From The University of California-Santa Cruz (US) : “A new way to find genetic variations removes bias from human genotyping”

From The University of California-Santa Cruz (US)

December 16, 2021
Tim Stephens
stephens@ucsc.edu

Using a pangenomic approach instead of a single reference genome allows a more comprehensive characterization of genetic variations and can improve the genomic analyses used by a wide range of researchers and clinicians. Photo by Elena Zhukova.

Overview of the experiments: Variant calls from long-read–based and large-scale sequencing studies were used to construct pangenome reference graphs (top). Giraffe (and competing mappers) mapped reads to the graph or to linear references, and mapping accuracy, allele coverage balance, and speed were evaluated (middle). Then, mapped reads were used for variant calling, and variant call accuracy was evaluated (bottom). Structural variant calls were analyzed alongside expression data to identify population frequency estimates. Credit: Sirén et al., Science 2021.

Since the first sequencing of a human genome more than 20 years ago, the study of human genomes has relied almost exclusively on a single reference genome to which others are compared to identify genetic variations. Scientists have long recognized that a single reference genome cannot represent human diversity and that using it introduces a pervasive bias into these studies. Now, they finally have a practical alternative.

In a paper published December 16 in Science, researchers at the UC Santa Cruz Genomics Institute have introduced a new tool called Giraffe that can efficiently map new genome sequences to a “pangenome” representing many diverse human genome sequences. They show that this approach allows a more comprehensive characterization of genetic variations and can improve the genomic analyses used by a wide range of researchers and clinicians.

“We’ve been working toward this for years, and now for the first time we have something practical that works fast and works better than the single reference genome,” said corresponding author Benedict Paten, associate professor of biomolecular engineering at UC Santa Cruz and associate director of the Genomics Institute. “It’s important for the future of biomedicine that genomics helps everyone equally, so we need tools that account for the diversity of human populations and are not biased.”

All humans have the same genes but there are many variations in the exact sequences of the genes—meaning the sequence of DNA subunits (abbreviated A, C, T, G) that spell out the genetic code—as well as in the vast stretches of the genome outside of the protein-coding genes. A difference in a single letter of code is called a single nucleotide variant (SNV), and insertions or deletions of short sequences are known collectively as “indels”.

Structural variations

The most complex variants are structural variations involving rearrangements of large segments of code (50 or more letters). These are especially hard to find using a single reference genome, yet they can have significant effects and are known to play an important role in some diseases. The average person has millions of SNVs and indels and tens of thousands of larger structural variants, and collectively the structural variants actually involve more letters of code than the other types of variants do.

“The workhorses of genomics have been SNVs and short indels, because structural variants have been hidden from view,” Paten said. “Pangenomics is making structural variants visible so we can study them the same way we do SNVs and short indels. There are a lot of structural variants and they can have a big impact, so this is critical for the future of genetic studies of disease.”

A pangenome reference can be created from multiple genome sequences using a mathematical graph structure to represent the relationships between different sequences. In the new paper, the researchers built two human genome reference graphs using publicly available data. These were used to evaluate the new tool, Giraffe, which is a set of algorithms for mapping new sequence data to a pangenome reference.

First author Jouni Sirén, a research scientist at the Genomics Institute, pioneered many of Giraffe’s key algorithmic innovations. Giraffe can accurately map new sequence data to thousands of genomes embedded in a pangenome reference as quickly as existing tools map to a single reference genome. The study also showed that using Giraffe reduces mapping bias, the tendency to incorrectly map sequences that differ from the reference genome.

“Not only is the analysis better, it is also as fast as current methods that use a linear reference genome,” said co-first author Jean Monlong, a postdoctoral researcher at the Genomics Institute.

Genotyping

Inexpensive short-read sequencing is a mainstay of modern genomics, yielding snippets of sequence that must be mapped to a reference genome to make sense of them. Mapping shows where each snippet belongs on one of the 23 human chromosomes and identifies the variants present at each location in an individual’s genome, a process known as genotyping.

The researchers found that Google Health’s deep-learning variant caller, DeepVariant, could more accurately identify SNVs and indels using Giraffe’s alignments against a pangenome than it could using alignments against a single reference genome.

Monlong said he was most excited about using pangenomics to study structural variants.

“A lot of structural variants have been discovered recently using long-read sequencing,” he said. “With pangenomes, we can look for these structural variants in large datasets of short-read sequencing. It’s exciting because this will allow us to study those new structural variants across many people and ask questions about their functional impact, association with disease, or role in evolution.”

The researchers used Giraffe to map sequence reads from a diverse group of 5202 people and determine their genotypes for 167000 recently discovered structural variations. This enabled them to estimate the frequency of different versions of these structural variants in the human population as a whole and within individual subpopulations. They showed that the frequency of some variants differs considerably between subpopulations and could be misinterpreted if analyzed only in, for example, European-ancestry populations where the frequency of a particular variant is low.

A single reference genome must choose one version of any variation to represent, leaving the other versions unrepresented. By making more broadly representative pangenome references practical, Giraffe can make genomics more inclusive.

Paten and others at the UC Santa Cruz Genomics Institute are involved in a major effort funded by the National Human Genome Research Institute to build a comprehensive human pangenome reference, which they expect to release next year as a resource for the scientific community.

In addition to Sirén and Monlong, the new paper has three other co-first authors who contributed equally: Xian Chang, Adam Novak, and Jordan Eizenga, all at the UC Santa Cruz Genomics Institute. In addition to other coauthors at the Genomics Institute, including Director David Haussler, the coauthors also include researchers at Google Health, Broad Institute of MIT (US) and Harvard (US), The University of Michigan (US), The University of Virginia (US), Harbor-University of California at Los Angeles(US) Medical Center, and The University of Tennessee-Knoxville (US) Health Science Center. This research was funded by The National Institutes of Health (US).

See the full article here .

five-ways-keep-your-child-safe-school-shootings

Please help promote STEM in your local schools.

Stem Education Coalition

UC Santa Cruz (US) Lick Observatory Since 1888 Mt Hamilton, in San Jose, California, Altitude 1,283 m (4,209 ft)

UC Observatories Lick Automated Planet Finder fully robotic 2.4-meter optical telescope at Lick Observatory, situated on the summit of Mount Hamilton, east of San Jose, California, USA.

The UCO Lick C. Donald Shane telescope is a 120-inch (3.0-meter) reflecting telescope located at the Lick Observatory, Mt Hamilton, in San Jose, California, Altitude 1,283 m (4,209 ft).
UC Santa Cruz (US) campus.

The University of California-Santa Cruz (US) , opened in 1965 and grew, one college at a time, to its current (2008-09) enrollment of more than 16,000 students. Undergraduates pursue more than 60 majors supervised by divisional deans of humanities, physical & biological sciences, social sciences, and arts. Graduate students work toward graduate certificates, master’s degrees, or doctoral degrees in more than 30 academic fields under the supervision of the divisional and graduate deans. The dean of the Jack Baskin School of Engineering oversees the campus’s undergraduate and graduate engineering programs.

UCSC is the home base for the Lick Observatory.

UCO Lick Observatory’s 36-inch Great Refractor telescope housed in the South (large) Dome of main building.

Search for extraterrestrial intelligence expands at Lick Observatory
New instrument scans the sky for pulses of infrared light
March 23, 2015
By Hilary Lebow

The NIROSETI instrument saw first light on the Nickel 1-meter Telescope at Lick Observatory on March 15, 2015. (Photo by Laurie Hatch.)

Astronomers are expanding the search for extraterrestrial intelligence into a new realm with detectors tuned to infrared light at UC’s Lick Observatory. A new instrument, called NIROSETI, will soon scour the sky for messages from other worlds.

Alumna Shelley Wright, now an assistant professor of physics at UC San Diego (US), discusses the dichroic filter of the NIROSETI instrument, developed at the U Toronto Dunlap Institute for Astronomy and Astrophysics (CA) and brought to UCSD and installed at the UC Santa Cruz (US) Lick Observatory Nickel Telescope (Photo by Laurie Hatch).

“Infrared light would be an excellent means of interstellar communication,” said Shelley Wright, an assistant professor of physics at UC San Diego (US) who led the development of the new instrument while at the U Toronto Dunlap Institute for Astronomy and Astrophysics (CA).

Shelley Wright of UC San Diego with (US) NIROSETI, developed at U Toronto Dunlap Institute for Astronomy and Astrophysics (CA) at the 1-meter Nickel Telescope at Lick Observatory at UC Santa Cruz

NIROSETI team from left to right Rem Stone UCO Lick Observatory Dan Werthimer, UC Berkeley; Jérôme Maire, U Toronto; Shelley Wright, UCSD; Patrick Dorval, U Toronto; Richard Treffers, Starman Systems. (Image by Laurie Hatch).

Wright worked on an earlier SETI project at Lick Observatory as a UC Santa Cruz undergraduate, when she built an optical instrument designed by University of California-Berkeley (US) researchers. The infrared project takes advantage of new technology not available for that first optical search.

Infrared light would be a good way for extraterrestrials to get our attention here on Earth, since pulses from a powerful infrared laser could outshine a star, if only for a billionth of a second. Interstellar gas and dust is almost transparent to near infrared, so these signals can be seen from great distances. It also takes less energy to send information using infrared signals than with visible light.

Frank Drake, professor emeritus of astronomy and astrophysics at UC Santa Cruz and director emeritus of the SETI Institute, said there are several additional advantages to a search in the infrared realm.

Frank Drake with his Drake Equation. Credit Frank Drake.

Drake Equation, Frank Drake, Seti Institute (US).

“The signals are so strong that we only need a small telescope to receive them. Smaller telescopes can offer more observational time, and that is good because we need to search many stars for a chance of success,” said Drake.

The only downside is that extraterrestrials would need to be transmitting their signals in our direction, Drake said, though he sees this as a positive side to that limitation. “If we get a signal from someone who’s aiming for us, it could mean there’s altruism in the universe. I like that idea. If they want to be friendly, that’s who we will find.”

Scientists have searched the skies for radio signals for more than 50 years and expanded their search into the optical realm more than a decade ago. The idea of searching in the infrared is not a new one, but instruments capable of capturing pulses of infrared light only recently became available.

“We had to wait,” Wright said. “I spent eight years waiting and watching as new technology emerged.”

Now that technology has caught up, the search will extend to stars thousands of light years away, rather than just hundreds. NIROSETI, or Near-Infrared Optical Search for Extraterrestrial Intelligence, could also uncover new information about the physical universe.

“This is the first time Earthlings have looked at the universe at infrared wavelengths with nanosecond time scales,” said Dan Werthimer, UC Berkeley SETI Project Director. “The instrument could discover new astrophysical phenomena, or perhaps answer the question of whether we are alone.”

NIROSETI will also gather more information than previous optical detectors by recording levels of light over time so that patterns can be analyzed for potential signs of other civilizations.

“Searching for intelligent life in the universe is both thrilling and somewhat unorthodox,” said Claire Max, director of UC Observatories and professor of astronomy and astrophysics at UC Santa Cruz. “Lick Observatory has already been the site of several previous SETI searches, so this is a very exciting addition to the current research taking place.”

NIROSETI will scan the skies several times a week on the Nickel 1-meter telescope at Lick Observatory, located on Mt. Hamilton east of San Jose.

From The Massachusetts Institute of Technology (US) : “Taking some of the guesswork out of drug discovery”

From The Massachusetts Institute of Technology (US)

December 6, 2021
Adam Zewe

MIT researchers have developed a deep learning model that can rapidly predict the likely 3D shapes of a molecule given a 2D graph of its structure. This technique could accelerate drug discovery. Image: Courtesy of the researchers edited by MIT News.

In their quest to discover effective new medicines, scientists search for drug-like molecules that can attach to disease-causing proteins and change their functionality. It is crucial that they know the 3D shape of a molecule to understand how it will attach to specific surfaces of the protein.

But a single molecule can fold in thousands of different ways, so solving that puzzle experimentally is a time consuming and expensive process akin to searching for a needle in a molecular haystack.

MIT researchers are using machine learning to streamline this complex task. They have created a deep learning model that predicts the 3D shapes of a molecule solely based on a graph in 2D of its molecular structure. Molecules are typically represented as small graphs.

Their system, GeoMol, processes molecules in only seconds and performs better than other machine learning models, including some commercial methods. GeoMol could help pharmaceutical companies accelerate the drug discovery process by narrowing down the number of molecules they need to test in lab experiments, says Octavian-Eugen Ganea, a postdoc in the Computer Science and Artificial Intelligence Laboratory (CSAIL) and co-lead author of the paper.

“When you are thinking about how these structures move in 3D space, there are really only certain parts of the molecule that are actually flexible, these rotatable bonds. One of the key innovations of our work is that we think about modeling the conformational flexibility like a chemical engineer would. It is really about trying to predict the potential distribution of rotatable bonds in the structure,” says Lagnajit Pattanaik, a graduate student in the Department of Chemical Engineering and co-lead author of the paper.

Other authors include Connor W. Coley, the Henri Slezynger Career Development Assistant Professor of Chemical Engineering; Regina Barzilay, the School of Engineering Distinguished Professor for AI and Health in CSAIL; Klavs F. Jensen, the Warren K. Lewis Professor of Chemical Engineering; William H. Green, the Hoyt C. Hottel Professor in Chemical Engineering; and senior author Tommi S. Jaakkola, the Thomas Siebel Professor of Electrical Engineering in CSAIL and a member of the Institute for Data, Systems, and Society. The research will be presented this week at the Conference on Neural Information Processing Systems.

Mapping a molecule

In a molecular graph, a molecule’s individual atoms are represented as nodes and the chemical bonds that connect them are edges.

GeoMol leverages a recent tool in deep learning called a message passing neural network, which is specifically designed to operate on graphs. The researchers adapted a message passing neural network to predict specific elements of molecular geometry.

Given a molecular graph, GeoMol initially predicts the lengths of the chemical bonds between atoms and the angles of those individual bonds. The way the atoms are arranged and connected determines which bonds can rotate.

GeoMol then predicts the structure of each atom’s local neighborhood individually and assembles neighboring pairs of rotatable bonds by computing the torsion angles and then aligning them. A torsion angle determines the motion of three segments that are connected, in this case, three chemical bonds that connect four atoms.

“Here, the rotatable bonds can take a huge range of possible values. So, the use of these message passing neural networks allows us to capture a lot of the local and global environments that influences that prediction. The rotatable bond can take multiple values, and we want our prediction to be able to reflect that underlying distribution,” Pattanaik says.

Overcoming existing hurdles

One major challenge to predicting the 3D structure of molecules is to model chirality. A chiral molecule can’t be superimposed on its mirror image, like a pair of hands (no matter how you rotate your hands, there is no way their features exactly line up). If a molecule is chiral, its mirror image won’t interact with the environment in the same way.

This could cause medicines to interact with proteins incorrectly, which could result in dangerous side effects. Current machine learning methods often involve a long, complex optimization process to ensure chirality is correctly identified, Ganea says.

Because GeoMol determines the 3D structure of each bond individually, it explicitly defines chirality during the prediction process, eliminating the need for optimization after-the-fact.

After performing these predictions, GeoMol outputs a set of likely 3D structures for the molecule.

“What we can do now is take our model and connect it end-to-end with a model that predicts this attachment to specific protein surfaces. Our model is not a separate pipeline. It is very easy to integrate with other deep learning models,” Ganea says.

A “super-fast” model

The researchers tested their model using a dataset of molecules and the likely 3D shapes they could take, which was developed by Rafael Gomez-Bombarelli, the Jeffrey Cheah Career Development Chair in Engineering, and graduate student Simon Axelrod.

They evaluated how many of these likely 3D structures their model was able to capture, in comparison to machine learning models and other methods.

In nearly all instances, GeoMol outperformed the other models on all tested metrics.

“We found that our model is super-fast, which was really exciting to see. And importantly, as you add more rotatable bonds, you expect these algorithms to slow down significantly. But we didn’t really see that. The speed scales nicely with the number of rotatable bonds, which is promising for using these types of models down the line, especially for applications where you are trying to quickly predict the 3D structures inside these proteins,” Pattanaik says.

In the future, the researchers hope to apply GeoMol to the area of high-throughput virtual screening, using the model to determine small molecule structures that would interact with a specific protein. They also want to keep refining GeoMol with additional training data so it can more effectively predict the structure of long molecules with many flexible bonds.

“Conformational analysis is a key component of numerous tasks in computer-aided drug design, and an important component in advancing machine learning approaches in drug discovery,” says Pat Walters, senior vice president of computation at Relay Therapeutics, who was not involved in this research. “I’m excited by continuing advances in the field and thank MIT for contributing to broader learnings in this area.”

See the full article here .

five-ways-keep-your-child-safe-school-shootings
Please help promote STEM in your local schools.

Stem Education Coalition

USPS “Forever” postage stamps celebrating Innovation at MIT.

The Massachusetts Institute of Technology (US) is a private land-grant research university in Cambridge, Massachusetts. The institute has an urban campus that extends more than a mile (1.6 km) alongside the Charles River. The institute also encompasses a number of major off-campus facilities such as the MIT Lincoln Laboratory (US), the MIT Bates Research and Engineering Center (US), and the Haystack Observatory (US), as well as affiliated laboratories such as the Broad Institute of MIT and Harvard(US) and Whitehead Institute (US).

Massachusettes Institute of Technology-Haystack Observatory(US) Westford, Massachusetts, USA, Altitude 131 m (430 ft).

Founded in 1861 in response to the increasing industrialization of the United States, Massachusetts Institute of Technology (US) adopted a European polytechnic university model and stressed laboratory instruction in applied science and engineering. It has since played a key role in the development of many aspects of modern science, engineering, mathematics, and technology, and is widely known for its innovation and academic strength. It is frequently regarded as one of the most prestigious universities in the world.

As of December 2020, 97 Nobel laureates, 26 Turing Award winners, and 8 Fields Medalists have been affiliated with MIT as alumni, faculty members, or researchers. In addition, 58 National Medal of Science recipients, 29 National Medals of Technology and Innovation recipients, 50 MacArthur Fellows, 80 Marshall Scholars, 3 Mitchell Scholars, 22 Schwarzman Scholars, 41 astronauts, and 16 Chief Scientists of the U.S. Air Force have been affiliated with The Massachusetts Institute of Technology (US) . The university also has a strong entrepreneurial culture and MIT alumni have founded or co-founded many notable companies. Massachusetts Institute of Technology (US) is a member of the Association of American Universities (AAU).

Foundation and vision

In 1859, a proposal was submitted to the Massachusetts General Court to use newly filled lands in Back Bay, Boston for a “Conservatory of Art and Science”, but the proposal failed. A charter for the incorporation of the Massachusetts Institute of Technology, proposed by William Barton Rogers, was signed by John Albion Andrew, the governor of Massachusetts, on April 10, 1861.

Rogers, a professor from the University of Virginia (US), wanted to establish an institution to address rapid scientific and technological advances. He did not wish to found a professional school, but a combination with elements of both professional and liberal education, proposing that:

“The true and only practicable object of a polytechnic school is, as I conceive, the teaching, not of the minute details and manipulations of the arts, which can be done only in the workshop, but the inculcation of those scientific principles which form the basis and explanation of them, and along with this, a full and methodical review of all their leading processes and operations in connection with physical laws.”

The Rogers Plan reflected the German research university model, emphasizing an independent faculty engaged in research, as well as instruction oriented around seminars and laboratories.

Early developments

Two days after Massachusetts Institute of Technology (US) was chartered, the first battle of the Civil War broke out. After a long delay through the war years, MIT’s first classes were held in the Mercantile Building in Boston in 1865. The new institute was founded as part of the Morrill Land-Grant Colleges Act to fund institutions “to promote the liberal and practical education of the industrial classes” and was a land-grant school. In 1863 under the same act, the Commonwealth of Massachusetts founded the Massachusetts Agricultural College, which developed as the University of Massachusetts Amherst (US)). In 1866, the proceeds from land sales went toward new buildings in the Back Bay.

Massachusetts Institute of Technology (US) was informally called “Boston Tech”. The institute adopted the European polytechnic university model and emphasized laboratory instruction from an early date. Despite chronic financial problems, the institute saw growth in the last two decades of the 19th century under President Francis Amasa Walker. Programs in electrical, chemical, marine, and sanitary engineering were introduced, new buildings were built, and the size of the student body increased to more than one thousand.

The curriculum drifted to a vocational emphasis, with less focus on theoretical science. The fledgling school still suffered from chronic financial shortages which diverted the attention of the MIT leadership. During these “Boston Tech” years, Massachusetts Institute of Technology (US) faculty and alumni rebuffed Harvard University (US) president (and former MIT faculty) Charles W. Eliot’s repeated attempts to merge MIT with Harvard College’s Lawrence Scientific School. There would be at least six attempts to absorb MIT into Harvard. In its cramped Back Bay location, MIT could not afford to expand its overcrowded facilities, driving a desperate search for a new campus and funding. Eventually, the MIT Corporation approved a formal agreement to merge with Harvard, over the vehement objections of MIT faculty, students, and alumni. However, a 1917 decision by the Massachusetts Supreme Judicial Court effectively put an end to the merger scheme.

In 1916, the Massachusetts Institute of Technology (US) administration and the MIT charter crossed the Charles River on the ceremonial barge Bucentaur built for the occasion, to signify MIT’s move to a spacious new campus largely consisting of filled land on a one-mile-long (1.6 km) tract along the Cambridge side of the Charles River. The neoclassical “New Technology” campus was designed by William W. Bosworth and had been funded largely by anonymous donations from a mysterious “Mr. Smith”, starting in 1912. In January 1920, the donor was revealed to be the industrialist George Eastman of Rochester, New York, who had invented methods of film production and processing, and founded Eastman Kodak. Between 1912 and 1920, Eastman donated $20 million ($236.6 million in 2015 dollars) in cash and Kodak stock to MIT.

Curricular reforms

In the 1930s, President Karl Taylor Compton and Vice-President (effectively Provost) Vannevar Bush emphasized the importance of pure sciences like physics and chemistry and reduced the vocational practice required in shops and drafting studios. The Compton reforms “renewed confidence in the ability of the Institute to develop leadership in science as well as in engineering”. Unlike Ivy League schools, Massachusetts Institute of Technology (US) catered more to middle-class families, and depended more on tuition than on endowments or grants for its funding. The school was elected to the Association of American Universities (US)in 1934.

Still, as late as 1949, the Lewis Committee lamented in its report on the state of education at Massachusetts Institute of Technology (US) that “the Institute is widely conceived as basically a vocational school”, a “partly unjustified” perception the committee sought to change. The report comprehensively reviewed the undergraduate curriculum, recommended offering a broader education, and warned against letting engineering and government-sponsored research detract from the sciences and humanities. The School of Humanities, Arts, and Social Sciences and the MIT Sloan School of Management were formed in 1950 to compete with the powerful Schools of Science and Engineering. Previously marginalized faculties in the areas of economics, management, political science, and linguistics emerged into cohesive and assertive departments by attracting respected professors and launching competitive graduate programs. The School of Humanities, Arts, and Social Sciences continued to develop under the successive terms of the more humanistically oriented presidents Howard W. Johnson and Jerome Wiesner between 1966 and 1980.

Massachusetts Institute of Technology (US)‘s involvement in military science surged during World War II. In 1941, Vannevar Bush was appointed head of the federal Office of Scientific Research and Development and directed funding to only a select group of universities, including MIT. Engineers and scientists from across the country gathered at Massachusetts Institute of Technology (US)’s Radiation Laboratory, established in 1940 to assist the British military in developing microwave radar. The work done there significantly affected both the war and subsequent research in the area. Other defense projects included gyroscope-based and other complex control systems for gunsight, bombsight, and inertial navigation under Charles Stark Draper’s Instrumentation Laboratory; the development of a digital computer for flight simulations under Project Whirlwind; and high-speed and high-altitude photography under Harold Edgerton. By the end of the war, Massachusetts Institute of Technology (US) became the nation’s largest wartime R&D contractor (attracting some criticism of Bush), employing nearly 4000 in the Radiation Laboratory alone and receiving in excess of $100 million ($1.2 billion in 2015 dollars) before 1946. Work on defense projects continued even after then. Post-war government-sponsored research at MIT included SAGE and guidance systems for ballistic missiles and Project Apollo.

These activities affected Massachusetts Institute of Technology (US) profoundly. A 1949 report noted the lack of “any great slackening in the pace of life at the Institute” to match the return to peacetime, remembering the “academic tranquility of the prewar years”, though acknowledging the significant contributions of military research to the increased emphasis on graduate education and rapid growth of personnel and facilities. The faculty doubled and the graduate student body quintupled during the terms of Karl Taylor Compton, president of Massachusetts Institute of Technology (US) between 1930 and 1948; James Rhyne Killian, president from 1948 to 1957; and Julius Adams Stratton, chancellor from 1952 to 1957, whose institution-building strategies shaped the expanding university. By the 1950s, Massachusetts Institute of Technology (US) no longer simply benefited the industries with which it had worked for three decades, and it had developed closer working relationships with new patrons, philanthropic foundations and the federal government.

In late 1960s and early 1970s, student and faculty activists protested against the Vietnam War and Massachusetts Institute of Technology (US)’s defense research. In this period Massachusetts Institute of Technology (US)’s various departments were researching helicopters, smart bombs and counterinsurgency techniques for the war in Vietnam as well as guidance systems for nuclear missiles. The Union of Concerned Scientists was founded on March 4, 1969 during a meeting of faculty members and students seeking to shift the emphasis on military research toward environmental and social problems. Massachusetts Institute of Technology (US) ultimately divested itself from the Instrumentation Laboratory and moved all classified research off-campus to the MIT (US) Lincoln Laboratory facility in 1973 in response to the protests. The student body, faculty, and administration remained comparatively unpolarized during what was a tumultuous time for many other universities. Johnson was seen to be highly successful in leading his institution to “greater strength and unity” after these times of turmoil. However six Massachusetts Institute of Technology (US) students were sentenced to prison terms at this time and some former student leaders, such as Michael Albert and George Katsiaficas, are still indignant about MIT’s role in military research and its suppression of these protests. (Richard Leacock’s film, November Actions, records some of these tumultuous events.)

In the 1980s, there was more controversy at Massachusetts Institute of Technology (US) over its involvement in SDI (space weaponry) and CBW (chemical and biological warfare) research. More recently, Massachusetts Institute of Technology (US)’s research for the military has included work on robots, drones and ‘battle suits’.

Recent history

Massachusetts Institute of Technology (US) has kept pace with and helped to advance the digital age. In addition to developing the predecessors to modern computing and networking technologies, students, staff, and faculty members at Project MAC, the Artificial Intelligence Laboratory, and the Tech Model Railroad Club wrote some of the earliest interactive computer video games like Spacewar! and created much of modern hacker slang and culture. Several major computer-related organizations have originated at MIT since the 1980s: Richard Stallman’s GNU Project and the subsequent Free Software Foundation were founded in the mid-1980s at the AI Lab; the MIT Media Lab was founded in 1985 by Nicholas Negroponte and Jerome Wiesner to promote research into novel uses of computer technology; the World Wide Web Consortium standards organization was founded at the Laboratory for Computer Science in 1994 by Tim Berners-Lee; the MIT OpenCourseWare project has made course materials for over 2,000 Massachusetts Institute of Technology (US) classes available online free of charge since 2002; and the One Laptop per Child initiative to expand computer education and connectivity to children worldwide was launched in 2005.

Massachusetts Institute of Technology (US) was named a sea-grant college in 1976 to support its programs in oceanography and marine sciences and was named a space-grant college in 1989 to support its aeronautics and astronautics programs. Despite diminishing government financial support over the past quarter century, MIT launched several successful development campaigns to significantly expand the campus: new dormitories and athletics buildings on west campus; the Tang Center for Management Education; several buildings in the northeast corner of campus supporting research into biology, brain and cognitive sciences, genomics, biotechnology, and cancer research; and a number of new “backlot” buildings on Vassar Street including the Stata Center. Construction on campus in the 2000s included expansions of the Media Lab, the Sloan School’s eastern campus, and graduate residences in the northwest. In 2006, President Hockfield launched the MIT Energy Research Council to investigate the interdisciplinary challenges posed by increasing global energy consumption.

In 2001, inspired by the open source and open access movements, Massachusetts Institute of Technology (US) launched OpenCourseWare to make the lecture notes, problem sets, syllabi, exams, and lectures from the great majority of its courses available online for no charge, though without any formal accreditation for coursework completed. While the cost of supporting and hosting the project is high, OCW expanded in 2005 to include other universities as a part of the OpenCourseWare Consortium, which currently includes more than 250 academic institutions with content available in at least six languages. In 2011, Massachusetts Institute of Technology (US) announced it would offer formal certification (but not credits or degrees) to online participants completing coursework in its “MITx” program, for a modest fee. The “edX” online platform supporting MITx was initially developed in partnership with Harvard and its analogous “Harvardx” initiative. The courseware platform is open source, and other universities have already joined and added their own course content. In March 2009 the Massachusetts Institute of Technology (US) faculty adopted an open-access policy to make its scholarship publicly accessible online.

Massachusetts Institute of Technology (US) has its own police force. Three days after the Boston Marathon bombing of April 2013, MIT Police patrol officer Sean Collier was fatally shot by the suspects Dzhokhar and Tamerlan Tsarnaev, setting off a violent manhunt that shut down the campus and much of the Boston metropolitan area for a day. One week later, Collier’s memorial service was attended by more than 10,000 people, in a ceremony hosted by the Massachusetts Institute of Technology (US) community with thousands of police officers from the New England region and Canada. On November 25, 2013, Massachusetts Institute of Technology (US) announced the creation of the Collier Medal, to be awarded annually to “an individual or group that embodies the character and qualities that Officer Collier exhibited as a member of the Massachusetts Institute of Technology (US) community and in all aspects of his life”. The announcement further stated that “Future recipients of the award will include those whose contributions exceed the boundaries of their profession, those who have contributed to building bridges across the community, and those who consistently and selflessly perform acts of kindness”.

In September 2017, the school announced the creation of an artificial intelligence research lab called the MIT-IBM Watson AI Lab. IBM will spend $240 million over the next decade, and the lab will be staffed by MIT and IBM scientists. In October 2018 MIT announced that it would open a new Schwarzman College of Computing dedicated to the study of artificial intelligence, named after lead donor and The Blackstone Group CEO Stephen Schwarzman. The focus of the new college is to study not just AI, but interdisciplinary AI education, and how AI can be used in fields as diverse as history and biology. The cost of buildings and new faculty for the new college is expected to be $1 billion upon completion.

The Caltech/MIT Advanced aLIGO (US) was designed and constructed by a team of scientists from California Institute of Technology (US), Massachusetts Institute of Technology (US), and industrial contractors, and funded by the National Science Foundation (US) .

Caltech /MIT Advanced aLigo

It was designed to open the field of gravitational-wave astronomy through the detection of gravitational waves predicted by general relativity. Gravitational waves were detected for the first time by the LIGO detector in 2015. For contributions to the LIGO detector and the observation of gravitational waves, two Caltech physicists, Kip Thorne and Barry Barish, and Massachusetts Institute of Technology (US) physicist Rainer Weiss won the Nobel Prize in physics in 2017. Weiss, who is also an Massachusetts Institute of Technology (US) graduate, designed the laser interferometric technique, which served as the essential blueprint for the LIGO.

The mission of Massachusetts Institute of Technology (US) is to advance knowledge and educate students in science, technology, and other areas of scholarship that will best serve the nation and the world in the twenty-first century. We seek to develop in each member of The Massachusetts Institute of Technology community the ability and passion to work wisely, creatively, and effectively for the betterment of humankind.

From The University of Toronto (CA) : “‘A really big deal’ U of T’s Colin Furness on why ventilation is key to fighting COVID-19”

From The University of Toronto (CA)

November 24, 2021
Mariam Matti

Photo by Steve Russell/Toronto Star via Getty Images.

As the weather turns colder and people move indoors, the University of Toronto’s Colin Furness is emphasizing the importance of proper ventilation to combat the spread of the virus that causes COVID-19.

The expert in infection control epidemiology and COVID-19 pandemic management says it’s well-established in the medical community that airborne transmission is major contributor to the spread SARS‑CoV‑2. But he notes that public health regulations have often been slow to catch up, leaving many businesses and other organizations with less-than-optimal safeguards.

There is, however, a notable exception: post-secondary institutions.

Furness recently spoke to University Affairs about how some universities – including U of T – are at the forefront of addressing ventilation by retrofitting HVAC systems.

At U of T for example, HVAC experts made recommendations that were quickly adopted. Centralized HVAC system filters that service all parts of buildings including offices, meeting rooms and hallways, were replaced with enhanced MERV 13 filters (or the highest compatible with the existing HVAC infrastructure). Demand-control ventilation measures (typically in place to support energy conservation efforts) were disabled to maintain consistent in-air flow. Ventilation systems are turned on two hours before occupancy every morning to replace the air in entire buildings, a process known as flushing.

“Universities have expertise. They’ve got respect for expertise. And they have decision-making that actually incorporates that expertise,” says Furness, an assistant professor, teaching stream, in the Faculty of Information with a cross-appointment to the Institute of Health Policy, Management and Evaluation at the Dalla Lana School of Public Health.

He adds that such qualities make universities “incredibly resilient.”

Furness has even gone so far as to test the air quality in his own classroom.

To learn more about why HVAC systems matter, U of T News spoke with Furness about airborne transmission of SARS‑CoV‑2 and how to guard against it.
____________________________________________________________________________________

Why is having proper ventilation so important in combatting COVID-19?

In the earliest days of the pandemic, we relied on our existing knowledge around transmission. It was a model that said large droplets are it and therefore we don’t need to worry about air – but that view was flawed. It allowed us to explain a communicable respiratory disease, even though it wasn’t quite correct.

We now know that not only does COVID-19 move through the air, but that air seems to be the dominant mode of transmission. That’s a very new way of thinking. It means we have to unlearn a lot about what we thought we knew about respiratory disease. We’ve learned more about respiratory disease transmission in the last year and a half than I think we ever have. It’s a really big deal.

It seems like universities adapted fairly quickly, compared to other organizations. Why do you think that is?

Universities have expertise. They’ve got respect for expertise. And they have decision-making that actually incorporates that expertise. Those are three things that make universities incredibly resilient.

We didn’t wait for others to say air matters. The leading voices in Canada are here at the U of T with respect to infectious disease and epidemiology. We consulted our own internal expertise.

U of T jumped in from the beginning and started prioritizing air and ventilation, which is really smart.

Can you explain why proper HVAC systems are effective in combating the virus?

What we understand with airborne transmission is that, if you’re infected and you exhale, the virions of the virus – viral particles – are going to stay in the air for a long time and they’re going to accumulate in the air. In other words, an infected person sitting in a room is going to continue to add to the concentration of dangerous virions in the room.

What ventilation does is it take those virions and flush them out of the room by changing the air.

You can have two people in a very well-ventilated room – one sick, one not, and the person who’s not sick is perhaps not going to get sick because they’re not breathing in the unadulterated exhalations of the other person. They’re also breathing in fresh air.

Can you talk about what you’ve found testing the air quality in your classroom?

I work in a building that has forced air circulation. It has mechanical systems that can be adjusted to do what they do best. They not only circulate air, but they also exchange air from the inside the room with the air from outside the building.

In my classroom, I’ve measured the CO2 levels. The more carbon dioxide there is in the room, the more exhalations you have as opposed to fresh air. Outdoor air is about 400 parts per million in carbon dioxide. That’s the gold standard. If you’ve got air that is higher than 1,500 parts per million, you’ve got stale air.

With COVID-19, the best practice says you should try and stay under 800 parts per million, which is very aggressive. I found my classroom is usually around 460 to 520 – so very, very close to outdoor air. I’ve got 25 students in this class and the room is big and the other thing is, at the moment, the building is sparsely populated. So, as more people start to spend more time there, we might expect those numbers to creep up a little bit. But I was flabbergasted. I bought a second unit because I didn’t think the air could be that good.

I want to point out that I’m lucky. There are many buildings that don’t have forced air where managing air quality is going to be a lot harder. And you’ve got other kinds of challenging places like university residences and labs that have people working in close proximity and pretty complicated infrastructure. I mean, a university is a city within a city. So, I do want to acknowledge it’s not always easy.

I’m going to run through three scenarios that people might find themselves in this winter. Can you weigh in on what can be done to improve air flow?

a. On public transit or in a taxi

If you’re on a bus, streetcar or taxi, open a window. There was an interesting study [Science Advances] done around where’s the best place to sit in a taxi – in the backseat, kitty-corner to the driver.

They came to that conclusion not by measuring distance, but by modelling airflow when you have the windows open. But regardless of where you’re sitting, open the windows and let the air move through. And wear an N95 mask. That’s what people should be doing to stay maximally safe.

b. In your own home

Part of it will depend on who else is in your home. Do you share air with other dwellings? Condos and apartment buildings might have a higher risk profile depending on how air moves. But even if you’re in a single-family house and you have control of your own air, then you still want to ask: What are the risks in my house?

In my case, we’ve got two kids. One of them is under 12 and they’re both in school. They’re getting exposed to a lot of other kids and the younger one is not vaccinated. What we did at my home last fall was buy portable HEPA filters – about eight of them. I thought: If someone comes home with COVID-19, we may see transmission before we know it’s a problem. We’re not going to wear masks at home, so I thought we should be scrubbing the air as much as possible.

Opening your door or window for 10 minutes can be transformational. If you want to measure carbon dioxide in your house, you can buy a detector – which I recommend – and you can really start to get a sense of what it takes, in terms of human activity in one room, for carbon dioxide to go way up, and what it takes in terms of opening a window or a door for 10 minutes for carbon dioxide levels to go back down.

So, it’s opening windows, periodically measuring carbon dioxide and deploying HEPA filters.

c. In a bar or restaurant

Unfortunately, my advice is not to go. At this point in the pandemic, sharing air with people who you don’t know and not wearing a mask while you’re indoors is not something I would do. I’ll re-evaluate that position when I see HEPA filters in restaurants, in gyms or in public places where people are together and not wearing masks. This, to me, is extremely high risk.

We should be putting up HEPA filters in restaurants, gyms, movie theatres and other kinds of places where people are going to be gathered together and not wearing masks.

My family loves to support our local businesses by getting takeout and that’s what we’ll keep doing until COVID-19 is subdued or we know that we’re getting clean, scrubbed air in a restaurant.

Is an air purifier a useful investment for a household?

I’m a big fan of portable HEPA filters. You do need to change the filters periodically. But the filters can be vacuumed and their life can be extended. It doesn’t need to be extremely expensive. They help with a lot – with allergies, mould, and all kinds of bacterial spores in the air.

I have just purchased a HEPA unit for my furnace as well. It’s a long-term investment in air quality – above and beyond COVID-19.

See the full article here .

five-ways-keep-your-child-safe-school-shootings

Please help promote STEM in your local schools.

Stem Education Coalition

The The University of Toronto (CA) is a public research university in Toronto, Ontario, Canada, located on the grounds that surround Queen’s Park. It was founded by royal charter in 1827 as King’s College, the oldest university in the province of Ontario.

Originally controlled by the Church of England, the university assumed its present name in 1850 upon becoming a secular institution.

As a collegiate university, it comprises eleven colleges each with substantial autonomy on financial and institutional affairs and significant differences in character and history. The university also operates two satellite campuses located in Scarborough and Mississauga.

University of Toronto has evolved into Canada’s leading institution of learning, discovery and knowledge creation. We are proud to be one of the world’s top research-intensive universities, driven to invent and innovate.

Our students have the opportunity to learn from and work with preeminent thought leaders through our multidisciplinary network of teaching and research faculty, alumni and partners.

The ideas, innovations and actions of more than 560,000 graduates continue to have a positive impact on the world.

Academically, the University of Toronto is noted for movements and curricula in literary criticism and communication theory, known collectively as the Toronto School.

The university was the birthplace of insulin and stem cell research, and was the site of the first electron microscope in North America; the identification of the first black hole Cygnus X-1; multi-touch technology, and the development of the theory of NP-completeness.

The university was one of several universities involved in early research of deep learning. It receives the most annual scientific research funding of any Canadian university and is one of two members of the Association of American Universities (US) outside the United States, the other being McGill(CA).

The Varsity Blues are the athletic teams that represent the university in intercollegiate league matches, with ties to gridiron football, rowing and ice hockey. The earliest recorded instance of gridiron football occurred at University of Toronto’s University College in November 1861.

The university’s Hart House is an early example of the North American student centre, simultaneously serving cultural, intellectual, and recreational interests within its large Gothic-revival complex.

The University of Toronto has educated three Governors General of Canada, four Prime Ministers of Canada, three foreign leaders, and fourteen Justices of the Supreme Court. As of March 2019, ten Nobel laureates, five Turing Award winners, 94 Rhodes Scholars, and one Fields Medalist have been affiliated with the university.

Early history

The founding of a colonial college had long been the desire of John Graves Simcoe, the first Lieutenant-Governor of Upper Canada and founder of York, the colonial capital. As an University of Oxford (UK)-educated military commander who had fought in the American Revolutionary War, Simcoe believed a college was needed to counter the spread of republicanism from the United States. The Upper Canada Executive Committee recommended in 1798 that a college be established in York.

On March 15, 1827, a royal charter was formally issued by King George IV, proclaiming “from this time one College, with the style and privileges of a University … for the education of youth in the principles of the Christian Religion, and for their instruction in the various branches of Science and Literature … to continue for ever, to be called King’s College.” The granting of the charter was largely the result of intense lobbying by John Strachan, the influential Anglican Bishop of Toronto who took office as the college’s first president. The original three-storey Greek Revival school building was built on the present site of Queen’s Park.

Under Strachan’s stewardship, King’s College was a religious institution closely aligned with the Church of England and the British colonial elite, known as the Family Compact. Reformist politicians opposed the clergy’s control over colonial institutions and fought to have the college secularized. In 1849, after a lengthy and heated debate, the newly elected responsible government of the Province of Canada voted to rename King’s College as the University of Toronto and severed the school’s ties with the church. Having anticipated this decision, the enraged Strachan had resigned a year earlier to open Trinity College as a private Anglican seminary. University College was created as the nondenominational teaching branch of the University of Toronto. During the American Civil War the threat of Union blockade on British North America prompted the creation of the University Rifle Corps which saw battle in resisting the Fenian raids on the Niagara border in 1866. The Corps was part of the Reserve Militia lead by Professor Henry Croft.

Established in 1878, the School of Practical Science was the precursor to the Faculty of Applied Science and Engineering which has been nicknamed Skule since its earliest days. While the Faculty of Medicine opened in 1843 medical teaching was conducted by proprietary schools from 1853 until 1887 when the faculty absorbed the Toronto School of Medicine. Meanwhile the university continued to set examinations and confer medical degrees. The university opened the Faculty of Law in 1887, followed by the Faculty of Dentistry in 1888 when the Royal College of Dental Surgeons became an affiliate. Women were first admitted to the university in 1884.

A devastating fire in 1890 gutted the interior of University College and destroyed 33,000 volumes from the library but the university restored the building and replenished its library within two years. Over the next two decades a collegiate system took shape as the university arranged federation with several ecclesiastical colleges including Strachan’s Trinity College in 1904. The university operated the Royal Conservatory of Music from 1896 to 1991 and the Royal Ontario Museum from 1912 to 1968; both still retain close ties with the university as independent institutions. The University of Toronto Press was founded in 1901 as Canada’s first academic publishing house. The Faculty of Forestry founded in 1907 with Bernhard Fernow as dean was Canada’s first university faculty devoted to forest science. In 1910, the Faculty of Education opened its laboratory school, the University of Toronto Schools.

World wars and post-war years

The First and Second World Wars curtailed some university activities as undergraduate and graduate men eagerly enlisted. Intercollegiate athletic competitions and the Hart House Debates were suspended although exhibition and interfaculty games were still held. The David Dunlap Observatory in Richmond Hill opened in 1935 followed by the University of Toronto Institute for Aerospace Studies in 1949. The university opened satellite campuses in Scarborough in 1964 and in Mississauga in 1967. The university’s former affiliated schools at the Ontario Agricultural College and Glendon Hall became fully independent of the University of Toronto and became part of University of Guelph (CA) in 1964 and York University (CA) in 1965 respectively. Beginning in the 1980s reductions in government funding prompted more rigorous fundraising efforts.

Since 2000

In 2000 Kin-Yip Chun was reinstated as a professor of the university after he launched an unsuccessful lawsuit against the university alleging racial discrimination. In 2017 a human rights application was filed against the University by one of its students for allegedly delaying the investigation of sexual assault and being dismissive of their concerns. In 2018 the university cleared one of its professors of allegations of discrimination and antisemitism in an internal investigation after a complaint was filed by one of its students.

The University of Toronto was the first Canadian university to amass a financial endowment greater than c. $1 billion in 2007. On September 24, 2020 the university announced a $250 million gift to the Faculty of Medicine from businessman and philanthropist James C. Temerty- the largest single philanthropic donation in Canadian history. This broke the previous record for the school set in 2019 when Gerry Schwartz and Heather Reisman jointly donated $100 million for the creation of a 750,000-square foot innovation and artificial intelligence centre.

Research

Since 1926 the University of Toronto has been a member of the Association of American Universities (US) a consortium of the leading North American research universities. The university manages by far the largest annual research budget of any university in Canada with sponsored direct-cost expenditures of $878 million in 2010. In 2018 the University of Toronto was named the top research university in Canada by Research Infosource with a sponsored research income (external sources of funding) of $1,147.584 million in 2017. In the same year the university’s faculty averaged a sponsored research income of $428,200 while graduate students averaged a sponsored research income of $63,700. The federal government was the largest source of funding with grants from the Canadian Institutes of Health Research; the Natural Sciences and Engineering Research Council; and the Social Sciences and Humanities Research Council amounting to about one-third of the research budget. About eight percent of research funding came from corporations- mostly in the healthcare industry.

The first practical electron microscope was built by the physics department in 1938. During World War II the university developed the G-suit- a life-saving garment worn by Allied fighter plane pilots later adopted for use by astronauts.Development of the infrared chemiluminescence technique improved analyses of energy behaviours in chemical reactions. In 1963 the asteroid 2104 Toronto was discovered in the David Dunlap Observatory (CA) in Richmond Hill and is named after the university. In 1972 studies on Cygnus X-1 led to the publication of the first observational evidence proving the existence of black holes. Toronto astronomers have also discovered the Uranian moons of Caliban and Sycorax; the dwarf galaxies of Andromeda I, II and III; and the supernova SN 1987A. A pioneer in computing technology the university designed and built UTEC- one of the world’s first operational computers- and later purchased Ferut- the second commercial computer after UNIVAC I. Multi-touch technology was developed at Toronto with applications ranging from handheld devices to collaboration walls. The AeroVelo Atlas which won the Igor I. Sikorsky Human Powered Helicopter Competition in 2013 was developed by the university’s team of students and graduates and was tested in Vaughan.

The discovery of insulin at the University of Toronto in 1921 is considered among the most significant events in the history of medicine. The stem cell was discovered at the university in 1963 forming the basis for bone marrow transplantation and all subsequent research on adult and embryonic stem cells. This was the first of many findings at Toronto relating to stem cells including the identification of pancreatic and retinal stem cells. The cancer stem cell was first identified in 1997 by Toronto researchers who have since found stem cell associations in leukemia; brain tumors; and colorectal cancer. Medical inventions developed at Toronto include the glycaemic index; the infant cereal Pablum; the use of protective hypothermia in open heart surgery; and the first artificial cardiac pacemaker. The first successful single-lung transplant was performed at Toronto in 1981 followed by the first nerve transplant in 1988; and the first double-lung transplant in 1989. Researchers identified the maturation promoting factor that regulates cell division and discovered the T-cell receptor which triggers responses of the immune system. The university is credited with isolating the genes that cause Fanconi anemia; cystic fibrosis; and early-onset Alzheimer’s disease among numerous other diseases. Between 1914 and 1972 the university operated the Connaught Medical Research Laboratories- now part of the pharmaceutical corporation Sanofi-Aventis. Among the research conducted at the laboratory was the development of gel electrophoresis.

The University of Toronto is the primary research presence that supports one of the world’s largest concentrations of biotechnology firms. More than 5,000 principal investigators reside within 2 kilometres (1.2 mi) from the university grounds in Toronto’s Discovery District conducting $1 billion of medical research annually. MaRS Discovery District is a research park that serves commercial enterprises and the university’s technology transfer ventures. In 2008, the university disclosed 159 inventions and had 114 active start-up companies. Its SciNet Consortium operates the most powerful supercomputer in Canada.

From Asociacion RUVID via phys.org : “Portable device capable of monitoring gamma radiation and neutrons in radioactive and nuclear processes”

From Asociacion RUVID(ES)

via

phys.org

November 15, 2021

Credit: Asociacion RUVID(ES)

A group of researchers from the Institute of Corpuscular Physics (IFIC), a joint center of The University of Valencia [Universitat de València](ES) and the Spanish National Research Council (CSIC), has patented a compact and portable device capable of simultaneously monitoring gamma radiation and neutrons produced in radioactive processes and nuclear reactions. This detector also makes it possible to measure these radiations with a wide range of energy and visualize them spatially, which can give rise to multiple applications: from the detection of radioactive materials in nuclear safety programs to mitigating the side effects of hadron therapy, a novel way to treat cancer.

The development of this detector arises from a basic research project funded by the European Research Council (ERC) for IFIC researcher César Domingo Pardo through the Consolidator Grant program. The HYMNS project tries to reproduce in the laboratory the nuclear reactions that occur inside stars, and thus study the formation of elements heavier than iron in the Universe. In these processes, photons are produced, the particles that make up light, in the form of gamma radiation, and also neutrons, one of the components of the atom’s nucleus along with protons.

“To reduce this neutron radiation and better study the nuclear processes that occur inside stars, we have developed a series of advanced measurement techniques and instruments capable of minimizing this neutron background,” explains César Domingo, who is leading the experiment. “We quickly realized that these techniques could have applications in the field of nuclear security, port surveillance and even in medical cancer therapies such as hadrontherapy.”

The device consists of a special collimator enriched with a lithium isotope that allows the absorption of neutrons and prevents the background radiation produced by the collimator itself. “By using this collimator in the foreground, a pinhole camera is formed that allows an image of neutron radiation to be made with great precision and detection efficiency while simultaneously allowing gamma imaging techniques to be applied,” he says.

IFIC. Detector compacto de radiaciones gamma y de neutrones.

On the other hand, gamma radiation is visualized using electronic collimation with two detection planes: in the first, the gamma ray is scattered, and in the second it is completely absorbed. “By uniting the energy and spatial information from both planes, we are able to reconstruct the spatial origin of this gamma radiation,” says Jorge Lerendegui, a CSIC researcher participating in this project.

Applications

Among the main applications of this device is nuclear safety. “The detector would make it possible to identify sources of nuclear radiation that may point to uranium or plutonium, which emit these two types of radiation,” says Lerendegui. In addition to detecting gamma and neutron radiation at the same time, the device developed at the IFIC is more compact and lightweight, “and makes a difference with other older, bulkier devices, which implies greater portability and increases the range of applications of this new system,” says César Domingo.

The researchers place another of the possible applications of this device in hadron therapy. This type of therapy uses protons to treat certain types of very localized tumors. The advantage over conventional radiotherapy, which uses photons, is that hadrontherapy mainly affects the tumor and minimizes damage to surrounding healthy tissues.

In the path of the protons towards the tumor, gamma rays are produced, “which can be analyzed with this device to know with great precision their trajectory and if they really deposit most of their energy in the tumor,” says Jorge Lerendegui. “On the other hand, neutrons are also produced, which represent the main source of secondary dose in this type of therapy. Therefore, monitoring both types of radiation would represent a significant breakthrough in this field.”

See the full article here .

five-ways-keep-your-child-safe-school-shootings

Please help promote STEM in your local schools.

Stem Education Coalition

About Science X in 100 words
Science X™ is a leading web-based science, research and technology news service which covers a full range of topics. These include physics, earth science, medicine, nanotechnology, electronics, space, biology, chemistry, computer sciences, engineering, mathematics and other sciences and technologies. Launched in 2004 (Physorg.com), Science X’s readership has grown steadily to include 5 million scientists, researchers, and engineers every month. Science X publishes approximately 200 quality articles every day, offering some of the most comprehensive coverage of sci-tech developments world-wide. Science X community members enjoy access to many personalized features such as social networking, a personal home page set-up, article comments and ranking, the ability to save favorite articles, a daily newsletter, and other options.
Mission 12 reasons for reading daily news on Science X Organization Key editors and writers include 1.75 million scientists, researchers, and engineers every month. Phys.org publishes approximately 100 quality articles every day, offering some of the most comprehensive coverage of sci-tech developments world-wide. Quancast 2009 includes Phys.org in its list of the Global Top 2,000 Websites. Phys.org community members enjoy access to many personalized features such as social networking, a personal home page set-up, RSS/XML feeds, article comments and ranking, the ability to save favorite articles, a daily newsletter, and other options.

From Yale University (US) : “Study examines severe breakthrough cases of COVID-19”

From Yale University (US)

September 7, 2021
Mallory Locklear

(Illustration by Michael S. Helfenbein)

A new Yale study provides important insights into breakthrough COVID-19 cases — instances where fully vaccinated individuals are infected by SARS-CoV-2 — and who is particularly vulnerable to serious illness.

In a study of hospitalized patients in the Yale New Haven Health System, researchers identified 969 individuals who tested positive for the SARS-CoV-2 infection during a 14-week period between March and July 2021. Of that group, 54 were fully vaccinated.

“These cases are extremely rare, but they are becoming more frequent as variants emerge and more time passes since patients are vaccinated,” said Hyung Chun, associate professor of medicine (cardiology) at Yale and senior author of the study published Sept. 7 in Lancet Infectious Diseases.

As of Aug. 30, the Centers for Disease Control and Prevention (US) had received reports of 12,908 patients with breakthrough infections who were hospitalized or died — less than 0.008% of fully vaccinated individuals in the United States. “Identifying who is more likely to develop severe COVID-19 illness after vaccination will be critical to ongoing efforts to mitigate the impact of these breakthrough infections.”

While researchers in the new study observed a wide range of illness severity among the fully vaccinated patients who were hospitalized and tested positive for COVID-19, more than a quarter of this group were found to have severe or critical disease. All patients with severe or critical cases — 14 in total — required supplementary oxygen support, four were admitted to the intensive care unit, and three died.

These patients tended to be older — between 65 and 95 years old with a median age of 80.5 — and had preexisting comorbidities, such as cardiovascular disease and Type 2 diabetes. A subset of patients was also on immunosuppressive drugs that may affect vaccine efficacy.

“The majority of fully vaccinated patients experience mild or no symptoms if infected with SARS-CoV-2,” Chun said. “This research identifies those who suffered more severe disease, and we need a better understanding of how to best manage these patients.”

Chun noted that many of the patients with severe breakthrough infections in the study were hospitalized before the Delta variant became the predominant variant of SARS-CoV-2 in the United States. Additional research will be needed to determine the impact of the Delta variant on the rate of breakthrough COVID-19, he said.

Chun and his colleagues are now investigating severe breakthrough cases to examine what is taking place at the molecular level. His team plans to study these patients to identify any unique mechanisms that may be driving disease severity in the breakthrough cases compared with COVID-19 infections in those yet to be vaccinated.

“It’s clear that the vaccines are highly effective, and without them we would be facing a much deadlier pandemic,” he said. “As effective as the vaccines are, with emerging variants and increasing cases of breakthrough infections, we need to continue to be vigilant in taking measures such as indoor masking and social distancing.”

Prerak Juthani, Akash Gupta, and Kelly Borges were co-lead authors of the study. Other Yale authors include Christina Price, Alfred Lee, and Christine Won.

See the full article here .

five-ways-keep-your-child-safe-school-shootings

Please help promote STEM in your local schools.

Stem Education Coalition

Yale University (US) is a private Ivy League research university in New Haven, Connecticut. Founded in 1701 as the Collegiate School, it is the third-oldest institution of higher education in the United States and one of the nine Colonial Colleges chartered before the American Revolution. The Collegiate School was renamed Yale College in 1718 to honor the school’s largest private benefactor for the first century of its existence, Elihu Yale. Yale University is consistently ranked as one of the top universities and is considered one of the most prestigious in the nation.

Chartered by Connecticut Colony, the Collegiate School was established in 1701 by clergy to educate Congregational ministers before moving to New Haven in 1716. Originally restricted to theology and sacred languages, the curriculum began to incorporate humanities and sciences by the time of the American Revolution. In the 19th century, the college expanded into graduate and professional instruction, awarding the first PhD in the United States in 1861 and organizing as a university in 1887. Yale’s faculty and student populations grew after 1890 with rapid expansion of the physical campus and scientific research.

Yale is organized into fourteen constituent schools: the original undergraduate college, the Yale Graduate School of Arts and Sciences and twelve professional schools. While the university is governed by the Yale Corporation, each school’s faculty oversees its curriculum and degree programs. In addition to a central campus in downtown New Haven, the university owns athletic facilities in western New Haven, a campus in West Haven, Connecticut, and forests and nature preserves throughout New England. As of June 2020, the university’s endowment was valued at $31.1 billion, the second largest of any educational institution. The Yale University Library, serving all constituent schools, holds more than 15 million volumes and is the third-largest academic library in the United States. Students compete in intercollegiate sports as the Yale Bulldogs in the NCAA Division I – Ivy League.

As of October 2020, 65 Nobel laureates, five Fields Medalists, four Abel Prize laureates, and three Turing award winners have been affiliated with Yale University. In addition, Yale has graduated many notable alumni, including five U.S. Presidents, 19 U.S. Supreme Court Justices, 31 living billionaires, and many heads of state. Hundreds of members of Congress and many U.S. diplomats, 78 MacArthur Fellows, 252 Rhodes Scholars, 123 Marshall Scholars, and nine Mitchell Scholars have been affiliated with the university.

Research

Yale is a member of the Association of American Universities (AAU) (US) and is classified among “R1: Doctoral Universities – Very high research activity”. According to the National Science Foundation (US), Yale spent $990 million on research and development in 2018, ranking it 15th in the nation.

Yale’s faculty include 61 members of the National Academy of Sciences (US), 7 members of the National Academy of Engineering (US) and 49 members of the American Academy of Arts and Sciences (US). The college is, after normalization for institution size, the tenth-largest baccalaureate source of doctoral degree recipients in the United States, and the largest such source within the Ivy League.

Yale’s English and Comparative Literature departments were part of the New Criticism movement. Of the New Critics, Robert Penn Warren, W.K. Wimsatt, and Cleanth Brooks were all Yale faculty. Later, the Yale Comparative literature department became a center of American deconstruction. Jacques Derrida, the father of deconstruction, taught at the Department of Comparative Literature from the late seventies to mid-1980s. Several other Yale faculty members were also associated with deconstruction, forming the so-called “Yale School”. These included Paul de Man who taught in the Departments of Comparative Literature and French, J. Hillis Miller, Geoffrey Hartman (both taught in the Departments of English and Comparative Literature), and Harold Bloom (English), whose theoretical position was always somewhat specific, and who ultimately took a very different path from the rest of this group. Yale’s history department has also originated important intellectual trends. Historians C. Vann Woodward and David Brion Davis are credited with beginning in the 1960s and 1970s an important stream of southern historians; likewise, David Montgomery, a labor historian, advised many of the current generation of labor historians in the country. Yale’s Music School and Department fostered the growth of Music Theory in the latter half of the 20th century. The Journal of Music Theory was founded there in 1957; Allen Forte and David Lewin were influential teachers and scholars.

In addition to eminent faculty members, Yale research relies heavily on the presence of roughly 1200 Postdocs from various national and international origin working in the multiple laboratories in the sciences, social sciences, humanities, and professional schools of the university. The university progressively recognized this working force with the recent creation of the Office for Postdoctoral Affairs and the Yale Postdoctoral Association.

Notable alumni

Over its history, Yale has produced many distinguished alumni in a variety of fields, ranging from the public to private sector. According to 2020 data, around 71% of undergraduates join the workforce, while the next largest majority of 16.6% go on to attend graduate or professional schools. Yale graduates have been recipients of 252 Rhodes Scholarships, 123 Marshall Scholarships, 67 Truman Scholarships, 21 Churchill Scholarships, and 9 Mitchell Scholarships. The university is also the second largest producer of Fulbright Scholars, with a total of 1,199 in its history and has produced 89 MacArthur Fellows. The U.S. Department of State Bureau of Educational and Cultural Affairs ranked Yale fifth among research institutions producing the most 2020–2021 Fulbright Scholars. Additionally, 31 living billionaires are Yale alumni.

At Yale, one of the most popular undergraduate majors among Juniors and Seniors is political science, with many students going on to serve careers in government and politics. Former presidents who attended Yale for undergrad include William Howard Taft, George H. W. Bush, and George W. Bush while former presidents Gerald Ford and Bill Clinton attended Yale Law School. Former vice-president and influential antebellum era politician John C. Calhoun also graduated from Yale. Former world leaders include Italian prime minister Mario Monti, Turkish prime minister Tansu Çiller, Mexican president Ernesto Zedillo, German president Karl Carstens, Philippine president José Paciano Laurel, Latvian president Valdis Zatlers, Taiwanese premier Jiang Yi-huah, and Malawian president Peter Mutharika, among others. Prominent royals who graduated are Crown Princess Victoria of Sweden, and Olympia Bonaparte, Princess Napoléon.

Yale alumni have had considerable presence in U.S. government in all three branches. On the U.S. Supreme Court, 19 justices have been Yale alumni, including current Associate Justices Sonia Sotomayor, Samuel Alito, Clarence Thomas, and Brett Kavanaugh. Numerous Yale alumni have been U.S. Senators, including current Senators Michael Bennet, Richard Blumenthal, Cory Booker, Sherrod Brown, Chris Coons, Amy Klobuchar, Ben Sasse, and Sheldon Whitehouse. Current and former cabinet members include Secretaries of State John Kerry, Hillary Clinton, Cyrus Vance, and Dean Acheson; U.S. Secretaries of the Treasury Oliver Wolcott, Robert Rubin, Nicholas F. Brady, Steven Mnuchin, and Janet Yellen; U.S. Attorneys General Nicholas Katzenbach, John Ashcroft, and Edward H. Levi; and many others. Peace Corps founder and American diplomat Sargent Shriver and public official and urban planner Robert Moses are Yale alumni.

Yale has produced numerous award-winning authors and influential writers, like Nobel Prize in Literature laureate Sinclair Lewis and Pulitzer Prize winners Stephen Vincent Benét, Thornton Wilder, Doug Wright, and David McCullough. Academy Award winning actors, actresses, and directors include Jodie Foster, Paul Newman, Meryl Streep, Elia Kazan, George Roy Hill, Lupita Nyong’o, Oliver Stone, and Frances McDormand. Alumni from Yale have also made notable contributions to both music and the arts. Leading American composer from the 20th century Charles Ives, Broadway composer Cole Porter, Grammy award winner David Lang, and award-winning jazz pianist and composer Vijay Iyer all hail from Yale. Hugo Boss Prize winner Matthew Barney, famed American sculptor Richard Serra, President Barack Obama presidential portrait painter Kehinde Wiley, MacArthur Fellow and contemporary artist Sarah Sze, Pulitzer Prize winning cartoonist Garry Trudeau, and National Medal of Arts photorealist painter Chuck Close all graduated from Yale. Additional alumni include architect and Presidential Medal of Freedom winner Maya Lin, Pritzker Prize winner Norman Foster, and Gateway Arch designer Eero Saarinen. Journalists and pundits include Dick Cavett, Chris Cuomo, Anderson Cooper, William F. Buckley, Jr., and Fareed Zakaria.

In business, Yale has had numerous alumni and former students go on to become founders of influential business, like William Boeing (Boeing, United Airlines), Briton Hadden and Henry Luce (Time Magazine), Stephen A. Schwarzman (Blackstone Group), Frederick W. Smith (FedEx), Juan Trippe (Pan Am), Harold Stanley (Morgan Stanley), Bing Gordon (Electronic Arts), and Ben Silbermann (Pinterest). Other business people from Yale include former chairman and CEO of Sears Holdings Edward Lampert, former Time Warner president Jeffrey Bewkes, former PepsiCo chairperson and CEO Indra Nooyi, sports agent Donald Dell, and investor/philanthropist Sir John Templeton,

Yale alumni distinguished in academia include literary critic and historian Henry Louis Gates, economists Irving Fischer, Mahbub ul Haq, and Nobel Prize laureate Paul Krugman; Nobel Prize in Physics laureates Ernest Lawrence and Murray Gell-Mann; Fields Medalist John G. Thompson; Human Genome Project leader and National Institutes of Health (US) director Francis S. Collins; brain surgery pioneer Harvey Cushing; pioneering computer scientist Grace Hopper; influential mathematician and chemist Josiah Willard Gibbs; National Women’s Hall of Fame inductee and biochemist Florence B. Seibert; Turing Award recipient Ron Rivest; inventors Samuel F.B. Morse and Eli Whitney; Nobel Prize in Chemistry laureate John B. Goodenough; lexicographer Noah Webster; and theologians Jonathan Edwards and Reinhold Niebuhr.

In the sporting arena, Yale alumni include baseball players Ron Darling and Craig Breslow and baseball executives Theo Epstein and George Weiss; football players Calvin Hill, Gary Fenick, Amos Alonzo Stagg, and “the Father of American Football” Walter Camp; ice hockey players Chris Higgins and Olympian Helen Resor; Olympic figure skaters Sarah Hughes and Nathan Chen; nine-time U.S. Squash men’s champion Julian Illingworth; Olympic swimmer Don Schollander; Olympic rowers Josh West and Rusty Wailes; Olympic sailor Stuart McNay; Olympic runner Frank Shorter; and others.

From Yale University (US) : “New model helps map the individual variations of mental illness”

From Yale University (US)

July 27, 2021
Bill Hathaway

Illustration: Michael S. Helfenbein.

The diagnosis of mental illnesses such as major depression, schizophrenia, or anxiety disorder is typically based on coarse groupings of symptoms. These symptoms, however, vary widely among individuals as do the brain circuits that cause them. This complexity explains why drug treatments work for some patients, but not others.

Now Yale researchers have developed a novel framework for “computational psychiatry” that blends neuroimaging, pharmacology, biophysical modeling, and neural gene expression that maps these variations in individual symptoms to specific neural circuits.

The findings, reported in tandem papers published in the journal eLife, promise to help create more targeted therapies for individual patients. The two studies were led, respectively, by Alan Anticevic and John Murray, associate professors of psychiatry at Yale School of Medicine.

In one study [eLife], a team led by Anticevic and Jie Lisa Ji, a Ph.D. student at Yale, used advanced statistical approaches to identify precise sets of symptoms that describe specific patients more accurately than traditional coarse diagnoses of mental illness, which do not account for individual variation of symptoms or the neural biology which causes them. The researchers found that these refined symptom signatures revealed precise neural circuits that more precisely captured variation across hundreds of patients diagnosed with psychotic disorders.

For instance, they found patients diagnosed with schizophrenia exhibited a diverse array of neural circuitry, the network of neurons which carry out brain function, that could be linked to specific symptoms of individual patients.

“This study shows the promise of computational psychiatry for personalized patient selection and treatment design using human brain imaging technology,” Anticevic said.

In the related study [eLife], led by Murray and Ph.D. student Joshua Burt, researchers simulated the effects of drugs on brain circuits. They used a new neuroimaging technology which incorporates a computational model that includes data on patterns of neural gene expression.

Specifically, the team studied the effects of LSD, a well-known hallucinogen known to alter consciousness and perception. Murray and colleagues were able to map personalized brain and psychological effects induced by LSD.

Understanding the neural effects of such substances can advance the treatment of mental illness, the researchers said. LSD is of particular interest to researchers because it can mimic symptoms of psychosis found in diseases like schizophrenia. It also activates a serotonin receptor which is a major target of antidepressants.

“We can develop a mechanistic view of how drugs alter brain function in specific regions and use that information to understand the brains of individual patients,” said Murray.

By linking personalized brain patterns to symptoms and simulating the effect of drugs on the human brain, these technologies can not only help clinicians to predict which drugs might best help patients but spur development of new drugs tailored to individuals, the authors say.

See the full article here .

five-ways-keep-your-child-safe-school-shootings

Please help promote STEM in your local schools.

Stem Education Coalition

Yale University (US) is a private Ivy League research university in New Haven, Connecticut. Founded in 1701 as the Collegiate School, it is the third-oldest institution of higher education in the United States and one of the nine Colonial Colleges chartered before the American Revolution. The Collegiate School was renamed Yale College in 1718 to honor the school’s largest private benefactor for the first century of its existence, Elihu Yale. Yale University is consistently ranked as one of the top universities and is considered one of the most prestigious in the nation.

Chartered by Connecticut Colony, the Collegiate School was established in 1701 by clergy to educate Congregational ministers before moving to New Haven in 1716. Originally restricted to theology and sacred languages, the curriculum began to incorporate humanities and sciences by the time of the American Revolution. In the 19th century, the college expanded into graduate and professional instruction, awarding the first PhD in the United States in 1861 and organizing as a university in 1887. Yale’s faculty and student populations grew after 1890 with rapid expansion of the physical campus and scientific research.

Yale is organized into fourteen constituent schools: the original undergraduate college, the Yale Graduate School of Arts and Sciences and twelve professional schools. While the university is governed by the Yale Corporation, each school’s faculty oversees its curriculum and degree programs. In addition to a central campus in downtown New Haven, the university owns athletic facilities in western New Haven, a campus in West Haven, Connecticut, and forests and nature preserves throughout New England. As of June 2020, the university’s endowment was valued at $31.1 billion, the second largest of any educational institution. The Yale University Library, serving all constituent schools, holds more than 15 million volumes and is the third-largest academic library in the United States. Students compete in intercollegiate sports as the Yale Bulldogs in the NCAA Division I – Ivy League.

As of October 2020, 65 Nobel laureates, five Fields Medalists, four Abel Prize laureates, and three Turing award winners have been affiliated with Yale University. In addition, Yale has graduated many notable alumni, including five U.S. Presidents, 19 U.S. Supreme Court Justices, 31 living billionaires, and many heads of state. Hundreds of members of Congress and many U.S. diplomats, 78 MacArthur Fellows, 252 Rhodes Scholars, 123 Marshall Scholars, and nine Mitchell Scholars have been affiliated with the university.

Research

Yale is a member of the Association of American Universities (AAU) (US) and is classified among “R1: Doctoral Universities – Very high research activity”. According to the National Science Foundation (US), Yale spent $990 million on research and development in 2018, ranking it 15th in the nation.

Yale’s faculty include 61 members of the National Academy of Sciences (US), 7 members of the National Academy of Engineering (US) and 49 members of the American Academy of Arts and Sciences (US). The college is, after normalization for institution size, the tenth-largest baccalaureate source of doctoral degree recipients in the United States, and the largest such source within the Ivy League.

Yale’s English and Comparative Literature departments were part of the New Criticism movement. Of the New Critics, Robert Penn Warren, W.K. Wimsatt, and Cleanth Brooks were all Yale faculty. Later, the Yale Comparative literature department became a center of American deconstruction. Jacques Derrida, the father of deconstruction, taught at the Department of Comparative Literature from the late seventies to mid-1980s. Several other Yale faculty members were also associated with deconstruction, forming the so-called “Yale School”. These included Paul de Man who taught in the Departments of Comparative Literature and French, J. Hillis Miller, Geoffrey Hartman (both taught in the Departments of English and Comparative Literature), and Harold Bloom (English), whose theoretical position was always somewhat specific, and who ultimately took a very different path from the rest of this group. Yale’s history department has also originated important intellectual trends. Historians C. Vann Woodward and David Brion Davis are credited with beginning in the 1960s and 1970s an important stream of southern historians; likewise, David Montgomery, a labor historian, advised many of the current generation of labor historians in the country. Yale’s Music School and Department fostered the growth of Music Theory in the latter half of the 20th century. The Journal of Music Theory was founded there in 1957; Allen Forte and David Lewin were influential teachers and scholars.

In addition to eminent faculty members, Yale research relies heavily on the presence of roughly 1200 Postdocs from various national and international origin working in the multiple laboratories in the sciences, social sciences, humanities, and professional schools of the university. The university progressively recognized this working force with the recent creation of the Office for Postdoctoral Affairs and the Yale Postdoctoral Association.

Notable alumni

Over its history, Yale has produced many distinguished alumni in a variety of fields, ranging from the public to private sector. According to 2020 data, around 71% of undergraduates join the workforce, while the next largest majority of 16.6% go on to attend graduate or professional schools. Yale graduates have been recipients of 252 Rhodes Scholarships, 123 Marshall Scholarships, 67 Truman Scholarships, 21 Churchill Scholarships, and 9 Mitchell Scholarships. The university is also the second largest producer of Fulbright Scholars, with a total of 1,199 in its history and has produced 89 MacArthur Fellows. The U.S. Department of State Bureau of Educational and Cultural Affairs ranked Yale fifth among research institutions producing the most 2020–2021 Fulbright Scholars. Additionally, 31 living billionaires are Yale alumni.

At Yale, one of the most popular undergraduate majors among Juniors and Seniors is political science, with many students going on to serve careers in government and politics. Former presidents who attended Yale for undergrad include William Howard Taft, George H. W. Bush, and George W. Bush while former presidents Gerald Ford and Bill Clinton attended Yale Law School. Former vice-president and influential antebellum era politician John C. Calhoun also graduated from Yale. Former world leaders include Italian prime minister Mario Monti, Turkish prime minister Tansu Çiller, Mexican president Ernesto Zedillo, German president Karl Carstens, Philippine president José Paciano Laurel, Latvian president Valdis Zatlers, Taiwanese premier Jiang Yi-huah, and Malawian president Peter Mutharika, among others. Prominent royals who graduated are Crown Princess Victoria of Sweden, and Olympia Bonaparte, Princess Napoléon.

Yale alumni have had considerable presence in U.S. government in all three branches. On the U.S. Supreme Court, 19 justices have been Yale alumni, including current Associate Justices Sonia Sotomayor, Samuel Alito, Clarence Thomas, and Brett Kavanaugh. Numerous Yale alumni have been U.S. Senators, including current Senators Michael Bennet, Richard Blumenthal, Cory Booker, Sherrod Brown, Chris Coons, Amy Klobuchar, Ben Sasse, and Sheldon Whitehouse. Current and former cabinet members include Secretaries of State John Kerry, Hillary Clinton, Cyrus Vance, and Dean Acheson; U.S. Secretaries of the Treasury Oliver Wolcott, Robert Rubin, Nicholas F. Brady, Steven Mnuchin, and Janet Yellen; U.S. Attorneys General Nicholas Katzenbach, John Ashcroft, and Edward H. Levi; and many others. Peace Corps founder and American diplomat Sargent Shriver and public official and urban planner Robert Moses are Yale alumni.

Yale has produced numerous award-winning authors and influential writers, like Nobel Prize in Literature laureate Sinclair Lewis and Pulitzer Prize winners Stephen Vincent Benét, Thornton Wilder, Doug Wright, and David McCullough. Academy Award winning actors, actresses, and directors include Jodie Foster, Paul Newman, Meryl Streep, Elia Kazan, George Roy Hill, Lupita Nyong’o, Oliver Stone, and Frances McDormand. Alumni from Yale have also made notable contributions to both music and the arts. Leading American composer from the 20th century Charles Ives, Broadway composer Cole Porter, Grammy award winner David Lang, and award-winning jazz pianist and composer Vijay Iyer all hail from Yale. Hugo Boss Prize winner Matthew Barney, famed American sculptor Richard Serra, President Barack Obama presidential portrait painter Kehinde Wiley, MacArthur Fellow and contemporary artist Sarah Sze, Pulitzer Prize winning cartoonist Garry Trudeau, and National Medal of Arts photorealist painter Chuck Close all graduated from Yale. Additional alumni include architect and Presidential Medal of Freedom winner Maya Lin, Pritzker Prize winner Norman Foster, and Gateway Arch designer Eero Saarinen. Journalists and pundits include Dick Cavett, Chris Cuomo, Anderson Cooper, William F. Buckley, Jr., and Fareed Zakaria.

In business, Yale has had numerous alumni and former students go on to become founders of influential business, like William Boeing (Boeing, United Airlines), Briton Hadden and Henry Luce (Time Magazine), Stephen A. Schwarzman (Blackstone Group), Frederick W. Smith (FedEx), Juan Trippe (Pan Am), Harold Stanley (Morgan Stanley), Bing Gordon (Electronic Arts), and Ben Silbermann (Pinterest). Other business people from Yale include former chairman and CEO of Sears Holdings Edward Lampert, former Time Warner president Jeffrey Bewkes, former PepsiCo chairperson and CEO Indra Nooyi, sports agent Donald Dell, and investor/philanthropist Sir John Templeton,

Yale alumni distinguished in academia include literary critic and historian Henry Louis Gates, economists Irving Fischer, Mahbub ul Haq, and Nobel Prize laureate Paul Krugman; Nobel Prize in Physics laureates Ernest Lawrence and Murray Gell-Mann; Fields Medalist John G. Thompson; Human Genome Project leader and National Institutes of Health (US) director Francis S. Collins; brain surgery pioneer Harvey Cushing; pioneering computer scientist Grace Hopper; influential mathematician and chemist Josiah Willard Gibbs; National Women’s Hall of Fame inductee and biochemist Florence B. Seibert; Turing Award recipient Ron Rivest; inventors Samuel F.B. Morse and Eli Whitney; Nobel Prize in Chemistry laureate John B. Goodenough; lexicographer Noah Webster; and theologians Jonathan Edwards and Reinhold Niebuhr.

In the sporting arena, Yale alumni include baseball players Ron Darling and Craig Breslow and baseball executives Theo Epstein and George Weiss; football players Calvin Hill, Gary Fenick, Amos Alonzo Stagg, and “the Father of American Football” Walter Camp; ice hockey players Chris Higgins and Olympian Helen Resor; Olympic figure skaters Sarah Hughes and Nathan Chen; nine-time U.S. Squash men’s champion Julian Illingworth; Olympic swimmer Don Schollander; Olympic rowers Josh West and Rusty Wailes; Olympic sailor Stuart McNay; Olympic runner Frank Shorter; and others.

From University of California-Santa Cruz (US) : “NIH grant funds collaborative research on protein-RNA interactions in cancer”

From University of California-Santa Cruz (US)

August 03, 2021
Tim Stephens
stephens@ucsc.edu

Jeremy Sanford

Jeremy Sanford, professor of molecular, cell, and developmental biology at UC Santa Cruz, has received major funding from the National Cancer Institute for research on the role of protein-RNA interactions in cancer. Sanford and Dr. Dinesh Rao at University of California-Los Angeles (US) are co-principal investigators on the grant, which will provide more than $3 million over five years for their research.

Sanford and Rao, who have been friends since they met in college, have been collaborating for several years to investigate aggressive forms of leukemia that remain highly resistant to treatment. Their recent studies have shown that one determinant of the aggressive behavior of leukemia is an RNA-binding protein that regulates gene expression. The new grant supports their ongoing research to investigate the function of this RNA-binding protein, called IGF2BP3, in the initiation and maintenance of leukemia.

“Protein-RNA interactions are fundamental to the inner working of our cells,” Sanford said. “The expression of all genetic information is controlled through a network of protein-RNA interactions. When this network is disrupted, myriad human diseases, including cancer, can occur.”

In a study published July 29 in Leukemia, Sanford and Rao’s team presented new evidence for IGF2BP3 as an attractive target for novel therapies to treat leukemia. The researchers showed that deletion of the gene for IGF2BP3 significantly increases the survival of mice with a type of leukemia in which the RNA-binding protein is over-expressed. In addition, they found that mice lacking the protein developed normally, suggesting that blocking the protein would not have serious side effects.

“Importantly, IGF2BP3 goes rogue in a variety of other cancers,” Sanford said. “We anticipate that our work on IGF2BP3 will have broad impacts on cancer biology, diagnostics, and future therapies.”

Sanford noted that the preliminary research supporting their proposal for the new grant was funded by smaller grants from the Santa Cruz Cancer Benefit Group and the UC Cancer Research Coordinating Committee.

See the full article here .

five-ways-keep-your-child-safe-school-shootings

Please help promote STEM in your local schools.

Stem Education Coalition
The University of California-Santa Cruz (US), opened in 1965 and grew, one college at a time, to its current (2008-09) enrollment of more than 16,000 students. Undergraduates pursue more than 60 majors supervised by divisional deans of humanities, physical & biological sciences, social sciences, and arts. Graduate students work toward graduate certificates, master’s degrees, or doctoral degrees in more than 30 academic fields under the supervision of the divisional and graduate deans. The dean of the Jack Baskin School of Engineering oversees the campus’s undergraduate and graduate engineering programs.

Lick Observatory Since 1888 Mt Hamilton, in San Jose, California, Altitude 1,283 m (4,209 ft)

UC Observatories Lick Automated Planet Finder fully robotic 2.4-meter optical telescope at Lick Observatory, situated on the summit of Mount Hamilton, east of San Jose, California, USA.

The UCO Lick C. Donald Shane telescope is a 120-inch (3.0-meter) reflecting telescope located at the Lick Observatory, Mt Hamilton, in San Jose, California, Altitude 1,283 m (4,209 ft).

UC Santa Cruz (US)campus.

UCSC is the home base for the Lick Observatory.

UCO Lick Observatory’s 36-inch Great Refractor telescope in the South (large) Dome of main building.

From University of Washington (US) School of Medicine : “Study links autism to new set of rare gene variants”

From University of Washington (US) School of Medicine

July 26, 2021

Brian Donohue
206.543.7856
bdonohue@uw.edu

The effects of these newly identified genes are unknown but some are associated with protein networks known to play a role in autism.

A child with autism plays with blocks. Credit: University of Washington (US) School of Medicine./Getty Images.

“These ultra-rare variants involve a set of genes that have not been associated with autism before,” said Amy B. Wilfert, a senior research fellow in the Department of Genome Sciences at the University of Washington School of Medicine. She was the lead author of the report published July 26 in the journal Nature Genetics. Evan Eichler, UW professor of genome sciences, led the team that conducted the study.

The findings should help researchers better understand how the genetic risk of developing autism is inherited and how mutations in these variants might contribute to the disorder.

Autism, or autism spectrum disorder (ASD), affects about 1 in 59 children in the United States. The exact cause is unknown, but certain genes with deleterious mutation are known to increase the risk of developing the disorder.

To date, most research has focused on genes with mutations not found in the parents’ genomes but which originate in the sperm, the egg, or very early in the development of the fertilized egg. Such “de novo” variants have been shown to greatly increase a child’s risk of developing ASD, but account for a relatively small percentage of cases.

To better understand how children might inherit mutations in genes from a parent that put them at risk of developing ASD, the Seattle researchers and their collaborators looked for variants in genes so rare that they appeared in only one parent in a study group involving thousands of families. Such variants are called ultra-rare or private variants.

To find these ultra-rare variants, the researchers examined the genome sequences of nearly 3,500 families that had at least one child with ASD. They limited their search to changes in the genes that would likely disable the gene, called likely-gene disruptive (LGD) variants. They then repeated the analysis in a larger dataset of nearly 6,000 families. Overall, they analyzed nearly 35,000 genomes.

In the end, they identified 163 candidate genes with private LGD variants that collectively increase the risk of ASD. These genes had not been previously identified as ASD-risk genes by studies of de novo variants. The researchers estimate these mutations in these genes may account for as much as 4.5% of autism cases. That’s on par with the percentage ascribed to the more intensely studied de novo variants.

Inheriting one or more of these variants is not enough to cause ASD as none of the parents who carried the variants had ASD, the researchers found. Some additional factors, either genetic or environmental, must therefore have to be present for the child to go on to develop ASD. This finding supports the theory that changes in multiple genes must be present for a child to develop ASD, known as the “multi-hit” model. “Our study suggests that one inherited mutation is not enough,” said Wilfert. “You need at least one other mutation to push a child over the threshold required to be diagnosed with autism.”

One reason why these variants are so rare is that they appear to be relatively short-lived, persisting in a family for only a few generations, perhaps because those children that inherit them are less likely to go on to have children of their own, the researchers said.

Just how these ultra-rare variants increase a child’s risk of ASD is unknown, Wilfert said, but many of the genes are involved in protein networks that play a role in biochemical pathways that have been previously linked to the development of ASD.

“The availability of large whole genome and exome datasets made it possible to identify such rare variants. Without the sequencing efforts by our collaborators at the Centers for Common Disease Genomics, and the study coordination efforts from Simons Foundation this study would have been impossible,” she said. “Our findings won’t be brought into the clinic tomorrow,” Wilfert said, “but they do give researchers new areas to focus on and may lead to clinically relevant knowledge in the future.”

Study collaborators included researchers from the Allen Institute for Brain Science in Seattle, the New York Genome Center in New York, and the Center for Medical Genetic & Hunan Key Laboratory of Medical Genetics, Central South University, in Changsha, China.

This work was supported in part by grants from the National Institutes of Health (US) (R01 MH101221, R01 MH100047, K99 MH117165, K99 HG011041, UM1 HG008901); The National Human Genome Research Institute (US); The National Heart, Lung, and Blood Institute (US); The Genome Sequencing Program Coordinating Center (U24 HG008956); The National Institute of Mental Health (US) via Autism Speaks (1U24MH081810); The Howard Hughes Medical Institute (US); and The Simons Foundation (US).

See the full article here .

five-ways-keep-your-child-safe-school-shootings

Please help promote STEM in your local schools.

Stem Education Coalition

The University of Washington School of Medicine (UWSOM) is a large public medical school in the northwest United States, located in Seattle and affiliated with the University of Washington. According to U.S. News & World Report’s 2022 Best Graduate School rankings, University of Washington School of Medicine ranked #1 in the nation for primary care education, and #7 for research.

UWSOM is the first public medical school in the states of Washington, Wyoming, Alaska, Montana, and Idaho. The school maintains a network of teaching facilities in more than 100 towns and cities across the five-state region. As part of this “WWAMI” partnership, medical students from Wyoming, Alaska, Montana, and Idaho spend their first year and a half at The University of Wyoming (US), The University of Alaska-Anchorage (US), Montana State University (US), or The University of Idaho (US), respectively. In addition, sixty first-year students and forty second-year students from Washington are based at Gonzaga University (US) in Spokane. Preference is given to residents of the WWAMI states.

The University of Washington (US) is one of the world’s preeminent public universities. Our impact on individuals, on our region, and on the world is profound — whether we are launching young people into a boundless future or confronting the grand challenges of our time through undaunted research and scholarship. Ranked number 10 in the world in Shanghai Jiao Tong University rankings and educating more than 54,000 students annually, our students and faculty work together to turn ideas into impact and in the process transform lives and our world. For more about our impact on the world, every day.

So what defines us —the students, faculty and community members at the University of Washington? Above all, it’s our belief in possibility and our unshakable optimism. It’s a connection to others, both near and far. It’s a hunger that pushes us to tackle challenges and pursue progress. It’s the conviction that together we can create a world of good. Join us on the journey.

The University of Washington (US) is a public research university in Seattle, Washington, United States. Founded in 1861, University of Washington is one of the oldest universities on the West Coast; it was established in downtown Seattle approximately a decade after the city’s founding to aid its economic development. Today, the university’s 703-acre main Seattle campus is in the University District above the Montlake Cut, within the urban Puget Sound region of the Pacific Northwest. The university has additional campuses in Tacoma and Bothell. Overall, University of Washington encompasses over 500 buildings and over 20 million gross square footage of space, including one of the largest library systems in the world with more than 26 university libraries, as well as the UW Tower, lecture halls, art centers, museums, laboratories, stadiums, and conference centers. The university offers bachelor’s, master’s, and doctoral degrees through 140 departments in various colleges and schools, sees a total student enrollment of roughly 46,000 annually, and functions on a quarter system.

University of Washington is a member of the Association of American Universities(US) and is classified among “R1: Doctoral Universities – Very high research activity”. According to the National Science Foundation(US), UW spent $1.41 billion on research and development in 2018, ranking it 5th in the nation. As the flagship institution of the six public universities in Washington state, it is known for its medical, engineering and scientific research as well as its highly competitive computer science and engineering programs. Additionally, University of Washington continues to benefit from its deep historic ties and major collaborations with numerous technology giants in the region, such as Amazon, Boeing, Nintendo, and particularly Microsoft. Paul G. Allen, Bill Gates and others spent significant time at Washington computer labs for a startup venture before founding Microsoft and other ventures. The University of Washington’s 22 varsity sports teams are also highly competitive, competing as the Huskies in the Pac-12 Conference of the NCAA Division I, representing the United States at the Olympic Games, and other major competitions.

The university has been affiliated with many notable alumni and faculty, including 21 Nobel Prize laureates and numerous Pulitzer Prize winners, Fulbright Scholars, Rhodes Scholars and Marshall Scholars.

In 1854, territorial governor Isaac Stevens recommended the establishment of a university in the Washington Territory. Prominent Seattle-area residents, including Methodist preacher Daniel Bagley, saw this as a chance to add to the city’s potential and prestige. Bagley learned of a law that allowed United States territories to sell land to raise money in support of public schools. At the time, Arthur A. Denny, one of the founders of Seattle and a member of the territorial legislature, aimed to increase the city’s importance by moving the territory’s capital from Olympia to Seattle. However, Bagley eventually convinced Denny that the establishment of a university would assist more in the development of Seattle’s economy. Two universities were initially chartered, but later the decision was repealed in favor of a single university in Lewis County provided that locally donated land was available. When no site emerged, Denny successfully petitioned the legislature to reconsider Seattle as a location in 1858.

In 1861, scouting began for an appropriate 10 acres (4 ha) site in Seattle to serve as a new university campus. Arthur and Mary Denny donated eight acres, while fellow pioneers Edward Lander, and Charlie and Mary Terry, donated two acres on Denny’s Knoll in downtown Seattle. More specifically, this tract was bounded by 4th Avenue to the west, 6th Avenue to the east, Union Street to the north, and Seneca Streets to the south.

John Pike, for whom Pike Street is named, was the university’s architect and builder. It was opened on November 4, 1861, as the Territorial University of Washington. The legislature passed articles incorporating the University, and establishing its Board of Regents in 1862. The school initially struggled, closing three times: in 1863 for low enrollment, and again in 1867 and 1876 due to funds shortage. University of Washington awarded its first graduate Clara Antoinette McCarty Wilt in 1876, with a bachelor’s degree in science.

19th century relocation

By the time Washington state entered the Union in 1889, both Seattle and the University had grown substantially. University of Washington’s total undergraduate enrollment increased from 30 to nearly 300 students, and the campus’s relative isolation in downtown Seattle faced encroaching development. A special legislative committee, headed by University of Washington graduate Edmond Meany, was created to find a new campus to better serve the growing student population and faculty. The committee eventually selected a site on the northeast of downtown Seattle called Union Bay, which was the land of the Duwamish, and the legislature appropriated funds for its purchase and construction. In 1895, the University relocated to the new campus by moving into the newly built Denny Hall. The University Regents tried and failed to sell the old campus, eventually settling with leasing the area. This would later become one of the University’s most valuable pieces of real estate in modern-day Seattle, generating millions in annual revenue with what is now called the Metropolitan Tract. The original Territorial University building was torn down in 1908, and its former site now houses the Fairmont Olympic Hotel.

The sole-surviving remnants of Washington’s first building are four 24-foot (7.3 m), white, hand-fluted cedar, Ionic columns. They were salvaged by Edmond S. Meany, one of the University’s first graduates and former head of its history department. Meany and his colleague, Dean Herbert T. Condon, dubbed the columns as “Loyalty,” “Industry,” “Faith”, and “Efficiency”, or “LIFE.” The columns now stand in the Sylvan Grove Theater.

20th century expansion

Organizers of the 1909 Alaska-Yukon-Pacific Exposition eyed the still largely undeveloped campus as a prime setting for their world’s fair. They came to an agreement with Washington’s Board of Regents that allowed them to use the campus grounds for the exposition, surrounding today’s Drumheller Fountain facing towards Mount Rainier. In exchange, organizers agreed Washington would take over the campus and its development after the fair’s conclusion. This arrangement led to a detailed site plan and several new buildings, prepared in part by John Charles Olmsted. The plan was later incorporated into the overall University of Washington campus master plan, permanently affecting the campus layout.

Both World Wars brought the military to campus, with certain facilities temporarily lent to the federal government. In spite of this, subsequent post-war periods were times of dramatic growth for the University. The period between the wars saw a significant expansion of the upper campus. Construction of the Liberal Arts Quadrangle, known to students as “The Quad,” began in 1916 and continued to 1939. The University’s architectural centerpiece, Suzzallo Library, was built in 1926 and expanded in 1935.

After World War II, further growth came with the G.I. Bill. Among the most important developments of this period was the opening of the School of Medicine in 1946, which is now consistently ranked as the top medical school in the United States. It would eventually lead to the University of Washington Medical Center, ranked by U.S. News and World Report as one of the top ten hospitals in the nation.

In 1942, all persons of Japanese ancestry in the Seattle area were forced into inland internment camps as part of Executive Order 9066 following the attack on Pearl Harbor. During this difficult time, university president Lee Paul Sieg took an active and sympathetic leadership role in advocating for and facilitating the transfer of Japanese American students to universities and colleges away from the Pacific Coast to help them avoid the mass incarceration. Nevertheless many Japanese American students and “soon-to-be” graduates were unable to transfer successfully in the short time window or receive diplomas before being incarcerated. It was only many years later that they would be recognized for their accomplishments during the University of Washington’s Long Journey Home ceremonial event that was held in May 2008.

From 1958 to 1973, the University of Washington saw a tremendous growth in student enrollment, its faculties and operating budget, and also its prestige under the leadership of Charles Odegaard. University of Washington student enrollment had more than doubled to 34,000 as the baby boom generation came of age. However, this era was also marked by high levels of student activism, as was the case at many American universities. Much of the unrest focused around civil rights and opposition to the Vietnam War. In response to anti-Vietnam War protests by the late 1960s, the University Safety and Security Division became the University of Washington Police Department.

Odegaard instituted a vision of building a “community of scholars”, convincing the Washington State legislatures to increase investment in the University. Washington senators, such as Henry M. Jackson and Warren G. Magnuson, also used their political clout to gather research funds for the University of Washington. The results included an increase in the operating budget from $37 million in 1958 to over $400 million in 1973, solidifying University of Washington as a top recipient of federal research funds in the United States. The establishment of technology giants such as Microsoft, Boeing and Amazon in the local area also proved to be highly influential in the University of Washington’s fortunes, not only improving graduate prospects but also helping to attract millions of dollars in university and research funding through its distinguished faculty and extensive alumni network.

21st century

In 1990, the University of Washington opened its additional campuses in Bothell and Tacoma. Although originally intended for students who have already completed two years of higher education, both schools have since become four-year universities with the authority to grant degrees. The first freshman classes at these campuses started in fall 2006. Today both Bothell and Tacoma also offer a selection of master’s degree programs.

In 2012, the University began exploring plans and governmental approval to expand the main Seattle campus, including significant increases in student housing, teaching facilities for the growing student body and faculty, as well as expanded public transit options. The University of Washington light rail station was completed in March 2015, connecting Seattle’s Capitol Hill neighborhood to the University of Washington Husky Stadium within five minutes of rail travel time. It offers a previously unavailable option of transportation into and out of the campus, designed specifically to reduce dependence on private vehicles, bicycles and local King County buses.

University of Washington has been listed as a “Public Ivy” in Greene’s Guides since 2001, and is an elected member of the American Association of Universities. Among the faculty by 2012, there have been 151 members of American Association for the Advancement of Science, 68 members of the National Academy of Sciences(US), 67 members of the American Academy of Arts and Sciences, 53 members of the National Academy of Medicine(US), 29 winners of the Presidential Early Career Award for Scientists and Engineers, 21 members of the National Academy of Engineering(US), 15 Howard Hughes Medical Institute Investigators, 15 MacArthur Fellows, 9 winners of the Gairdner Foundation International Award, 5 winners of the National Medal of Science, 7 Nobel Prize laureates, 5 winners of Albert Lasker Award for Clinical Medical Research, 4 members of the American Philosophical Society, 2 winners of the National Book Award, 2 winners of the National Medal of Arts, 2 Pulitzer Prize winners, 1 winner of the Fields Medal, and 1 member of the National Academy of Public Administration. Among UW students by 2012, there were 136 Fulbright Scholars, 35 Rhodes Scholars, 7 Marshall Scholars and 4 Gates Cambridge Scholars. UW is recognized as a top producer of Fulbright Scholars, ranking 2nd in the US in 2017.

The Academic Ranking of World Universities (ARWU) has consistently ranked University of Washington as one of the top 20 universities worldwide every year since its first release. In 2019, University of Washington ranked 14th worldwide out of 500 by the ARWU, 26th worldwide out of 981 in the Times Higher Education World University Rankings, and 28th worldwide out of 101 in the Times World Reputation Rankings. Meanwhile, QS World University Rankings ranked it 68th worldwide, out of over 900.

U.S. News & World Report ranked University of Washington 8th out of nearly 1,500 universities worldwide for 2021, with University of Washington’s undergraduate program tied for 58th among 389 national universities in the U.S. and tied for 19th among 209 public universities.

In 2019, it ranked 10th among the universities around the world by SCImago Institutions Rankings. In 2017, the Leiden Ranking, which focuses on science and the impact of scientific publications among the world’s 500 major universities, ranked University of Washington 12th globally and 5th in the U.S.

In 2019, Kiplinger Magazine’s review of “top college values” named University of Washington 5th for in-state students and 10th for out-of-state students among U.S. public colleges, and 84th overall out of 500 schools. In the Washington Monthly National University Rankings University of Washington was ranked 15th domestically in 2018, based on its contribution to the public good as measured by social mobility, research, and promoting public service.

From University of Strathclyde [Oilthigh Shrath Chluaidh] (SCT): “The paradox of a free-electron laser without the laser: a new source of coherent radiation”

From University of Strathclyde [Oilthigh Shrath Chluaidh] (SCT)

16 July 2021

A new way of producing coherent light in the ultra-violet spectral region, which points the way to developing brilliant table-top x-ray sources, has been produced in research led at the University of Strathclyde.

The scientists have developed a type of ultra-short wavelength coherent light source that does not require laser action to produce coherence. Common electron-beam based light sources-known as fourth-generation light sources-are based on the free-electron laser (FEL) which uses an undulator to convert electron beam energy into X-rays.

Coherent light sources are powerful tools that enable research in many areas of medicine, biology, material sciences, chemistry and physics.

Making ultraviolet and X-ray coherent light sources more widely available would transform the way science is done; a university could have one of the devices in a single room, on a table top, for a reasonable price.

The group is now planning a proof-of-principle experiment in the ultraviolet spectral range to demonstrate this new way of producing coherent light. If successful, it should dramatically accelerate the development of even shorter wavelength coherent sources based on the same principle. The Strathclyde group has set up a facility to investigate these types of sources: the Scottish Centre for the Application of Plasma-based Accelerators (SCAPA), which hosts one of the highest power lasers in the UK.

The new research has been published in Scientific Reports.

Professor Dino Jaroszynski, of Strathclyde’s Department of Physics, led the research. He said: “This work significantly advances the state-of-the-art of synchrotron sources by proposing a new method of producing short-wavelength coherent radiation, using a short undulator and attosecond duration electron bunches.

“This is more compact and less demanding on the electron beam quality than free-electron lasers and could provide a paradigm shift in light sources, which would stimulate a new direction of research. It proposes to use bunch compression – as in chirped pulse amplification lasers – within the undulator to significantly enhance the radiation brightness.

“The new method presented would be of wide interest to a diverse community developing and using light sources.”

In FELs, as in all lasers, the intensity of light is amplified by a feedback mechanism that locks the phases of individual radiators, which in this case are “free” electrons. In the FEL, this is achieved by passing a high energy electron beam through the undulator, which is an array of alternating polarity magnets.

Light emitted from the electrons as they wiggle through the undulator creates a force called the ponderomotive force that bunches the electrons – some are slowed down, some are sped up, which causes bunching, similar to traffic on a motorway periodically slowing and speeding up.

Electrons passing through the undulator radiate incoherent light if they are uniformly distributed – for every electron that emits light, there is another electron that partially cancels out the light because they radiate out of phase. An analogy of this partial cancelling out is rain on the sea: it produces many small ripples that partially cancel each other out, effectively quelling the waves – reducing their amplitude. In contrast, steady or pulsating wind will cause the waves to amplify through the mutual interaction of the wind with the sea.

In the FEL, electron bunching causes amplification of the light and the increase in its coherence, which usually takes a long time – thus very long undulators are required. In an X-ray FEL, the undulators can be more than a hundred metres long. The accelerators driving these X-ray FELs are kilometres long, which makes these devices very expensive and some of the largest instruments in the world.

However, using a free-electron laser to produce coherent radiation is not the only way; a “pre-bunched” beam or ultra-short electron bunch can also be used to achieve exactly the same coherence in a very short undulator that is less than a metre in length. As long as the electron bunch is shorter than the wavelength of the light produced by the undulator, it will automatically produce coherent light – all the light waves will add up or interfere constructively, which leads to very brilliant light with exactly the same properties of light from a laser.

The researchers have demonstrated theoretically that this can be achieved using a laser-plasma wakefield accelerator, which produces electron bunches that can have a length of a few tens of nanometres. They show that if these ultra-short bunches of high energy electrons pass through a short undulator, they can produce as may photons as a very expensive FEL can produce. Moreover, they have also shown that by producing an electron bunch that has an energy “chirp”, they can ballistically compress the bunch to a very short duration inside the undulator, which provides a unique way of going to even shorter electron bunches and therefore produce even shorter wavelength light.

The research collaboration also involved the University of Manchester (UK), Pulsar Physics (NL) and the STFC ASTeC group at Daresbury Laboratories. The study has received funding from the EPSRC (Engineering and Physical Sciences Research Council), to support a project named “Lab in a Bubble”.

See the full article here.

five-ways-keep-your-child-safe-school-shootings

Please help promote STEM in your local schools.

Stem Education Coalition

The University of Strathclyde [Oilthigh Shrath Chluaidh] (SCT)) is a public research university located in Glasgow, Scotland. Founded in 1796 as the Andersonian Institute, it is Glasgow’s second-oldest university, having received its royal charter in 1964 as the first technological university in the United Kingdom. Taking its name from the historic Kingdom of Strathclyde, it is Scotland’s third-largest university by number of students, with students and staff from over 100 countries.

The institution was named University of the Year 2012 by Times Higher Education and again in 2019, becoming the first university to receive this award twice. The annual income of the institution for 2019–20 was £334.8 million of which £81.2 million was from research grants and contracts, with an expenditure of £298.8 million. It is one of the 39 old universities in the UK comprising the distinctive second cluster of elite universities after Oxbridge.

Research

In 2011 the University’s Advanced Forming Research Centre was announced as a leading partner in the first UK-wide Technology Strategy Board Catapult Centre. The Government also announced that the University is to lead the UK-wide EPSRC Centre for Innovative Manufacturing in Continuous Manufacturing and Crystallisation.

The University has become the base for the first Fraunhofer Centre to be established in the UK. Fraunhofer-Gesellschaft, Europe’s largest organisation for contract research, is creating the new Fraunhofer Centre for Applied Photonics in collaboration with Strathclyde, for research in sectors including healthcare, security, energy and transport.

Strathclyde was chosen in 2012 as the exclusive European partner university for South Korea’s global research and commercialisation programme – the Global Industry-Academia Cooperation Programme, funded by South Korea’s Ministry of Knowledge and Economics.

In 2012 the University became a key partner in its second UK Catapult Centre. Plans for the Catapult Centre for Offshore Renewable Energy were announced at Strathclyde by Business Secretary Vince Cable. The University has also become a partner in the Industrial Doctorate Centre for Offshore Renewable Energy, which is one of 11 doctoral centres at Strathclyde.

Engineers at the University are leading the €4 million, Europe-wide Stardust project, a research-based training network investigating the removal of space debris and the deflection of asteroids.

Strathclyde has become part of the new ESRC Enterprise Research Centre, a £2.9 million venture generating world-class research to help stimulate growth for small and medium-sized enterprises.

The University has centres in pharmacy, drug delivery and development, micro and ultrasonic engineering, biophotonics and photonics, biomedical engineering, medical devices, new therapies,prosthetics and orthotics, public health history, law, crime and justice and social work. The University is involved in 11 partnerships with other universities through the Scottish Funding Councils’ Research Pooling Programme, covering areas such as engineering, life sciences, energy, marine science and technology, physics, chemistry, computer sciences and economics.

Several Strathclyde staff have been elected to Fellowships in the Royal Societies of Edinburgh and London.

From Carnegie Mellon University (US) : “DARPA Selects CMU to Develop AI for Portable Ultrasound”

From Carnegie Mellon University (US)

June 21, 2021
Aaron Aupperlee
aaupperlee@cmu.edu

The Defense Advanced Research Projects Agency (DARPA) has selected Carnegie Mellon University as one of five teams to develop artificial intelligence that will help field medics better use portable ultrasound devices to diagnose and treat injuries on the battlefield.

Point-of-Care Ultrasound Automated Interpretation (POCUS AI). DARPA.

DARPA’s Point-of-Care Ultrasound Automated Interpretation (POCUS AI) program will challenge the teams to create an extensible AI model that can be trained to identify injuries and assist with interventions using limited data — 15 to 30 images or video clips instead of thousands.

“Because we cannot train the AI on large datasets, we are going to incorporate knowledge straight from doctors,” said John Galeotti, director of the Biomedical Image Guidance Laboratory in the Robotics Institute and head of the CMU team. “We are going to collect information from clinical experts and put it on top of the AI system so the model does not have to learn as many new concepts on its own for each new application.”

Portable point-of-care ultrasound devices could help frontline medics quickly capture images of injuries and confirm whether interventions to temporarily treat them or alleviate pain were administered properly or should be tried again. These devices could increase the speed and accuracy of the care provided on the battlefield or in other scenarios where evacuations could take time. But frontline medical personnel often lack significant training with these instruments, hindering their deployment. AI promises to bridge that gap.

DARPA selected five research teams to create an AI model for the 18-month challenge: CMU, Drexel University (US), Netrias, Novateur Research Solutions and Kitware Inc.

The CMU team, which includes Artur Dubrawski, Alumni Research Professor of Computer Science and head of the Auton Laboratory, will work to train an AI model that combines computer vision and machine learning to help medics identify what they see through the ultrasound. They’ll also incorporate clinical rules and best practices from medical experts to guide and evaluate the interventions when assessing for traumatic brain injury. DARPA requires the system to diagnose a life-threatening pneumothorax condition, which prevents the lungs from inflating, and measure the diameter of the optic nerve sheath to detect high intracranial pressure. The system must also tell a medic whether a nerve block injection needle was administered in the correct place and if a breathing tube was inserted correctly.

The value of the technology extends far beyond the military and battlefield, Galeotti said. It could be used with devices in ambulances to provide better treatment to roadside accident victims and be carried by paramedics, EMTs and other first responders to offer more effective aid outside hospital settings.

“This could help first responders provide better aid earlier, which would lead directly to not only saving more lives but also to alleviating pain and preventing long-lasting injuries,” Galeotti said.

See the full article here .

five-ways-keep-your-child-safe-school-shootings

Please help promote STEM in your local schools.

Stem Education Coalition

Carnegie Mellon University (US) is a global research university with more than 12,000 students, 95,000 alumni, and 5,000 faculty and staff.
CMU has been a birthplace of innovation since its founding in 1900.
Today, we are a global leader bringing groundbreaking ideas to market and creating successful startup businesses.
Our award-winning faculty members are renowned for working closely with students to solve major scientific, technological and societal challenges. We put a strong emphasis on creating things—from art to robots. Our students are recruited by some of the world’s most innovative companies.
We have campuses in Pittsburgh, Qatar and Silicon Valley, and degree-granting programs around the world, including Africa, Asia, Australia, Europe and Latin America.

The university was established by Andrew Carnegie as the Carnegie Technical Schools, the university became the Carnegie Institute of Technology in 1912 and began granting four-year degrees. In 1967, the Carnegie Institute of Technology merged with the Mellon Institute of Industrial Research, formerly a part of the University of Pittsburgh. Since then, the university has operated as a single institution.

The university has seven colleges and independent schools, including the College of Engineering, College of Fine Arts, Dietrich College of Humanities and Social Sciences, Mellon College of Science, Tepper School of Business, Heinz College of Information Systems and Public Policy, and the School of Computer Science. The university has its main campus located 3 miles (5 km) from Downtown Pittsburgh, and the university also has over a dozen degree-granting locations in six continents, including degree-granting campuses in Qatar and Silicon Valley.

Past and present faculty and alumni include 20 Nobel Prize laureates, 13 Turing Award winners, 23 Members of the American Academy of Arts and Sciences (US), 22 Fellows of the American Association for the Advancement of Science (US), 79 Members of the National Academies, 124 Emmy Award winners, 47 Tony Award laureates, and 10 Academy Award winners. Carnegie Mellon enrolls 14,799 students from 117 countries and employs 1,400 faculty members.
Research

Carnegie Mellon University is classified among “R1: Doctoral Universities – Very High Research Activity”. For the 2006 fiscal year, the university spent $315 million on research. The primary recipients of this funding were the School of Computer Science ($100.3 million), the Software Engineering Institute ($71.7 million), the College of Engineering ($48.5 million), and the Mellon College of Science ($47.7 million). The research money comes largely from federal sources, with a federal investment of $277.6 million. The federal agencies that invest the most money are the National Science Foundation (US) and the Department of Defense (US), which contribute 26% and 23.4% of the total university research budget respectively.

The recognition of Carnegie Mellon as one of the best research facilities in the nation has a long history—as early as the 1987 Federal budget Carnegie Mellon University was ranked as third in the amount of research dollars with $41.5 million, with only Massachusetts Institute of Technology (US) and Johns Hopkins University (US) receiving more research funds from the Department of Defense.

The Pittsburgh Supercomputing Center (PSC) (US) is a joint effort between Carnegie Mellon, University of Pittsburgh (US), and Westinghouse Electric Company. Pittsburgh Supercomputing Center was founded in 1986 by its two scientific directors, Dr. Ralph Roskies of the University of Pittsburgh and Dr. Michael Levine of Carnegie Mellon. Pittsburgh Supercomputing Center is a leading partner in the TeraGrid, the National Science Foundation’s cyberinfrastructure program.
Scarab lunar rover is being developed by the RI.

The Robotics Institute (RI) is a division of the School of Computer Science and considered to be one of the leading centers of robotics research in the world. The Field Robotics Center (FRC) has developed a number of significant robots, including Sandstorm and H1ghlander, which finished second and third in the DARPA Grand Challenge, and Boss, which won the DARPA Urban Challenge. The Robotics Institute has partnered with a spinoff company, Astrobotic Technology Inc., to land a CMU robot on the moon by 2016 in pursuit of the Google Lunar XPrize. The robot, known as Andy, is designed to explore lunar pits, which might include entrances to caves. The RI is primarily sited at Carnegie Mellon’s main campus in Newell-Simon hall.

The Software Engineering Institute (SEI) is a federally funded research and development center sponsored by the U.S. Department of Defense and operated by Carnegie Mellon, with offices in Pittsburgh, Pennsylvania, USA; Arlington, Virginia, and Frankfurt, Germany. The SEI publishes books on software engineering for industry, government and military applications and practices. The organization is known for its Capability Maturity Model (CMM) and Capability Maturity Model Integration (CMMI), which identify essential elements of effective system and software engineering processes and can be used to rate the level of an organization’s capability for producing quality systems. The SEI is also the home of CERT/CC, the federally funded computer security organization. The CERT Program’s primary goals are to ensure that appropriate technology and systems management practices are used to resist attacks on networked systems and to limit damage and ensure continuity of critical services subsequent to attacks, accidents, or failures.

The Human–Computer Interaction Institute (HCII) is a division of the School of Computer Science and is considered one of the leading centers of human–computer interaction research, integrating computer science, design, social science, and learning science. Such interdisciplinary collaboration is the hallmark of research done throughout the university.

The Language Technologies Institute (LTI) is another unit of the School of Computer Science and is famous for being one of the leading research centers in the area of language technologies. The primary research focus of the institute is on machine translation, speech recognition, speech synthesis, information retrieval, parsing and information extraction. Until 1996, the institute existed as the Center for Machine Translation that was established in 1986. From 1996 onwards, it started awarding graduate degrees and the name was changed to Language Technologies Institute.

Carnegie Mellon is also home to the Carnegie School of management and economics. This intellectual school grew out of the Tepper School of Business in the 1950s and 1960s and focused on the intersection of behavioralism and management. Several management theories, most notably bounded rationality and the behavioral theory of the firm, were established by Carnegie School management scientists and economists.

Carnegie Mellon also develops cross-disciplinary and university-wide institutes and initiatives to take advantage of strengths in various colleges and departments and develop solutions in critical social and technical problems. To date, these have included the Cylab Security and Privacy Institute, the Wilton E. Scott Institute for Energy Innovation, the Neuroscience Institute (formerly known as BrainHub), the Simon Initiative, and the Disruptive Healthcare Technology Institute.

Carnegie Mellon has made a concerted effort to attract corporate research labs, offices, and partnerships to the Pittsburgh campus. Apple Inc., Intel, Google, Microsoft, Disney, Facebook, IBM, General Motors, Bombardier Inc., Yahoo!, Uber, Tata Consultancy Services, Ansys, Boeing, Robert Bosch GmbH, and the Rand Corporation have established a presence on or near campus. In collaboration with Intel, Carnegie Mellon has pioneered research into claytronics.