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Category: chemistry – Page 276

Researchers at MIT and IBM Propose an Efficient Machine Learning Method That Uses Graph Grammar to Generate New Molecules

Chemical engineers and materials scientists are continuously looking for the following groundbreaking material, chemical, or medication. The emergence of machine-learning technologies has accelerated the discovery process, which may typically take years. Ideally, the objective is to train a machine-learning model on a few known chemical samples and then let it build as many manufacturable molecules of the same class with predictable physical attributes as feasible. You can develop new molecules with ideal characteristics if you have all of these components and the know-how to synthesize them.

However, current approaches need large datasets for training models. Many class-specific chemical databases only contain a few example compounds, restricting their capacity to generalize and construct biological molecules that might be generated in the real world.

This issue was addressed by a team of researchers from MIT and IBM by employing a generative graph model to create new synthesizable compounds within the same training data’s chemical class. The research was presented in a research paper. They model the production of atoms and chemical bonds as a graph and create a graph grammar — a linguistic analog of systems and structures for word ordering — that provides a set of rules for constructing compounds like monomers and polymers.

Age of skin cells reversed by 30 years

The researchers looked at multiple measures of cellular age. First, they used the epigenetic clock, where chemical tags throughout the genome indicate age. Secondly, they looked at the transcriptome, all the gene readouts produced by the cell. By these two measures, the reprogrammed cells matched the profile of cells that were 30 years younger, compared to reference data sets. In other words, cells from a woman of 53 now appeared like those of a woman aged 23.

The potential applications of this technique are dependent on cells not only appearing younger, but functioning like young cells too. Fibroblasts produce collagen – a molecule found in bones, skin tendons, and ligaments, helping provide structure to tissues and heal wounds. In this study, the rejuvenated fibroblasts produced more collagen proteins compared to control cells that did not undergo the reprogramming process. Fibroblasts also move into areas that need repairing. Researchers tested the partially rejuvenated cells by creating an artificial cut in a layer of cells in a dish, seen in the video below. The treated fibroblasts moved into the gap faster than older cells. This is a promising sign that one day this research could eventually be used to create cells that are better at healing wounds.

In the future, this research may also open up other therapeutic possibilities; the researchers observed that their method also influenced other genes linked to age-related diseases and symptoms. The APBA2 gene – associated with Alzheimer’s, and the MAF gene with a role in the development of cataracts – both showed changes towards youthful levels of transcription.

Dr. Peter J. Hotez — Baylor College of Medicine — Scientist, Researcher, Author, Science Explainer

Coming off multiple country approvals for his “patent free” Covid vaccine, Scientist, Researcher, Author, Science Explainer, Dr. Peter Hotez, MD, Ph.D. Baylor College of Medicine, drops by for an episode of Progress, Potential, And Possibilities.

Dr. Peter J. Hotez, M.D., Ph.D. (https://peterhotez.org/), is Dean of the National School of Tropical Medicine and Professor of Pediatrics and Molecular Virology and Microbiology at Baylor College of Medicine (https://www.bcm.edu/people-search/peter-hotez-23229), where he is also Chief of the Section of Pediatric Tropical Medicine and the Texas Children’s Hospital Endowed Chair of Tropical Pediatrics (https://www.texaschildrens.org/find-a-doctor/peter-jay-hotez-md-phd).

Dr. Hotez is also Rice University’s Baker Institute fellow in disease and poverty (https://www.bakerinstitute.org/experts/peter-j-hotez/) and Co-Director of Parasites Without Borders (https://parasiteswithoutborders.com/), a global nonprofit organization with a focus on those suffering from parasitic diseases in subtropical environments.

Dr. Hotez is an internationally recognized physician-scientist with expertise in neglected tropical diseases and vaccine development. He leads the only product development partnership for developing new vaccines for hookworm, schistosomiasis and Chagas disease, and is just coming off a major win for emergency use approval of his team’s Corbevax protein sub-unit COVID-19 vaccine, of which he, and previous guest to the show, Dr. Maria Elena Bottazzi, were recently nominated for a Nobel Prize.

Dr. Hotez is the author of more than 400 original papers, as well as the books Forgotten People, Forgotten Diseases — The Neglected Tropical Diseases and Their Impact on Global Health and Development, Blue Marble Health — An Innovative Plan to Fight Diseases of the Poor amid Wealth, Vaccines Did Not Cause Rachel’s Autism: My Journey as a Vaccine Scientist, Pediatrician, and Autism Dad, and Preventing the Next Pandemic: Vaccine Diplomacy in a Time of Anti-science.

Continue reading “Dr. Peter J. Hotez — Baylor College of Medicine — Scientist, Researcher, Author, Science Explainer” | >

Blue Brain builds neurons with mathematics

Santiago Ramón y Cajal, a Spanish physician from the turn of the 19th century, is considered by most to be the father of modern neuroscience. He stared down a microscope day and night for years, fascinated by chemically stained neurons he found in slices of human brain tissue. By hand, he painstakingly drew virtually every new type of neuron he came across using nothing more than pen and paper. As the Charles Darwin for the brain, he mapped every detail of the forest of neurons that make up the brain, calling them the “butterflies of the brain”. Today, 200 years later, Blue Brain has found a way to dispense with the human eye, pen and paper, and use only mathematics to automatically draw neurons in 3D as digital twins. Math can now be used to capture all the “butterflies of the brain”, which allows us to use computers to build any and all the billons of neurons that make up the brain. And that means we are getting closer to being able to build digital twins of brains.

These billions of neurons form trillions of synapses – where neurons communicate with each other. Such complexity needs comprehensive neuron models and accurately reconstructed detailed brain networks in order to replicate the healthy and disease states of the brain. Efforts to build such models and networks have historically been hampered by the lack of experimental data available. But now, scientists at the EPFL Blue Brain Project using algebraic topology, a field of Math, have created an algorithm that requires only a few examples to generate large numbers of unique cells. Using this algorithm – the Topological Neuronal Synthesis (TNS), they can efficiently synthesize millions of unique neuronal morphologies.

A million times faster: DNA nanotechnology could speed up pharmaceutical development while minimizing costs

A new tool speeds up development of vaccines and other pharmaceutical products by more than 1 million times while minimizing costs.

In search of pharmaceutical agents such as new vaccines, industry will routinely scan thousands of related candidate molecules. A novel technique allows this to take place on the nano scale, minimizing use of materials and energy. The work is published in the journal Nature Chemistry.

More than 40,000 molecules can be synthesized and analyzed within an area smaller than a pinhead. The method, developed through a highly interdisciplinary research effort in Denmark, promises to drastically reduce the amounts of material, energy, and economic cost for .

Revolutionary DNA Nanotechnology Speeds Up Development of Vaccines

Revolutionary tool will meet future pandemics with accelerated response.

A new tool speeds up development of vaccines and other pharmaceutical products by more than one million times while minimizing costs.

In search of pharmaceutical agents such as new vaccines, industry will routinely scan thousands of related candidate molecules. A novel technique allows this to take place on the nano scale, minimizing use of materials and energy. The work is published in the prestigious journal Nature Chemistry.

Chemical-to-mechanical molecular computation using DNA-based motors with onboard logic

Current DNA computation techniques are slow in generating chemical outputs in response to chemical inputs and rely heavily on fluorescence readouts. Here, the authors introduce a new paradigm for DNA computation where the chemical input is processed and transduced into a mechanical output in the form of macroscopic locomotion using dynamic DNA-based motors.

Hyper-CEST NMR technique reveals missing structure of a novel container molecule

Using the Hyper-CEST NMR technique, the team led by Leif Schröder from the Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) and the Deutsches Krebsforschungszentrum (DKFZ) has managed to reveal two previously little researched variants of a type of transport container from the class of metal–organic polyhedra (MOPs). The researchers want to use this knowledge to develop a novel type of contrast agent in MR (magnetic resonance) imaging.

The concept of a modular construction system proves useful in many applications for assembling complex structures for specific functions from individual, repeated sub-units. In chemistry, the principle can be used to construct a self-assembling network from smaller molecular units that acts as a transport container of a defined size. For example, several can be linked with . These MOPs (metal–organic polyhedra) are used, for instance, to capture or to pave the way for more effective chemotherapeutic agents by loading them with certain drugs, which they then release in the tumor. Several aspects of the behavior of these structures have not yet been adequately explored. This is partly because there are not always appropriate techniques available to observe the loading and unloading of these MOPs at the —often, no differences can be measured between the empty and loaded variants for either the container or its contents.

In cooperation with a team from the University of Oulu in Finland, Leif Schröder’s research group has now investigated MOPs that spontaneously assemble in solution from iron ions and an organic compound to form tetrahedra. In the process, the organic struts can be attached differently to the iron “nodes.” Essentially, this influences the properties of MOPs, such as their capacity to kill tumor cells. In the case of the MOP under study, however, it was previously thought that only one of the three theoretically predicted variants existed. The other two variants were considered too unstable because no were able to detect them. Using a new method of (hyper-CEST NMR), Schröder’s team member Jabadurai Jayapaul has now succeeded in demonstrating that these previously unknown variants do exist.

Scientists Achieve Record Energy Efficiency for Thin Solar Panels

Scientists from the University of Surrey and Imperial College London have achieved an increase in energy absorption in ultra-thin solar panels by 25%, a record for panels of this size.

The team, which collaborated with AMOLF in Amsterdam, used solar panels just one micrometer thick with a disordered honeycomb layer on top of the silicon panel. The biophilic design draws inspiration from butterfly wings and bird eyes to absorb sunlight from every possible angle, making the panels more efficient.

The research led to a 25% increase in levels of energy absorption by the panels, making these solar panels more efficient than other one-micrometer-thick panels. They published their findings in the American Chemical Society’s journal, Photonics.