BE Seminar: "Reaction-Coupled Solid-State Nanopore Digital Counting: Towards Sensitive, Selective and Fast Nucleic Acid Testing" (Weihua Guan)
2021-04-08 15:00 - 16:00 (America/New_York)
This seminar will be held virtually on Zoom (details coming soon).
Due to their conceptual simplicity, the nanopore sensors have attracted intense research interest in electronic single molecule detection. While considerable success has been achieved, the solid-state nanopores still face three significant challenges, including repeatable nanopore size control, introduction sensing specificity, and prolonged sensor response time at low concentrations. In this talk, I will discuss a calibration-free solid-state nanopore counting method and two representative applications in nucleic acid testing. One is an isothermal amplification-coupled nanopore counting for malaria analysis. The other is the CRISPR-cas12a-coupled nanopore counting for HIV analysis. Finally, I will also discuss how we can develop a fully integrated ‘sample-to-result’ nucleic acid testing device using the solid-state counting strategy. I believe the reaction-coupled solid-state nanopore digital counting could open a new avenue towards compact, robust, low-cost electronic nucleic acid testing at the point of care.

CIS Seminar: "AI for Population Health: Melding Data and Algorithms on Networks"
2021-04-08 15:00 - 16:00 | Zoom – Email CIS for link, cherylh@cis.upenn.edu
As exemplified by the COVID-19 pandemic, our health and wellbeing depend on a difficult-to-measure web of societal factors and individual behaviors. My research aims to build AI which can impact such social challenges, advancing health and equity on a population level. This effort requires new algorithmic and data-driven paradigms which span the full process of gathering costly data, developing machine learning models to understand and predict interactions, and optimizing the use of limited resources in interventions. In response to these needs, I will present methodological developments at the intersection of machine learning, optimization, and social networks which are motivated by on-the-ground collaborations on HIV prevention, tuberculosis treatment, and the COVID-19 response. These projects have produced deployed applications and policy impact. For example, I will present the development of an AI-augmented intervention for HIV prevention among homeless youth. This system was evaluated in a field test enrolling over 700 youth and found to significantly reduce key risk behaviors for HIV.

GRASP On Robotics: “Perspectives on Machine Learning for Adaptive Robotic Systems”
2021-04-09 11:00 - 12:30 | https://upenn.zoom.us/j/96715197752
Abstract: Recent advances in machine learning are leading to new tools for designing intelligent robots: functions relied on to govern a robot’s behavior can be learned from a robot’s interaction with its environment rather than hand-designed by an engineer. Many machine learning methods assume little prior knowledge and are extremely flexible, they can model almost anything! But, this flexibility comes at a cost. The same algorithms are often notoriously data hungry and computationally expensive, two problems that can be debilitating for robotics. In this talk I’ll discuss how machine learning can be combined with prior knowledge and structure to build effective solutions to robotics problems. I’ll introduce an online learning perspective on robot adaptation that unifies well-known algorithms and suggests new approaches. I’ll discuss how structure and simulation can augment learning and how imperfect models, simple policies, and hierarchical abstractions can help to build adaptive, resilient systems. I will also show how we have applied some of these ideas to several robotics tasks that require impressive sensing, speed, and agility to complete.
Click here to join the Zoom Webinar

ODEI Spotlight: Career Tools Webinar Series: Navigating the Job Search & Workplace Authentically
2021-04-09 12:00 - 13:00
Friday, April 9th at 12pm
Register HERE
One’s identity is multi-faceted and complex, shaped by different affinities and experiences that impact the way we see (and are seen) and operate in the world. However, research shows that having to hide parts of your identity at work can be exhausting and mentally draining.
This panel will feature Penn alumni discussing strategies for both finding inclusive employers that welcome and value your identities and ways to effectively navigate the work environment as your authentic self in terms of cultural and socioeconomic backgrounds, sexual orientation, and lived experiences. Individuals who supervise others will also find the panel useful for tips on creating the most inclusive workplace culture possible.
Moderator: Malik Muhammad, Associate Director, University of Pennsylvania’s (Penn) LGBT Center.
Panelists:

Misha Chakrabarti is a speaker, podcaster, comedian, and coach.
Karen Lithgow innovates and transforms brands and businesses
Victor Anthony Scotti, Jr. is a DEI practitioner and Black student advocate.

In partnership with Career Services and Alumni Relations

Spring 2021 GRASP Seminar: “Propelling Robot Manipulation of Unknown Objects using Learned Object Centric Models”
2021-04-09 14:00 - 15:00 | Zoom
Abstract: There is a growing interest in using data-driven methods to scale up manipulation capabilities of robots for handling a large variety of objects. Many of these methods are oblivious to the notion of objects and they learn monolithic policies from the whole scene in image space. As a result, they don’t generalize well to different scenes, viewpoints, and lighting changes. In addition, these models cannot be combined with other components and constraints without re-training. In this talk, I will present our approach for learning object centric models trained on 3D depth data. I will show how these approaches are combined with each other to accomplish tasks on unseen objects and environments. In particular, I will cover our works on grasping and segmenting unknown objects, obstacle avoidance, and task planning for unknown object rearrangement task.
Click here to join the Zoom meeting

PICS: " Houdini Presentation"
2021-04-09 14:00 - 16:00 | Zoom – email kathom@seas.upenn.edu
Cinematic scientific visualization makes three dimensional scientific phenomena approachable for mass audiences by using the artistic language of film including elements like camera choreography, lighting design, comprehensive scenic environments, and more. Cinematic scientific visualizations are an engaging way for domain experts to communicate niche information with the public, to refute widely held misconceptions, and to inspire the scientists of the future. Science films that feature these visualizations are screened at science centers to millions of viewers over the span of 10+ years and bridge different languages and cultures. They are shared widely on social media, featured regularly in television programs, and contribute to the success of public lectures.
If you are a domain expert looking to share your data more widely, or a visualization designer who has focused on more analytical tools, what better way is there to get started with a Hollywood style than by using Hollywood tools? This workshop will introduce participants to Houdini, a visual effects software package that can generate cinematic-quality data visualizations with ease and efficiency. It is used and appreciated by most major animation and visual effects film studios for its procedural architecture, its modular design, and out-of-the-box rendering algorithms, all important features for ease-of-use in the field of data visualization. Houdini is a general-purpose image-making software that differs from most traditional scientific visualization tools in that it is optimized for look development and design functionality.
This session will consist of a presentation about using scientific data in Houdini, and a demonstration breakdown of a working Houdini scene file.

No registration is necessary.

PSOC Webinar: “Biophysical Regulation of Macrophages in Tissue Repair” (Wendy Liu)
2021-04-12 12:00 - 13:00
Physical Sciences in Oncology Center PSOC@Penn
Spring 2021 Webinar Series Mondays at 12:00 noon (EST)
For webinar links, please contact manu@seas.upenn.edu.

The Jack Keil Wolf Lecture: "Coordination of Distributed Energy Resources (DERs)"
2021-04-12 15:00 - 16:00 | Zoom – Email ESE for Link jbatter@seas.upenn.edu
DERs are small-scale energy resources that can generate electricity, such as roof-top solar PV, store electricity, such as Tesla’s Powerwall, or whose electricity consumption can be flexibly controlled, such as EV chargers, HVACs, water heaters, and large industrial fans. DERs are located behind the meters of electricity consumers, such as in homes, commercial building and EV charging stations. With few exceptions, DERs today are mostly uncoordinated, that is, they don’t operate together toward explicitly optimizing consumer or grid objectives. I will first talk about the benefits of coordinating DERs both behind-the-meter and across the meters of different electricity consumers, and the challenges of coordinating a large number of DERs owned by different entities with different objectives and privacy constraints. I will then describe a cloud-based coordination system we developed that can overcome these challenges and its first field deployment in a California dairy farm.
The talk is based on joint work with Kyle Anderson, Thomas Navidi and Professor Ram
Rajagopal’s group at Stanford.

CIS Diversity Summit
2021-04-12 16:00 - 18:00 | https://upenn.zoom.us/j/96715197752
Help make CIS a supportive and welcoming environment.
All students, faculty, staff and postdocs are invited.
Summit themes include increasing community in CIS; peer collaboration; how faculty can help; how to respond to microaggressions and implicit bias–both victims and bystanders; the value of a diverse TA force; productive TA-Student interaction.
Zoom link:
https://upenn.zoom.us/j/95364173714?pwd=[REDACTED]

ODEI Spotlight: CHOP Diversity Symposium, Striving for Equity in STEM
2021-04-13 10:00 - 11:00
“Gaslighting in the Academy: Actually Making Black Lives Matter”
Manu Platt, PhD
Professor, Biomedical Engineering Georgia Tech and Emory University
Date: April 13, 2021
Time: 10:00 – 11:00 am
BlueJeans Link: https://primetime.bluejeans.com/a2m/live-event/kaqbajsb
In honor of Diversity Month, we are pleased to host the first annual CHOP Diversity Symposium. This is a time for us to come together and reflect on the importance of diversity, and to highlight opportunities to make science more diverse, equitable, and accessible to all. This year’s theme is “Striving for Equity in STEM” and our inaugural speaker is Manu Platt, PhD. Integrated with his research program are his mentoring goals of changing the look of the next generation of scientists and engineers to include all colors, genders, and backgrounds. Dr. Platt will address systemic barriers impeding underrepresented minorities in STEM, and discuss methods to counteract the overt and implicit barriers contributing to this phenomenon.

MEAM Seminar: "Design, Fabrication, and Control of Biologically Inspired Soft Robots"
2021-04-13 10:30 - 12:00 | Zoom – Email MEAM for Link, peterlit@seas.upenn.edu
Robotics has the potential to address many of today’s pressing problems in fields ranging from healthcare to manufacturing to disaster relief. However, the traditional approaches used on the factory floor do not perform well in unstructured environments. The key to solving many of these challenges is to explore new, non-traditional designs. Fortunately, nature surrounds us with examples of novel ways to navigate and interact with the real world. Dr. Tolley’s Bioinspired Robotics and Design Lab seeks to borrow the key principles of operation from biological systems and apply them to robotic design. This talk will give an overview of recent projects in the lab that investigate the ways in which the use of non-rigid materials can help solve challenging problems in robotics. These projects seek to develop bioinspired systems capable of, for example, navigating the world by walking, digging, and swimming (inspired by animals like turtles, worms, and squid) and of interacting safely with humans and delicate objects.

Neuroengineering Seminar: "Advancing Deep Brain Stimulation Therapy in Movement Disorders: from surgical implantation to behavior-based responsive therapeutic stimulation" (Enrico Opri)
2021-04-13 16:00 - 17:00 | https://upenn.zoom.us/j/96715197752
Sponsored by the Center for Neuroengineering and Therapeutics, and the Departments of Neurosurgery and Bioengineering.
Join Zoom Meeting
https://pennmedicine.zoom.us/j/97483734781
Meeting ID: 974 8373 4781
Deep brain stimulation (DBS) has become standard therapy for medically refractory patients with Parkinson’s disease (PD), essential tremor (ET), and other neurological disorders. The two main challenges for DBS standard-of-care are rooted in the accurate positioning of the DBS leads during intraoperative implantation and the postoperative programming of the implanted DBS device, both needed to achieve the sought optimal therapeutic benefit. However, both processes rely on subjective patient exams, on expert neurophysiologists to optimize implant trajectory and programming, and on time-consuming trial-and-error approaches. Furthermore, existing commercially available stimulation approaches (continuous stimulation, also known as open-loop stimulation) lack integration with patient behavior and environmental factors. We sought to address these shortcomings in the ET population, by demonstrating the feasibility of on-demand responsive stimulation using only thalamocortical neuromarkers that modulate movement related-behavior. This led to the design and implementation of the first fully embedded closed-loop algorithm for chronic neurostimulators (CL-DBS) in humans affected by ET, which achieved an equally effective treatment compared to current DBS approaches while having a more efficient stimulation energy profile. Furthermore, CL-DBS demonstrated potential in decreasing DBS-related side effects (e.g. speech impairments). Additionally, the unique window provided by intraoperative acute recordings, allowed us to further our understanding of the thalamocortical network. We showed that there is significant cross-rhythm communication between thalamocortical regions and that changes in motor behavior correspond to changes in thalamocortical phase-amplitude coupling (PAC) profiles, demonstrating it is a crucial mechanism for gating motor behavior. We then sought to improve intraoperative DBS implantation for the PD population by leveraging a novel biomarker, DBS local evoked potential (DLEP), which strongly correlates with the location of the typical target-subregions of the nuclei of interest, the subthalamic nucleus (STN) and globus pallidus internus (GPi). Most importantly, the proposed methodology requires no patient interaction and could be leveraged for implementing an objective, real-time guided placement of the DBS lead, with a less time-consuming process and subjectivity compared to traditional mapping procedures.

CBE Seminar: "Robots That Eat, Breathe and Bleed"
2021-04-14 15:00 - 16:00 | Zoom – Email CBE for link
Abstract
Modern robots lack the multifunctional, interconnected chemical systems found in living organisms and, consequently, exhibit reduced efficiency and autonomy. At the same time, new advancements in chemistry are enabling synthetic materials with capabilities that surpass biological materials. This talk will discuss how advances in electrochemistry and soft materials can transform the way we build and use robots, with the ultimate goal of surpassing the capabilities of living organisms. Specifically, fundamental insights will be applied to improve the performance and capabilities of structural materials and energy storage in robots. The discussion on energy storage will cover materials and manufacturing techniques, funded by DARPA’s SHRIMP program, that triple the energy density of batteries for small scale robots, approaches that break the scaling laws of energy storage technologies by allowing robots to eat metal in their environment, and multifunctional synthetic vascular systems that increase the energy density of robots by up to 4x that of robots that only use lithium ion batteries. The talk will finish with a discussion on how old tools like self-assembly enable metals with the strength of titanium and density of water, and how new approaches to healing, through transport mediated in water, allow bone-inspired room-temperature healing of metals.

CIS Seminar: "Digital humans that move, interact, express, and feel, just like us!"
2021-04-14 15:00 - 16:00 | Zoom – Email CIS for link, cherylh@cis.upenn.edu
The creation of intelligent virtual agents (IVAs) or digital humans is vital for many virtual and augmented reality systems. As the world increasingly uses digital and virtual platforms for everyday communication and interactions, there is a heightened need to create human-like virtual avatars and agents endowed with social and emotional intelligence. Interactions between humans and virtual agents are being used in different areas including, VR, games and story-telling, computer-aided design, social robotics, and healthcare. Designing and building intelligent agents that can communicate and connect with people is necessary but not sufficient. Researchers must also consider how these IVAs will inspire trust and desire among humans. Knowing the perceived affective states and social-psychological constructs (such as behavior, emotions, psychology, motivations, and beliefs) of humans in such scenarios allows the agents to make more informed decisions and navigate and interact in a socially-intelligent manner.
When humans communicate with each other, they frequently use a combination of verbal communications, interpersonal relationships between the people involved, and non-verbal body expressions during communication to complement, contradict, substitute, or regulate what is being said. These signals are essential for understanding each other, particularly regarding expressing changing moods and affective states. In this talk, I will give an overview of our recent work on simulating intelligent, interactive, and immersive human-like agents who can also learn, understand and be sentient to the world around them using a combination of emotive gestures, gaits, and expressions. This problem arises in the context of human motion and behavior computation that takes environmental, sociological, and psychological factors into account. Finally, I will also talk about our many on-going projects which use our AI-driven IVAs, including intelligent digital humans for urban simulation, crowd simulation, mental health and therapy applications, and social robotics

ODEI Spotlight: Race, Solidarity, and Allyship
2021-04-14 17:30 - 19:00
Moderated by:
Malik Muhammad
Assoc. Director – LGBT Center
Panelists:
Dr. Valerie Dorsey Allen
Director – African American Resource Center
Elizabeth Cannon
Co-Founder – White Educators Committed to Anti-Racism & Equity

Zoom ID: 970 2429 7938

CBE PhD Dissertation Defense | A Computational Approach to the Study of Trauma
2021-04-15 10:00 - 11:30 | Zoom – Email CBE for link
Abstract:
Trauma with hypovolemic shock is an extreme pathological state that challenges the body to maintain blood pressure and oxygenation in the face of hemorrhagic blood loss. In conjunction with surgical actions and transfusion therapy, survival requires the patient’s blood to maintain hemostasis to stop bleeding. The physics of the problem are multiscale: (1) the systemic circulation sets the global blood pressure in response to blood loss and resuscitation therapy, (2) local tissue perfusion is altered by localized vasoregulatory mechanisms and bleeding, and (3) altered blood and vessel biology resulting from the trauma as well as local hemodynamics control the assembly of clotting components at the site of injury. Building upon ongoing modeling efforts to simulate arterial or venous thrombosis in a diseased vasculature, we have developed models of trauma (both multiscale and machine-learning based) to understand patient risk and predict response. Key results were: (1) the upstream vascular network rapidly depressurizes to reduce blood loss, (2) wall shear rates at the hemorrhaging wound exit are sufficiently high (~10,000 s-1) to drive von Willebrand Factor unfolding, (3) full coagulopathy results in >2L blood loss in 2 hours for severing all vessels of 0.13 to 0.005 mm diameter within the bifurcating network, whereas full hemostasis limits blood loss to <100 mL within 2 min, and (4) hemodilution from transcapillary refill increases blood loss and could be implicated in trauma induced coagulopathy. Machine learning based methods were also implemented to understand trauma patient outcomes. A 400-estimator gradient boosting classifier was trained to predict survival probability and the model is able to predict a survival probability for any trauma patient and accurately distinguish between a deceased and survived patient in 92.4% of all cases. Partial dependence curves (Psurvival vs. feature value) obtained from the trained model revealed the global importance of Glasgow coma score, age, and systolic blood pressure while pulse rate, respiratory rate, temperature, oxygen saturation, and gender had more subtle single variable influences. Shapley values, which measure the relative contribution of each of the 8 features to individual patient risk, were computed for several patients and quantified patient-specific warning signs.

MSE Doctoral Student Seminar
2021-04-15 10:45 - 11:45

BE Seminar: "Understanding Spatiotemporal Cell Reprogramming for Precision Medicine" (Xiling Shen)
2021-04-15 15:00 - 16:00
This seminar will be held virtually on zoom (check email for link or contact ksas@seas.upenn.edu).
Bodily cells undergo transformations in space and time during development, disease progression, and therapeutic treatment. A holistic approach that combines engineering tools, patient-derived models, and analytical methods is needed to map cellular reprogramming and expose new therapeutic opportunities. The talk will cover our effort across the entire spectrum from bench to bedside, including organogenesis during embryonic development, epigenetic and metabolic reprogramming of cancer metastasis and COVID-19 patients, and organoid technology to guide precision- and immune-oncology.

CIS Seminar: "Exploiting latent structure and bisimulation metrics for better generalization in reinforcement learning"
2021-04-15 15:00 - 16:00 | Zoom – Email CIS for link, cherylh@cis.upenn.edu
The advent of deep learning has shepherded unprecedented progress in various fields of machine learning. Despite recent advances in deep reinforcement learning (RL) algorithms, however, there is no method today that exhibits anywhere near the generalization that we have seen in computer vision and NLP. Indeed, one might ask whether deep RL algorithms are even capable of the kind of generalization that is needed for open-world environments. This challenge is fundamental and will not be solved with incremental algorithmic advances.
In this talk, we propose to incorporate different assumptions that better reflect the real world and allow the design of novel algorithms with theoretical guarantees to address this fundamental problem. We first present how state abstractions can accelerate reinforcement learning from rich observations, such as images, without relying either on domain knowledge or pixel-reconstruction. Our goal is to learn state abstractions that both provide for effective downstream control and invariance to task-irrelevant details. We use bisimulation metrics to quantify behavioral similarity between states, and learn robust latent representations which encode only the task-relevant information from observations. We provide theoretical guarantees for the learned approximate abstraction and extend this notion to families of tasks with varying dynamics.

GRASP On Robotics: “Learning and Games in Self-Driving”
2021-04-16 11:00 - 12:30
Abstract: In this talk, I’ll explore the power of a game-theoretic viewpoint in self-driving and in machine learning. We begin by considering the application of machine learning to Aurora’s advanced self-driving system in both perception and decision making. We discuss complexities that arise from multi-actor interaction.
We then explore the, perhaps surprising, role a game-theoretic view can take in developing algorithms for learning to make decisions. In particular, we review a “no-regret” game-theoretic perspective on model-based RL, Approximate Policy Iteration, and Inverse Optimal Control.
Click here to join the Zoom Webinar

ODEI Spotlight: Blindspot: Hidden Biases of Good People
2021-04-16 12:00 - 13:00
The purpose of the seminar, Blindspot: Hidden Biases of Good People, is to reveal the surprising and even perplexing ways in which we make errors in assessing and evaluating others when we recruit and hire, onboard and promote, lead teams, undertake succession planning, and work on behalf of our clients or the public we serve. It is Professor Banaji’s belief that people intend well and that the inconsistency we see, between values and behavior, comes from a lack of awareness. But because implicit bias is pervasive, we must rely on scientific evidence to “outsmart” our minds. If we do so, we will be more likely to reach the life goals we have chosen for ourselves and to serve better the organizations for which we work.

The Benjamin and Anne A. Pinkel Endowed Lecture Fund was established though a generous gift from Sheila Pinkel on behalf of the estate of her parents, Benjamin and Anne A. Pinkel, and serves as a memorial tribute to the lives of her parents. Benjamin Pinkel, who received a BSE in Electrical Engineering from the University of Pennsylvania in 1930, was actively interested in the philosophy of the mind and published a monograph on the subject, Consciousness, Matter, and Energy: The Emergence of Mind in Nature, in 1992, the objective of which is a “re-examination of the mind-body problem in the light of…new scientific information.” The lecture series is intended to advance the discussion and rigorous study of the deep questions which engaged Dr. Pinkel’s investigations.

http://web.sas.upenn.edu/pinkel-lectures/current
Click here to register!

ESE Ph.D. Thesis Defense: “The Development of A Fingertip Implantable MEMS Tactile Sensing System”
2021-04-16 12:00 - 14:00 | Zoom – email dulin@seas.upenn.edu for link
Abstract: This thesis explores the development of a fingertip implantable MEMS tactile sensing system to provide tactile sensing capabilities for paralyzed people using a brain machine interface (BMI) technology. With the BMI-controlled stimulation, paralyzed people are able to restore hand movement with their native hands without sensation. However, sensory feedback for these BMI-controlled stimulators is still missing. To overcome the barrier, development of a tactile sensing system is necessary. In previous studies, multiple approaches have been exploited to realize fingertip tactile recognition for wearable electronics, prosthetics, and robotics. Compared with these existing tactile sensors with wearable devices or robotic arms, we are interested in combining tactile sensing with implantable MEMS technologies. In this dissertation, we build an implantable tactile sensing system with wireless power and signal transmission capabilities for somatosensory feedback of BMI systems.
Toward these goals, a fused silica package with good hermeticity to moisture, biocompatibility, CMOS compatibility, as well as multiple feed-throughs for electronic access was developed and characterized. A localized fusion bonding technology by using CO2 laser-assisted machining was proposed to achieve simultaneous bonding and dicing of fused silica wafer stacks.
To demonstrate an implantable tactile sensor, a capacitive force-sensing technology based on the packaging technology was developed to satisfy hermetic and biocompatible requirements for implantation applications. The performance of this tactile sensor is investigated with quantitative static and dynamic loading measurements. In addition, both in vitro study with the sensor embedded under skin-phantom and implantation in a monkey hand are examined.
To further develop an implantable tactile sensing system with wireless communication capability, a multilayer fused silica structure incorporating a capacitive force sensor, an ASIC for wireless power and data communication, and the hermetic package technology for encapsulating the electronics is built. The development of an antenna coil integrated with the system was presented and the fabrication process of the system is discussed. To characterize the tactile sensing system, a customized experimental setup is employed and static loading measurement with dynamic loading analyzer is performed verifying that both of the pressure sensing and wireless transmission of the system are functional. This wafer-level technology will be very useful for other implantable pressure sensing and MOEMS applications.

Advisor: Mark G. Allen, Alfred Fitler Moore Professor of Electrical and Systems Engineering, University of Pennsylvania
Dissertation Committee:
Chair: Jan Van der Spiegel, Professor of Electrical and Systems Engineering, University of Pennsylvania
Member: Firooz Aflatouni, Associate Professor of Electrical and Systems Engineering, University of Pennsylvania
Member: Igor Bargatin, Associate Professor of Mechanical Engineering and Applied Mechanics, University of Pennsylvania
Member: Troy Olsson, Assistant Professor of Electrical and Systems Engineering, University of Pennsylvania

BE Doctoral Dissertation: "Silver sulfide nanoparticles for breast cancer imaging with dual energy mammography and other modalities"
2021-04-16 13:30 - 15:30 | https://upenn.zoom.us/j/96715197752
The Department of Bioengineering at the University of Pennsylvania and Dr. David Cormode are pleased to announce the Doctoral Dissertation Defense of Jessica Hsu.

Title: Silver sulfide nanoparticles for breast cancer imaging with dual energy mammography and other modalities

Date: April 16, 2021
Time: 1:30 pm (Eastern Time)

Please join via the zoom link below:
https://upenn.zoom.us/j/92408719412?pwd=[REDACTED]

The public is welcome to attend.

PICS Colloquium: "Modeling and simulations of protein conformational changes and virus entry"
2021-04-16 14:00 - 15:00 | Zoom – email kathom@seas.upenn.edu
Abstract: Virus infections remain major threats to human health worldwide. Viruses are intracellular parasites, and must enter host cells and deliver their genetic material to initiate infection. Virus entry is a highly complex process that may involve hundreds of trans-membrane and peripheral membrane proteins. This highly complex process is dictated by various events, such as virus motion, membrane deformation and merging as well as molecular scale protein-protein, protein- lipid interactions and drastic protein conformational changes, occurring at multiple stages and at multiple length and time scales. The question of how these biochemical and biomechanical events work together culminating in productive entry is not well understood but fundamentally important for development of vaccine candidates and identification of new targets for inhibitor design. Modeling and simulations of virus entry at different scales can provide mechanistic insights into this complex process. In this talk, we will present our recent simulation research on membrane deformation and protein conformational changes for virus entry. A mesoscale stochanstic membrane model has been implemented to investigate the membrane deformations during the entry process. We will also discuss our development of the coase-grained force field to capture the protein conforamtional changes, and the on-going work of machaine-learning facilitated sampling of protein structures.

ESE Thesis Defense: "A Microwell-Based Impedance Sensor in Microneedle Shape for Cytokine Detection"
2021-04-16 14:00 - 16:00 | Zoom – email naixins@seas.upenn.edu for link
Monitoring cytokine profiles plays a crucial role in predictive and early disease diagnosis, as well as in research in many biological fields, thus multiple approaches have been investigated. Despite the promise of these techniques, many still require specialized instrumentation or have not been shown in real-time applications, impeding their clinical adoption as point-of-care systems. Impedance-based protein detection sensors for point-of-care diagnostics require quantitative specificity as well as rapid or real-time operation. Furthermore, microfabrication of these sensors can lead to form factors suitable for in vivo operation.
Herein, we present microfabricated needle-shaped microwell impedance sensors for rapid sample-to-answer, label-free detection of cytokines. The sensor utilizes a micro-well array configuration at the microneedle tip to enable label-free detection while simultaneously maintaining the capability of high sensitivity detection, despite the high salt concentration of complex biological fluids. The microneedle form factor allows the sensors to be utilized in transcutaneous or transvascular sensing applications. In vitro experimental characterization confirmed sensor specificity and sensitivity to multiple proteins of interest. Mechanical characterization demonstrated sufficient microneedle robustness for transcutaneous insertion, as well as preserved sensor function post-insertion. We further utilized these sensors to carry out real-time in vivo quantification of human interleukin 8 (hIL8) concentration levels in the blood of transgenic mice that endogenously express hIL8. To assess sensor functionality, hIL8 concentration levels in serum samples from the same mice were quantified by ELISA. Excellent agreement between real-time in vivo sensor readouts in blood and subsequent ELISA serum assays was observed over multiple transgenic mice expressing hIL8 concentrations from 62 pg/mL to 539 ng/mL. Further, to reduce large mechanical mismatch between fused silica microneedle and surrounding soft tissue thus explore potential chronic applications, materials with lower Young’s modulus (e.g., Parylene materials) have been employed in the microneedle fabrication. Moreover, the relative sizes of microwell array and needle footprint offer the potential for multiple bioassay sensors on a single microneedle by functionalizing the surface of each sensor with distinct antibodies, forming a full sensor platform. Such multiplexed sensors could allow the real-time assessment of more complex diseases or conditions in vivo.
Advisor: Dr. Mark G. Allen, Alfred Fitler Moore Professor, Department of Electrical and Systems Engineering
Dissertation Committee:
Chair:
Dr. David Issadore, Associate Professor, Department of Bioengineering, University of Pennsylvania
Members:
Dr. A.T. Charlie Johnson, Rebecca W. Bushnell Professor, Department of Electrical and Systems Engineering, University of Pennsylvania
Dr. Flavia Vitale, Assistant Professor, Department of Bioengineering, University of Pennsylvania

MSE Senior Design Presentations
2021-04-16 14:30 - 17:00

CBE PhD Dissertation Defense | A Scalable, Point-of-Care Microfluidic Approach for Assessing Thrombosis and Hemostasis
2021-04-19 10:00 - 11:30 | Zoom – Email CBE for link
Abstract:
Coagulation testing is an important diagnostic tool for the detection of excessive bleeding risk or obstructive clot formation (thrombosis), using blood samples from patients. Microfluidic flow devices have been well established to provide insights on the impacts of shear rate, drug action, and disease state on coagulation and platelet biology. The bulk of the microfluidic devices and assays used in the past have relied upon manufactured using polydimethyl siloxane (PDMS), a material and construction method not well suited to use in a clinical setting. This thesis describes the design and testing of a single-use, storage stable evolution of previous PDMS microfluidic designs, manufactured via injection molding and pressure-sensitive adhesive bonding. Using this device, we demonstrate the ability to make consistent and repeatable measurements of platelet and fibrin fluorescence intensity in a clot forming under venous shear rate, using a benchtop LED microscope and physiologically consistent constant-pressure driven flow. We also demonstrate the ability to detect a strong, dose-dependent inhibition in the fibrin fluorescence intensity signal to in vitro spiking of direct oral anticoagulants (DOACs). Further, we showed the ability to reverse this inhibition, through small quantities of reversal agents to the anticoagulant drugs. In addition, the presence of the direct oral anticoagulants in the blood of patients on the medications was clearly detected as well. By comparing the response of a DOAC patient’s blood to reversal agent with the dose response established via spiking of healthy blood, quantitation of the current level of DOAC present in the patient’s blood was demonstrated as well. The field of coagulation testing has lacked a fast, reliable means of accurately assessing patient anticoagulation status. Taken together, the ability to identify the presence of and quantitate the amount of DOAC present in a patient’s blood using a single-use microfluidic chip approach as described in this thesis represents a potential promising new direction for coagulation testing at the bed-side.

BE Doctoral Dissertation: "Development of Nanoparticle-based Contrast Agents for Applications with Conventional and Photon-counting CT Imaging"
2021-04-19 13:30 - 15:30 | https://upenn.zoom.us/j/96715197752
The Department of Bioengineering at the University of Pennsylvania and Dr. David Cormode are pleased to announce the Doctoral Dissertation Defense of Johoon Kim.

Title: Development of nanoparticle-based contrast agents for applications with conventional and photon-counting CT imaging
Date/time: April 19, 2021
Time: 1:30pm

You are invited to attend via zoom:

Zoom link: https://upenn.zoom.us/j/94279939416

MEAM Seminar: "Micromechanics of Near-ideal Polymer Networks"
2021-04-20 10:30 - 12:00 | Zoom – Email MEAM for Link, peterlit@seas.upenn.edu
Understanding the relationships between the structure of polymer networks and their mechanical properties remains a long-standing challenge in polymer physics. In recent years, a new paradigm for network formation has emerged, whereby near-ideal hydrogels are produced by the cross-coupling of branched macromolecules with well-defined chain length. Such near-ideal networks constitute an excellent model system to revisit this question, as well as a promising platform for the design of new materials with tuneable properties. In this work, we systematically investigate the relative contributions of various network parameters (chain length, crosslink coordination, second-order loops) to the elasticity of near-ideal polymer networks using a computational random network model. Numerical results are compared to classical estimates of rubber elasticity theory. Our results highlight the role of the chain pre-stretch on the mechanical response, as well as the importance of topological defects on the elastic properties. We also compare our results to experimental data for near-ideal tetra-arm PEG hydrogels.

BE Dissertation: "Large Scale Integration of Microengineered Tissue Models for High-content, High-throughput analysis of Complex Human Physiological Systems"
2021-04-20 14:00 - 15:00 | https://upenn.zoom.us/j/96715197752
The Department of Bioengineering at the University of Pennsylvania and Dr. Dan Huh are pleased to announce the Doctoral Dissertation Defense of Andrei Georgescu.

Title: Large scale integration of microengineered tissue models for high-content, high-throughput analysis of complex human physiological systems.

Date: Tuesday April 20, 2021
Time: 2:00pm

You are invited to attend via zoom:

Zoom link: https://upenn.zoom.us/j/93808399625?pwd=[REDACTED]
