Computations and Modeling

Researchers from Sechenov University and University of Pittsburgh discovered that the resistance of innate immune cells, macrophages, to ferroptosis – a type of programmed cell death – depends on the type of their activation. It turned out that cells helping tissues to recover from inflammation were more vulnerable. The researchers identified the mechanisms underlying the cells’ resistance and explained how this research would help regulate inflammation in a paper published in Nature Chemical Biology.  McGowan Institute for Regenerative Medicine affiliated faculty members Valerian Kagan, PhD, DSc, Professor and Vice-Chairman in the Department of Environmental and Occupational Health as well as a Professor in the Department of Pharmacology and Chemical Biology, the Department of Radiation Oncology, and the Department of Chemistry at the University of Pittsburgh, and Ivet Bahar, PhD, Distinguished Professor, the John K. Vries Chair, and the Founding Chair in the Department of Computational & Systems Biology at the University of Pittsburgh’s School of Medicine, are co-authors on the study.

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In the Mechanics of Morphogenesis Lab, team members carry out interdisciplinary research at the interface of physics, engineering, mathematics, and developmental biology.  What you cannot follow in real time in the body, these researchers follow with sophisticated micromechanical test devices and imaging systems.  Once this data is gathered, they then create elaborate computer modeling simulations which can be easily and frequently changed to produce knowledge out of the reach of mathematical analysis or natural experimentation alone.

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McGowan Institute for Regenerative Medicine affiliated faculty member Thomas Rando, MD, PhD, is the co-founder and chair of the board of directors of Fountain Therapeutics.  At Fountain Therapeutics, the research team has combined the expertise of leaders in aging research and computation to build a pipeline of therapeutics aimed at reversing cellular aging. The company’s mission is to decouple aging from disease and significantly extend human health span.

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When a person contracts a respiratory viral infection like COVID-19 or influenza, the immune system responds in a myriad of ways to eliminate the virus. Respiratory viral infections are so dangerous, however, because excessive immune responses may cause extreme lung inflammation. However, new modeling research may help doctors better predict and treat patients who are most at risk to that extreme response.

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Led by Shandong Wu, PhD, associate professor in the Department of Radiology at Pitt, and supported by McGowan Institute for Regenerative Medicine David Vorp, PhD, associate dean for research and John A. Swanson Professor of Bioengineering, the “Pittsburgh Center for Artificial Intelligence Innovation in Medical Imaging” project won a University of Pittsburgh Scaling Grant.  The Scaling Grant provide $400,000 over two years to support detailed project planning, gathering proof-of-concept results, and reduction of technical risk for teams pursuing an identified large extramural funding opportunity. The Scaling Grants are part of the University’s Pitt Momentum Funds, which offer funding across multiple stages of large, ambitious projects.

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The twisting and bending capabilities of the human muscle system enable a varied and dynamic range of motion, from walking and running to reaching and grasping. Replicating something as seemingly simple as waving a hand in a robot, however, requires a complex series of motors, pumps, actuators and algorithms. Researchers at the University of Pittsburgh and Harvard University have recently designed a polymer known as a liquid crystal elastomer (LCE) that can be “programmed” to both twist and bend in the presence of light.

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The paper published by Steven Abramowitch, Associate Professor of Bioengineering at the University of Pittsburgh, and McGowan Institute for Regenerative Medicine affiliated faculty member Pamela Moalli, MD, PhD, Associate Professor, Department of Obstetrics, Gynecology & Reproductive Sciences, Division of Urogynecology & Pelvic Reconstructive Surgery, Magee-Womens Hospital of UPMC, University of Pittsburgh, was recently recognized by the editors of the Journal of Biomechanical ok work. The article details complications associated with mechanical loads on synthetic mesh used in pelvic organ prolapse and will be listed as an Editors’ Choice paper in JBME’s Annual Special Issue February 2020.

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Advances in biomimicry – creating biological responses within non-biological substances – will enable synthetic materials to behave in ways that were typically only found in Nature. Light provides an especially effective tool for triggering life-like, dynamic responses within a range of materials. The problem, however, is that the applied light is typically dispersed throughout the sample and thus, it is difficult to localize the bio-inspired behavior to the desired, specific portions of the material.

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The internet of things (IoT) widely spans from the smart speakers and Wi-Fi-connected home appliances to manufacturing machines that use connected sensors to time tasks on an assembly line, warehouses that rely on automation to manage inventory, and surgeons who can perform extremely precise surgeries with robots. But for these applications, timing is everything: a lagging connection could have disastrous consequences.

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Break any bone in the human body and the body can repair the tissue and fix the damage. Yet tooth enamel — the strongest tissue in the human body — cannot repair itself. Still, our teeth last a lifetime.

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Mantle cell lymphoma is an aggressive subtype of non-Hodgkin’s lymphoma that claims the lives of tens of thousands of people every year. Mantle cell lymphoma is considered incurable, even though new treatments have yielded promising results.

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Study: A bioengineering group from the University of Pittsburgh Swanson School of Engineering is bringing the worlds of computational modeling and experimentation closer together by developing a methodology to help analyze the wealth of imaging data provided by advancements in imaging tools and automated microscopes.

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The University of Pittsburgh School of Medicine and Carnegie Mellon University each have been awarded four-year contracts totaling more than $7.2 million from the U.S. Department of Defense to create an autonomous trauma care system that fits in a backpack and can treat and stabilize soldiers injured in remote locations.

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Collaboration and competition are basic instincts among biological species, from the simplest single-celled organisms to reptiles, fish and primates, as well as humans. This dynamic behavior – the result of millions of years of evolution – is difficult to replicate in synthetic systems. However, chemical engineers at the University of Pittsburgh Swanson School of Engineering have recreated these responses in an environment of microscopic particles, sheets, and catalysts, effectively mimicking responses of feeding, fighting, and fleeing.

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McGowan Institute for Regenerative Medicine affiliated faculty member Anna Balazs, PhD, has been at the Swanson School of Engineering since 1987 and is now a Distinguished Professor in chemical and petroleum engineering.  As reported by Amerigo Allegretto for Pittwire, Dr. Balazs is working to transform the future through her research of soft robotics, which could have revolutionary applications across a variety of fields — from surgery in hospitals to rehabilitating patients to providing safer industrial manufacturing conditions.

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The “magic carpet” featured in tales from “One Thousand and One Nights” to Disney’s “Aladdin” captures the imagination not only because it can fly, but because it can also wave, flap, and alter its shape to serve its riders. With that inspiration, and the assistance of catalytic chemical reactions in solutions, a team from the University of Pittsburgh’s Swanson School of Engineering has designed a two-dimensional, shape-changing sheet that moves autonomously in a reactant-filled fluid.

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The University of Pittsburgh research team of

• Piervincenzo Rizzo, PhD, associate professor of civil and environmental engineering,
• Samuel Dickerson, PhD, assistant professor of electrical and computer engineering, and
• McGowan Institute for Regenerative Medicine affiliated faculty member Ian Conner, MD, PhD, assistant professor of ophthalmology and bioengineering,

recently received funding via a $360,000 grant from the National Science Foundation.  Dr. Rizzo and his team are currently measuring the internal pressure of objects, such as a piece of steel girder and a tennis ball, with the end goal of calculating corrosive deterioration in pipelines in the natural gas, hazardous liquid and liquefied natural gas plant industries.  Other applications being researched for this technology include, most notably, for measuring and monitoring eye pressure in glaucoma patients.

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McGowan Institute for Regenerative Medicine affiliated faculty member Shilpa Sant, PhD, Assistant Professor of Pharmaceutical Sciences, has received a 7-year R37 MERIT Award from the National Cancer Institute (NCI), NIH, for her project entitled, “Three-dimensional organoid models to study breast cancer progression.” This grant is funded by the NCI under the Cancer Tissue Engineering Collaborative (TEC) Research Program that aims to support the development and characterization of state-of-the-art biomimetic tissue-engineered technologies for cancer research. The total funding for the first 5 years is $2.7 million.

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Buprenorphine (BUP) is approved for the treatment of opioid addiction. The current dosing regimen of BUP in pregnant women is based on recommendations designed for non-pregnant adults, but physiological changes during pregnancy may alter BUP exposure and efficacy.

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Embedding a decision support tool in the hospital electronic health record increases detection of acute kidney injury, reducing its severity, and improving survival, according to new research from the University of Pittsburgh and UPMC.

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The National Institutes of Health (NIH) has awarded a $1.2 million grant to a multi-institutional project led by the University of Pittsburgh to engineer a 3-dimensional joint-on-a-chip called the “microJoint,” to replicate a human joint on a small scale. The microJoint will be used to study and test drugs for the treatment of arthritic joint diseases. McGowan Institute for Regenerative Medicine associate director Rocky Tuan, PhD, is the principal investigator of the award.

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Molecular chelating agents are used in many areas ranging from laundry detergents to paper pulp processing to precious metal refining. However, some chelating agents, especially the most effective ones, do not degrade in nature and may pollute the environment. With support from the National Science Foundation (NSF), researchers at the University of Pittsburgh Swanson School of Engineering are developing machine learning procedures to discover new chelating agents that are both effective and degradable.

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“When there are one or two bacteria, they behave in a certain way,” said McGowan Institute for Regenerative Medicine affiliated faculty member Anna Balazs, PhD, Distinguished Professor of Chemical Engineering and the John A. Swanson Chair of Engineering at the University of Pittsburgh’s Swanson School of Engineering. “But suddenly, when there is a critical threshold of bacteria, the bacteria can sense this increase in population and they dramatically change their behavior.”

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McGowan Institute for Regenerative Medicine affiliated faculty members at the University of Pittsburgh have been awarded grants from the National Science Foundation (NSF) and the National Institutes of Health (NIH) to study diverse aspects of how the brain works.

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From the smallest cell to humans, most organisms can sense their local population density and change behavior in crowded environments. For bacteria and social insects, this behavior is referred to as “quorum sensing.” Researchers at the University of Pittsburgh’s Swanson School of Engineering have utilized computational modeling to mimic such quorum sensing behavior in synthetic materials, which could lead to devices with the ability for self-recognition and self-regulation.

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The National Science Foundation recently awarded a 3-year, $300K grant entitled, “SusChEM: machine learning blueprints for greener chelants.”  McGowan Institute for Regenerative Medicine affiliated faculty member Eric Beckman, PhD, Bevier Professor of Engineering in the Chemical Engineering Department at the University of Pittsburgh and a Co-Director of the Mascaro Center for Sustainable Innovation, is the project co-principal investigator along with principal investigator John Keith, PhD, R.K. Mellon Faculty Fellow in Energy, Department of Chemical Engineering.  The award begins August 1, 2017, and extends through July 31, 2020.

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McGowan Institute for Regenerative Medicine Director William Wagner, PhD, Professor of Surgery, Bioengineering and Chemical Engineering at the University of Pittsburgh, Chairman of the Tissue Engineering and Regenerative Medicine International Society (TERMIS) – Americas, Deputy Director of the NSF Engineering Research Center on Revolutionizing Metallic Biomaterials, and Chief Scientific Officer of the Armed Forces Institute of Regenerative Medicine, was a member of the keynote panel of the recently held RAPID + TCT, North America’s preeminent event for discovery, innovation, and networking in 3D manufacturing.

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The U.S. Department of Defense recently announced the awarding of their 2017 large, multi-university grants in their MURI program.  One of the 23 awards will go to a team of researchers led by McGowan Institute for Regenerative Medicine affiliated faculty member Anna Balazs, PhD, Distinguished Professor of Chemical Engineering and the Robert v. d. Luft Professor, Department of Chemical & Petroleum Engineering, University of Pittsburgh.  Dr. Balazs will serve as the PI on the project entitled “Adaptive Self‐Assembled Systems:  Exploiting Multifunctionality for Bottom‐up Large Scale Engineering” with the team spanning the University of Pittsburgh, Harvard, Northwestern, and the University of Illinois.  The award is for 5 years at $1.5 million per year.

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Capitalizing on previous studies in self-powered chemo-mechanical movement, researchers at the University of Pittsburgh’s Swanson School of Engineering and Penn State University’s Department of Chemistry have developed a novel method of transporting particles that utilizes chemical reactions to drive fluid flow within microfluidic devices. Their research, “Harnessing catalytic pumps for directional delivery of microparticles in microchambers,” was published recently in the journal, Nature Communications.

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The work of McGowan Institute for Regenerative Medicine affiliated faculty members Ruben Zamora, PhD, Research Associate Professor at the University of Pittsburgh in the Department of Surgery, and Yoram Vodovotz, PhD, Professor in the Department of Surgery with secondary appointments in the Department of Computational & Systems Biology, the Department of Bioengineering, the Department of Immunology, the Department of Communication Science and Disorders (of the School of Health and Rehabilitation Science), and the Clinical and Translational Science Institute, and also the Director of the Center for Inflammation and Regenerative Modeling at the McGowan Institute, is featured in the November 2016 issue of the publication, Molecular Medicine.

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For as long as scientists have been listening in on the activity of the brain, they have been trying to understand the source of its noisy, apparently random, activity. In the past 20 years, “balanced network theory” has emerged to explain this apparent randomness through a balance of excitation and inhibition in recurrently coupled networks of neurons. A team of scientists has extended the balanced model to provide deep and testable predictions linking brain circuits to brain activity.

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Visual hallucinations … everyone has heard of them, and many people have experienced the sensation of “seeing” something that isn’t there. But studying the phenomenon of hallucinations is difficult: they are irregular, transitory, and highly personal—only the person experiencing the hallucination knows what he or she is seeing, and representations of what’s being seen are limited to verbal descriptions or drawings.

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As additive manufacturing, or 3D printing, continues to advance in industry and academia, knowledge gaps can appear as researchers push the technology to new limits. To solve some of industry’s most difficult additive manufacturing problems, Oberg Industries and the University of Pittsburgh’s Swanson School of Engineering have partnered to combine Oberg expertise in manufacturing complex tooling and precision machined or stamped metal components with Pitt’s ANSYS Additive Manufacturing Research Laboratory (AMRL).  McGowan Institute for Regenerative Medicine faculty member David Vorp, PhD, Associate Dean for Research, Swanson School of Engineering, William Kepler Whiteford Professor of Bioengineering, Director of the Center for Vascular Remodeling and Regeneration, Co-Director of the Center for Medical Innovation, and Director of the Vascular Bioengineering Laboratory, is a member of the Pitt team.

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The National Heart, Lung, and Blood Institute of the National Institutes of Health has awarded McGowan Institute for Regenerative Medicine affiliated faculty member Robert Parker, PhD, Professor in the University of Pittsburgh’s Department of Chemical and Petroleum Engineering, member of the Molecular Therapeutics/Drug Discovery Program at the University of Pittsburgh Cancer Institute, and a member of the Clinical Research, Investigation, and Systems Modeling of Acute Illness (CRISMA) Center in the Department of Critical Care Medicine at the University of Pittsburgh, and, secondary Chemical and Petroleum Engineering faculty member Timothy Corcoran, PhD, a U01 Award.  The Award work is entitled “Building Multilevel Models of Therapeutic Response in the Lungs.”  The total amount funded will be $1.7M.

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The potential to develop “materials that compute” has taken another leap at the University of Pittsburgh’s Swanson School of Engineering, where researchers for the first time have demonstrated that the material can be designed to recognize simple patterns. This responsive, hybrid material, powered by its own chemical reactions, could one day be integrated into clothing and used to monitor the human body or developed as a skin for “squishy” robots.

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McGowan Institute for Regenerative Medicine Associate Director Rocky Tuan, PhD, has received a research grant from the Center for the Advancement of Science in Space (CASIS) to continue his work on a 3D microphysiological system (MPS) to be conducted on board the International Space Station (ISS) to evaluate the accelerated aging and degeneration process of bones that occurs in space.

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Researchers at the University of Pittsburgh Cancer Institute (UPCI) and materials and biomedical engineers at Carnegie Mellon University (CMU) including McGowan Institute for Regenerative Medicine affiliated faculty member Adam Feinberg, PhD, associate professor in CMU’s departments of Materials Science and Engineering and Biomedical Engineering, will address the overdiagnosis and overtreatment of a non-invasive precancerous breast tumor by creating the first-ever 3D bioprinted breast ductal structure to identify markers for low-risk premalignant disease.

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A novel investigation of how enzymatic reactions can direct the motion and organization of microcapsules may point toward a new theory of how protocells – the earliest biological cells – could have organized into colonies and thus, could have ultimately formed larger, differentiated structures.

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At the University of Pittsburgh, Yoram Vodovotz, PhD, is a professor in the Department of Surgery with secondary appointments in the Department of Computational & Systems Biology, the Department of Bioengineering, the Department of Immunology, the Department of Communication Science and Disorders (of the School of Health and Rehabilitation Science), and the Clinical and Translational Science Institute. He also is the director of the Center for Inflammation and Regenerative Modeling at the McGowan Institute for Regenerative Medicine.  In this latter role, his research interests, carried out in the context of an interdisciplinary research team, include systems biology and mathematical modeling of inflammation and wound healing in various disease states, especially infection, trauma/hemorrhage, wound healing, and liver failure, as well as the application of these computational approaches (i.e. in silico) to regenerative medicine, biomarker discovery, and rational drug/device design.  In silico study in medicine is thought to have the potential to speed the rate of discovery while reducing the need for expensive lab work and clinical trials.

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Combining photo-responsive fibers with thermo-responsive gels, researchers at the University of Pittsburgh’s Swanson School of Engineering and Clemson University have modeled a new hybrid material that could reconfigure itself multiple times into different shapes when exposed to light and heat, allowing for the creation of devices that not only adapt to their environment, but also display distinctly different behavior in the presence of different stimuli.

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