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Computer scientist researches interpretable machine learning, develops AI to explain its discoveries

Artificial intelligence helps scientists make discoveries, but not everyone can understand how it reaches its conclusions. One UMaine computer scientist is developing deep neural networks that explain their findings in ways users can comprehend, applying his work to biology, medicine and other fields.

Interpretable machine learning, or AI that creates explanations for the findings it reaches, defines the focus of Chaofan Chen’s research. The assistant professor of computer science says interpretable machine learning also allows AI to make comparisons among images and predictions from data, and at the same time, elaborate on its reasoning.

Scientists can use interpretable machine learning for a variety of applications, from identifying birds in images for wildlife surveys to analyzing mammograms.

Science of Building Bones with Eggshells and Origami

Origami-inspired tissue engineering — using eggshells, plant leaves, marine sponges, and paper as substrates.


Ira Pastor ideaXme life sciences ambassador interviews Dr. Gulden Camci-Unal, Ph.D. Assistant Professor, at the Department Chemical Engineering, Francis College of Engineering, UMass Lowell.

Ira Pastor comments:

A few episodes ago ideaXme hosted the University of Michigan’s Dr. Bruce Carlson. We spoke to him about the interesting topic of the importance of “substrate” in regenerative processes, for both the maintenance of normal tissue functions, and in the migration of cells or changes to tissue architecture that are part of healing processes.

Substrate is broadly defined as the surface or material on, or from which, cells / tissues live, grow, or obtain nourishment, and have both biochemical, as well as biomechanical functions.

Israeli innovation plugs into emerging energy-tech sector

“There are two critical factors in this world: time and energy. Time is the only limited resource and therefore the most important one in our lives. Energy moves everything — our bodies, our lives and even all the digital revolution that is not physical depends on energy to be shared. We have no more time to cure the world and the Covid-19 is an amazing gift to better understand the important and critical things of our lives. It is a very important wake-up call for everyone.”

As more Israeli companies continue to seek solutions to economic and environmental challenges, we’ll see more local investors deploy capital in this space. Lack of acquisitions in this space – as opposed to a vertical like cybersecurity — are one main reason for the initial hesitancy of Israeli VCs.

Regardless of social impact or double bottom line investing, Israel is poised to lead another vertical impacting our global community. This has life-altering ramifications for future generations.

PerkinElmer snaps up CRISPR provider Horizon Discovery in $383M deal

PerkinElmer has moved to expand its life sciences portfolio with CRISPR and gene editing offerings by snapping up the cell engineering specialist Horizon Discovery.

The $383 million, all-cash deal will add gene modulation tools that—in combination with its own work in applied genomics solutions—aims to provide next-generation research tools and the customized cell lines necessary for developers of new targeted therapies, and broaden PerkinElmer’s partnership work with academic researchers and the biopharma industry.

The Cambridge, U.K.-based Horizon, with about 400 employees worldwide with offices in the U.S. and Japan, provides genetic base editing technologies for living cell models using CRISPR reagents, as well as gene modulation products using RNA interference methods.

Melding biology and physical sciences yields deeper understanding of cancer

In a review published in the journal *Science*, Jain and Steele Laboratories colleagues Hadi T. Nia, PhD, and Lance L. Munn, PhD, describe four distinct physical hallmarks of cancer that affect both cancer cells and the tumor microenvironment, contributing to both tumor growth and the development of resistance to powerful cancer drugs.

One widely accepted model of cancer holds that a normal cell goes rogue because of genetic mutations or an environmental insult. In this model, the altered cell starts replicating out of control and takes over normal tissues, displaying eight hallmarks that include the ability to promote and sustain the growth of tumors, evade immune system attempts to suppress growth, stimulate blood flow to tumors and both invade local tissues and metastasize (spread) elsewhere in the body.

But this model fails to take into account how physical processes affect tumor progression and treatment, say the authors. In addition to the aforementioned eight biological hallmarks of cancer proposed by Robert Weinberg, PhD, from MIT, and Douglas Hanahan, PhD, from the Swiss Federal Institute of Technology in Lausanne, Jain and colleagues propose adding four distinct physical hallmarks that capture the biomechanical abnormalities in tumors: elevated solid stress; elevated interstitial fluid pressure; increased stiffness and altered material properties; and altered tissue micro-architecture.

Three decades of research in the Steele Laboratories led to the discovery and clinical translation of the first two hallmarks. “Solid stresses are created as proliferating and migrating cells push and stretch solid components of the surrounding tissue. They are large enough to compress blood and lymphatic vessels in and around tumors, impairing blood flow and the delivery of oxygen, drugs and immune cells,” Jain says.

Elevated interstitial fluid pressure is caused by abnormally permeable blood vessels in tumors leaking blood plasma into tissues surrounding the tumor, and by insufficient drainage of lymphatic fluid. The interstitial fluid carries various growth factors with it, causing edema (swelling), elution (release) of drugs and growth factors, and facilitating cancer invasion of local and distant tissues.

Increased stiffness is caused by the deposition of cellular matrix (scaffolding) and remodeling of tissues. This stiffness has traditionally been used as a diagnostic marker for tumor growth, and more recently it has come to be recognized as a marker for prognosis. Increased stiffness activates signaling pathways that promote proliferation, invasiveness and metastasis of cancer cells, Jain explains.

“Finally, when normal tissue architecture is disrupted by cancer growth and invasion, micro-architecture is altered,” he says. “Stromal (supporting) cells, cancer cells and extracellular matrix adopt new organization. This changes the interactions between an individual cell and its surrounding matrix and cells, which affects signaling pathways associated with invasion and metastasis.”

OneSkin Progress Report | Carolina Reis, CEO Oneskin

In this interview to Allison Duettmann, Carolina Reis, OneSkin’s CEO, describes the results of the prove of concept clinical study that the company performed for the product launched in the market some weeks ago, and explains more thoroughly the possible mechanisms of action involved in the reduction of senescent cells in the skin.


Zoom Transcription: https://otter.ai/s/DxPPE-AMSl6VdZa4K8dkDQ

How Coronavirus Can Be Stopped: 3D Atomic Map of COVID-19’s Viral Replication Mechanism

To better understand how the novel coronavirus behaves and how it can be stopped, scientists have completed a three-dimensional map that reveals the location of every atom in an enzyme molecule critical to SARS-CoV-2 reproduction.

Researchers at the Department of Energy’s Oak Ridge National Laboratory used neutron scattering to identify key information to improve the effectiveness of drug inhibitors designed to block the virus’s replication mechanism. The research is published in the Journal of Biological Chemistry.

The SARS-CoV-2 virus, which causes the COVID-19 disease, expresses long chains of proteins composed of approximately 1,900 amino acid residues. For the virus to reproduce, those chains have to be broken down and cut into smaller strands by an enzyme called the main protease. The active protease enzyme is formed from two identical protein molecules held together by hydrogen bonds. Developing a drug that inhibits or blocks the protease activity will prevent the virus from replicating and spreading to other cells in the body.

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