatment can hinder CSC driven development of chemoresistance in a phase II clinical trial.

In aim 2 we developed a heterogeneous tumoroid culture system that enabled culture of patient-derived tumor cells with controlled ratios of MSCs, ECs, and immune cells to study TME-mediated maintenance of CSCs and chemoresistance. Using this model, we found that changes in CD133+/-ALDH+/- CSC phenotypes in response to TME cells varied depending on the patient sample. We also observed increased tumorigenicity and chemoresistance in tumoroids compared to spheroids cultured with patient-derived tumor cells alone. Furthermore, we found evidence of epithelial-to-mesenchymal transition (EMT) in tumoroids accompanied by altered CSC phenotypes and a malignant matrisome signature. All of this together supports idea that the non-cancer cells in the TME contribute to the development of advanced, chemoresistant disease and implicates EMT, changes in CSC phenotypes, and matrix remodeling as the primary culprits.

Finally, in aim 3, we utilized this tumoroid system to generate tumoroids with 23 different cell compositions to evaluate the role of TME cell composition in response to therapy. Drug assays with novel and traditional chemotherapies revealed that tumoroids with different compositions respond differently to therapy and that the number of monocytes included in the culture was associated with the greatest resistance to therapy. Furthermore, our random forest models trained on the drug responses of each cell composition were able to predict drug response with moderate success. With these models we identified that nuanced differences in cell composition can influence drug response and that the strongest predictor of response to therapy was the total quantity of non-cancer cells. Overall, this model demonstrates the potential of using the TME composition to predict patient drug response and direct clinical management.

In these aims we demonstrate the clear utility of complex and realistic, yet practical in vitro model systems in the study of chemoresistance and CSC maintenance in ovarian cancer. Specifically, we identified the link between CSCs and the development of chemoresistance in long term 3D in vitro serial passage culture. Furthermore, we showed that the non-cancer cells in the TME can confer chemoresistance and promote EMT associated with altered CSC phenotypes and matrix remodeling. Lastly, we demonstrated the potential of TME composition in predicting drug response. Overall, the model systems presented in this study provide platforms that can be used to better understand the role of CSCs and the TME in chemoresistance and poor clinical outcomes. This could ultimately lead to the development of novel therapies, enhanced clinical management, and improved clinical outcomes.

Date: Wednesday, July 21, 2021
Time: 9:00 AM
Zoom: https://umich.zoom.us/j/96111622879
Password: 326862
Chair: Dr. Geeta Mehta

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Presentation Mon, 12 Jul 2021 12:13:44 -0400 2021-07-21T09:00:00-04:00 2021-07-21T10:00:00-04:00 Off Campus Location Biomedical Engineering Presentation BME Event
Precision Health Graduate Certificate Program (July 22, 2021 1:00pm) https://events.umich.edu/event/84318 84318-21623289@events.umich.edu Event Begins: Thursday, July 22, 2021 1:00pm
Location: Off Campus Location
Organized By: Department of Learning Health Sciences

The new U-M Precision Health Graduate Certificate Program has arrived to educate current and future practitioners and researchers in this emerging field so they can become better equipped to customize patient care.

**Only 12 credits of graduate coursework required
**Great opportunity for graduate students to design their own plan
**Network with other precision health students and faculty at seminars and professional development workshops

**Mentoring with faculty

The certificate is open to all graduate students enrolled at U-M. Application deadline is August 1.

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Presentation Fri, 18 Jun 2021 14:24:55 -0400 2021-07-22T13:00:00-04:00 2021-07-22T13:30:00-04:00 Off Campus Location Department of Learning Health Sciences Presentation researchers, learners and health professional in lab, classroom and clinic setting
Precision Health Graduate Certificate Program - Information Session (July 22, 2021 1:00pm) https://events.umich.edu/event/84201 84201-21620757@events.umich.edu Event Begins: Thursday, July 22, 2021 1:00pm
Location: Off Campus Location
Organized By: Department of Learning Health Sciences

Plan to attend this information session to learn more about the growing field of precision health which seeks to tailor health care for individuals via a multidisciplinary, data-driven approach.

The new U-M Precision Health Graduate Certificate Program has arrived to educate current and future practitioners and researchers in this emerging field so they can become better equipped to customize patient care.

**Only 12 credits of graduate coursework required
**Great opportunity for graduate students to design their own plan
**Network with other precision health students and faculty at seminars and professional development workshops
**Mentoring with faculty

The certificate is open to all graduate students enrolled at U-M. Application deadline is August 1.

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Other Thu, 03 Jun 2021 11:00:29 -0400 2021-07-22T13:00:00-04:00 2021-07-22T13:30:00-04:00 Off Campus Location Department of Learning Health Sciences Other learners and researchers in lab, classroom and research settings
BME Ph.D. Defense: Yuan Li (July 22, 2021 2:00pm) https://events.umich.edu/event/84452 84452-21624017@events.umich.edu Event Begins: Thursday, July 22, 2021 2:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Glioblastoma (GBM) is the most common and aggressive primary brain tumor in adults and has a poor prognosis with a median survival of approximately 14 months. Clinical standard assessment of therapy response and tumor progression is based upon post-contrast T1-weighted (T1W) and fluid-attenuated inversion recovery (FLAIR) T2-weighted (T2W) magnetic resonance images (MRI).  However, contrast enhancement observed on the post-contrast T1W MRI is affected not only by tumor growth but also effects of radiation, anti-angiogenesis drugs and chemotherapy, due to the fact that it represents blood-brain barrier disruption. Another problem is that abnormality on T2W FLAIR images is influenced by T2 changes of tumor cells as well as edema and necrosis that always co-exist within GBM. Diffusion weighted (DW) imaging has been proposed to overcome these limitations. Conventional DW images quantify apparent diffusion coefficient (ADC) with b-values between 0 and 1000 s/mm2 using a mono-exponential decay. One limitation is that co-existence of edema in clinical GBM elevates ADC.
 
In diffusion MRI, there are three dimensions of parameter spaces that we could explore in research —b value, diffusion time (t) and echo time (TE). Hence, we investigated and developed high order diffusion models in these three spaces and evaluated whether they could reveal more features of GBM.
 
In the b-value space, we investigated a microstructure model (MSM), in which modulation of diffusion gradient with cell size is considered, with high b-value diffusion images in the patients with GBM pre-radiation therapy (RT). We found apparent cell size (ARS), extracellular diffusion coefficient (Dex) and intracellular fractional volume (Vin) in tumor were significantly greater than ones in normal tissue and edema. In addition, we investigated diffusion kurtosis imaging (DKI) in GBM pre-RT and mid-RT, and found pre-RT mean kurtosis of the tumor could provide a predictive value of overall survival (OS) additional to clinical prognostic factors.
 
In the TE space, T2-Relaxation-Diffusion correlation experiments can be powerful in resolving water compartments with respect to their size and chemical composition, but the problem is ill-posed. We simplified the T2-Relaxation-Diffusion correlation to consider the T2 values and diffusion coefficients in a 2x2 fashion. We found that there were significant differences between fast and slow diffusion coefficients and between associated T2 values in tumor, cortex, deep GM, and edema. Multivariate Cox model showed the fractional volume of slow component (Vs) mid-RT may add a predictive value to clinical factors.
 
In diffusion time space, we applied three different diffusion times using pulsed diffusion gradients (PG) and oscillating gradients at frequencies of 30 Hz (OS30) and 50 Hz (OS50) using a prototype sequence. Using a random walk with barriers model, we estimated cell diameter, unrestricted diffusion coefficient (D0) at a short time limit, bulk diffusion coefficient (Dinf) at a long time limit, cell membrane permeability and effective restriction in the contrast-enhanced tumor. Those parameters provide microstructural information in the GBM and need to be further investigated and validated with pathology.
 
Previous studies have mainly investigated high order diffusion models in prostate cancer and xenograft tumor models, and only a few studies investigated GBM. The current knowledge about the relationship between model parameters and physiological/pathological features in GBM are still limited. Our research in GBM could lead to better imaging means for GBM diagnosis, tumor target definition for radiation therapy, and therapy response assessment.
 
Date: Thursday, July 22, 2021
Time: 2:00 PM
Zoom: https://umich.zoom.us/j/96213084276

Chair: Dr. Yue Cao

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Presentation Tue, 13 Jul 2021 13:47:02 -0400 2021-07-22T14:00:00-04:00 2021-07-22T15:00:00-04:00 Off Campus Location Biomedical Engineering Presentation BME Event
BME Ph.D. Defense: Alyse Krausz (July 30, 2021 10:00am) https://events.umich.edu/event/84644 84644-21624348@events.umich.edu Event Begins: Friday, July 30, 2021 10:00am
Location: Off Campus Location
Organized By: Biomedical Engineering

Diagnostic and monitoring devices based on protein biomarker measurements have the potential to inform courses of treatment in acute conditions and to help manage and prevent disease progression in chronic conditions. The importance of diagnostic and monitoring devices cannot be overstated as medicine is blind without them. However, prevalent conditions such as traumatic brain injury (TBI) and chronic kidney disease (CKD) lack adequate diagnostic and monitoring tools. 
 
Assessment of TBI is typically done through neurological examination and neuroimaging techniques. While these methods can identify direct tissue damage to the brain, they cannot assess the secondary damage stemming from the initial injury. The primary tissue damage sets off a cascade of secondary injuries, such as neuronal cell death, blood brain barrier breakdown, edema, and upregulation of inflammatory markers. Protein biomarkers have been proposed as a way of monitoring the progression of secondary TBI injury and of providing more sensitive diagnostic measures when used in conjunction with imaging and physical examination. However, FDA authorized biomarkers, glial fibrillary acidic protein (GFAP) and ubiquitin c-terminal hydrolase L1 (UCH-L1), can currently only be measured in a hospital laboratory. Analyzing TBI biomarker data in field and pre-hospital settings would enable rapid diagnosis and delivery of care, so we developed a glass and silicon microfluidic device for quantification of TBI protein biomarkers via bead-based immunoassay. The device consists of a single channel with a variable height profile fabricated by slowly lowering a glass wafer into hydrofluoric acid. The device can capture and separate beads with diameters ranging from 1 to 5 micrometers. We also developed bead-based quantum dot-linked immunosorbent assays (QLISAs) for GFAP, interleukin-6 (IL-6), and interleukin-8 (IL-8) by conjugating appropriate antibodies to 2.8, 4.5, and 1 micrometer diameter beads, respectively. We used the variable height device to passively separate a mixture of assay beads with completed immunocomplexes into distinct bands where the diameter of the beads matched the height of the channel. The fluorescent intensity of each band was used to quantify a different biomarker concentration, resulting in a customizable brain injury barcode. By changing out the bead size and antibodies used for each immunoassay, the variable height device can keep pace with the developing field of TBI biomarker discovery and validation or be applied to biomarkers for another condition of interest. 
 
We also developed an assay system to monitor CKD, which is one of the ten most common chronic conditions in adults aged 65 and older. Clinical guidelines currently recommend that the urinary albumin-to-creatinine ratio (ACR) be measured once a year to monitor disease progression. However, measuring the ACR at home can enable patients to self-identify the early signs of disease progression and consult their physicians, potentially leading to improved outcomes. We designed and analytically validated inexpensive, colorimetric assays for urinary albumin and creatinine intended to be used in a 3D-printed, disposable microfluidic device. Discrepancies between the results from the colorimetric albumin assay and the hospital albumin assay when clinical urine samples were tested highlight the importance of incorporating analytical validation as a checkpoint in the development of microfluidic monitoring systems. 
 
Overall, this work presents a novel method of multiplexing immunoassays in microfluidic systems that can be applied to measure protein biomarkers for TBI or another condition of interest and highlights the importance of integrating assay design with microfluidic device design to promote clinical translation.
 
Date: Friday, July 30, 2021
Time: 10:00 AM
Zoom: https://umich.zoom.us/meeting/register/tJYpdu2rrjsqH9LM0c4DZ8bs8Uj0BdggOEeE (pre-registration required)
Chair: Dr. Mark Burns

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Presentation Mon, 19 Jul 2021 11:02:10 -0400 2021-07-30T10:00:00-04:00 2021-07-30T11:00:00-04:00 Off Campus Location Biomedical Engineering Presentation BME Event
BME PhD Defense: Emine Sumeyra Turali-Emre (August 2, 2021 1:00pm) https://events.umich.edu/event/84794 84794-21624994@events.umich.edu Event Begins: Monday, August 2, 2021 1:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Biomimetic nanoparticles (NPs) are bio-inspired inorganic nanoscale materials that replicate some biological nanostructures functionalities including self-assembly, catalysis, and enzyme inhibition. These functionalities are being investigated for and, in some cases, are being utilized in optics and electronics such as chemical sensors, superhydrophobic coatings, and antireflective surfaces. This thesis examines the utilization of biomimetic inorganic NPs for various problems in biomedical engineering.

Specifically, in the first part of this thesis, I address the problem on controversial explanations of the antibacterial and other biological activity of zinc oxide NPs that are frequently utilized in cosmetics, textiles, and biomedical fields. In the second part of the thesis, I explore the self-organization of NPs into biomimetic supraparticles (SPs) for nucleic acid delivery that can be exploited as drug delivery agents.

NPs have been used in the antimicrobial field for a long time; however, their antibacterial mechanism of action against different types of bacteria remains unclear and, in many cases, misinterpreted. Most of the studies on antimicrobial NPs suggest reactive oxygen species (ROS) formation, ion release, and membrane damage as the primary source of antibacterial activity. In Chapter 2, we show that the mechanism of antibacterial activity for Staphylococcus aureus is remarkably more complex than generating ROS or the release of Zn2+ ions and is based on formation of biomimetic complexes of NPs with proteins. Gene expression analysis demonstrated that ZnO-NPs significantly affect carbohydrate metabolism and cell energetics, where the uridine monophosphate (UMP) biosynthesis pathway is highly upregulated. In Chapter 3, we explore the ZnO-NP mode of entry into S. aureus and the cell metabolism. Here, we showed that NPs enter the cells within 5 minutes of exposure and induce minimal membrane damage. We note that cells do not depolarize until 60 min post-NPs exposure. Thereby, we highlight that membrane damage is not the primary mechanism of action but rather a downstream effect of ZnO-NPs exposure to bacterial cells. Taken together, causing minimal ROS production and significant changes in carbohydrate metabolism and bioenergetics along with cell entry without immediate membrane damage imply the biomimetic function of these NPs. Further investigation into the antimicrobial mechanisms of biomimetic NPs is essential for future clinical translation.

Over the past few decades, there has been considerable interest in developing nanoscale constructs as effective delivery tools for high molecular weight drugs. In chapter 4, I explore the self-assembly of NPs into compartmentalized SPs, which mimics the structure of a virus to deliver nucleic acid into cells. The time-dependent self-assembly mechanism reveals that these SPs are formed from nanocup intermediates. We found that this intermediate stage is essential for the utilization of SP compartments. Nucleic acid is added to the system at this stage before SP formation, and high encapsulation is achieved. Similar to virus infections, once cells uptake the SP, SP disassociates in endosomes and releases the cargo.

Overall, the work presented in this thesis investigates and highlights the strong potential of biomimetic inorganic NPs use in next-generation biomedical applications.

Date: Monday, August 2, 2021
TIme: 1:00PM
Zoom: https://umich.zoom.us/j/95043183845
Chair: Prof. Nicholas Kotov

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Presentation Wed, 28 Jul 2021 12:34:40 -0400 2021-08-02T13:00:00-04:00 2021-08-02T14:00:00-04:00 Off Campus Location Biomedical Engineering Presentation BME Event
BME PhD Defense: Daniel Clough (August 4, 2021 10:00am) https://events.umich.edu/event/84844 84844-21625176@events.umich.edu Event Begins: Wednesday, August 4, 2021 10:00am
Location: Off Campus Location
Organized By: Biomedical Engineering

Type 1 diabetes is caused by the autoimmune destruction of insulin-producing β-cells, resulting in a chronic metabolic disorder typically treated with exogenous insulin. Even with the aid of advanced insulin pumps and real time feedback systems, blood glucose levels still deviate outside of the range maintained by native islets, which places the individual at risk for vascular complications and life-threatening hypoglycemic events. Cell replacement therapies have demonstrated the capacity to tightly control blood glucose levels. The wide adoption of cell replacement therapy is hindered by limited availability of donor islets, and the lack of effective methods to support the long-term function of these cells within a clinically accessible site. The results presented in this thesis address these limitations: through studying maturation of human pluripotent progenitor cell (hPPC) derived β cells within a transplantable biomaterial platform, and evaluating novel approaches to the implantation and support of these cells during their continued maturation in vivo.

First, I present a study that examined delivery of hPPC-derived pancreatic progenitors within microporous PLG scaffolds into the epididymal fat pad, the murine surrogate for the clinically relevant omental pouch. Kidney capsule injection, the site most commonly utilized to test stem cell-derived β cell function in murine models, was the comparison condition. We observed that the microporous scaffolds supported cell engraftment, however the levels of circulating C-peptide were lower when compared to the kidney capsule condition. The scaffolds were subsequently modified to provide sustained release of exendin-4, which led to significantly increased C-peptide production. Image analysis revealed that exendin-4 releasing scaffolds enhanced the proportion of pancreatic progenitors that matured to monohormonal insulin producing cells.

Next I present my findings from studying how hPPC-derived β cells mature and function within three transplantation sites: the i) scaffold delivery into the epididymal fat pad, ii) scaffold delivery into the subcutaneous space, and iii) the kidney capsule injection (control). Additionally, we investigated the impact of blood glucose levels on maturation of the hPPC-derived β cells by transplanting mice with pre- or post-engraftment diabetes induction. Hyperglycemia was ameliorated in the cohorts of mice that received scaffolds into the epididymal fat pad, following a period of in vivo maturation. The function of these cells was demonstrated by the reduction in blood glucose levels, healthy increase in weight, therapeutic levels of circulating human insulin, and healthy responses to glucose challenge tests. The function from the epididymal fat pad was superior to the subcutaneous space and was observed to be comparable to the kidney capsule. No differences were observed in graft function between the cohorts whose grafts matured in a diabetic or non-diabetic environment, yet several differences in gene expression were observed.

Many of the current differentiation protocols culture the cells above a feeder layer in monolayer, or in suspension within a bioreactor. Typically, these protocols require the disruption of the cell niche during key differentiation stages or pre-transplantation handling. Biomaterial scaffolds maintain the integrity of cell-to-cell and cell-to-matrix connections by providing both a space for cell niche development as well as a vehicle for transplantation into the body. Herein, I present results from testing the developmental stage in which progenitors are seeded into the 3D niche, and two differentiation strategies prior to seeding: monolayer and suspension culture. Maturation was characterized via gene expression analysis, glucose stimulated insulin secretion assay, and nondestructive microscopy utilizing a sfGFP-C-peptide cell line that reports C-peptide production and secretion. We observed that seeding clusters during the key transition phase from pancreatic progenitor to pancreatic endocrine enhanced commitment to the final beta cell fate.

This work enhances our understanding of hPPC-derived beta cell manufacturing within scaffolds, and delivery to an extrahepatic site to achieve normoglycemic blood glucose levels.

Date: Wednesday, August 4, 2021
Time: 10:00 AM
Zoom: https://umich.zoom.us/j/98009467275
Password: betacell
Chair: Dr. Lonnie Shea

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Presentation Mon, 02 Aug 2021 10:58:53 -0400 2021-08-04T10:00:00-04:00 2021-08-04T11:00:00-04:00 Off Campus Location Biomedical Engineering Presentation BME Event
BME PhD Defense: Dorsa Haji Ghaffari (August 5, 2021 11:00am) https://events.umich.edu/event/84795 84795-21624995@events.umich.edu Event Begins: Thursday, August 5, 2021 11:00am
Location: Off Campus Location
Organized By: Biomedical Engineering

Retinal prostheses have restored a sense of vision in patients blinded by photoreceptor degeneration. These electronic implants operate by electrically stimulating the remaining retinal cells. While retinal prosthesis users report improvements in light perception and performing basic visual tasks, their ability to perceive shapes and letters remains limited. Investigating stimulation strategies to reduce perceptual thresholds and create focal, non-overlapping phosphenes will increase the resolution of retinal prostheses and improve the overall patient outcomes. In this thesis I explore two main strategies for electrode-specific optimization of stimulation parameters: 1) a novel pulse paradigm for threshold reduction, and 2) an automated closed-loop method for adjusting stimulation parameters to create a focal retinal activation area.

I combined human subject testing and computational modeling to investigate the effect of waveform asymmetry on perception shapes and thresholds with epiretinal stimulation. Threshold measurement and phosphene shape analysis was performed on four Argus II users. A computational model of a retinal ganglion cell (RGC) was created in the NEURON simulation environment to allow for a more thorough parameter testing and to gain insight into the biophysical mechanisms. Our human subject results suggest that asymmetric waveforms could increase perception probabilities compared to a standard symmetric pulse, and this effect can be intensified by addition of an interphase gap (IPG). Our in silico model predicts that the most effective pulse for threshold reduction is asymmetric anodic-first stimulation with small duration ratios (≤ 5) and long IPGs (≥ 2 ms). Phosphene shape analysis revealed no significant difference in percept elongation with different pulse types. Average phosphene area was larger with asymmetric anodic-first stimulation compared to other pulse types.

Prosthetic vision quality is highly dependent on the capability to precisely activate target neurons and avoid off-target activation. However, studies show elongated and inconsistent responses to single electrode stimulation, indicating unintended stimulation of off-target neurons and electrode-specific activation patterns. While tuning stimulation parameters can transform the spatial RGC activity, a manual search for optimal parameters can be time consuming and tiring for patients. I developed a process for automatic optimization of stimulation parameters in silico, which involved training neural networks for quantifying the relationship between pulse parameters and spatial response descriptors, and a closed-loop algorithm to search for optimal parameters. Using this process, I was able to guide the parameter search effectively and converge to an optimal response within a few iterations.

Finally, I presented a process for automatic optimization of stimulation parameters in vitro using calcium imaging in mouse retina. This process involved training neural networks at each iteration based on a few images, using an interior point algorithm to find the optimal parameters, and classifying the resulting calcium images with a CNN trained on previous data. Our results indicate that we can converge to optimal stimulation parameters that create focal RGC activity by sampling less than 1/3 of the parameter space. This approach can shorten the exploration time significantly compared to a manual search, especially when the parameter space is large. Findings of this project could lead to the development of a clinically applicable system for electrode-specific optimization of stimulation protocol, improving the overall outcome of artificial vision.

Date: Thursday, August 5, 2021
Time: 11:00 AM
Zoom: https://umich.zoom.us/j/93552322970
Chair: Dr. James Weiland

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Presentation Wed, 28 Jul 2021 12:42:01 -0400 2021-08-05T11:00:00-04:00 2021-08-05T12:00:00-04:00 Off Campus Location Biomedical Engineering Presentation BME Event
BME PhD Defense: Ahmet Emre (August 9, 2021 2:00pm) https://events.umich.edu/event/84859 84859-21625204@events.umich.edu Event Begins: Monday, August 9, 2021 2:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Energy storage is an integral part of life. Living creatures have developed a distributed and structural energy storage system to survive under various and sometimes extreme conditions. Similarly, energy storage is critical for modern life to power from small biomedical instruments to large aircraft. There are still several challenges against efficient and safe energy storage utilization due to the mechanical, chemical, and physical limitations of existing materials. Inspired by biological structures, we present multifunctional nanocomposites from aramid nanofibers (ANF), a nanoscale version of Kevlar, to address the safety and efficiency of various battery chemistries and enable structural energy storage to increase energy density. High mechanical properties of ANF suppress dendrite formation, and tunability with different copolymers and fabrication methods allow ANF-based nanocomposites to meet specific needs of different battery chemistries.

In the first part of this thesis, we engineered biomimetic solid electrolyte from ANF and polyethylene oxide for zinc batteries inspired by the cartilage structure. These strong nanocomposites can block stiff zinc dendrite and prevent short circuits over cycles. Resilience to plastic deformation and damage while having no leaking fluids or cracks is essential for the safety of, for instance, electrical vehicles employing such batteries. These load-bearing batteries can be used as a structural component and increase energy density by simply avoiding inactive parts. As a proof of concept, we utilized this battery on a commercial drone as an auxiliary energy storage unit to extend flight endurance by about 20%.

The second part of the thesis addresses a specific polysulfide shuttle problem in lithium-sulfur batteries utilizing bioinspired ANF nanocomposites. Mimicking ion channels on the cell membrane, we engineered biomimetic nanochannels (1nm diameter) for selectively allowing lithium-ion passage while physically blocking lithium polysulfide species (>2nm) on the cathode side. Selective ion transport through nanochannels is also modeled by finite element analysis, COMSOL. These ion channels allow us to reach >3500 cycles.

In addition to previous solid and liquid electrolyte systems, here in the last part of the thesis, we present a tunable quasi-solid polymer electrolyte to take advantage of both electrolyte features while minimizing their individual risks and drawbacks. Similar to the kidney filtration system, specifically the glomerular basement membrane, this gel electrolyte filters ions depending on their size and charge. Selective permeability and regulated ion transport provide safe and stable charge/discharge cycles. High mechanical properties keep functionality under extreme conditions, including high temperature and nail penetration. We integrated pouch cells in various prototypes to show practical utilization of our structural batteries, including health monitoring devices, robotic prosthetics, and electric vehicles.

Taken together, mimicking structural and functional properties of multifunctional biological materials, i.e., cartilage, we present a novel multifunctional nanocomposite system that can be tailored to the specific needs of numerous structural energy storage applications.

Date: Monday, August 9, 2021
Time: 2:00 PM
Zoom: https://umich.zoom.us/j/92570283886
Chair: Prof. Nicholas Kotov

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Presentation Mon, 02 Aug 2021 12:53:44 -0400 2021-08-09T14:00:00-04:00 2021-08-09T15:00:00-04:00 Off Campus Location Biomedical Engineering Presentation BME Event
BME PhD Defense: Steven Cutlip (August 9, 2021 2:00pm) https://events.umich.edu/event/84858 84858-21625203@events.umich.edu Event Begins: Monday, August 9, 2021 2:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

For the sensorimotor system to complete motor tasks it controls the body, it controls objects that the sensorimotor system acts upon within the environment, and it anticipates future states of the environment. The sensorimotor system is known to adapt and improve in performance with practice in response to predictable phenomena. The literature explains motor adaptation and performance improvement in terms of models, called internal models, of future loads. The theory of internal models has been investigated in the neuroscience and human motor behavior communities, where electrophysiological data and motor performance experiments have yielded rich data in support of the role of predictive modeling.

Internal models can be divided into two types: internal models of the plant and internal models of exogenous processes. While internal models of the plant have a rich history and have been studied extensively, literature on internal models of exogenous processes is less developed. This dissertation introduces the Internal Model Principle (IMP) as a tool for modeling internal models of exogenous processes. This dissertation further extends the usefulness of the IMP for modeling human motor control by extending the model to handle sensorimotor tasks that feature signal blanking.

Haptic feedback can be considered as an exogenous signal (a disturbance) whose features can be predicted because they are produced by the plant under control. Haptic feedback is an information signal providing the receiver feedback about the state of the system. However, haptic feedback is also a power signal; sufficient force due to haptic feedback can backdrive the biomechanics of a participant. In this dissertation these topics are explored in two studies, one in the context of driving oscillations in a spring-mass system and the other in the context of shared control design for semi-autonomous vehicles.

Date: Monday, August 9, 2021
Time: 2:00 PM
Zoom: https://umich.zoom.us/j/97211413457
Chair: Brent Gillespie

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Presentation Mon, 02 Aug 2021 12:46:34 -0400 2021-08-09T14:00:00-04:00 2021-08-09T15:00:00-04:00 Off Campus Location Biomedical Engineering Presentation BME Event
BME Master's Defense: Hind AlYahya (August 10, 2021 1:00pm) https://events.umich.edu/event/84890 84890-21625248@events.umich.edu Event Begins: Tuesday, August 10, 2021 1:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Peripheral arterial disease (PAD) is a disorder that restricts the blood flow in arteries that carry blood to the limbs; it frequently affects the legs. This restriction occurs due to severe atherosclerosis (stenosis), an accumulation of fatty materials in the vessel lumen. Stents are used to manage this disease. However, in-stent restenosis can occur at an unpredictable time, leading to emergency hospitalization or death.

The wireless magnetoelastic monitoring system showed its potential to detect restenosis. The main components of this system are a miniaturized wireless sensor integrated into the stent and a bias magnet. The purpose of using a magnet is to provide a uniform magnetic field for the sensor to operate. This work aims to improve the design of the system components to be compatible with the commercial self-expanding vascular stents. The magnetoelastic sensor was designed to fit with a conventional self-expanding stent (e.g., Innova™ from Boston Scientific Corp.) used to treat superficial femoral artery lesions. It is designed to be a single layer of MetglasTM 2826MB (12 mm x 0.85 mm x 29 um). However, the sensor could be damaged during the stent deployment. As a result, it is necessary to encapsulate the sensor. A polymeric package was designed to house the sensor and the biasing magnet. The package is attached to the stent structure by two helical wires made of nitinol material. The biasing magnet is a strip of ArnokromeTM 5 (13.2 mm x 0.85 mm x 50 um). FEA tool was used to evaluate the performance of the sensor and the magnetic strip. The results showed that the sensor vibrates at 149 kHz. The magnetic field distribution confirmed that the ArnokromeTM 5 generates a sufficient magnetic field strength for the sensor to operate. This work also covers an analytical analysis of using electromagnetic coils to provide DC bias for the system. However, the results showed that the heat dissipated from the coils could be hard to manage.

If implanting this package is successful *in vivo* experiments, the detection of restenosis will be achieved in an earlier stage, saving the patient from undergoing another surgery. Therefore, the wireless monitoring system can reduce emergency surgeries and mortality that results from PAD, leading to healthier patients and a lower burden on hospital resources.

Date: Tuesday, August 10, 2021
Time: 1:00 PM
Zoom: https://umich.zoom.us/j/99281419966
Chair: Prof. Yogesh B. Gianchandani

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Presentation Tue, 03 Aug 2021 10:09:05 -0400 2021-08-10T13:00:00-04:00 2021-08-10T14:00:00-04:00 Off Campus Location Biomedical Engineering Presentation BME Event
SWE x Disclosed Panel "How to make yourself stand out?" (September 1, 2021 7:00pm) https://events.umich.edu/event/86185 86185-21631883@events.umich.edu Event Begins: Wednesday, September 1, 2021 7:00pm
Location: Off Campus Location
Organized By: Society of Women Engineers

Worried about how to stand out as an applicant at Career Fair when you haven't had any experience? Want to hear advice from managers at Nissan and LinkedIn? Then come to our panel, Wednesday, September 8th at 7 pm EST!! Fill out the form to submit questions and receive notes after the event! Please email Gabrielle & Eva at swe.car.directors@umich.edu if you have any questions!

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Careers / Jobs Wed, 01 Sep 2021 19:51:56 -0400 2021-09-01T19:00:00-04:00 2021-09-01T20:00:00-04:00 Off Campus Location Society of Women Engineers Careers / Jobs
BME 500 Seminar: Sheng Zhong, Ph.D. (September 2, 2021 4:00pm) https://events.umich.edu/event/85887 85887-21629515@events.umich.edu Event Begins: Thursday, September 2, 2021 4:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Sheng Zhong, Ph.D.
Professor of Bioengineering,
University of California, San Diego

“Revealing protein-protein interactions at the transcriptome scale by sequencing”

Abstract:

We describe PROPER-seq (protein-protein interaction sequencing) to map protein-protein interactions (PPIs) en masse. PROPER-seq first converts transcriptomes of input cells into RNA-barcoded protein libraries, in which all interacting protein pairs are captured through nucleotide barcode ligation, recorded as chimeric DNA sequences, and decoded at once by sequencing and mapping. We applied PROPER-seq to human embryonic kidney cells, T lymphocytes, and endothelial cells and identified 210,518 human PPIs (collected in the PROPER v.1.0 database). Among these, 1,365 and 2,480 PPIs are supported by published co-immunoprecipitation (coIP) and affinity purification-mass spectrometry (AP-MS) data, 17,638 PPIs are predicted by the prePPI algorithm without previous experimental validation, and 100 PPIs overlap human synthetic lethal gene pairs. In addition, four previously uncharacterized interaction partners with poly(ADP-ribose) polymerase 1 (PARP1) (a critical protein in DNA repair) known as XPO1, MATR3, IPO5, and LEO1 are validated in vivo. PROPER-seq presents a time-effective technology to map PPIs at the transcriptome scale, and PROPER v.1.0 provides a rich resource for studying PPIs.

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Lecture / Discussion Fri, 27 Aug 2021 14:36:18 -0400 2021-09-02T16:00:00-04:00 2021-09-02T17:00:00-04:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Event
Department of Computational Medicine & Bioinformatics || Weekly Seminar Series (September 8, 2021 4:00pm) https://events.umich.edu/event/86237 86237-21632210@events.umich.edu Event Begins: Wednesday, September 8, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract:

Structural variants (SVs) are a source of pathogenic variants in a clinical referral population, however, they are often under-reported due to technical limitations of detection and difficulty with clinical interpretation. For example, mobile element insertions (MEIs) are estimated to lead to a positive finding in 1 out of 1000 rare genetic disease cases, yet the numbers are far lower in clinical diagnostic laboratories. Targeted NGS with short insert size libraries, unlike genome sequencing, will have very few discordant read pairs to indicate the presence of an SV. We, therefore, developed an SV detection tool called SCRAMble (Soft Clipped Read Alignment Mapper) to identify SV breakpoints in targeted NGS.

We applied SCRAMble to a prospective clinical referral cohort for exome sequencing to identify deletions and MEIs. We also applied SCRAMble to a hereditary cancer panel assay for the identification of a large inversion involving the MSH2 gene that causes Lynch syndrome. Adding breakpoint detection to clinical targeted sequencing identifies positive findings which were missed by prior testing and by other variant callers. Detecting breakpoints allows for more precise interpretation and for more targeted confirmation assays. By applying SV breakpoint detection, we are able to diagnose ~0.3% more cases. While this is a modest gain in diagnostic yield, for the patients and families involved, a positive diagnosis, even after prior testing, can have a meaningful impact on their lives.

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

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Livestream / Virtual Thu, 02 Sep 2021 14:28:18 -0400 2021-09-08T16:00:00-04:00 2021-09-08T17:00:00-04:00 Off Campus Location DCMB Seminar Series Livestream / Virtual Rebecca Torene, Associate Director of Genomics Research | Data Science at GeneDx
BME 500 Seminar: A machine learning-based predictive model of genome-wide binding of the Aryl Hydrocarbon Receptor (September 9, 2021 4:00pm) https://events.umich.edu/event/86318 86318-21632715@events.umich.edu Event Begins: Thursday, September 9, 2021 4:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Abstract:

The Aryl Hydrocarbon Receptor (AhR) is an inducible transcription factor (TF) whose ligands include the potent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). TCDD-mediated toxicity is believed to occur through activation of AhR and its binding to the 5'-GCGTG-3' DNA motif, referred to as the Dioxin Response Element (DRE). However, AhR binding in intact human cells is highly dynamic and tissue-specific. Approximately 50% of all experimentally verified AhR binding sites do not contain a DRE, and a great number of otherwise accessible DREs are not bound by AhR. Identification of the determinants of tissue-specific AhR binding is crucial for understanding downstream gene regulatory effects and potential adverse health outcomes of TCDD exposure, such as liver toxicity and immune suppression. We applied XGBoost, a supervised machine learning architecture, to predict genome-wide AhR binding as a function of DNA sequences immediately flanking the DRE, and local chromatin context features such as DNase-seq, histone modifications, and TF ChIP-Seq signals, as well as DRE proximity to gene promoters. We predicted binding of induced AhR in MCF-7 breast cancer cells, human hepatocytes, and the human lymphoblastoid cell line GM17212, as well as constitutive AhR binding in HepG2 cells. Our results demonstrate highly accurate and robust models of within-tissue binding, with several specific TFs and HMs identified as predictive of AhR binding within and across tissues. Additionally, we show that tissue-specific AhR binding is driven by a complex interplay of DNA flanking sequence and local chromatin context.

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Lecture / Discussion Fri, 03 Sep 2021 12:47:39 -0400 2021-09-09T16:00:00-04:00 2021-09-09T17:00:00-04:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Event
RNA Innovation Seminar (September 13, 2021 4:00pm) https://events.umich.edu/event/86155 86155-21631746@events.umich.edu Event Begins: Monday, September 13, 2021 4:00pm
Location: Off Campus Location
Organized By: Center for RNA Biomedicine

"Recent improvements in modeling and design of RNA-only structures"

ABSTRACT: The discovery and design of biologically important RNA molecules is outpacing three-structural characterization. I'll describe results from my and Wah Chiu's groups that demonstrate that cryo-electron microscopy can resolve maps of several kinds of RNA-only systems. These maps enable subnanometer-resolution 3D coordinate estimation when complemented with multidimensional chemical mapping and Rosetta DRRAFTER computational modeling. If time allows, I'll describe work from the Eterna project to stabilize mRNA molecules to help accelerate worldwide COVID immunization.

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Lecture / Discussion Thu, 02 Sep 2021 12:54:16 -0400 2021-09-13T16:00:00-04:00 2021-09-13T17:00:00-04:00 Off Campus Location Center for RNA Biomedicine Lecture / Discussion Rhiju Das, Stanford University
Department of Computational Medicine & Bioinformatics Weekly Seminar Series (September 15, 2021 4:00pm) https://events.umich.edu/event/86598 86598-21635116@events.umich.edu Event Begins: Wednesday, September 15, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract:

Chromosomal instability (CIN) results in the accumulation of large-scale losses, gains, and rearrangements of DNA. The broad genomic complexity caused by CIN is a hallmark of cancer, however, there is no systematic framework to measure different types of CIN and their impact on clinical phenotypes. Here, we evaluate the extent, diversity and origin of chromosomal instability across 7,880 tumors representing 33 cancer types from the TCGA collection. We present a compendium of 17 copy number signatures characterizing specific types of CIN, with putative aetiologies supported by multiple independent data sources. The signatures predict drug response and identify new drug targets. Our framework refines the understanding of impaired homologous recombination, one of the most therapeutically targetable types of CIN. Our results illuminate a fundamental structure underlying genomic complexity and provide a resource to guide future CIN
research in human cancers.

Bio:

Florian Markowetz is a Senior Group Leader at the Cancer Research UK Cambridge Institute. He is a Royal Society Wolfson Research Merit Award holder and received a CRUK Future Leader in Cancer Research prize. He holds degrees in Mathematics (Dipl. math.) and Philosophy (M.A.) from the University of Heidelberg and a Dr. rer. nat. (PhD equivalent) in Computational Biology from Free University Berlin, for which he was awarded an Otto-Hahn Medal by the Max Planck Society. His group at the CRUK Cambridge Institute combines computational work on cancer evolution and image analysis of the tumor tissue with experimental work on understanding key cancer mechanisms like the estrogen receptor.

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

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Livestream / Virtual Thu, 09 Sep 2021 11:24:05 -0400 2021-09-15T16:00:00-04:00 2021-09-15T17:00:00-04:00 Off Campus Location DCMB Seminar Series Livestream / Virtual Florian Markowetz (Senior Group Leader at the Cancer Research UK Cambridge Institute)
BME 500 Seminar: Nicholas A. Graham, Ph.D. (September 16, 2021 4:00pm) https://events.umich.edu/event/87034 87034-21638155@events.umich.edu Event Begins: Thursday, September 16, 2021 4:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Nicholas A. Graham, Ph.D.
Mork Family Department of Chemical Engineering and Materials Science,
University of Southern California

“Systems biology approaches to drug discovery for cancer and aging”

Abstract:

“Omics” technologies have enabled network-level measurements of genes, proteins, and metabolites from cellular models of disease. Systems biology attempts to synthesize these quantitative measurements into data-driven models to explain biological function and identify targeted therapeutic drugs. Here, I will discuss three different engineering systems biology approaches using metabolomics, proteomics, and bioinformatics to identify or discover drugs for cancer and aging. First, using metabolomics, we designed a synergistic drug combination that mimics nutrient deprivation to kill cancer cells. Second, by integrating a proteomic signature of cellular senescence with large-scale drug screening databases, we predicted and then validated that EGFR inhibitors are toxic to a model of cellular aging, specifically senescent human mammary epithelial cells. Finally, we developed a bioinformatic approach to integrate gene expression data with drug screening data from hundreds of cancer cell lines to identify clinically approved drugs whose efficacy depends on metabolic pathway activity. Taken together, these studies demonstrate how metabolomics, proteomics, and bioinformatics can all serve to identify drugs for cancer and aging.

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Lecture / Discussion Wed, 15 Sep 2021 15:08:08 -0400 2021-09-16T16:00:00-04:00 2021-09-16T17:00:00-04:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Event
Opportunity Kick-Off: Preparing a Competitive NIH S10 Instrumentation Proposal (September 17, 2021 12:00pm) https://events.umich.edu/event/85468 85468-21626488@events.umich.edu Event Begins: Friday, September 17, 2021 12:00pm
Location: Off Campus Location
Organized By: OVPR Office of Research Development

Hosted by U-M Research Development and the Biosciences Initiative, this webinar will provide an overview of NIH S10 Instrumentation Grants, including U-M success rates, common reviewer critiques, a timeline for developing a strong proposal, and resources to support your efforts.
Recent S10 awardees will join our panel to discuss their experiences, offer tips for success and answer your questions.

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Workshop / Seminar Thu, 19 Aug 2021 16:59:13 -0400 2021-09-17T12:00:00-04:00 2021-09-17T13:00:00-04:00 Off Campus Location OVPR Office of Research Development Workshop / Seminar Closeup of microscope
Using Network Analysis to Understand Teamwork in Engineering: Novel Approaches, Limitations, and Future Directions (September 22, 2021 10:30am) https://events.umich.edu/event/87143 87143-21639089@events.umich.edu Event Begins: Wednesday, September 22, 2021 10:30am
Location: Off Campus Location
Organized By: Engineering Education Research

Curricular and co-curricular design experiences are an increasingly popular mechanism for delivering opportunities for students to connect technical engineering knowledge to professional skills, such as teamwork, fabrication, communication, and design ability. As such, ensuring equal participation in design activities is a critical aspect of team-based pedagogies. In this research, using data from 12 student design teams in a first-year cornerstone design course, I describe a novel approach to examining the nature of working relationships in student teams. I use the multilayer exponential random graph model (ERGM) to examine perceptions of contributions (i.e., whether one is contributing ideas to their team) and enactments (i.e., whether one’s ideas are being utilized).

The purpose of this talk is both to introduce the multilayer ERGM as novel approach to understanding teamwork in engineering, as well as to draw on this method to describe processes of inequity in undergraduate engineering education experiences. I conclude with implications for future
research and practice.

BIOGRAPHICAL SKETCH: Trevion Henderson is an Assistant Professor of Mechanical Engineering at Tufts University. He earned his Ph.D. in Higher Education from the University of Michigan, as well as his M.A. in Higher Education and Student Affairs and his B.S. in Computer Science and Engineering from The Ohio State University. Dr. Henderson holds secondary appointments in the STEM Education program in the Department of Education and the Institute for Research on Learning and Instruction (IRLI). As a first-year professor at Tufts, Dr. Henderson teaches courses on engineering design education and engineering education research methods.

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Lecture / Discussion Fri, 17 Sep 2021 10:53:52 -0400 2021-09-22T10:30:00-04:00 2021-09-22T11:45:00-04:00 Off Campus Location Engineering Education Research Lecture / Discussion EER Logo
Department of Computational Medicine & Bioinformatics Weekly Seminar (September 22, 2021 4:00pm) https://events.umich.edu/event/87282 87282-21640718@events.umich.edu Event Begins: Wednesday, September 22, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract:

Histones are small proteins that package DNA into chromosomes, and a large number of studies have showed that several post-translational modification (PTM) sites on the histones are associated with both gene activation and silencing. Along with DNA and small non-coding RNA, histone PTMs make up epigenetic mechanisms that control gene expression patterns outside of DNA sequence mutations. Dysregulation of these chromatin networks underlie several human diseases such as cancer. Here I will give an update on technology advancements that have allowed for high-throughput quantitative analyses of histone PTMs and chromatin structure, and how we are applying these methods to understand epigenetic reprogramming found in malignant peripheral nerve sheath tumors (MPNSTs). MPNST is an aggressive sarcoma with recurrent loss of function alterations in polycomb-repressive complex 2 (PRC2), a histone-modifying complex involved in transcriptional silencing.

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

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Livestream / Virtual Mon, 20 Sep 2021 15:27:41 -0400 2021-09-22T16:00:00-04:00 2021-09-22T17:00:00-04:00 Off Campus Location DCMB Seminar Series Livestream / Virtual
DCM&B Tools and Technology Seminar (September 23, 2021 12:00pm) https://events.umich.edu/event/85310 85310-21626212@events.umich.edu Event Begins: Thursday, September 23, 2021 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.

URL for remote viewing: https://umich-health.zoom.us/j/94886745590?pwd=LzhLU243K2ZhbXNzU1BJRHQ5V25BZz09

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Presentation Wed, 18 Aug 2021 09:24:07 -0400 2021-09-23T12:00:00-04:00 2021-09-23T13:00:00-04:00 Palmer Commons DCMB Tools and Technology Seminar Presentation
Oral Health Sciences Master's Program Information Session (September 27, 2021 9:00am) https://events.umich.edu/event/87517 87517-21642908@events.umich.edu Event Begins: Monday, September 27, 2021 9:00am
Location: Off Campus Location
Organized By: Office of Research School of Dentistry

This is a virtual information session for prospective Oral Health Sciences Master's students. You can listen to a brief presentation from the program director and there will be time for questions and answers.
Please Register to receive a Zoom link.

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Meeting Fri, 24 Sep 2021 15:03:50 -0400 2021-09-27T09:00:00-04:00 2021-09-27T10:00:00-04:00 Off Campus Location Office of Research School of Dentistry Meeting logo
Department of Computational Medicine & Bioinformatics Weekly Seminar (September 29, 2021 4:00pm) https://events.umich.edu/event/87515 87515-21642906@events.umich.edu Event Begins: Wednesday, September 29, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract:

Human complex traits result from genetic and environmental factors, and from their interactions. Many of these effects are mediated by changes in gene regulation. Indeed, most genetic variants associated with complex trait variation in humans are in regulatory regions. I will present some of our recent studies on gene-environment interactions in gene regulation, with a specific focus on cardiovascular health. I will present evidence that gene-environment interactions in molecular phenotypes are frequent, account for a substantial portion of complex trait variation and modify genetic risk for disease.

Research Focus:

My lab is interested in understanding the genetic and molecular basis of inter-individual and inter-population differences in complex phenotypes. We combine evolutionary and functional genomics approaches to study intermediate phenotypes (e.g.: transcription factor binding, gene expression, protein secretion, etc.) and how they are affected by gene-environment interactions. Our research is funded by the NIH.

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

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Livestream / Virtual Fri, 24 Sep 2021 14:01:53 -0400 2021-09-29T16:00:00-04:00 2021-09-29T17:00:00-04:00 Off Campus Location DCMB Seminar Series Livestream / Virtual Francesca Luca, PhD (Wayne State University)
DCM&B Tools and Technology Seminar (September 30, 2021 12:00pm) https://events.umich.edu/event/85355 85355-21626295@events.umich.edu Event Begins: Thursday, September 30, 2021 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.

URL for remote viewing: https://umich-health.zoom.us/j/94886745590?pwd=LzhLU243K2ZhbXNzU1BJRHQ5V25BZz09

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Presentation Wed, 18 Aug 2021 09:19:10 -0400 2021-09-30T12:00:00-04:00 2021-09-30T13:00:00-04:00 Palmer Commons DCMB Tools and Technology Seminar Presentation
LHS Collaboratory 2021-2022 Kick-off Session (September 30, 2021 12:00pm) https://events.umich.edu/event/84725 84725-21624492@events.umich.edu Event Begins: Thursday, September 30, 2021 12:00pm
Location: Off Campus Location
Organized By: Department of Learning Health Sciences

Presentation 1
The Learning Health (Record) System

Speaker:
Philip R.O. Payne, PhD, FACMI, FAMIA, FAIMBE, FIAHSI
Janet and Bernard Becker Professor and Director, Institute for Informatics (I2), Associate Dean for Health information and Data Science, Chief Data Scientist, at Washington University in St. Louis

This presentation will explore the ways in Biomedical Data Science and Informatics research are helping to realize the potential of EHR technologies in the context of creating an LHS, from the optimization of workflow and human factors, to the generation of reproducible and systematic clinical phenotypes, to the delivery of emergent knowledge to both providers and patients via advance clinical decision support systems.

Presentation 2
Techniques and Challenges for EHR Phenotyping

Speaker:
Lisa Bastarache, MS
Research Associate Professor Department of Biomedical Informatics,
Vanderbilt University

Electronic health records (EHR) contain a wealth of real world data that can be used for research purposes. However, extracting phenotype information from EHRs can be challenging. EHR phenotyping can be divided into two types: (1) Fast phenotyping which seeks to capture a broad swath of the medical phenome, and is often accomplished using coded EHR data (e.g. billing codes) and (2) slow phenotyping that seeks to achieve high precision and recall for a single phenotype, and often uses multiple EHR data types (e.g. medications, text, lab results). This talk will describe specific use-cases for both fast and slow phenotyping, and review challenges that are commonly encountered in creating research-grade EHR phenotypes.

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Lecture / Discussion Mon, 27 Sep 2021 11:13:17 -0400 2021-09-30T12:00:00-04:00 2021-09-30T13:30:00-04:00 Off Campus Location Department of Learning Health Sciences Lecture / Discussion LHS Collaboratory Logo
RNA Innovation Seminar (October 4, 2021 4:00pm) https://events.umich.edu/event/86162 86162-21631753@events.umich.edu Event Begins: Monday, October 4, 2021 4:00pm
Location: 1027 E. Huron Building
Organized By: Center for RNA Biomedicine

"Fluorescent nucleoside analogues with new properties"

HYBRID EVENT
in-person: Forum Hall, Palmer Commons
Zoom: https://umich.zoom.us/webinar/register/WN__vvE2dtHQi-R3h05JUHBzQ

ABSTRACT
Fluorescent nucleoside analogues (FNAs) are powerful probes for studying the structure and dynamics of nucleic acids, which are vital to understanding RNA function, DNA damage repair, nucleic acid–protein interactions, regulatory mechanisms for gene expression, and other aspects of nucleic acid function. Existing FNAs are prone to quenching by base pairing and stacking, are clustered at the blue–green end of the visible spectrum, and have limited brightness as compared with conventional fluorophores. Studies of nucleic acid function would benefit greatly from overcoming these limitations. We have designed, synthesized, and studied a series of fluorescent pyrimidine analogues, aiming to address these limitations and develop a detailed understanding of the relationships between chemical structure and fluorescent responses to local environment in nucleic acids. Included in this series is a tricyclic cytidine analogue DEAtC that is nearly non-fluorescent as a nucleoside, but responds to matched base pairing and stacking with a fluorescence turn-on. A chlorinated tricyclic cytidine 8-Cl-tCO reports on local environment by changes in the vibrational fine structure of its emission spectra. To address the problem of limited brightness, we have design and synthesized a new NFA that we call ABN, which has a conjugated push–pull system similar to those found in bright fluorophores such as rhodamines. ABN is the brightest known FNA when present in duplex nucleic acids, and it is readily detected in single-molecule fluorescence measurements using both 1-photon and 2-photon excitation. Collectively, these FNAs offer new capabilities for biophysical studies on nucleic acids. Comparisons of their structure and properties help to reveal mechanisms for fluorescence changes in response to local environment in nucleic acids.

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Lecture / Discussion Fri, 10 Sep 2021 11:29:04 -0400 2021-10-04T16:00:00-04:00 2021-10-04T17:00:00-04:00 1027 E. Huron Building Center for RNA Biomedicine Lecture / Discussion Byron Purse, San Diego State University
DCM&B Tools and Technology Seminar (October 7, 2021 12:00pm) https://events.umich.edu/event/85356 85356-21626297@events.umich.edu Event Begins: Thursday, October 7, 2021 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.

URL for remote viewing: https://umich-health.zoom.us/j/94886745590?pwd=LzhLU243K2ZhbXNzU1BJRHQ5V25BZz09

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Presentation Sun, 03 Oct 2021 10:17:29 -0400 2021-10-07T12:00:00-04:00 2021-10-07T13:00:00-04:00 Palmer Commons DCMB Tools and Technology Seminar Presentation
BME 500 Seminar: Imaging neural, hemodynamic, and cerebrospinal fluid dynamics in the sleeping brain (October 7, 2021 4:00pm) https://events.umich.edu/event/87782 87782-21645945@events.umich.edu Event Begins: Thursday, October 7, 2021 4:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Sleep is essential for cognition and maintenance of healthy brain function. Sleep changes diverse aspects of brain physiology, and exhibits unique behavioral states, electrophysiological oscillations, vascular dynamics, and waste clearance properties. Our research integrates multiple neuroimaging technologies to understand the neural circuits controlling sleep and the consequences of sleep for brain physiology. To investigate how these multiple aspects might be coupled during sleep, we used simultaneous fast fMRI and EEG to measure fluid and neural dynamics in the human brain. We found a coherent pattern of coupled electrophysiological, hemodynamic, and cerebrospinal fluid (CSF) dynamics that appears during non-rapid eye movement sleep. Our results demonstrate that the sleeping brain exhibits waves of CSF flow on a macroscopic scale, and suggests a neural mechanism that can regulate CSF flow. Next, using fast fMRI at ultra-high field (7 Tesla), we tracked subsecond dynamics throughout thalamocortical networks across transitions between sleep and wakefulness. We identified a temporal sequence of activity across individual thalamic nuclei that appears at the moment of awakening from sleep and predicts subsequent behaviour. Together, these studies develop multimodal imaging approaches for tracking human brain physiology at fast timescales, and identify neural and fluid dynamics unique to the sleeping brain.

Zoom Link: https://umich.zoom.us/j/97723483179

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Lecture / Discussion Mon, 04 Oct 2021 09:29:19 -0400 2021-10-07T16:00:00-04:00 2021-10-07T17:00:00-04:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Seminar Event
2021 EER Prospective Student Open House (October 8, 2021 9:30am) https://events.umich.edu/event/85934 85934-21630496@events.umich.edu Event Begins: Friday, October 8, 2021 9:30am
Location: Hatcher Graduate Library
Organized By: Engineering Education Research

IN-PERSON OR VIRTUAL OPTION

We invite students from all institutions to attend the University of Michigan Engineering Education Research (EER) graduate student open house!

THE OPEN HOUSE AGENDA FEATURES:
An overview about the program
Discussions with faculty
Meet the EER Grad Coordinator & Financial Administrator
Discussions with current EER graduate students
A tour of the beautiful University of Michigan campus

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Workshop / Seminar Fri, 17 Sep 2021 10:43:37 -0400 2021-10-08T09:30:00-04:00 2021-10-08T16:00:00-04:00 Hatcher Graduate Library Engineering Education Research Workshop / Seminar EER Logo
Department of Computational Medicine & Bioinformatics Weekly Seminar (October 13, 2021 4:00pm) https://events.umich.edu/event/86441 86441-21634316@events.umich.edu Event Begins: Wednesday, October 13, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract:

Understanding the genetic and molecular architecture of human disease is accelerated by robust model development and large-scale molecular profiling. I will present two studies leveraging big data analytics or automated machine learning to dissect human disease complexities: 1) Molecular and clinical signatures of SARS-CoV-2 infection in the US marines. This analysis revealed strong antiviral innate immunity set point in females contributing to sex differences in both molecular and clinical response to SARS-CoV-2 infection. A set of accurate biomarkers capable of detecting PCR false negative infections was implemented on small footprint devices. 2) Automated machine learning to interpret the effects of genetic variants. An automated framework, AMBER, was developed for efficiently searching neural network architectures to model genomic sequences. AMBER is useful in various biological applications, including fine mapping variants, partitioning genetic heritability, and in personalized medicine enabled by CRISPR/Cas9 genome editing. Together, these efforts demonstrate quantitative methods coupled with large-scale biomedical data as an effective avenue to decode human regulatory and disease biology.

Short Bio:

Frank Zhang is a Flatiron research fellow with Olga Troyanskaya at the Simons Foundation and Princeton University since 2019. Prior to that, he obtained his PhD at UCLA with Yi Xing. His research focuses on machine learning and statistical method developments for the prediction and interpretation of human molecular and genetic variations using biological big data. Recently, he works on adopting and developing cutting-edge neural architecture search methods to automate the design of deep neural networks in genomics. He is also interested in making deep learning in biomedicine more interpretable and equitable.

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

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Livestream / Virtual Tue, 07 Sep 2021 14:45:38 -0400 2021-10-13T16:00:00-04:00 2021-10-13T17:00:00-04:00 Off Campus Location DCMB Seminar Series Livestream / Virtual
DCM&B Tools and Technology Seminar (October 14, 2021 12:00pm) https://events.umich.edu/event/85358 85358-21626298@events.umich.edu Event Begins: Thursday, October 14, 2021 12:00pm
Location: Palmer Commons
Organized By: DCMB Tools and Technology Seminar

In the Molecular Transducers of Physical Activity Consortium (MoTrPAC), we seek to understand the acute exercise response at the molecular level. In our first multi-omics dataset—a 15 tissue dataset from 6-month-old rats—there was evidence that circadian rhythms were contributing to data signatures, and thus, our ability to differentiate these circadian patterns from our primary measurement—the acute exercise response. To quantify the effects, we created distinct models for acute exercise response and circadian rhythm. We combined the models and allowed them to simultaneously compete for the percent variance explained of gene expression patterns in bulk RNA sequencing data. Analyses were performed on every gene and every tissue. Preliminary evidence suggests that our models were on the right track; for instance, the variances of many known circadian genes (in human and mouse) were primarily explained by the circadian model. However, more analyses are required to rigorously vet these models. We hope these techniques of competing models encourage others to employ similar strategies to distinguish unintended cofounding factors in experiments.

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

URL for remote viewing: https://umich-health.zoom.us/j/94886745590?pwd=LzhLU243K2ZhbXNzU1BJRHQ5V25BZz09

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Presentation Fri, 24 Sep 2021 15:26:28 -0400 2021-10-14T12:00:00-04:00 2021-10-14T13:00:00-04:00 Palmer Commons DCMB Tools and Technology Seminar Presentation
Grad School in the Biosciences (October 15, 2021 3:00pm) https://events.umich.edu/event/88102 88102-21650295@events.umich.edu Event Begins: Friday, October 15, 2021 3:00pm
Location: Off Campus Location
Organized By: Futures in Research, Science, Teaching - FIRST

A Zoom panel on applying and preparing for grad school, doing thesis research, and pursuing careers post-degree.

Professor, Postdoc, and Grad Student speakers from the Department of Molecular, Cellular, and Developmental Biology.

Zoom: https://umich.zoom.us/j/91884583350

Question Submission: https://forms.gle/KSiZLTCicKygKcWg9

FIRST Events: https://linktr.ee/FIRST_Org

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Workshop / Seminar Mon, 11 Oct 2021 14:43:59 -0400 2021-10-15T15:00:00-04:00 2021-10-15T15:00:00-04:00 Off Campus Location Futures in Research, Science, Teaching - FIRST Workshop / Seminar FIRST Logo
RNA Innovation Seminar: Tim Stasevich, Ph.D., Colorado State University (October 18, 2021 4:00pm) https://events.umich.edu/event/86166 86166-21631758@events.umich.edu Event Begins: Monday, October 18, 2021 4:00pm
Location: Off Campus Location
Organized By: Center for RNA Biomedicine

KEYWORDS: translational regulation, gene expression, fluorescence microscopy, intrabodies, single-molecule imaging

ABSTRACT: My lab is creating technology to image mRNA translation in real time and with single-molecule precision in living cells. In this talk, I will introduce our technology and describe how it can be used to amplify fluorescence from newly synthesized proteins as they are being translated from single mRNAs. I will show how we quantify these signals to determine the size, shape, subcellular localization, and mobilities of mRNA translation sites, as well as their protein synthesis dynamics. I will then highlight a few recent applications of our technology, focusing mainly on a new biosensor we have developed to quantify how individual regulatory factors impact single mRNA translation dynamics. Using this biosensor, we provide evidence that human Argonaute2 (Ago2) shuts down translation by down regulating translation initiation on the minutes timescale and helping usher translationally silent mRNAs into P-bodies on the hours timescale. I will conclude by discussing new fluorescent intrabodies my lab is engineering to light up nascent and mature proteins in multiple colors. As these intrabodies can be encoded on plasmids, they can easily be adapted by other labs to image gene activity in diverse living systems.
Timothy J. Stasevich is an Associate Professor in the Department of Biochemistry and Molecular Biology at Colorado State University (CSU). His lab uses a combination of advanced fluorescence microscopy, genetic engineering, and computational modeling to study the dynamics of gene regulation in living mammalian cells. His lab helped pioneer the imaging of real-time single-mRNA translation dynamics in living cells1. Dr. Stasevich received his B.S. in Physics and Mathematics from the University of Michigan, Dearborn, and his Ph. D. in Physics from the University of Maryland, College Park. He transitioned into experimental biophysics as a post-doctoral research fellow in the laboratory of Dr. James G. McNally at the National Cancer Institute. During this time, he developed technology based on fluorescence microscopy to help establish gold-standard measurements of live-cell protein dynamics. Dr. Stasevich next moved to Osaka University, where he worked with Dr. Hiroshi Kimura as a Japan Society for the Promotion of Science Foreign Postdoctoral Research Fellow. While there, he helped create technology to image endogenous proteins and their post-translation modifications in vivo. This allowed him to image the live-cell dynamics of epigenetic histone modifications during gene activation for the first time2. Before joining the faculty at CSU, Dr. Stasevich spent a year as a Visiting Fellow at the HHMI Janelia Research Campus, where he applied superresolution fluorescence microscopy to improve the spatiotemporal resolution of endogenous protein imaging in live cells.
1. Morisaki, T. et al. Real-time quantification of single RNA translation dynamics in living cells. Science 352, 1425–1429 (2016).
2. Stasevich, T. J. et al. Regulation of RNA polymerase II activation by histone acetylation in single living cells. Nature 516, 272–275 (2014).

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Lecture / Discussion Thu, 30 Sep 2021 10:17:54 -0400 2021-10-18T16:00:00-04:00 2021-10-18T17:00:00-04:00 Off Campus Location Center for RNA Biomedicine Lecture / Discussion Tim Stasevich, Colorado State University
Understanding the Productive Beginnings of Engineering Judgement (October 20, 2021 10:30am) https://events.umich.edu/event/87988 87988-21648635@events.umich.edu Event Begins: Wednesday, October 20, 2021 10:30am
Location: Duderstadt Center
Organized By: Engineering Education Research

In 200- and 300-level engineering science courses, students are traditionally asked to use mathematical models to solve well-defined textbook homework problems. While these problems are important for practicing mathematical problem-solving, they lack the complexity of ill-defined, sociotechnical engineering projects in the real world. In my current research I seek to bridge this gap between the engineering classroom and engineering workplace by understanding how students engage in the productive beginnings of professional practices and how instructors can support these productive beginnings.   This seminar will focus on one particular practice, engineering judgment, which is the use of mathematical models in design and analysis. I will begin by discussing my background and own personal motivation for this interpretivist research. I will then present my work in progress on the development of a new theoretical framework of the productive beginnings of engineering judgment. This research has been conducted symbiotically with a new innovative type of assignment in which students model a real-world system by making and justifying their own assumptions. I will conclude by outlining my future work on students’ development of macroethical reasoning and formative assessment strategies instructors can use to engage students in the productive beginnings of professional practices.

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Lecture / Discussion Thu, 07 Oct 2021 13:32:51 -0400 2021-10-20T10:30:00-04:00 2021-10-20T11:45:00-04:00 Duderstadt Center Engineering Education Research Lecture / Discussion Professor Aaron Johnson
Department of Computational Medicine & Bioinformatics Weekly Seminar (October 20, 2021 4:00pm) https://events.umich.edu/event/88315 88315-21652404@events.umich.edu Event Begins: Wednesday, October 20, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract:

The Ye lab is focused on harnessing the power of single cell and computational genomics to understand how immune cells sense and respond to their environment. Utilizing new experimental methods we have developed to enable multiplexed single-cell sequencing, I will describe results from sequencing 1.2M cells from ~250 samples to understand the cellular and molecular bases of systemic lupus erythmatosus and COVID-19. I will also describe how population scale single cell sequencing can enable dissection of the genetic architecture of gene expression and annotation of disease associated variants. Finally, I’ll touch on novel experimental workflows to further increase the throughput of single-cell genomics and for encoding orthogonal information into single-cell sequencing assays.

Research Overview:

The Ye lab is interested in how the interaction between genetics and environment affect human variation at the level of molecular phenotypes. To study these interactions, the lab couples high-throughput sequencing approaches that measure cellular response under environmental challenges with population genetics where such measurements are collected and analyzed across large patient cohorts. The lab develops novel experimental approaches that enable the large-scale collection of functional genomic data *en masse* and computational approaches that translate the data into novel biological insights. This approach is used to initially study primary human immune cells in both healthy and diseased patients to understand host pathogen interactions and its role in autoimmunity.

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

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Livestream / Virtual Fri, 15 Oct 2021 14:50:45 -0400 2021-10-20T16:00:00-04:00 2021-10-20T17:00:00-04:00 Off Campus Location DCMB Seminar Series Livestream / Virtual
DCM&B Tools and Technology Seminar (October 21, 2021 12:00pm) https://events.umich.edu/event/85359 85359-21626300@events.umich.edu Event Begins: Thursday, October 21, 2021 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.

URL for remote viewing: https://umich-health.zoom.us/j/94886745590?pwd=LzhLU243K2ZhbXNzU1BJRHQ5V25BZz09

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Presentation Wed, 18 Aug 2021 09:43:20 -0400 2021-10-21T12:00:00-04:00 2021-10-21T13:00:00-04:00 Palmer Commons DCMB Tools and Technology Seminar Presentation
BME 500 Seminar: “Elucidating and engineering microbial communities: systems and synthetic biology approaches” (October 21, 2021 4:00pm) https://events.umich.edu/event/88452 88452-21654121@events.umich.edu Event Begins: Thursday, October 21, 2021 4:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Microbes are everywhere in nature and they live in diverse communities that show remarkable metabolic capabilities and robustness. On the other hand, disruption of microbiome homeostasis and associated changes in the community’s structure/function underlies numerous health or environmental issues. My lab has been developing methods and tools rooted in engineering to study microbial communities in order to discover the underlying cellular and molecular mechanisms. In particular, we have pioneered a technological pipeline, based on nanoliter-scale microfluidic droplets, to co-cultivate sub-communities and characterize interactions between community members. A number of technological modules have been created and the pipeline is being applied to the investigation of a range of health or environment related microbiomes. A second distinct yet complementary research thrust in my lab, inspired by naturally occurring synergistic microbial communities, has been the design and construction of synthetic microbial consortia for microbial engineering and biochemical production. One application focus has been synthesis of fuels and chemicals from lignocellulosic biomass. For instance, we designed and optimized a consortium consisting of a cellulolytic fungus capable of hydrolyzing hemicellulose and cellulose (main components of lignocellulosic biomass) into mono and oligosaccharides and a genetically engineered bacterium for converting mono and oligosaccharides into isobutanol, an advanced biofuel. The general framework of engineering defined co-cultures of coordinated specialists also offers exciting new opportunities for the efficient and flexible production of many valuable chemicals from other non-conventional bio-feedstocks.

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Workshop / Seminar Wed, 20 Oct 2021 10:08:36 -0400 2021-10-21T16:00:00-04:00 2021-10-21T17:00:00-04:00 Off Campus Location Biomedical Engineering Workshop / Seminar BME LOGO
CANCELLED: SAVE THE DATE 11th INTERNATIONAL SYMPOSIUM (October 25, 2021 10:00am) https://events.umich.edu/event/84621 84621-21631581@events.umich.edu Event Begins: Monday, October 25, 2021 10:00am
Location:
Organized By: Center for Cell Plasticity and Organ Design

With the current state of things we have decide to cancel the Save the Date for the CPOD International Symposium.

We will update you with the new details as soon as we have a new date.

Thank you for your understanding as we work to make adjustments with the safety of all participants in mind.

Questions/Comments please contact us at: organogenesis@umich.edu

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Conference / Symposium Wed, 01 Sep 2021 10:40:09 -0400 2021-10-25T10:00:00-04:00 2021-10-25T11:00:00-04:00 Center for Cell Plasticity and Organ Design Conference / Symposium CPOD Center for Cell Plasticity and Organ Design
Department of Computational Medicine & Bioinformatics Weekly Seminar (October 27, 2021 4:00pm) https://events.umich.edu/event/88276 88276-21652019@events.umich.edu Event Begins: Wednesday, October 27, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract:
Molecular classification has transformed the diagnosis and treatment of diffuse gliomas, creating targets for precision therapies. However, timely and efficient access to molecular diagnostic methods remains difficult, causing a significant barrier to deliver molecularly-targeted therapies. We aim to develop an innovative point-of-care diagnostic screening method that provides rapid and accurate molecular classification of diffuse gliomas through artificial intelligence and optical imaging in order to improve the comprehensive care of brain tumor patients.

Bio:
Dr. Todd Hollon is a neurosurgeon and research scientist who specializes in brain tumors. He is an Assistant Professor of Neurosurgery. He completed his postdoctoral training in the UM Translational Molecular Imaging Laboratory under the supervision of Drs. Daniel Orringer and Honglak Lee. His postdoctoral work focused on the application of deep neural networks to advanced imaging methods to improve the speed and accuracy of intraoperative brain tumor diagnosis. He hopes to be part of the next generation of young scientists that uses computation and machine learning to make scientific breakthroughs.

Host: Josh Welch, PhD

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

In-Person: Forum Hall, Palmer Commons

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Livestream / Virtual Thu, 14 Oct 2021 14:26:31 -0400 2021-10-27T16:00:00-04:00 2021-10-27T17:00:00-04:00 Off Campus Location DCMB Seminar Series Livestream / Virtual
DCM&B Tools and Technology Seminar (October 28, 2021 12:00pm) https://events.umich.edu/event/85361 85361-21626301@events.umich.edu Event Begins: Thursday, October 28, 2021 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.

URL for remote viewing: https://umich-health.zoom.us/j/94886745590?pwd=LzhLU243K2ZhbXNzU1BJRHQ5V25BZz09

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Presentation Wed, 18 Aug 2021 09:46:40 -0400 2021-10-28T12:00:00-04:00 2021-10-28T13:00:00-04:00 Palmer Commons DCMB Tools and Technology Seminar Presentation
“The role of muscle activity in structure-function relationships of embryonic tendon development” (October 28, 2021 4:00pm) https://events.umich.edu/event/88592 88592-21656086@events.umich.edu Event Begins: Thursday, October 28, 2021 4:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

BME 500 Seminar Series
Thursday, October 28, 2021
4:00 – 5:00 pm

Zoom Link: https://umich.zoom.us/j/97723483179

Spencer Szczesny, Ph.D.
Biomedical Engineering,
Pennsylvania State University

“The role of muscle activity in structure-function relationships of embryonic tendon development”

Abstract:

While there is significant interest in using tissue engineering techniques to create tendon and ligament replacements, no engineered biomaterial has been successful in replicating their physiological function. This is because there is a fundamental lack of understanding of how to produce a robust tensile load-bearing biological tissue. Previous work suggests that tendon maturation is driven by rapid increases in collagen fibril length and molecular crosslinking mediated by mechanical stimulation due to muscle activity. However, the effect of mechanical stimulation on the tensile mechanics of developing tendons and the functional significance of the structural changes that occur during development are still unclear. To address this knowledge gap, we investigated the multiscale structure-function relationships of embryonic tendons during normal development and following the loss of mechanical stimulation via immobilization. Using multiscale mechanical testing, we found that the strain transmitted to the collagen fibrils in tendons at embryonic days 16, 18, and 20 is less than the strain applied to the tissue, suggesting the collagen fibrils remain discontinuous throughout embryonic development. However, the ratio of the fibril strains to the tissue strains increased with developmental age; this indicates that more strain is being transmitted to the fibrils and that there is less interfibrillar sliding, which is consistent with an increase in the average fibril length and an increase in the macroscale mechanics during this period of development. Additionally, there was a decrease in the macroscale tensile modulus and the fibril:tissue strain ratio with flaccid (but not rigid) immobilization, suggesting that complete loss of mechanical stimulation inhibits fibril elongation and strain transmission to the collagen fibrils, resulting in impaired functional maturation. Consistent with these mechanical assessments, we found that collagen fibril bundling was impaired with immobilization. Interestingly, while the enthalpy required to denature the tendons increased with increasing age, there was no effect with immobilization. This suggests that although intermolecular crosslinks in embryonic tendons increase with development, the loss of tensile mechanical properties with immobilization is potentially not due to a reduction in functional crosslinking. Together, these data suggest that the key structural change induced by mechanical stimulation during tendon development is an increase in the strain transmitted to the collagen fibrils, which is consistent with fibril elongation. These data provide fundamental insight into the mechanisms driving tendon development and will guide the design of improved techniques for engineering tendon/ligament replacements.

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Lecture / Discussion Mon, 25 Oct 2021 09:25:42 -0400 2021-10-28T16:00:00-04:00 2021-10-28T17:00:00-04:00 Off Campus Location Biomedical Engineering Lecture / Discussion U-M BME Event
Writing Graduate School Application Statements (October 29, 2021 3:00pm) https://events.umich.edu/event/88774 88774-21657750@events.umich.edu Event Begins: Friday, October 29, 2021 3:00pm
Location: Off Campus Location
Organized By: Futures in Research, Science, Teaching - FIRST

What to include/avoid and how to frame your story while writing academic and personal statements for research-based grad programs.

Seminar/Discussion

Zoom Link: https://umich.zoom.us/j/95163992475

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Workshop / Seminar Fri, 29 Oct 2021 12:12:00 -0400 2021-10-29T15:00:00-04:00 2021-10-29T16:00:00-04:00 Off Campus Location Futures in Research, Science, Teaching - FIRST Workshop / Seminar FIRST Logo
RISE November Virtual Talking Circle (November 1, 2021 12:00pm) https://events.umich.edu/event/87910 87910-21647679@events.umich.edu Event Begins: Monday, November 1, 2021 12:00pm
Location: Off Campus Location
Organized By: RISE (Research. Innovation. Scholarship. Education.)

Please join us for our next Virtual Taking Circle on Monday, November 1 at 12:00 PM. We will be hosting a conversation about how educators are finding ways to innovate within the clinical setting. We look forward to learning more about current innovations happening in the clinical setting and what it takes to be innovative within this setting. We will also explore synergies that might better enable innovation and what is next for innovation in the clinical setting.
All are welcome to join!

Register via Eventbrite: https://www.eventbrite.com/e/rise-virtual-talking-circle-tickets-176292163607

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Workshop / Seminar Tue, 05 Oct 2021 12:17:38 -0400 2021-11-01T12:00:00-04:00 2021-11-01T13:00:00-04:00 Off Campus Location RISE (Research. Innovation. Scholarship. Education.) Workshop / Seminar RISE Virtual Talking Circle
STEM Incubators: Centering Black Families' Rightful Presence in STEM (November 3, 2021 10:30am) https://events.umich.edu/event/88372 88372-21653523@events.umich.edu Event Begins: Wednesday, November 3, 2021 10:30am
Location: Duderstadt Center
Organized By: Engineering Education Research

Black families act as STEM incubators. Despite stereotypical representations that are often rooted in deficit framing, Black families provide their children access to STEM opportunities, resources, capital, ways of thinking, behaving, and sense-making Scholars have identified that Black parents influence the college-going and completion process through practices such as sharing information, developing expectations around school completion, positioning students as examples to younger siblings/family members, and by sharing advice on how to persist when faced with challenging situations.  Building on this work, I will present some of my research on Black family life and the lineage Black contributions to STEM in order to provide evidence of the ways that Black families incubate STEM learning and aspirations. I have found that families – with emphasis on parents – leverage capital and establish family cultures values and practices that support STEM exploration and confidence. This talk will highlight some of my recent contributions along with implications for research on informal/family learning spaces

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Lecture / Discussion Wed, 27 Oct 2021 14:27:20 -0400 2021-11-03T10:30:00-04:00 2021-11-03T11:45:00-04:00 Duderstadt Center Engineering Education Research Lecture / Discussion DeLean Tolbert Smith
Department of Computational Medicine & Bioinformatics Weekly Seminar (November 3, 2021 4:00pm) https://events.umich.edu/event/88449 88449-21654119@events.umich.edu Event Begins: Wednesday, November 3, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract
My research group works in the area of mathematical oncology, where we use mathematical models to decipher the complex networks of reactions inside of cancer cells and interactions between cells. Immune cells use hundreds of biochemical reactions to respond to their environment, become activated, and kill cancer cells. Understanding the complexity of these reaction networks requires computational tools and mathematical models. We combine detailed, mechanistic modeling with machine learning to study these networks, better understand cancer and immune cells, and predict ways to control tumor growth. In this talk, I will present our recent work aimed at predicting the dynamics of immune cell behaviors across three scales: intracellular signaling pathways in CAR T cells, the collective behavior of a heterogeneous population of immune cells, and tumor-immune interactions at the tissue scale. Our models generate novel mechanistic insight into immune cell activation and predict the effects of immunotherapeutic strategies.


Biography
Stacey D. Finley is the Gordon S. Marshall Early Career Chair and Associate Professor of Biomedical Engineering at the University of Southern California. Dr. Finley received her B.S. in Chemical Engineering from Florida A & M University and obtained her Ph.D. in Chemical Engineering from Northwestern University. She completed postdoctoral training at Johns Hopkins University in the Department of Biomedical Engineering. Dr. Finley joined the faculty at USC in 2013, and she leads the Computational Systems Biology Laboratory. Dr. Finley has joint appointments in the Departments of Chemical Engineering and Materials Science and Quantitative and Computational Biology, and she is a member of the USC Norris Comprehensive Cancer Center. Dr. Finley is also the Founding Director of the Center for Computational Modeling of Cancer at USC. Her research is supported by grants from NSF, NIH, and the American Cancer Society.

Selected honors. 2016 NSF Faculty Early CAREER Award; 2016 Young Innovator by the Cellular and Molecular Bioengineering journal; Leah Edelstein-Keshet Prize from the Society of Mathematical Biology; Junior Research Award from the USC Viterbi School of Engineering; the Hanna Reisler Mentorship Award; 2018 AACR NextGen Star; 2018 Orange County Engineering Council Outstanding Young Engineer; Elected Fellow of the American Institute for Medical and Biological Engineering (2021)

Hosted by: Alan Boyle, PhD

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

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Livestream / Virtual Wed, 20 Oct 2021 09:54:50 -0400 2021-11-03T16:00:00-04:00 2021-11-03T17:00:00-04:00 Off Campus Location DCMB Seminar Series Livestream / Virtual Stacey D. Finley, Ph.D. (USC)
DCM&B Tools and Technology Seminar (November 4, 2021 12:00pm) https://events.umich.edu/event/85368 85368-21626321@events.umich.edu Event Begins: Thursday, November 4, 2021 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.

URL for remote viewing: https://umich-health.zoom.us/j/94886745590?pwd=LzhLU243K2ZhbXNzU1BJRHQ5V25BZz09

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Presentation Wed, 18 Aug 2021 14:35:23 -0400 2021-11-04T12:00:00-04:00 2021-11-04T13:00:00-04:00 Palmer Commons DCMB Tools and Technology Seminar Presentation
"Cell cycle regulation in microbes" (November 4, 2021 4:00pm) https://events.umich.edu/event/88883 88883-21658814@events.umich.edu Event Begins: Thursday, November 4, 2021 4:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

BME 500 Seminar Series
Ariel Amir, Ph.D.
Applied Mathematics and Physics
Harvard University

"Cell cycle regulation in microbes"

Abstract:
Microbial cells are remarkable in their abilities to adapt to different environments while maintaining cellular homeostasis. How cells coordinate the various events within the cell cycle, notably cell division and DNA replication, remains an outstanding problem for cells of all domains of life. I will discuss our current understanding of cell cycle regulation in microbes, including recent results demonstrating a tight coupling between DNA replication and cell division in E. coli.

DATE: Thursday, November 4, 2021
TIME: 4:00-5:00 pm
ZOOM LINK: https://umich.zoom.us/j/97723483179

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Presentation Tue, 02 Nov 2021 09:04:43 -0400 2021-11-04T16:00:00-04:00 2021-11-04T17:00:00-04:00 Off Campus Location Biomedical Engineering Presentation BME Logo
Oral Health Sciences Master's Program Information Session (November 8, 2021 11:00am) https://events.umich.edu/event/87517 87517-21642909@events.umich.edu Event Begins: Monday, November 8, 2021 11:00am
Location: Off Campus Location
Organized By: Office of Research School of Dentistry

This is a virtual information session for prospective Oral Health Sciences Master's students. You can listen to a brief presentation from the program director and there will be time for questions and answers.
Please Register to receive a Zoom link.

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Meeting Fri, 24 Sep 2021 15:03:50 -0400 2021-11-08T11:00:00-05:00 2021-11-08T12:00:00-05:00 Off Campus Location Office of Research School of Dentistry Meeting logo
RNA Innovation Seminar (November 8, 2021 4:00pm) https://events.umich.edu/event/86167 86167-21631759@events.umich.edu Event Begins: Monday, November 8, 2021 4:00pm
Location: Off Campus Location
Organized By: Center for RNA Biomedicine

"Harnessing diverse compact CRISPR-Cas3 for long-range genome engineering"
Zhonggang Hou, Ph.D.
Research Investigator
Biological Chemistry

and

"Microscopic Examination of Spatial Transcriptome through Seq-Scope"
Jun Hee Lee, PhD
Associate Professor
Molecular & Integrative Physiology

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Lecture / Discussion Mon, 25 Oct 2021 13:33:17 -0400 2021-11-08T16:00:00-05:00 2021-11-08T20:00:00-05:00 Off Campus Location Center for RNA Biomedicine Lecture / Discussion Zhonggang Hou, Biological Chemistry & Jun Hee Lee, Molecular & Integrative Physiology
Veterans Week Special: How the Wars in Iraq and Afghanistan Impacted Military and Civilian Critical Care (November 9, 2021 6:00pm) https://events.umich.edu/event/88857 88857-21658649@events.umich.edu Event Begins: Tuesday, November 9, 2021 6:00pm
Location: Off Campus Location
Organized By: Veteran and Military Services

During this interactive session, Dr. Ward will discuss some of the medical innovations spurred by the wars in Iraq and Afghanistan, how civilian trauma care has been impacted by military medical advancements, and the future of critical care.
This event is free, and we welcome all members of the University of Michigan Medical School and larger university community including students, faculty, and staff.

Kevin Ward, MD, is a Professor of Emergency Medicine, a Lieutenant Colonel in the U.S. Army Reserve Medical Corps, founder of the Michigan Center for Integrative Research in Critical Care (MCIRCC), and Executive Director of Michigan Medicine’s Fast Forward Medical Innovation (FFMI), 2013-2018

NextGen Med is a group of medical students committed to inviting local and global leaders to discuss current challenges in medicine with the UMMS community. Questions? NextGenMed@umich.edu

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Lecture / Discussion Mon, 01 Nov 2021 13:59:33 -0400 2021-11-09T18:00:00-05:00 2021-11-09T19:00:00-05:00 Off Campus Location Veteran and Military Services Lecture / Discussion Dr. Kevin Ward
Integrative Systems + Design Open House (November 10, 2021 9:00am) https://events.umich.edu/event/88203 88203-21651464@events.umich.edu Event Begins: Wednesday, November 10, 2021 9:00am
Location:
Organized By: Integrative Systems + Design

YOU'RE INVITED
Integrative Systems + Design
Informational Open House

Wednesday, November 10, 2021
9:00 - 10:00 a.m. Virtually in Zoom
10:00 - 11:00 a.m. In-person for U-M Only Students

1075 Beal Ave.
Ann Arbor, MI
SI-North 2nd Floor Commons Area

Come learn about our exciting interdisciplinary engineering graduate programs.
Courses are available both on-campus and online!

Integrative Systems + Design (ISD) is dedicated to educating dynamic global leaders who can think transformatively to create innovative solutions for society’s challenges and the future.

Our six graduate programs include dual degrees, SUGS, masters, and doctoral* degrees in:
Automotive Engineering
Energy Systems Engineering
Manufacturing Engineering*
Systems Engineering and Design
Global Automotive & Manufacturing Engineering
Design Science*

Register here: https://docs.google.com/forms/d/1yqO9GUdjQIDooe9JqJipdIfQ919NhWwL3n092sroLmk/edit

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Reception / Open House Wed, 13 Oct 2021 12:33:29 -0400 2021-11-10T09:00:00-05:00 2021-11-10T11:00:00-05:00 Integrative Systems + Design Reception / Open House Open House Invite
Department of Computational Medicine & Bioinformatics Weekly Seminar (November 10, 2021 4:00pm) https://events.umich.edu/event/88540 88540-21654960@events.umich.edu Event Begins: Wednesday, November 10, 2021 4:00pm
Location: Off Campus Location
Organized By: DCMB Seminar Series

Abstract:

Subspace classifiers have been around for a long time, beginning with feature selection, which in essence was a subspace selection technique. This talk will discuss the kind of subspace classifiers that Bledsoe and Browning presented in their 1959 paper and from which there have been a variety of extensions which we will discuss.

The Bledsoe and Browning subspace classifier quantizes measurement space. Each quantized observation tuple corresponds to a cell in measurement space. A collection of subspaces are selected at random. In the original form the subspaces were mutually exclusive. For each class, each cell of a subspace contained a number dependent on the number of observations of the training data that fell into that cell. For each class those numbers were combined in ways not dissimilar to random forests. For a given observation tuple, the class with the highest vote count was selected as the assigned class.

We will discuss a variety of principled extensions of the technique and make some comparisons with Neural Networks.

Research Interests:

High-dimensional space clustering, pattern recognition, knowledge discovery and artificial intelligence

Professor Haralick began his work as one of the principal investigators of the NASA ERTS satellite data doing remote sensing image analysis.

He has made a series of contributions in the field of computer vision. In the high-level vision area, he has worked on inferring 3D geometry from one or more perspective projection views.] He has also identified a variety of vision problems which are special cases of the consistent labeling problem. His papers on consistent labeling, arrangements, relation homomorphism, matching, and tree search translate some specific computer vision problems to the more general combinatorial consistent labeling problem and then discuss the theory of the look-ahead operators that speed up the tree search. The most basic of these is called Forward Checking. This gives a framework for the control structure required in high-level vision problems. He has also extended the forward-checking tree search technique to propositional logic.

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

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Livestream / Virtual Fri, 22 Oct 2021 09:28:27 -0400 2021-11-10T16:00:00-05:00 2021-11-10T17:00:00-05:00 Off Campus Location DCMB Seminar Series Livestream / Virtual Robert M. Haralick, PhD (City University of New York)
DCM&B Tools and Technology Seminar (November 11, 2021 12:00pm) https://events.umich.edu/event/85369 85369-21626322@events.umich.edu Event Begins: Thursday, November 11, 2021 12:00pm
Location: Palmer Commons
Organized By: DCMB Tools and Technology Seminar

Tool link: https://prsweb.sph.umich.edu/

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

URL for remote viewing: https://umich-health.zoom.us/j/94886745590?pwd=LzhLU243K2ZhbXNzU1BJRHQ5V25BZz09

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Presentation Wed, 18 Aug 2021 14:40:06 -0400 2021-11-11T12:00:00-05:00 2021-11-11T13:00:00-05:00 Palmer Commons DCMB Tools and Technology Seminar Presentation
"Diet and metabolic therapeutics in cancer metabolism" (November 11, 2021 4:00pm) https://events.umich.edu/event/89035 89035-21660280@events.umich.edu Event Begins: Thursday, November 11, 2021 4:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

BME 500 Seminar Series
Jason Locasale, Ph.D.
Pharmacology and Cancer Biology
Duke University

"Diet and metabolic therapeutics in cancer metabolism"
Abstract:
This presentation will focus on methionine metabolism in health and cancer. I will first
discuss methionine content in human food and dietary patterns . I will next focus on
how changes to dietary methionine can produce defined consequences on cellular
metabolism. I will then discuss work on dietary influences on the activity of the
pathway and its relation to the regulation of one carbon metabolism in cancer. How
methionine restricted diets may allow for interventions in cancer treatment and relevant
mechanisms will be discussed including how changes to dietary methionine can
influence interventions that target one carbon metabolism involving radiation and
antimetabolite chemotherapies such as 5-fluorouracil. The link between nutritional
methionine status and chromatin biology and epigenetics will also be introduced in this
talk.
Details:
DATE: Thursday, November 11, 2021
TIME: 4:00-5:00 pm
ZOOM LINK: https://umich.zoom.us/j/97723483179

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Presentation Mon, 08 Nov 2021 10:30:52 -0500 2021-11-11T16:00:00-05:00 2021-11-11T17:00:00-05:00 Off Campus Location Biomedical Engineering Presentation BME Event
Presenting Your Research & Project Design (November 12, 2021 3:00pm) https://events.umich.edu/event/89144 89144-21660677@events.umich.edu Event Begins: Friday, November 12, 2021 3:00pm
Location: Off Campus Location
Organized By: Futures in Research, Science, Teaching - FIRST

A Zoom seminar on presenting to academic audiences, including basics of project design. Useful for those considering careers in science and/or preparing for grad school interviews that require a presentation.

Zoom link: https://umich.zoom.us/j/95315038837

FIRST linktree: https://linktr.ee/FIRST_Org

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Workshop / Seminar Wed, 10 Nov 2021 13:18:06 -0500 2021-11-12T15:00:00-05:00 2021-11-12T16:00:00-05:00 Off Campus Location Futures in Research, Science, Teaching - FIRST Workshop / Seminar FIRST Logo. The letters of "FIRST" are made up of chromosomes tethered to spindles during mitosis.
Michigan Institute of Data Science Annual Symposium (November 15, 2021 3:45pm) https://events.umich.edu/event/88887 88887-21658823@events.umich.edu Event Begins: Monday, November 15, 2021 3:45pm
Location: Off Campus Location
Organized By: Michigan Institute for Data Science

3:45 PM - 4:00 PM: H.V. Jagadish, Opening Remarks
4:00 PM - 5:00 PM: Dr. Rebecca Fiebrink, Keynote Address: “How machine learning can support human creators"

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Workshop / Seminar Tue, 02 Nov 2021 10:42:22 -0400 2021-11-15T15:45:00-05:00 2021-11-15T17:00:00-05:00 Off Campus Location Michigan Institute for Data Science Workshop / Seminar MIDAS Symposium 2021
Michigan Institute of Data Science Annual Symposium (November 16, 2021 9:00am) https://events.umich.edu/event/88888 88888-21658824@events.umich.edu Event Begins: Tuesday, November 16, 2021 9:00am
Location: Michigan League
Organized By: Michigan Institute for Data Science

Workshops

Sign up to attend one of the four mini-workshops as part of the 2021 U-M Data Science and AI Symposium. Bring your own laptop!

Nov. 16th | 9:00am - 11:00am @ Michigan League

1. Introduction to data visualization on the web with D3.js. Led by Prof. Fred Feng (Industrial and Manufacturing Systems Engineering)

2. Using text as data: Introduction to machine learning for natural language processing. Led by Drs. Jule Krueger (Institute for Social Research) and Meghan Dailey (Advanced Research Computing)

3. Diversity and equity in data science - a community forum. Led by Drs. Lia Corrales (Astronomy), Tayo Fabusuyi (U-M Transportation Research Institute), H. V. Jagadish (MIDAS Director), and Rada Mihalcea (U-M AI Lab Director). Presenters will highlight technical designs to detect and adjust for data and algorithmic biases, and programs that promote diversity in data science and AI research community. Attendees will be encouraged to share their work and discuss ways to collaborate.

4. Developing best practices for reproducible data science. Led by Drs. Jing Liu (MIDAS Managing Director), Johann Gagnon-Bartsch (Statistics), Tom Valley (Internal Medicine) and Sharon Glotzer's Lab. The presenters will offer tutorials on building reproducible workflows, data and code review and sharing. They will also answer questions for those who are interested in entering the MIDAS 2021 Reproducibility Challenge.

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Workshop / Seminar Tue, 02 Nov 2021 10:48:50 -0400 2021-11-16T09:00:00-05:00 2021-11-16T11:00:00-05:00 Michigan League Michigan Institute for Data Science Workshop / Seminar MIDAS Symposium 2021
DCMB / CCMB Weekly Seminar Series (November 17, 2021 4:00pm) https://events.umich.edu/event/89137 89137-21660643@events.umich.edu Event Begins: Wednesday, November 17, 2021 4:00pm
Location: Palmer Commons
Organized By: DCMB Seminar Series

Talk title: Clinical Trajectory analysis to determine risk-factors of Copd: A COPDGene Study

Abstract:

Background

Chronic obstructive pulmonary disease (COPD) presents significant clinical heterogeneity and a wide variety of progression trajectories [1]. Clinical trajectory analysis (ClinTrajAn) is a powerful tool based on elastic principal graphs for the calculation of trajectories from large cross-sectional clinical data sets [2].

Aims and objectives

Our objective was to determine potential risk-factors by evaluate progression trajectories in COPD using ClinTrajAn on the COPDGene Phase I (baseline visit) dataset.

Methods

7883 participants, current and former smokers with GOLD 0 thru 4 COPD, from Phase I of the COPDGene study, were utilized for this work. 55 features were obtained for each subject, including demographics, spirometry, smoking history and computed tomography (CT), which included Parametric Response Mapping (PRM). Developed by our group, PRM is capable of simultaneously measuring small airways disease and emphysema which are the main contributors of airflow limitations in COPD. The resulting data matrix was analyzed with ClinTrajAn.

Results

A principal tree, with 13 branch segments and 8 termini, was generated (Figure 1). There was a clearly recognized trajectory from healthier subjects through decreasing lung function and increasing age (Figure 1 A), increasing in GOLD (Figure 1 B), to an emphysema high terminus (Figure 1 C). Notably this method illustrated numerous branching points along this trajectory.

Conclusions

In this study we used ClinTrajAn to obtain a map of disease progression trajectories in COPD including clinically recognized pathogenesis. Our next steps will be to further validate this approach using longitudinal data from the COPDGene follow-up visits.

References

1. Han MK, Agusti A, Calverley PM, Celli BR, Criner G, Curtis JL, Fabbri LM, Goldin JG, Jones PW, MacNee W, Make BJ. Chronic obstructive pulmonary disease phenotypes: the future of COPD. American journal of respiratory and critical care medicine. 2010 Sep 1;182(5):598-604.

2. Golovenkin SE, Bac J, Chervov A, Mirkes EM, Orlova YV, Barillot E, Gorban AN, Zinovyev A. Trajectories, bifurcations, and pseudo-time in large clinical datasets: applications to myocardial infarction and diabetes data. GigaScience. 2020 Nov;9(11):giaa128.

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

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Lecture / Discussion Wed, 10 Nov 2021 09:47:40 -0500 2021-11-17T16:00:00-05:00 2021-11-17T17:00:00-05:00 Palmer Commons DCMB Seminar Series Lecture / Discussion
DCM&B Tools and Technology Seminar (November 18, 2021 12:00pm) https://events.umich.edu/event/85370 85370-21626323@events.umich.edu Event Begins: Thursday, November 18, 2021 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.

URL for remote viewing: https://umich-health.zoom.us/j/94886745590?pwd=LzhLU243K2ZhbXNzU1BJRHQ5V25BZz09

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Presentation Mon, 30 Aug 2021 08:08:26 -0400 2021-11-18T12:00:00-05:00 2021-11-18T13:00:00-05:00 Palmer Commons DCMB Tools and Technology Seminar Presentation
BME 500 Seminar: "Engineering next-generation T cells for cancer immunotherapy" (November 18, 2021 4:00pm) https://events.umich.edu/event/89279 89279-21661695@events.umich.edu Event Begins: Thursday, November 18, 2021 4:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Abstract:
The adoptive transfer of T cells expressing chimeric antigen receptors (CARs) has demonstrated clinical efficacy in the treatment of advanced cancers, with anti-CD19 CAR-T cells achieving up to 90% complete remission among patients with relapsed B-cell malignancies. However, challenges such as antigen escape and immunosuppression limit the long-term efficacy of adoptive T-cell therapy. Here, I will discuss the development of and clinical data on next-generation T cells that can target multiple cancer antigens and resist antigen escape. I will also present recent work on tuning CAR signaling activities via rational protein design to achieve greater in vivo anti-tumor efficacy. This presentation will highlight the potential of synthetic biology in generating novel mammalian cell systems with multifunctional outputs for therapeutic applications.
Details:
DATE: Thursday, November 18, 2021
TIME: 4:00-5:00 pm
ZOOM LINK: https://umich.zoom.us/j/97723483179

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Lecture / Discussion Mon, 15 Nov 2021 15:53:04 -0500 2021-11-18T16:00:00-05:00 2021-11-18T17:00:00-05:00 Off Campus Location Biomedical Engineering Lecture / Discussion Yvonne Chen, Ph.D.
Alan J. Hunt Memorial Lecture: "Moving takes energy: the intersection of cell motility with cellular metabolism" (November 19, 2021 2:00pm) https://events.umich.edu/event/89276 89276-21661669@events.umich.edu Event Begins: Friday, November 19, 2021 2:00pm
Location: Lurie Biomedical Engineering (formerly ATL)
Organized By: Biomedical Engineering

2021 Alan J. Hunt Memorial Lecture

"Moving takes energy: the intersection of cell motility with cellular metabolism"

Cynthia Reinhart-King, Ph.D.
Cornelius Vanderbilt Professor of Engineering
Professor of Biomedical Engineering
Vanderbilt University

November 19, 2021, 2:00 PM - 3:30 PM

Please save the date and RSVP below for the 2021 Alan J. Hunt Memorial Lecture on Friday, November 19, 2021, from 2:00 PM - 3:30 PM. The lecture will take place in 1130 Lurie Biomedical Engineering Building (classroom) featuring Cynthia Reinhart-King, Ph.D. the Cornelius Vanderbilt Professor of Engineering and Professor of Biomedical Engineering at Vanderbilt University. Following the lecture, a reception will be held in the BME Commons.

Details:
DATE: Friday, November 19, 2021
TIME: 2:00 PM - 3:30 PM (Reception; 3:30 PM - 4:30 PM)
LOCATION: 1130 Lurie Biomedical Engineering; A reception will follow in the BME Commons

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Lecture / Discussion Mon, 15 Nov 2021 15:16:23 -0500 2021-11-19T14:00:00-05:00 2021-11-19T16:30:00-05:00 Lurie Biomedical Engineering (formerly ATL) Biomedical Engineering Lecture / Discussion Alan J Hunt
Exploring students’ expectations towards and experiences with a new engineering interdisciplinary curriculum (December 1, 2021 10:30am) https://events.umich.edu/event/89044 89044-21660326@events.umich.edu Event Begins: Wednesday, December 1, 2021 10:30am
Location: Off Campus Location
Organized By: Engineering Education Research

The University College London (UCL) Centre for Engineering Education is a joint venture between Faculty of Engineering Sciences and the Institute of Education (IoE). Through research and active engagement, it aims to encourage the study of engineering and allied subjects and drive curriculum innovations to help create the next generation of engineering graduates needed to address complex global challenges. The Centre for Engineering Education is heavily involved in the running and dissemination of UCL Engineering's Integrated Engineering Programme (IEP) – one of the four case studies described in the MIT report “Reimagining and rethinking engineering education” – a pedagogical framework by which undergraduate students study using innovative and interdisciplinary approaches. In this session, I will focus on CEE’s research with IEP students and recent graduates to understand their experiences in the programme. Findings suggest gender differences in the awareness of the societal impact of engineering, and that communication skills are essential to engineering practice. Finally, I will highlight contributions for future longitudinal research on engineering student learning and career pathways in the UK.

Register here: tinyurl.com/eerseminar-direito

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Workshop / Seminar Mon, 08 Nov 2021 14:23:40 -0500 2021-12-01T10:30:00-05:00 2021-12-01T11:45:00-05:00 Off Campus Location Engineering Education Research Workshop / Seminar Inês Direito
Department of Computational Medicine & Bioinformatics Weekly Seminar (December 1, 2021 4:00pm) https://events.umich.edu/event/88514 88514-21654664@events.umich.edu Event Begins: Wednesday, December 1, 2021 4:00pm
Location: Palmer Commons
Organized By: DCMB Seminar Series

Abstract:

Epigenetic control of gene expression is highly cell-type- and context-specific. Yet, despite its complexity, gene regulatory logic can be broken down into modular components consisting of a transcription factor (TF) activating or repressing the expression of a target gene through its binding to a cis-regulatory region. Recent advances in joint profiling of transcription and chromatin accessibility with single-cell resolution offer unprecedented opportunities to interrogate such regulatory logic. Here, we propose a nonparametric approach, TRIPOD, to detect and characterize three-way relationships between a TF, its target gene, and the accessibility of the TF’s binding site, using single-cell RNA and ATAC multiomic data. We apply TRIPOD to interrogate cell-type-specific regulatory logic in peripheral blood mononuclear cells and contrast our results to detections from enhancer databases, cis-eQTL studies, ChIP-seq experiments, and TF knockdown/knockout studies. We then apply TRIPOD to mouse embryonic brain data during neurogenesis and gliogenesis and identified known and novel putative regulatory relationships, validated by ChIP-seq and PLAC-seq. Finally, we demonstrate TRIPOD on SHARE-seq data of differentiating mouse hair follicle cells and identify lineage-specific regulation supported by histone marks for gene activation and super-enhancer annotations.

Hosted by: Joshua Welch, PhD

Speaker will be in-person and the seminar will be live-streamed via Zoom.

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

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Lecture / Discussion Thu, 21 Oct 2021 14:55:35 -0400 2021-12-01T16:00:00-05:00 2021-12-01T17:00:00-05:00 Palmer Commons DCMB Seminar Series Lecture / Discussion Yuchao Jiang (Assistant Professor in the Departments of Biostatistics and Genetics at UNC)
DCM&B Tools and Technology Seminar (December 2, 2021 12:00pm) https://events.umich.edu/event/85371 85371-21626324@events.umich.edu Event Begins: Thursday, December 2, 2021 12:00pm
Location: Palmer Commons
Organized By: DCMB Tools and Technology Seminar

A linear approach is the simplest way to model the relationship between an exposure and an outcome. But a linear approach is limited in only capturing the association that is either strictly increasing or strictly decreasing. This might not adequately represent the associations at the extremes of the distribution for an exposure. For example, in Nguyen et al. 2021, we found that modeling a linear association between an exposure, body mass index (BMI) and an outcome, all-cause mortality resulted in a null relationship (i.e. there is no association between BMI and mortality risk.) This is nonsensical as we intuitively understand that participants with the lowest and highest BMI are at increased risk for all-cause mortality. Our intuition was confirmed when we considered non-linear associations between BMI and all-cause mortality. Furthermore, we observed that the prediction performance for the linear model were on par with those of the non-linear models, but this creates challenges in selecting the most appropriate model. Thus, we developed a visualization tool, called the stairway plots, to compare the linear and non-linear shapes of the associations to help select the most appropriate model. In Nguyen et al. 2021, we used the stairway plots to characterize the non-linear associations between physiological indicators and all-cause mortality. These plots enable us to assess the relevance of the clinical thresholds in differentiating patients who are at high vs. low risk for mortality. Now, we are currently using this visualization tool to study the non-linear associations between chemical exposures and cancer-specific mortality to quantify the cancer mortality risk found at human relevant doses. We plan to deploy this tool as an R package to enable the characterization of linear vs non-linear associations between any exposures and any outcomes of interest.

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.

URL for remote viewing: https://umich-health.zoom.us/j/94886745590?pwd=LzhLU243K2ZhbXNzU1BJRHQ5V25BZz09

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Presentation Wed, 17 Nov 2021 07:53:51 -0500 2021-12-02T12:00:00-05:00 2021-12-02T13:00:00-05:00 Palmer Commons DCMB Tools and Technology Seminar Presentation
"Hybrid Models to Accelerate Discovery and Optimize Design in Neural Engineering" (December 2, 2021 4:00pm) https://events.umich.edu/event/89543 89543-21664063@events.umich.edu Event Begins: Thursday, December 2, 2021 4:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Abstract:
Neural engineers try to fight disease by interfacing directly with the nervous system to correct or circumvent the pathology, but the complexities of neurophysiology make designing these therapies very difficult. The sophisticated interactions of neural control systems with the body and mind has limited our ability to predict the effects of neural interfaces in advance, which forces the field to rely on painstaking animal experiments to test and design the devices. This work presents an alternate way forward using new functionally predictive hybrid models that let us prototype and test neural interfaces in cheap, low-risk settings to get the most out of the cumbersome and expensive animal and human studies that require implanted electrodes. The key innovation is to combine parts of traditionally separate model systems (animal, human, mathematical, or statistical) into hybrid frameworks that use the strengths of each type to make accurate, use-case predictions about the effects of new neural interfaces.
Details:
DATE: Thursday, December 2, 2021
TIME: 4:00-5:00 pm
LOCATION: Cooley G906
ZOOM LINK: https://umich.zoom.us/j/97723483179

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Lecture / Discussion Mon, 29 Nov 2021 09:57:50 -0500 2021-12-02T16:00:00-05:00 2021-12-02T17:00:00-05:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Event
Engineering Education Research Information Session: EER Certificate and Master's Degree (December 3, 2021 11:00am) https://events.umich.edu/event/89355 89355-21662211@events.umich.edu Event Begins: Friday, December 3, 2021 11:00am
Location: Off Campus Location
Organized By: Engineering Education Research

Are you an engineering PhD student who wants to study approaches for improving learning in the engineering classroom and beyond? Are you interested in diversifying STEM education and the engineering workforce? Do you have ideas for developing engineers who think like entrepreneurs, design creative solutions to the nations’ grand challenges, and make a difference in the world? Pursuing an Engineering Education Research (EER) Certificate or Master's Degree may be a way for you to achieve those goals.

Join us for an information session about the EER Certificate and Master's Degree:
11:00 - 12:30 p.m. | Friday, December 3, 2021
Zoom link provided upon registration


You can read more information about the program is at this site: https://eer.engin.umich.edu/academics/rackham-certificate/

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Workshop / Seminar Thu, 18 Nov 2021 08:55:30 -0500 2021-12-03T11:00:00-05:00 2021-12-03T12:00:00-05:00 Off Campus Location Engineering Education Research Workshop / Seminar Engineering Education Research (EER)
RISE December Virtual Talking Circle (December 6, 2021 12:00pm) https://events.umich.edu/event/87913 87913-21647681@events.umich.edu Event Begins: Monday, December 6, 2021 12:00pm
Location: Off Campus Location
Organized By: RISE (Research. Innovation. Scholarship. Education.)

Please join us for our next Virtual Taking Circle on Monday, December 6 at 12:00 PM. We will be hosting a conversation about how educators are finding ways to innovate within the laboratory setting. We look forward to learning more about current innovations happening in the laboratory setting and what it takes to be innovative within this setting. We will also explore synergies that might better enable innovation and what is next for innovation in the laboratory setting.

All are welcome to join!

Register via Eventbrite https://www.eventbrite.com/e/rise-virtual-talking-circle-tickets-177410468487

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Workshop / Seminar Tue, 05 Oct 2021 12:29:32 -0400 2021-12-06T12:00:00-05:00 2021-12-06T13:00:00-05:00 Off Campus Location RISE (Research. Innovation. Scholarship. Education.) Workshop / Seminar RISE Virtual Talking Circle
SCSAP Monthly Seminar Series (December 6, 2021 1:00pm) https://events.umich.edu/event/89632 89632-21664587@events.umich.edu Event Begins: Monday, December 6, 2021 1:00pm
Location: Off Campus Location
Organized By: Single Cell Spatial Analysis Program (SCSAP)

Title: The mutational landscape and clonal dynamics of Human Somatic and Germline cells

During the course of a lifetime normal human cells accumulate mutations. Studying these mutations provides important insight into the development, maintenance and structure of normal tissues, the mutational processes that have been operative, and the role of selection in shaping cell populations. It can elucidate how each of these are altered by, or contribute to, cancer, other diseases, and ageing. However, characterising such mutations has been technically challenging, as normal cell populations consist of myriad small clones, with the mutations differing between clones. We employed laser capture microscopy combined with low input-DNA whole genome sequencing, to study clonal units across multiple cell types from the same individuals. We compared the mutational landscape in 29 cell types from the soma and germline. Our results revealed the extent of variation in clonal dynamics across tissues. Mutation rates vary between different cell types, with stem cells of the intestinal epithelium exhibiting the highest mutation rates and germ-cells in testis exhibited the lowest mutation rates thus far reported. Several mutational signatures were observed among normal cell types. However, most mutations in almost all cell types were due to SBS1 and SBS5, which are likely due to endogenous mutagenic processes. The relative contributions of these signatures differed between cell types, indicating that their rates of generation are, at least partially, independently regulated.

Register on Zoom at https://tinyurl.com/b59rmbk6

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Workshop / Seminar Tue, 30 Nov 2021 16:22:15 -0500 2021-12-06T13:00:00-05:00 2021-12-06T14:00:00-05:00 Off Campus Location Single Cell Spatial Analysis Program (SCSAP) Workshop / Seminar Dr. Raheleh Rahbari, Sanger Institute
LHS Collaboratory (December 7, 2021 12:30pm) https://events.umich.edu/event/88230 88230-21651558@events.umich.edu Event Begins: Tuesday, December 7, 2021 12:30pm
Location: Off Campus Location
Organized By: Department of Learning Health Sciences

Julia Adler-Milstein, PhD
Professor of Medicine and Director of the Center for Clinical Informatics and Improvement Research (CLIIR)
University of California San Francisco

Interoperability is considered a key capability of a high-performing healthcare system and has been a top policy priority for more than a decade. Implementing interoperability is, however, a complex undertaking – requiring stakeholder coordination that tackles incentives, governance, technology, standards, and more. In this talk, Dr. Adler-Milstein will describe current approaches to interoperability and where we stand with respect to current levels of national adoption. She will then discuss the implications for Learning Health System efforts at different levels of scale.

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Livestream / Virtual Wed, 13 Oct 2021 13:59:31 -0400 2021-12-07T12:30:00-05:00 2021-12-07T14:00:00-05:00 Off Campus Location Department of Learning Health Sciences Livestream / Virtual Collaboratory logo
BME PhD Defense: Melissa Lemke (December 8, 2021 1:00pm) https://events.umich.edu/event/89542 89542-21664062@events.umich.edu Event Begins: Wednesday, December 8, 2021 1:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Department of Biomedical Engineering Final Oral Examination

Melissa Lemke

A Systems Approach to Elucidate Personalized Mechanistic Complexities of Antibody-Fc Receptor Activation Post-Vaccination

One of the most significant challenges to current human healthcare is the emergence of antigenically variable viruses that evade traditional vaccination approaches. Human immunodeficiency virus (HIV) is one such virus that emerged over 30 years ago and still has no effective vaccine. Like many other antigenically variable viruses, after infection, HIV quickly mutates to evade broadly neutralizing antibodies that bind tightly to key sites to prevent infection. Over 250 clinical trials have been performed to date to develop an effective HIV vaccine, with only one providing moderate protection; the RV144 Thai trial, estimated to be 31% effective but has not been replicated in other populations. Rather than broadly neutralizing antibodies, the trial identified IgG antibodies with the capacity to induce Fc effector functions as a correlate of protection. These functions are triggered by less specific antibodies that bind HIV antigen and Fc receptors on the surface of innate immune cells to form immune complexes to activate protective cellular functions. Understanding how to increase the formation of IgG-FcR complexes may improve vaccine efficacy, but variation in IgG and FcR features across individuals suggests that protective mechanisms need to be understood on a personalized basis. There are multiple subclasses of protective IgGs, each having different concentrations and affinities to FcRs in different individuals. Genetics can also play a role, with FcR polymorphisms changing FcR binding affinity and IgG1 allotypes changing IgG subclass concentrations. Mechanistic ordinary differential equation (ODE) modeling of this system offers the opportunity to account for these factors on a personalized basis and deconvolve which are most influential and determine how to improve protection universally.


We developed an ODE model of IgG-FcγRIIIa immune complex formation to elucidate how personalized variability in IgG subclass concentration and genetic factors may contribute to complex formation after vaccination. We validated the model with RV144 plasma samples and used it to discover new mechanisms that underpin complex formation. This enabled the identification of genetic and post-translational features that influenced complex formation and suggested the best interventions on a personalized basis. For example, although IgG3 was associated with protection in RV144 and has the highest affinity to FcγRIIIas, the model suggested that IgG1 may play a more essential role, though it also may be highly variable; due to high IgG1 concentration variability across individuals. The model identified RV144 vaccinees who were predicted to be sensitive, insensitive, or negatively affected by increases in HIV-specific IgG1, which was validated experimentally with the addition of HIV-specific IgG1 monoclonal antibodies to vaccine samples. The model also gave important insights into how to maximize IgG-FcγRIIIa complex formation in different genetic backgrounds. We found that individuals with certain IgG1 allotypes were predicted to be more responsive to vaccine adjuvant strategies that increase antibody affinity (e.g., glycosylation modifications) compared to other allotypes, which were predicted to be more responsive to vaccine boosting regimens that increase IgG1 antibody concentration. Finally, simulations in mixed-allotype populations suggest that the benefit of boosting IgG1 concentration versus IgG1 affinity may depend upon the frequency of a specific IgG1 allotype (G1m-1,3) in the population. Overall we believe that this approach represents a valuable tool that will help understand the role of personalized immune mechanisms in response to vaccination and address challenges related to under-represented genetic populations in vaccine trials.

Date: Wednesday, December 8, 2021
Time: 1:00 PM
Zoom: https://umich.zoom.us/j/96971889814
Meeting ID: 969 7188 9814 Passcode: 663036
Chair: Dr. Kelly Arnold

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Lecture / Discussion Mon, 29 Nov 2021 09:50:43 -0500 2021-12-08T13:00:00-05:00 2021-12-08T14:00:00-05:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Event
Precision Health Seminar Series (December 9, 2021 11:30am) https://events.umich.edu/event/88799 88799-21657772@events.umich.edu Event Begins: Thursday, December 9, 2021 11:30am
Location: Off Campus Location
Organized By: Precision Health

What goes on behind the scenes when clinicians use these tools to provide evidence-based care? Our panel weighs in on what is important for clinicians to know and how confident they can be when using these tools. Our panelists also describe training necessary to use these tools effectively to support medical decisions.

The panel includes varied perspectives from: an engineer, a learner, a clinician, and an educator.

* Rada Mihalcea, PhD, Professor, Electrical Engineering & Computer Science, College of Engineering
* Erkin Otles, Medical Scientist Training Program Fellow (MD-PhD student)
* Max Spadafore, MD, Resident, Emergency Medicine
* Cornelius James, MD, Assistant Professor, Internal Medicine & Pediatrics

The panel will be moderated by Vicki Ellingrod, PharmD, Associate Research Dean and Professor, Pharmacy.

This webinar is the third in the Precision Health educational series "Demystifying the Data, Processes, and Tools that Are Changing Clinical Care." Visit the Precision Health website to see recordings of previous webinars: https://precisionhealth.umich.edu/.

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Livestream / Virtual Thu, 11 Nov 2021 16:27:29 -0500 2021-12-09T11:30:00-05:00 2021-12-09T12:30:00-05:00 Off Campus Location Precision Health Livestream / Virtual Precision Health at U-M
"EPICode, a multiplexed epitope barcoding strategy that enables dynamic cellular phenotypic screens" (December 9, 2021 4:00pm) https://events.umich.edu/event/89887 89887-21666282@events.umich.edu Event Begins: Thursday, December 9, 2021 4:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Pooled genetic libraries have improved screening throughput for mapping genotypes to phenotypes. However, selectable phenotypes are limiting, restricting screening to outcomes with a low spatiotemporal resolution. Here, we integrated live-cell imaging with pooled library-based screening. To enable intracellular multiplexing, we developed a method, called EPICode (Epitope-Phenotype Immunofluorescence barCode), that uses a combination of short epitopes to facilitate optical screening. By using the subcellular localization of the barcode as an additional channel, our method exponentially increases multiplexing capacity. Thus, after using live-cell microscopy to characterize a phenotype of interest, subjected to sequential stimulatory/inhibitory manipulations, the genotype of each cell in the population can be identified. To demonstrate applicability, we developed a live-cell PKA kinase translocation reporter with improved sensitivity and specificity. The use of epitopes as fluorescent barcodes introduces a scalable strategy for high-throughput screening broadly applicable to protein engineering and drug discovery settings where image-based phenotyping is desired.
Details:
DATE: Thursday, December 9, 2021
TIME: 4:00-5:00 pm
ZOOM LINK: https://umich.zoom.us/j/97723483179

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Workshop / Seminar Wed, 08 Dec 2021 11:33:18 -0500 2021-12-09T16:00:00-05:00 2021-12-09T17:00:00-05:00 Off Campus Location Biomedical Engineering Workshop / Seminar BME Event
BME Ph.D. Defense: Thomas A. Davidson (December 10, 2021 8:00am) https://events.umich.edu/event/89701 89701-21665017@events.umich.edu Event Begins: Friday, December 10, 2021 8:00am
Location: Off Campus Location
Organized By: Biomedical Engineering

Nearly 90% of adults in the US will develop dental caries needing treatment with dental restorations within their lifetimes. An increasing number of restorations are done using composite rather than amalgams. Dental composites have some benefits, but the longevity of these restorations is shorter (5 to 7 years) than amalgams (10+ years). The leading cause of dental restoration failure is development of secondary caries. Secondary caries is decay at or near the margins of dental restorations that occurs when bacteria or acid infiltrate the interface and cause demineralization. A reduction in infiltration would prevent the development of secondary caries. The focus of this dissertation is the development of a method for improving the integrity of the interface using peptide engineering. It was hypothesized that a mineral binding peptide identified via phage display for affinity to apatite could be modified to A) chemically incorporate with dental composites during polymerization and increase bond strength and B) act as an anchor for a mineralization promoting peptide to increase remineralization at the interface.


First, this thesis describes the characterization of VTKHLNQISQSY (VTK) peptide and phosphorylated variants (pVTK) for their affinity to dentin and enamel and the increase in adhesion strength at the nano-scale. pVTK showed strong affinity to dentin and enamel, and both VTK and pVTK exhibited strong adhesion to dentin and enamel at the nanoscale under dry and wet conditions. Binding at the nanomolecular level translated to modest shear bond strength (SBS) increases at the interface when pVTK (7.4%) was modified with a cysteine that incorporated with the methacrylate-based bonding agent and composite during polymerization. Using a competitive risk model incorporating failure mode and SBS, a small increase in bond strength (VTK: 3%; pVTK: 10%) was observed.


The second modification to VTK was the addition of a remineralization domain using 8DSS, a known remineralization peptide consisting of 8 repeats of Asp-Ser-Ser (DSS). The dual-functioning peptide (VTK-8DSS) was applied to in vitro cross sections of dentin and enamel and an in situ model of class V dental restorations. Mineral deposition and quality were assessed over 7 days in remineralization solution. VTK-8DSS increased the mineral quality (recovering 75% of young’s modulus and hardness compared to 50% of 8DSS control) determined using nanoindentation over the 7 day time course of the study.


These modifications were also analyzed under challenging conditions for their protective effect to the interface. VTK and pVTK doped composites were exposed to thermal cycling and had a 43% and 49% reduction in microleakage as measured by silver nitrate penetration using micro CT. Cross sections and dental restorations were used to assess the function of VTK-8DSS in artificial saliva containing proteins that competitively bind to dentin and enamel and an acidic cycling model where samples were exposed to acid every day in addition to remineralization solution. VTK-8DSS in both artificial saliva and acidic cycling models showed a slight increase in mineral deposition (95% and 95% recovery) compared to 8DSS (80% and 50% respectively) and a large increase mineral quality (70% vs 10% and 60% vs 30%).


Taken together, the data in this dissertation demonstrates the ability to engineer interfacial surfaces using peptides derived for their affinity to specific tissues. This system could be applied more broadly to improve the interactions or integration of any number of biomaterials that directly interface with native tissue.


Date: Friday, December 10, 2021
Time: 8:00 AM EST
Zoom: https://umich.zoom.us/j/97816028147 (Zoom link requires prior registration)
Chair: Dr. David Kohn

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Lecture / Discussion Thu, 02 Dec 2021 09:36:52 -0500 2021-12-10T08:00:00-05:00 2021-12-10T09:00:00-05:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Event
BME PH.D. Defense: Christopher D. Davidson (December 10, 2021 1:00pm) https://events.umich.edu/event/89668 89668-21664759@events.umich.edu Event Begins: Friday, December 10, 2021 1:00pm
Location: Off Campus Location
Organized By: Biomedical Engineering

The ability of cells to communicate and coordinate their activity is crucial to the development and homeostatic function of all tissues. In addition to the well-established means of biochemically mediated signaling, a more recent body of evidence has indicated that cells can also communicate via cell-generated forces transmitted to neighboring cells through the extracellular matrix (ECM). One setting in which a deeper understanding of mechanical intercellular communication (MIC) would be extremely valuable is in vasculogenesis, or the de novo formation of a microvascular network. This dynamic process involves the assembly and organization of individual endothelial progenitor cells into an interconnected network of capillaries, thus requiring cellular communication and coordination over large spatial scales. If fully understood and harnessed, vasculogenic assembly presents a promising approach to vascularizing engineered tissue constructs for regenerative medicine applications. We hypothesize physical properties of the ECM are critical to MIC as the matrix context defines not only the generation of cell forces but also force transmission through the matrix to nearby cells. Thus, the focus of this dissertation is to study cell force propagation and MIC between endothelial cells (ECs) in controllable synthetic ECMs towards the informed design of biomaterials that drive rapid self-assembly of functional microvascular networks.



First, this thesis explores how physical attributes of the ECM regulate the assembly of ECs into interconnected multicellular networks. To mimic the fibrous microenvironments where neovascularization typically occurs in the body, we developed a novel model of the EC network formation assay utilizing 2.5D matrices of electrospun synthetic dextran methacrylate (DexMA) polymeric fibers. Our results revealed that active cell-mediated matrix deformations and fiber recruitment through actomyosin force generation occurs concurrently with the formation and stabilization of multicellular EC networks.



Next, this thesis describes the development and characterization of a new material system composed of electrospun dextran vinyl sulfone (DexVS) polymeric fibers that possess longer-term mechanical stability in culture as compared to DexMA matrices. These matrices were utilized for two major objectives: 1) investigating the role of matrix mechanics on the activation of fibroblasts into myofibroblasts, a key component of wound healing and the fibrotic progression, and 2) exploring the impact of nonlinear matrix mechanical properties on vasculogenic assembly by imbuing fibers with crimped microstructure.



Lastly, this thesis describes the mechanism of MIC between individual ECs during vasculogenic assembly. By combining electrospun DexMA fiber matrices with a microfabrication-based cell-patterning method, we investigated EC force-mediated matrix displacements and MIC as a function of matrix stiffness and identified the critical cellular machinery required for ECs to sense and respond to mechanical signals emanating from neighboring cells. We then sought to harness these observations in more translatable 3D hydrogel constructs by using a composite approach where fibrin hydrogels were reinforced with electrospun DexVS fiber segments. While traditional approaches to prevascularize 3D hydrogels require long-term co-cultures of ECs and support stromal cells, our work demonstrated that mechanical cues from synthetic fibers enable ECs alone to rapidly self-assemble into networks of lumenized capillary-like structures.



Overall, the work presented in this dissertation integrates biomaterials, tissue engineering, and microfabrication approaches to investigate the mechanobiology of how cell forces regulate intercellular communication during vasculogenic assembly. The results presented here are critical to the design of biomaterials that promote robust capillary network assembly for applications in tissue engineering and regenerative medicine.



Date: Friday, December 10, 2021

Time: 1:00 PM EST

Zoom: https://umich.zoom.us/meeting/register/tJAoceuhqD0rHdwL8duV6QwOcYjLXl14kysD (Zoom link requires prior registration)

Chair: Dr. Brendon Baker

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Lecture / Discussion Wed, 01 Dec 2021 11:44:48 -0500 2021-12-10T13:00:00-05:00 2021-12-10T14:00:00-05:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Event
RNA Faculty Candidate Seminar (December 13, 2021 4:00pm) https://events.umich.edu/event/89524 89524-21663803@events.umich.edu Event Begins: Monday, December 13, 2021 4:00pm
Location: Taubman Biomedical Science Research Building
Organized By: Center for RNA Biomedicine

In-person/Hybrid seminar co-hosted by the Center for RNA Biomedicine and the Department of Molecular, Cellular, and Developmental Biology

Talk title: “Resolving the localisation and dynamics of mRNA and protein synthesis within neurons”

Keywords: mRNA dynamics, local protein synthesis, neurons, neuronal cell biology, synaptic plasticity, in vivo imaging

If you are having trouble registering, please contact Martina Jerant at mjerant@umich.edu

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Lecture / Discussion Tue, 30 Nov 2021 13:12:23 -0500 2021-12-13T16:00:00-05:00 2021-12-13T17:00:00-05:00 Taubman Biomedical Science Research Building Center for RNA Biomedicine Lecture / Discussion Paul Donlin-Asp, Ph.D.,
RISE Virtual Talking Circle (January 10, 2022 12:00pm) https://events.umich.edu/event/90030 90030-21667626@events.umich.edu Event Begins: Monday, January 10, 2022 12:00pm
Location: Off Campus Location
Organized By: RISE (Research. Innovation. Scholarship. Education.)

Crowdsourcing your input on our preliminary ideas emerging from the Health Science Education Innovation Task Force

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Workshop / Seminar Wed, 15 Dec 2021 07:01:39 -0500 2022-01-10T12:00:00-05:00 2022-01-10T13:00:00-05:00 Off Campus Location RISE (Research. Innovation. Scholarship. Education.) Workshop / Seminar RISE Virtual Talking Circle
BME PhD Defense: Olga M. Wroblewski (January 12, 2022 10:00am) https://events.umich.edu/event/90462 90462-21671089@events.umich.edu Event Begins: Wednesday, January 12, 2022 10:00am
Location: Off Campus Location
Organized By: Biomedical Engineering

Volumetric muscle loss (VML) is a common pathological condition caused by traumatic loss of skeletal muscle that exceeds the muscle’s regenerative capabilities and results in functional impairment. Current surgical standards-of-care frequently fail to fully recover contractile function. To address these limitations, our laboratory has developed scaffold-free tissue engineered skeletal muscle units (SMUs) for the treatment of VML. Isolated skeletal muscle stem cells (satellite cells) and fibroblasts are cultured into a confluent cell monolayer before being rolled into a cylindrical 3D construct. Ideally, these SMUs could be engineered from small autogenic muscle biopsies, alleviating the limitations of donor site morbidity and immune rejection seen in current VML treatments. These SMUs are biocompatible, incorporate into surrounding muscle tissue upon implantation, and have shown efficacy to partially repair a 30% VML in rat and sheep models. There are two key challenges that must be resolved to successfully translate our technology to a human cell-sourced model. To date, it has been difficult to grow human cell-sourced SMUs with any noteworthy contractile function. Secondly, many satellite cells are required for SMU fabrication. Any methodology that can optimize the number of cells obtained in a human skeletal muscle biopsy and enhance the functional properties of the resultant muscle tissue will advance SMUs towards clinical use.

Human epidermal growth factor (hEGF), a mitogen, has shown promise enhancing myobundle formation and contractile function in vitro. Prior to this thesis work, the impact of hEGF treatment during the proliferation and differentiation phases of SMU fabrication had yet to be evaluated. We investigated the effects of hEGF on SMU fabrication, structure, and biomechanical function. Our results indicated that hEGF was critical for the development of contractile function in human cell-sourced SMUs.

Due to the small amount of satellite cells present in skeletal muscle, we also sought to optimize our methodologies so that fewer satellite cells are needed to be isolated to fabricate SMUs. Currently, we have been successful at fabricating functional SMUs using lower cell-seeding densities compared to rat and sheep models. By altering the timing of our fabrication protocol and allowing cell cultures to reach >90% confluency in media that promotes proliferation, we found that we could lower starting cell-seeding density by 90% compared to ovine models with no detrimental impact to monolayer development or SMU function.

To further expand the capabilities of satellite cells from a single autogenic skeletal muscle biopsy, we evaluated the impact of in vitro cell proliferation (increasing cell number by cell passaging) on human primary skeletal muscle cells within an engineered skeletal muscle tissue environment. While cell passaging decreased the percentage of myogenic cells in the total cell population, results indicated that human primary skeletal muscle cells can be passaged without negatively impacting the contractile function of a skeletal muscle construct compared to one created with unpassaged cells. A single passage can increase the total cell yield from a human skeletal muscle biopsy fiftyfold compared to cells harvested without a passage.

Overall, this work significantly contributed to the field of skeletal muscle tissue engineering by advancing fabrication methodologies to develop SMUs of appropriate structure and function for human application. We addressed two key limitations in human cell-sourced skeletal muscle tissue engineering by optimizing cell culture conditions to increase the cell yield from a single skeletal muscle biopsy while promoting SMU biomechanical function.

Date: Wednesday, January 12, 2022
Time: 10:00 AM EST
Zoom: https://umich.zoom.us/meeting/register/tJUocu2gqjMpGdelbor8Vj43NvRde859Q-EE
(Zoom link requires prior registration)
Chair: Dr. Lisa Larkin

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Lecture / Discussion Wed, 05 Jan 2022 08:59:08 -0500 2022-01-12T10:00:00-05:00 2022-01-12T11:00:00-05:00 Off Campus Location Biomedical Engineering Lecture / Discussion BME Event
A Truly Subject-Specific, Shared Model of the Human Tricuspid Valve (January 13, 2022 3:30pm) https://events.umich.edu/event/90763 90763-21673517@events.umich.edu Event Begins: Thursday, January 13, 2022 3:30pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Abstract: Computer simulations have become critical elements of the medical device design and regulatory approval process. Naturally, the predictability and therefore value of such simulations depends highly on their accuracy. Especially for the design of heart valve replacements and repair technologies computer simulations have become a critical tool. While much progress has been made in modeling the aortic valve and the mitral valve, much less effort has been spent on modeling the tricuspid valve. The reasons are multi-fold, but include the general neglect of the valve as well as the high complexity of the valve in comparison to the three other valves. In our most recent work, we are beginning to fulfill this gap. Specifically, our objective is to develop, validate, and then publicly provide a truly subject-specific, shared model of the human tricuspid valve. To this end, we combine multi imaging-modality based measurements in beating human hearts that have been prepared in an organ preservation system, with in-vitro measurements of heart valve geometric, structural, and mechanical properties. Once built, we conduct finite element simulations with this valve and validate dynamic simulations throughout the cardiac cycle against in-situ measurements. Finally, we show case our model by first mimicking a diseased valve, which we then repair using a surgical and an interventional approach.

Bio: Dr. Rausch is an assistant professor at the University of Texas at Austin where he directs the soft tissue biomechanics laboratory. His laboratory's objective is to use complimentary imaging modalities, mechanical testing, and numerical methods to understand and predict soft tissue disease. The specific problems he studies include pressure ulcers, right heart heart failure, tricuspid valve regurgitation, and thrombotic disease. Check out his work on www.manuelrausch.com and follow him on Twitter under @ManuelKRausch1.

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Workshop / Seminar Mon, 10 Jan 2022 16:14:23 -0500 2022-01-13T15:30:00-05:00 2022-01-13T16:30:00-05:00 Off Campus Location Biomedical Engineering Workshop / Seminar BME Seminar
UROP Summer Fellowship Applications Open (January 18, 2022 9:00am) https://events.umich.edu/event/91078 91078-21676398@events.umich.edu Event Begins: Tuesday, January 18, 2022 9:00am
Location: Off Campus Location
Organized By: UROP - Undergraduate Research Opportunity Program

U-M undergraduates interested in conducting research during the summer for a 10-week paid fellowship can apply to one of three available programs: Biomedical & Life Sciences, Engineering or Women and Gender. Previous research experience IS NOT required.

Applications are available at: https://myumi.ch/lxmbp

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Careers / Jobs Mon, 17 Jan 2022 09:34:51 -0500 2022-01-18T09:00:00-05:00 2022-01-18T23:00:00-05:00 Off Campus Location UROP - Undergraduate Research Opportunity Program Careers / Jobs Paid UROP Summer Fellowships
LHS Collaboratory (January 18, 2022 12:00pm) https://events.umich.edu/event/89940 89940-21666535@events.umich.edu Event Begins: Tuesday, January 18, 2022 12:00pm
Location: Off Campus Location
Organized By: Department of Learning Health Sciences

This presentation will explore how Big Data Science and Informatics research can overcome deficiencies within the electronic health record and optimize real world data collection. We will discuss examples of how standardized nomenclature integrated into clinical workflow can enable statistical AI methods to advance clinical decision support and improve outcome models. Our successes in radiation oncology come from single multi-institutional, multi-national and multi-professional society collaboration.

Presenters:
Charles Mayo, PhD
Professor
Director of Radiation Oncology Informatics and Analytics
Department of Radiation Oncology
University of Michigan Medical School

Michelle Mierzwa, MD
Associate Professor
Associate Chair of Clinical Research
Co-Chair of Head and Neck Clinical Trials
Department of Radiation Oncology
University of Michigan Medical School

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Lecture / Discussion Tue, 11 Jan 2022 15:56:37 -0500 2022-01-18T12:00:00-05:00 2022-01-18T13:30:00-05:00 Off Campus Location Department of Learning Health Sciences Lecture / Discussion Collaboratory logo
UROP Summer Fellowship Applications Open (January 19, 2022 9:00am) https://events.umich.edu/event/91078 91078-21676399@events.umich.edu Event Begins: Wednesday, January 19, 2022 9:00am
Location: Off Campus Location
Organized By: UROP - Undergraduate Research Opportunity Program

U-M undergraduates interested in conducting research during the summer for a 10-week paid fellowship can apply to one of three available programs: Biomedical & Life Sciences, Engineering or Women and Gender. Previous research experience IS NOT required.

Applications are available at: https://myumi.ch/lxmbp

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Careers / Jobs Mon, 17 Jan 2022 09:34:51 -0500 2022-01-19T09:00:00-05:00 2022-01-19T23:00:00-05:00 Off Campus Location UROP - Undergraduate Research Opportunity Program Careers / Jobs Paid UROP Summer Fellowships
Navigating at the Intersection of Two Pandemics: Exploring Black Engineering Graduate Students’ Simultaneous Experiences of COVID-19 and Racism-20 (January 19, 2022 10:30am) https://events.umich.edu/event/90470 90470-21671098@events.umich.edu Event Begins: Wednesday, January 19, 2022 10:30am
Location: Off Campus Location
Organized By: Engineering Education Research

In this seminar, the presenter will share findings from an in-progress work and facilitate a conversation anchored in the experiences of Black graduate students in engineering (BGSE) at the intersections of two pandemics. This engaging conversation will support our awareness of how the experiences of BGSE as a marginalized group in engineering have been compounded by the simultaneous realities of COVID-19 and Racism-20 (systemic racism). Specifically, the duality of BGSE as Black people in America and Black graduate students in U.S. engineering programs creates a unique set of experiences about which little is known. This seminar will amplify the experiences of BGSE in this moment and their explicit needs with the goal of increasing institutional awareness, and thus accountability, for best supporting their persistence and success.

Brooke C. Coley, Ph.D. is an Assistant Professor in Engineering at the Ira A. Fulton Schools of Engineering at Arizona State University. She is also Principal Investigator of the Shifting Perceptions, Attitudes and Cultures in Engineering (SPACE) Lab, which aspires to elevate the experiences of marginalized populations, dismantle systemic injustices, and transform the way inclusion is cultivated in engineering through the implementation of novel technologies and methodologies in engineering education. Her active NSF-supported research focuses on three specific areas: the role of identity-related professional organizations in engineering student success, factors impacting trajectory decisions of engineering students from underrepresented groups at community colleges and creating pathways to engineering education research. Dr. Coley recently received the 2021 Diversity and Inclusion Award from the Ira A. Fulton Schools of Engineering for her commitment to creating and fostering a diverse and inclusive environment. She holds a BS degree in Chemical Engineering from the University of Maryland Baltimore County.

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Workshop / Seminar Fri, 07 Jan 2022 09:24:14 -0500 2022-01-19T10:30:00-05:00 2022-01-19T11:45:00-05:00 Off Campus Location Engineering Education Research Workshop / Seminar Professor Brooke C. Coley
UROP Summer Fellowship Info Sessions (January 19, 2022 2:00pm) https://events.umich.edu/event/91076 91076-21676394@events.umich.edu Event Begins: Wednesday, January 19, 2022 2:00pm
Location: Off Campus Location
Organized By: UROP - Undergraduate Research Opportunity Program

Undergraduate Students interested in participating in a 10-week paid summer research fellowship can learn more about the Biomedical & Life Sciences, Engineering and Women & Gender programs during our virtual info sessions offered during the following dates:

January 19th (2pm-3pm)
January 25th (12pm-1pm)
February 3rd (5pm-6pm)
February 9th (5pm-6pm)

Register for an info session at: https://myumi.ch/7e36D

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Livestream / Virtual Mon, 17 Jan 2022 09:58:41 -0500 2022-01-19T14:00:00-05:00 2022-01-19T15:00:00-05:00 Off Campus Location UROP - Undergraduate Research Opportunity Program Livestream / Virtual UROP Paid Summer Fellowships
UROP Summer Fellowship Applications Open (January 20, 2022 9:00am) https://events.umich.edu/event/91078 91078-21676400@events.umich.edu Event Begins: Thursday, January 20, 2022 9:00am
Location: Off Campus Location
Organized By: UROP - Undergraduate Research Opportunity Program

U-M undergraduates interested in conducting research during the summer for a 10-week paid fellowship can apply to one of three available programs: Biomedical & Life Sciences, Engineering or Women and Gender. Previous research experience IS NOT required.

Applications are available at: https://myumi.ch/lxmbp

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Careers / Jobs Mon, 17 Jan 2022 09:34:51 -0500 2022-01-20T09:00:00-05:00 2022-01-20T23:00:00-05:00 Off Campus Location UROP - Undergraduate Research Opportunity Program Careers / Jobs Paid UROP Summer Fellowships
DCM&B Tools and Technology Seminar (January 20, 2022 12:00pm) https://events.umich.edu/event/89769 89769-21665747@events.umich.edu Event Begins: Thursday, January 20, 2022 12:00pm
Location: Off Campus Location
Organized By: DCMB Tools and Technology Seminar

This presentation will be given remotely, with the livestream available via Zoom.

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Presentation Mon, 17 Jan 2022 10:08:14 -0500 2022-01-20T12:00:00-05:00 2022-01-20T13:00:00-05:00 Off Campus Location DCMB Tools and Technology Seminar Presentation
Structure and Mechanics of the Myocardium: Modeling and Simulation (January 20, 2022 3:30pm) https://events.umich.edu/event/90947 90947-21674997@events.umich.edu Event Begins: Thursday, January 20, 2022 3:30pm
Location: Off Campus Location
Organized By: Biomedical Engineering

Bio:
Gerhard A. Holzapfel is Professor of Biomechanics and Head of the Institute of Biomechanics at Graz University of Technology (TUG), Austria, since 2007. He is also Adjunct Professor at the Norwegian University of Science and Technology (NTNU), Trondheim, Norway, and Visiting Professor at the University of Glasgow, Scotland. Until 2013 he was Professor of Biomechanics at the Royal Institute of Technology (KTH) in Stockholm, Sweden, for 9 years (7 years as an Adjunct Professor). After his PhD in Mechanical Engineering in Graz he received an Erwin-Schrödinger Scholarship for foreign countries to be a Visiting Scholar at Stanford University (1993-95). He achieved his Habilitation at TU Vienna in 1996 and received a START-Award in 1997, which is the most prestigious research award in Austria for young scientists. In the following years (1998-2004) he was the Head of a research group on "Computational Biomechanics" at TUG. Among several awards and honors in the past years he is listed in "The World's Most Influential Scientific Minds: 2014" (Thomas Reuters), he received the Erwin Schrödinger Prize 2011 from the Austrian Academy of Sciences for his lifetime achievements, and he was awarded the 2021 William Prager Medal and the 2021 Warner T. Koiter Medal.

Professor Holzapfel has authored a graduate textbook entitled "Nonlinear Solid Mechanics. A Continuum Approach for Engineering" (John Wiley & Sons), and co-edited seven books. He contributed chapters to 25 other books, and published 240+ peer-reviewed journal articles. He is the co-founder and co-editor of the International Journal "Biomechanics and Modeling in Mechanobiology" (Springer-Verlag, Berlin, Heidelberg).

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Workshop / Seminar Thu, 13 Jan 2022 11:51:20 -0500 2022-01-20T15:30:00-05:00 2022-01-20T16:30:00-05:00 Off Campus Location Biomedical Engineering Workshop / Seminar BME Seminar
UROP Summer Fellowship Applications Open (January 21, 2022 9:00am) https://events.umich.edu/event/91078 91078-21676401@events.umich.edu Event Begins: Friday, January 21, 2022 9:00am
Location: Off Campus Location
Organized By: UROP - Undergraduate Research Opportunity Program

U-M undergraduates interested in conducting research during the summer for a 10-week paid fellowship can apply to one of three available programs: Biomedical & Life Sciences, Engineering or Women and Gender. Previous research experience IS NOT required.

Applications are available at: https://myumi.ch/lxmbp

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Careers / Jobs Mon, 17 Jan 2022 09:34:51 -0500 2022-01-21T09:00:00-05:00 2022-01-21T23:00:00-05:00 Off Campus Location UROP - Undergraduate Research Opportunity Program Careers / Jobs Paid UROP Summer Fellowships
Grad School Interviews Office Hour (January 21, 2022 10:00am) https://events.umich.edu/event/91167 91167-21677027@events.umich.edu Event Begins: Friday, January 21, 2022 10:00am
Location: Off Campus Location
Organized By: Futures in Research, Science, Teaching - FIRST

If you would like to ask current biology grad students about what interviewing at different grad programs is like, or practice interviewing yourself, please stop by.

Zoom link: https://umich.zoom.us/j/99108550897

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Workshop / Seminar Tue, 18 Jan 2022 11:11:32 -0500 2022-01-21T10:00:00-05:00 2022-01-21T11:00:00-05:00 Off Campus Location Futures in Research, Science, Teaching - FIRST Workshop / Seminar FIRST Logo with the name made out of chromosomes separating during mitosis.
UROP Summer Fellowship Applications Open (January 22, 2022 9:00am) https://events.umich.edu/event/91078 91078-21676402@events.umich.edu Event Begins: Saturday, January 22, 2022 9:00am
Location: Off Campus Location
Organized By: UROP - Undergraduate Research Opportunity Program

U-M undergraduates interested in conducting research during the summer for a 10-week paid fellowship can apply to one of three available programs: Biomedical & Life Sciences, Engineering or Women and Gender. Previous research experience IS NOT required.

Applications are available at: https://myumi.ch/lxmbp

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Careers / Jobs Mon, 17 Jan 2022 09:34:51 -0500 2022-01-22T09:00:00-05:00 2022-01-22T23:00:00-05:00 Off Campus Location UROP - Undergraduate Research Opportunity Program Careers / Jobs Paid UROP Summer Fellowships