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Biotechnology

Jurassic fossils from northeastern China reveal morphological stasis in the catkin-yew

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The Taxaceae are a distinct conifer family widely used in ornamental horticulture and are an important source of chemotherapeutic drugs (e.g., Paclitaxel). Fossil evidence of Taxaceae is based mainly on isolated leaves or leafy shoots for which the reproductive structures are unknown. However, several more complete fossils with attached seed-bearing structures show that Taxaceae had diverged from other conifers by the earliest Jurassic and were probably diverse during the Jurassic and Cretaceous.

Dong and colleagues add to knowledge of early Taxaceae based on well-preserved fossils from the Middle-Late Jurassic (~160 Myr) Daohugou Bed in eastern Inner Mongolia, northeastern China. The material includes the terminal portion of a leafy shoot with attached seed-bearing structures, and a leafy shoot with two-orders of branching in which each ultimate shoot has a terminal conical bud. The fossil leafy shoots have opposite and decussate leaves. Attached seed-bearing structures arise singly from the axil of a normal vegetative leaf and consist of a short, naked axis bearing a single terminal seed that is enclosed by pairs of opposite and decussate bracts.

These fossils bear a striking resemblance to the leafy shoots and seed-bearing structures of extant catkin-yews Amentotaxus and only differ in having shorter seed-bearing axes. Assignment of the fossils to the living genus is also supported by cladistic analyses based on morphological characters of living and fossil Taxaceae. These fossils are among the most completely known of all fossil Taxaceae. Extant catkin-yews are endangered and have very restricted distributions in Eastern Asia. The Daohugou fossils document that among the diverse extinct Mesozoic Taxaceae were ancient catkin-yews. Like Ginkgo biloba, the catkin-yews are living fossils that have undergone little morphological change since the Middle-Late Jurassic.

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See the article:

Dong C., Shi G., Herrera F., Wang Y., Herendeen P.S., Crane P.R., 2020. Middle-Late Jurassic fossils from northeastern China reveal morphological stasis in the catkin-yew. National Science Review, nwaa138. DOI: 10.1093/nsr/nwaa138

Link: https://doi.org/10.1093/nsr/nwaa138

Source: https://bioengineer.org/jurassic-fossils-from-northeastern-china-reveal-morphological-stasis-in-the-catkin-yew/

Artificial Intelligence

Deep learning helps predict new drug combinations to fight Covid-19

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The existential threat of Covid-19 has highlighted an acute need to develop working therapeutics against emerging health concerns. One of the luxuries deep learning has afforded us is the ability to modify the landscape as it unfolds — so long as we can keep up with the viral threat, and access the right data. 

As with all new medical maladies, oftentimes the data need time to catch up, and the virus takes no time to slow down, posing a difficult challenge as it can quickly mutate and become resistant to existing drugs. This led scientists from MIT’s Computer Science and Artificial Intelligence Laboratory (CSAIL) and the Jameel Clinic for Machine Learning in Health to ask: How can we identify the right synergistic drug combinations for the rapidly spreading SARS-CoV-2? 

Typically, data scientists use deep learning to pick out drug combinations with large existing datasets for things like cancer and cardiovascular disease, but, understandably, they can’t be used for new illnesses with limited data.

Without the necessary facts and figures, the team needed a new approach: a neural network that wears two hats. Since drug synergy often occurs through inhibition of biological targets (like proteins or nucleic acids), the model jointly learns drug-target interaction and drug-drug synergy to mine new combinations. The drug-target predictor models the interaction between a drug and a set of known biological targets that are related to the chosen disease. The target-disease association predictor learns to understand a drug’s antiviral activity, which means determining the virus yield in infected tissue cultures. Together, they can predict the synergy of two drugs. 

Two new drug combinations were found using this approach: remdesivir (currently approved by the FDA to treat Covid-19) and reserpine, as well as remdesivir and IQ-1S, which, in biological assays, proved powerful against the virus. The study has been published in the Proceedings of the National Academy of Sciences.

“By modeling interactions between drugs and biological targets, we can significantly decrease the dependence on combination synergy data,” says Wengong Jin SM ’18, a postdoc at the Broad Institute of MIT and Harvard who recently completed his doctoral work in CSAIL, and who is the lead author on a new paper about the research. “In contrast to previous approaches using drug-target interaction as fixed descriptors, our method learns to predict drug-target interaction from molecular structures. This is advantageous since a large proportion of compounds have incomplete drug-target interaction information.” 

Using multiple medications to maximize potency, while also decreasing side effects, is practically ubiquitous for aforementioned cancer and cardiovascular disease, including a host of others such as tuberculosis, leprosy, and malaria. Using specialized drug cocktails can, quite importantly, reduce the grave and sometimes public threat of resistance (think methicillin-resistant Staphylococcus aureus known as “MRSA”), since many drug-resistant mutations are mutually exclusive. It’s much harder for a virus to develop two mutations at the same time and then become resistant to two drugs in a combination therapy. 

Importantly, the model isn’t limited to just one SARS-CoV-2 strain — it could also potentially be used for the increasingly contagious Delta variant or other variants of concern that may arise. To extend the model’s efficacy against these strains, you’d only need additional drug combination synergy data for the relevant mutation(s). In addition, the team applied their approach to HIV and pancreatic cancer.

To further refine their biological modeling down the line, the team plans to incorporate additional information such as protein-protein interaction and gene regulatory networks. 

Another direction for future work they’re exploring is something called “active learning.” Many drug combination models are biased toward certain chemical spaces due to their limited size, so there’s high uncertainty in predictions. Active learning helps guide the data collection process and improve accuracy in a wider chemical space. 

Jin wrote the paper alongside Jonathan M. Stokes, Banting Fellow at The Broad Institute of MIT and Harvard; Richard T. Eastman, a scientist at the National Center for Advancing Translational Sciences; Zina Itkin, a scientist at National Institutes of Health; Alexey V. Zakharo, informatics lead at the National Center for Advancing Translational Sciences (NCATS); James J. Collins, professor of biological engineering at MIT; and Tommi S. Jaakkola and Regina Barzilay, MIT professors of electrical engineering and computer science at MIT.

This project is supported by the Abdul Latif Jameel Clinic for Machine Learning in Health; the Defense Threat Reduction Agency; Patrick J. McGovern Foundation; the DARPA Accelerated Molecular Discovery program; and in part by the Intramural/Extramural Research Program of the National Center for Advancing Translational Sciences within the National Institutes of Health.

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Source: https://news.mit.edu/2021/deep-learning-helps-predict-new-drug-combinations-fight-covid-19-0924

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Biotechnology

New bionics center established at MIT with $24 million gift

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A deepening understanding of the brain has created unprecedented opportunities to alleviate the challenges posed by disability. Scientists and engineers are taking design cues from biology itself to create revolutionary technologies that restore the function of bodies affected by injury, aging, or disease — from prosthetic limbs that effortlessly navigate tricky terrain to digital nervous systems that move the body after a spinal cord injury.

With the establishment of the new K. Lisa Yang Center for Bionics, MIT is pushing forward the development and deployment of enabling technologies that communicate directly with the nervous system to mitigate a broad range of disabilities. The center’s scientists, clinicians, and engineers will work together to create, test, and disseminate bionic technologies that integrate with both the body and mind.

The center is funded by a $24 million gift to MIT’s McGovern Institute for Brain Research from philanthropist Lisa Yang, a former investment banker committed to advocacy for individuals with visible and invisible disabilities. Her previous gifts to MIT have also enabled the establishment of the K. Lisa Yang and Hock E. Tan Center for Molecular Therapeutics in Neuroscience, Hock E. Tan and K. Lisa Yang Center for Autism Research, Y. Eva Tan Professorship in Neurotechnology, and the endowed K. Lisa Yang Post-Baccalaureate Program.

“The K. Lisa Yang Center for Bionics will provide a dynamic hub for scientists, engineers, and designers across MIT to work together on revolutionary answers to the challenges of disability,” says MIT President L. Rafael Reif. “With this visionary gift, Lisa Yang is unleashing a powerful collaborative strategy that will have broad impact across a large spectrum of human conditions — and she is sending a bright signal to the world that the lives of individuals who experience disability matter deeply.”

Video thumbnail Play video

“K. Lisa Yang Center for Bionics”
Video by Jimmy Day/MIT Media Lab

An interdisciplinary approach

To develop prosthetic limbs that move as the brain commands or optical devices that bypass an injured spinal cord to stimulate muscles, bionic developers must integrate knowledge from a diverse array of fields — from robotics and artificial intelligence to surgery, biomechanics, and design. The K. Lisa Yang Center for Bionics will be deeply interdisciplinary, uniting experts from three MIT schools: Science, Engineering, and Architecture and Planning. With clinical and surgical collaborators at Harvard Medical School, the center will ensure that research advances are tested rapidly and reach people in need, including those in traditionally underserved communities.

To support ongoing efforts to move toward a future without disability, the center will also provide four endowed fellowships for MIT graduate students working in bionics or other research areas focused on improving the lives of individuals who experience disability.

“I am thrilled to support MIT on this major research effort to enable powerful new solutions that improve the quality of life for individuals who experience disability,” says Yang. “This new commitment extends my philanthropic investment into the realm of physical disabilities, and I look forward to the center’s positive impact on countless lives, here in the U.S. and abroad.”

The center will be led by Hugh Herr, a professor of media arts and sciences at MIT’s Media Lab, and Ed Boyden, the Y. Eva Tan Professor of Neurotechnology at MIT, a professor of biological engineering, brain and cognitive sciences, and media arts and sciences, and an investigator at MIT’s McGovern Institute and the Howard Hughes Medical Institute.

A double amputee himself, Herr is a pioneer in the development of bionic limbs to improve mobility for those with physical disabilities.“The world profoundly needs relief from the disabilities imposed by today’s nonexistent or broken technologies. We must continually strive towards a technological future in which disability is no longer a common life experience,” says Herr. “I am thrilled that the Yang Center for Bionics will help to measurably improve the human experience for so many.”

Boyden, who is a renowned creator of tools to analyze and control the brain, will play a key role in merging bionics technologies with the nervous system. “The Yang Center for Bionics will be a research center unlike any other in the world,” he says. “A deep understanding of complex biological systems, coupled with rapid advances in human-machine bionic interfaces, mean we will soon have the capability to offer entirely new strategies for individuals who experience disability. It is an honor to be part of the center’s founding team.”

Center priorities

In its first four years, the K. Lisa Yang Center for Bionics will focus on developing and testing three bionic technologies: 

  • digital nervous system, to eliminate movement disorders caused by spinal cord injuries using computer-controlled muscle activations to regulate limb movements while simultaneously stimulating spinal cord repair;
  • brain-controlled limb exoskeletons, to assist weak muscles and enable natural movement for people affected by stroke or musculoskeletal disorders; and
  • bionic limb reconstruction, to restore natural, brain-controlled movements as well as the sensation of touch and proprioception (awareness of position and movement) from bionic limbs.

A fourth priority will be developing a mobile delivery system to ensure patients in medically underserved communities have access to prosthetic limb services. Investigators will field-test a system that uses a mobile clinic to conduct the medical imaging needed to design personalized, comfortable prosthetic limbs and to fit the prostheses to patients where they live. Investigators plan to initially bring this mobile delivery system to Sierra Leone, where thousands of people suffered amputations during the country’s 11-year civil war. While the population of persons with amputation continues to increase each year in Sierra Leone, today less than 10 percent of persons in need benefit from functional prostheses. Through the mobile delivery system, a key center objective is to scale up production and access of functional limb prostheses for Sierra Leoneans in dire need.

“The mobile prosthetics service fueled by the K. Lisa Yang Center for Bionics at MIT is an innovative solution to a global problem,” says Julius Maada Bio, president of Sierra Leone. “I am proud that Sierra Leone will be the first site for deploying this state-of-the-art digital design and fabrication process. As leader of a government that promotes innovative technologies and prioritizes human capital development, I am overjoyed that this pilot project will give Sierra Leoneans (especially in rural areas) access to quality limb prostheses and thus improve their quality of life.”

Together, Herr and Boyden will launch research at the bionics center with three other MIT faculty: assistant professor of media arts and sciences Canan Dagdeviren, Walter A. Rosenblith Professor of Cognitive Neuroscience Nancy Kanwisher, and David H. Koch (1962) Institute Professor Robert Langer. They will work closely with three clinical collaborators at Harvard Medical School: Marco Ferrone, an orthopedic surgeon; Matthew Carty, a plastic surgeon; and Nancy Oriol, Faculty Associate Dean for Community Engagement in Medical Education.

“Lisa Yang and I share a vision for a future in which each and every person in the world has the right to live without a debilitating disability if they so choose,” adds Herr. “The Yang Center will be a potent catalyst for true innovation and impact in the bionics space, and I am overjoyed to work with my colleagues at MIT, and our accomplished clinical partners at Harvard, to make important steps forward to help realize this vision.”

PlatoAi. Web3 Reimagined. Data Intelligence Amplified.
Click here to access.

Source: https://news.mit.edu/2021/new-bionics-center-established-mit-24-million-gift-0923

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Biotechnology

New bionics center established at MIT with $24 million gift

Published

on

A deepening understanding of the brain has created unprecedented opportunities to alleviate the challenges posed by disability. Scientists and engineers are taking design cues from biology itself to create revolutionary technologies that restore the function of bodies affected by injury, aging, or disease — from prosthetic limbs that effortlessly navigate tricky terrain to digital nervous systems that move the body after a spinal cord injury.

With the establishment of the new K. Lisa Yang Center for Bionics, MIT is pushing forward the development and deployment of enabling technologies that communicate directly with the nervous system to mitigate a broad range of disabilities. The center’s scientists, clinicians, and engineers will work together to create, test, and disseminate bionic technologies that integrate with both the body and mind.

The center is funded by a $24 million gift to MIT’s McGovern Institute for Brain Research from philanthropist Lisa Yang, a former investment banker committed to advocacy for individuals with visible and invisible disabilities. Her previous gifts to MIT have also enabled the establishment of the K. Lisa Yang and Hock E. Tan Center for Molecular Therapeutics in Neuroscience, Hock E. Tan and K. Lisa Yang Center for Autism Research, Y. Eva Tan Professorship in Neurotechnology, and the endowed K. Lisa Yang Post-Baccalaureate Program.

“The K. Lisa Yang Center for Bionics will provide a dynamic hub for scientists, engineers, and designers across MIT to work together on revolutionary answers to the challenges of disability,” says MIT President L. Rafael Reif. “With this visionary gift, Lisa Yang is unleashing a powerful collaborative strategy that will have broad impact across a large spectrum of human conditions — and she is sending a bright signal to the world that the lives of individuals who experience disability matter deeply.”

Video thumbnail Play video

“K. Lisa Yang Center for Bionics”
Video by Jimmy Day/MIT Media Lab

An interdisciplinary approach

To develop prosthetic limbs that move as the brain commands or optical devices that bypass an injured spinal cord to stimulate muscles, bionic developers must integrate knowledge from a diverse array of fields — from robotics and artificial intelligence to surgery, biomechanics, and design. The K. Lisa Yang Center for Bionics will be deeply interdisciplinary, uniting experts from three MIT schools: Science, Engineering, and Architecture and Planning. With clinical and surgical collaborators at Harvard Medical School, the center will ensure that research advances are tested rapidly and reach people in need, including those in traditionally underserved communities.

To support ongoing efforts to move toward a future without disability, the center will also provide four endowed fellowships for MIT graduate students working in bionics or other research areas focused on improving the lives of individuals who experience disability.

“I am thrilled to support MIT on this major research effort to enable powerful new solutions that improve the quality of life for individuals who experience disability,” says Yang. “This new commitment extends my philanthropic investment into the realm of physical disabilities, and I look forward to the center’s positive impact on countless lives, here in the U.S. and abroad.”

The center will be led by Hugh Herr, a professor of media arts and sciences at MIT’s Media Lab, and Ed Boyden, the Y. Eva Tan Professor of Neurotechnology at MIT, a professor of biological engineering, brain and cognitive sciences, and media arts and sciences, and an investigator at MIT’s McGovern Institute and the Howard Hughes Medical Institute.

A double amputee himself, Herr is a pioneer in the development of bionic limbs to improve mobility for those with physical disabilities.“The world profoundly needs relief from the disabilities imposed by today’s nonexistent or broken technologies. We must continually strive towards a technological future in which disability is no longer a common life experience,” says Herr. “I am thrilled that the Yang Center for Bionics will help to measurably improve the human experience for so many.”

Boyden, who is a renowned creator of tools to analyze and control the brain, will play a key role in merging bionics technologies with the nervous system. “The Yang Center for Bionics will be a research center unlike any other in the world,” he says. “A deep understanding of complex biological systems, coupled with rapid advances in human-machine bionic interfaces, mean we will soon have the capability to offer entirely new strategies for individuals who experience disability. It is an honor to be part of the center’s founding team.”

Center priorities

In its first four years, the K. Lisa Yang Center for Bionics will focus on developing and testing three bionic technologies: 

  • digital nervous system, to eliminate movement disorders caused by spinal cord injuries using computer-controlled muscle activations to regulate limb movements while simultaneously stimulating spinal cord repair;
  • brain-controlled limb exoskeletons, to assist weak muscles and enable natural movement for people affected by stroke or musculoskeletal disorders; and
  • bionic limb reconstruction, to restore natural, brain-controlled movements as well as the sensation of touch and proprioception (awareness of position and movement) from bionic limbs.

A fourth priority will be developing a mobile delivery system to ensure patients in medically underserved communities have access to prosthetic limb services. Investigators will field-test a system that uses a mobile clinic to conduct the medical imaging needed to design personalized, comfortable prosthetic limbs and to fit the prostheses to patients where they live. Investigators plan to initially bring this mobile delivery system to Sierra Leone, where thousands of people suffered amputations during the country’s 11-year civil war. While the population of persons with amputation continues to increase each year in Sierra Leone, today less than 10 percent of persons in need benefit from functional prostheses. Through the mobile delivery system, a key center objective is to scale up production and access of functional limb prostheses for Sierra Leoneans in dire need.

“The mobile prosthetics service fueled by the K. Lisa Yang Center for Bionics at MIT is an innovative solution to a global problem,” says Julius Maada Bio, president of Sierra Leone. “I am proud that Sierra Leone will be the first site for deploying this state-of-the-art digital design and fabrication process. As leader of a government that promotes innovative technologies and prioritizes human capital development, I am overjoyed that this pilot project will give Sierra Leoneans (especially in rural areas) access to quality limb prostheses and thus improve their quality of life.”

Together, Herr and Boyden will launch research at the bionics center with three other MIT faculty: assistant professor of media arts and sciences Canan Dagdeviren, Walter A. Rosenblith Professor of Cognitive Neuroscience Nancy Kanwisher, and David H. Koch (1962) Institute Professor Robert Langer. They will work closely with three clinical collaborators at Harvard Medical School: Marco Ferrone, an orthopedic surgeon; Matthew Carty, a plastic surgeon; and Nancy Oriol, Faculty Associate Dean for Community Engagement in Medical Education.

“Lisa Yang and I share a vision for a future in which each and every person in the world has the right to live without a debilitating disability if they so choose,” adds Herr. “The Yang Center will be a potent catalyst for true innovation and impact in the bionics space, and I am overjoyed to work with my colleagues at MIT, and our accomplished clinical partners at Harvard, to make important steps forward to help realize this vision.”

PlatoAi. Web3 Reimagined. Data Intelligence Amplified.
Click here to access.

Source: https://news.mit.edu/2021/new-bionics-center-established-mit-24-million-gift-0923

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Artificial Intelligence

The next healthcare revolution will have AI at its center

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The global pandemic has heightened our understanding and sense of importance of our own health and the fragility of healthcare systems around the world. We’ve all come to realize how archaic many of our health processes are, and that, if we really want to, we can move at lightning speed. This is already leading to a massive acceleration in both the investment and application of artificial intelligence in the health and medical ecosystems.

Modern medicine in the 20th century benefited from unprec­edented scientific breakthroughs, resulting in improvements in every as­pect of healthcare. As a result, human life expectancy increased from 31 years in 1900 to 72 years in 2017. Today, I believe we are on the cusp of another healthcare revolution — one driven by artificial intelligence (AI). Advances in AI will usher in the era of modern medicine in truth.

Over the coming decades, we can expect medical diagnosis to evolve from an AI tool that provides analysis of options to an AI assistant that recommends treatments.

Digitization enables powerful AI

The healthcare sector is seeing massive digitization of everything from patient records and radiology data to wearable computing and multiomics. This will redefine healthcare as a data-driven industry, and when that happens, it will leverage the power of AI — its ability to continuously improve with more data.

When there is enough data, AI can do a much more accurate job of diagnosis and treatment than human doctors by absorbing and checking billions of cases and outcomes. AI can take into account everyone’s data to personalize treatment accordingly, or keep up with a massive number of new drugs, treatments and studies. Doing all of this well is beyond human capabilities.

AI-powered diagnosis

I anticipate diagnostic AI will surpass all but the best doctors in the next 20 years. Studies have shown that AI trained on sizable data can outperform physicians in several areas of medical diagnosis regarding brain tumors, eye disease, breast cancer, skin cancer and lung cancer. Further trials are needed, but as these technologies are deployed and more data is gathered, the AI stands to outclass doctors.

We will eventually see diagnostic AI for general practitioners, one disease at a time, to gradually cover all diagnoses. Over time, AI may become capable of acting as your general practitioner or family doctor.

PlatoAi. Web3 Reimagined. Data Intelligence Amplified.
Click here to access.

Source: https://techcrunch.com/2021/09/20/the-next-healthcare-revolution-will-have-ai-at-its-center/

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