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  • richardmitnick 1:59 pm on March 2, 2021 Permalink | Reply
    Tags: "Designing Soft Materials that Mimic Biological Functions", , Bioengineering, During embryonic development for instance flat sheets of embryonic cells morph through a series of folds into intricate three-dimensional structures such as branches; tubes; and furrows., , , , Researchers led by Monica Olvera de la Cruz designed computational and experimental systems that mimic these biological interactions., , Shape-forming processes however are controlled by chemical and mechanical signaling events which are not fully understood on the microscopic level., Soft materials that demonstrate autonomous oscillating properties that mimic biological functions., The long-term goal is to create autonomous hydrogels that can perform complex functions triggered by clues as simple as a local mechanical deformation., The researchers designed a chemical-responsive polymeric shell meant to mimic living matter., The researchers’ model could be used as the basis to develop other soft materials demonstrating diverse dynamic morphological changes., The scientists coupled the mechanical response of the hydrogel to changes in the concentration of the chemical species within the gel as a feedback loop., The work could also inform the future development of soft materials with robot-like functionality that operate autonomously., Therapeutics   

    From Northwestern University(US): “Designing Soft Materials that Mimic Biological Functions” 

    Northwestern U bloc
    From Northwestern University(US)

    Mar 1, 2021
    Alex Gerage

    1
    Soft material demonstrates autonomous, heartbeat-like oscillating properties.

    Northwestern Engineering researchers have developed a theoretical model to design soft materials that demonstrate autonomous oscillating properties that mimic biological functions. The work could advance the design of responsive materials used to deliver therapeutics as well as for robot-like soft materials that operate autonomously.

    The design and synthesis of materials with biological functions require a delicate balance between structural form and physiological function. During embryonic development for instance flat sheets of embryonic cells morph through a series of folds into intricate three-dimensional structures such as branches, tubes, and furrows. These, in turn, become dynamic, three-dimensional building blocks for organs performing vital functions like heartbeat, nutrient absorption, or information processing by the nervous system.

    Such shape-forming processes however are controlled by chemical and mechanical signaling events which are not fully understood on the microscopic level. To bridge this gap, researchers led by Monica Olvera de la Cruz designed computational and experimental systems that mimic these biological interactions. Hydrogels, a class of hydrophilic polymer materials, have emerged as candidates capable of reproducing shape changes upon chemical and mechanical stimulation observed in nature.

    The researchers developed a theoretical model for a hydrogel-based shell that underwent autonomous morphological changes when induced by chemical reactions.

    “We found that the chemicals modified the local gel microenvironment, allowing swelling and deswelling of materials via chemo-mechanical stresses in an autonomous manner,” said de la Cruz, Lawyer Taylor Professor of Materials Science and Engineering at the McCormick School of Engineering. “This generated dynamic morphological change, including periodic oscillations reminiscent of heartbeats found in living systems.”

    A paper, titled “Chemically Controlled Pattern Formation in Self-oscillating Elastic Shells,” was published March 1 in the journal PNAS. Siyu Li and Daniel Matoz-Fernandez, postdoctoral fellows in Olvera de la Cruz’s lab, were the paper’s co-first authors.

    In the study, the researchers designed a chemical-responsive polymeric shell meant to mimic living matter. They applied the water-based mechanical properties of the hydrogel shell to a chemical species, a chemical substance that produces specific patterned behavior — in this case, wave-like oscillations — located within the shell. After conducting a series of reduction-oxidation reactions — a chemical reaction that transfers of electrons between two chemical species — the shell generated microcompartments capable of expanding or contracting, or inducing buckling-unbuckling behavior when mechanical instability was introduced.

    “We coupled the mechanical response of the hydrogel to changes in the concentration of the chemical species within the gel as a feedback loop,” Matoz-Fernandez said. “If the level of chemicals goes past a certain threshold, water gets absorbed, swelling the gel. When the gel swells, the chemical species gets diluted, triggering chemical processes that expel the gel’s water, therefore contracting the gel.”

    The researchers’ model could be used as the basis to develop other soft materials demonstrating diverse dynamic morphological changes. This could lead to new drug delivery strategies with materials that enhance the rate of diffusion of compartmentalized chemicals or release cargos at specific rates.

    “One could, in principle, design catalytic microcompartments that expand and contract to absorb or release components at a specific frequency. This could lead to more targeted, time-based therapeutics to treat disease,” Li said.

    The work could also inform the future development of soft materials with robot-like functionality that operate autonomously. These ‘soft robotics’ have emerged as candidates to support chemical production, tools for environmental technologies, or smart biomaterials for medicine. Yet the materials rely on external stimuli, such as light, to function.

    “Our material operates autonomously, so there’s no external control involved,” Li said. “By ‘poking’ the shell with a chemical reaction, you trigger the movement.”

    The researchers plan to build on their findings and further bridge the gap between what’s possible in nature and the science lab.

    “The long-term goal is to create autonomous hydrogels that can perform complex functions triggered by clues as simple as a local mechanical deformation,” Olvera de la Cruz said.

    See the full article here .

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    Northwestern South Campus
    South Campus

    Northwestern University(US) is a private research university in Evanston, Illinois. Founded in 1851 to serve the former Northwest Territory, the university is a founding member of the Big Ten Conference.

    On May 31, 1850, nine men gathered to begin planning a university that would serve the Northwest Territory.

    Given that they had little money, no land and limited higher education experience, their vision was ambitious. But through a combination of creative financing, shrewd politicking, religious inspiration and an abundance of hard work, the founders of Northwestern University were able to make that dream a reality.

    In 1853, the founders purchased a 379-acre tract of land on the shore of Lake Michigan 12 miles north of Chicago. They established a campus and developed the land near it, naming the surrounding town Evanston in honor of one of the University’s founders, John Evans. After completing its first building in 1855, Northwestern began classes that fall with two faculty members and 10 students.
    Twenty-one presidents have presided over Northwestern in the years since. The University has grown to include 12 schools and colleges, with additional campuses in Chicago and Doha, Qatar.

    Northwestern is known for its focus on interdisciplinary education, extensive research output, and student traditions. The university provides instruction in over 200 formal academic concentrations, including various dual degree programs. The university is composed of eleven undergraduate, graduate, and professional schools, which include the Kellogg School of Management, the Pritzker School of Law, the Feinberg School of Medicine, the Weinberg College of Arts and Sciences, the Bienen School of Music, the McCormick School of Engineering and Applied Science, the Medill School of Journalism, the School of Communication, the School of Professional Studies, the School of Education and Social Policy, and The Graduate School. As of fall 2019, the university had 21,946 enrolled students, including 8,327 undergraduates and 13,619 graduate students.

    Valued at $12.2 billion, Northwestern’s endowment is among the largest university endowments in the United States. Its numerous research programs bring in nearly $900 million in sponsored research each year.

    Northwestern’s main 240-acre (97 ha) campus lies along the shores of Lake Michigan in Evanston, 12 miles north of Downtown Chicago. The university’s law, medical, and professional schools, along with its nationally ranked Northwestern Memorial Hospital, are located on a 25-acre (10 ha) campus in Chicago’s Streeterville neighborhood. The university also maintains a campus in Doha, Qatar and locations in San Francisco, California, Washington, D.C. and Miami, Florida.

    As of October 2020, Northwestern’s faculty and alumni have included 1 Fields Medalist, 22 Nobel Prize laureates, 40 Pulitzer Prize winners, 6 MacArthur Fellows, 17 Rhodes Scholars, 27 Marshall Scholars, 23 National Medal of Science winners, 11 National Humanities Medal recipients, 84 members of the American Academy of Arts and Sciences, 10 living billionaires, 16 Olympic medalists, and 2 U.S. Supreme Court Justices. Northwestern alumni have founded notable companies and organizations such as the Mayo Clinic, The Blackstone Group, Kirkland & Ellis, U.S. Steel, Guggenheim Partners, Accenture, Aon Corporation, AQR Capital, Booz Allen Hamilton, and Melvin Capital.

    The foundation of Northwestern University can be traced to a meeting on May 31, 1850, of nine prominent Chicago businessmen, Methodist leaders, and attorneys who had formed the idea of establishing a university to serve what had been known from 1787 to 1803 as the Northwest Territory. On January 28, 1851, the Illinois General Assembly granted a charter to the Trustees of the North-Western University, making it the first chartered university in Illinois. The school’s nine founders, all of whom were Methodists (three of them ministers), knelt in prayer and worship before launching their first organizational meeting. Although they affiliated the university with the Methodist Episcopal Church, they favored a non-sectarian admissions policy, believing that Northwestern should serve all people in the newly developing territory by bettering the economy in Evanston.

    John Evans, for whom Evanston is named, bought 379 acres (153 ha) of land along Lake Michigan in 1853, and Philo Judson developed plans for what would become the city of Evanston, Illinois. The first building, Old College, opened on November 5, 1855. To raise funds for its construction, Northwestern sold $100 “perpetual scholarships” entitling the purchaser and his heirs to free tuition. Another building, University Hall, was built in 1869 of the same Joliet limestone as the Chicago Water Tower, also built in 1869, one of the few buildings in the heart of Chicago to survive the Great Chicago Fire of 1871. In 1873 the Evanston College for Ladies merged with Northwestern, and Frances Willard, who later gained fame as a suffragette and as one of the founders of the Woman’s Christian Temperance Union (WCTU), became the school’s first dean of women (Willard Residential College, built in 1938, honors her name). Northwestern admitted its first female students in 1869, and the first woman was graduated in 1874.

    Northwestern fielded its first intercollegiate football team in 1882, later becoming a founding member of the Big Ten Conference. In the 1870s and 1880s, Northwestern affiliated itself with already existing schools of law, medicine, and dentistry in Chicago. Northwestern University Pritzker School of Law is the oldest law school in Chicago. As the university’s enrollments grew, these professional schools were integrated with the undergraduate college in Evanston; the result was a modern research university combining professional, graduate, and undergraduate programs, which gave equal weight to teaching and research. By the turn of the century, Northwestern had grown in stature to become the third largest university in the United States after Harvard University(US) and the University of Michigan(US).

    Under Walter Dill Scott’s presidency from 1920 to 1939, Northwestern began construction of an integrated campus in Chicago designed by James Gamble Rogers, noted for his design of the Yale University(US) campus, to house the professional schools. The university also established the Kellogg School of Management and built several prominent buildings on the Evanston campus, including Dyche Stadium, now named Ryan Field, and Deering Library among others. In the 1920s, Northwestern became one of the first six universities in the United States to establish a Naval Reserve Officers Training Corps (NROTC). In 1939, Northwestern hosted the first-ever NCAA Men’s Division I Basketball Championship game in the original Patten Gymnasium, which was later demolished and relocated farther north, along with the Dearborn Observatory, to make room for the Technological Institute.

    After the golden years of the 1920s, the Great Depression in the United States (1929–1941) had a severe impact on the university’s finances. Its annual income dropped 25 percent from $4.8 million in 1930-31 to $3.6 million in 1933-34. Investment income shrank, fewer people could pay full tuition, and annual giving from alumni and philanthropists fell from $870,000 in 1932 to a low of $331,000 in 1935. The university responded with two salary cuts of 10 percent each for all employees. It imposed hiring and building freezes and slashed appropriations for maintenance, books, and research. Having had a balanced budget in 1930-31, the university now faced deficits of roughly $100,000 for the next four years. Enrollments fell in most schools, with law and music suffering the biggest declines. However, the movement toward state certification of school teachers prompted Northwestern to start a new graduate program in education, thereby bringing in new students and much needed income. In June 1933, Robert Maynard Hutchins, president of the University of Chicago(US), proposed a merger of the two universities, estimating annual savings of $1.7 million. The two presidents were enthusiastic, and the faculty liked the idea; many Northwestern alumni, however, opposed it, fearing the loss of their Alma Mater and its many traditions that distinguished Northwestern from Chicago. The medical school, for example, was oriented toward training practitioners, and alumni feared it would lose its mission if it were merged into the more research-oriented University of Chicago Medical School. The merger plan was ultimately dropped. In 1935, the Deering family rescued the university budget with an unrestricted gift of $6 million, bringing the budget up to $5.4 million in 1938-39. This allowed many of the previous spending cuts to be restored, including half of the salary reductions.

    Like other American research universities, Northwestern was transformed by World War II (1939–1945). Regular enrollment fell dramatically, but the school opened high-intensity, short-term programs that trained over 50,000 military personnel, including future president John F. Kennedy. Northwestern’s existing NROTC program proved to be a boon to the university as it trained over 36,000 sailors over the course of the war, leading Northwestern to be called the “Annapolis of the Midwest.” Franklyn B. Snyder led the university from 1939 to 1949, and after the war, surging enrollments under the G.I. Bill drove dramatic expansion of both campuses. In 1948, prominent anthropologist Melville J. Herskovits founded the Program of African Studies at Northwestern, the first center of its kind at an American academic institution. J. Roscoe Miller’s tenure as president from 1949 to 1970 saw an expansion of the Evanston campus, with the construction of the Lakefill on Lake Michigan, growth of the faculty and new academic programs, and polarizing Vietnam-era student protests. In 1978, the first and second Unabomber attacks occurred at Northwestern University. Relations between Evanston and Northwestern became strained throughout much of the post-war era because of episodes of disruptive student activism, disputes over municipal zoning, building codes, and law enforcement, as well as restrictions on the sale of alcohol near campus until 1972. Northwestern’s exemption from state and municipal property-tax obligations under its original charter has historically been a source of town-and-gown tension.

    Although government support for universities declined in the 1970s and 1980s, President Arnold R. Weber was able to stabilize university finances, leading to a revitalization of its campuses. As admissions to colleges and universities grew increasingly competitive in the 1990s and 2000s, President Henry S. Bienen’s tenure saw a notable increase in the number and quality of undergraduate applicants, continued expansion of the facilities and faculty, and renewed athletic competitiveness. In 1999, Northwestern student journalists uncovered information exonerating Illinois death-row inmate Anthony Porter two days before his scheduled execution. The Innocence Project has since exonerated 10 more men. On January 11, 2003, in a speech at Northwestern School of Law’s Lincoln Hall, then Governor of Illinois George Ryan announced that he would commute the sentences of more than 150 death-row inmates.

    In the 2010s, a 5-year capital campaign resulted in a new music center, a replacement building for the business school, and a $270 million athletic complex. In 2014, President Barack Obama delivered a seminal economics speech at the Evanston campus.

    Organization and administration

    Governance

    Northwestern is privately owned and governed by an appointed Board of Trustees, which is composed of 70 members and, as of 2011, has been chaired by William A. Osborn ’69. The board delegates its power to an elected president who serves as the chief executive officer of the university. Northwestern has had sixteen presidents in its history (excluding interim presidents). The current president, economist Morton O. Schapiro, succeeded Henry Bienen whose 14-year tenure ended on August 31, 2009. The president maintains a staff of vice presidents, directors, and other assistants for administrative, financial, faculty, and student matters. Kathleen Haggerty assumed the role of interim provost for the university in April 2020.

    Students are formally involved in the university’s administration through the Associated Student Government, elected representatives of the undergraduate students, and the Graduate Student Association, which represents the university’s graduate students.

    The admission requirements, degree requirements, courses of study, and disciplinary and degree recommendations for each of Northwestern’s 12 schools are determined by the voting members of that school’s faculty (assistant professor and above).

    Undergraduate and graduate schools

    Evanston Campus:

    Weinberg College of Arts and Sciences (1851)
    School of Communication (1878)
    Bienen School of Music (1895)
    McCormick School of Engineering and Applied Science (1909)
    Medill School of Journalism (1921)
    School of Education and Social Policy (1926)
    School of Professional Studies (1933)

    Graduate and professional

    Evanston Campus

    Kellogg School of Management (1908)
    The Graduate School

    Chicago Campus

    Feinberg School of Medicine (1859)
    Kellogg School of Management (1908)
    Pritzker School of Law (1859)
    School of Professional Studies (1933)

    Northwestern University had a dental school from 1891 to May 31, 2001, when it closed.

    Endowment

    In 1996, Princess Diana made a trip to Evanston to raise money for the university hospital’s Robert H. Lurie Comprehensive Cancer Center at the invitation of then President Bienen. Her visit raised a total of $1.5 million for cancer research.

    In 2003, Northwestern finished a five-year capital campaign that raised $1.55 billion, exceeding its fundraising goal by $550 million.

    In 2014, Northwestern launched the “We Will” campaign with a fundraising goal of $3.75 billion. As of December 31, 2019, the university has received $4.78 billion from 164,026 donors.

    Sustainability

    In January 2009, the Green Power Partnership (sponsored by the EPA) listed Northwestern as one of the top 10 universities in the country in purchasing energy from renewable sources. The university matches 74 million kilowatt hours (kWh) of its annual energy use with Green-e Certified Renewable Energy Certificates (RECs). This green power commitment represents 30 percent of the university’s total annual electricity use and places Northwestern in the EPA’s Green Power Leadership Club. The Initiative for Sustainability and Energy at Northwestern (ISEN), supporting research, teaching and outreach in these themes, was launched in 2008.

    Northwestern requires that all new buildings be LEED-certified. Silverman Hall on the Evanston campus was awarded Gold LEED Certification in 2010; Wieboldt Hall on the Chicago campus was awarded Gold LEED Certification in 2007, and the Ford Motor Company Engineering Design Center on the Evanston campus was awarded Silver LEED Certification in 2006. New construction and renovation projects will be designed to provide at least a 20% improvement over energy code requirements where feasible. At the beginning of the 2008–09 academic year, the university also released the Evanston Campus Framework Plan, which outlines plans for future development of the university’s Evanston campus. The plan not only emphasizes sustainable building construction, but also focuses on reducing the energy costs of transportation by optimizing pedestrian and bicycle access. Northwestern has had a comprehensive recycling program in place since 1990. The university recycles over 1,500 tons of waste, or 30% of all waste produced on campus, each year. All landscape waste at the university is composted.

    Academics

    Education and rankings

    Northwestern is a large, residential research university, and is frequently ranked among the top universities in the United States. The university is a leading institution in the fields of materials engineering, chemistry, business, economics, education, journalism, and communications. It is also prominent in law and medicine. Accredited by the Higher Learning Commission and the respective national professional organizations for chemistry, psychology, business, education, journalism, music, engineering, law, and medicine, the university offers 124 undergraduate programs and 145 graduate and professional programs. Northwestern conferred 2,190 bachelor’s degrees, 3,272 master’s degrees, 565 doctoral degrees, and 444 professional degrees in 2012–2013. Since 1951, Northwestern has awarded 520 honorary degrees. Northwestern also has chapters of academic honor societies such as Phi Beta Kappa (Alpha of Illinois), Eta Kappa Nu, Tau Beta Pi, Eta Sigma Phi (Beta Chapter), Lambda Pi Eta, and Alpha Sigma Lambda (Alpha Chapter).

    The four-year, full-time undergraduate program comprises the majority of enrollments at the university. Although there is no university-wide core curriculum, a foundation in the liberal arts and sciences is required for all majors; individual degree requirements are set by the faculty of each school. The university heavily emphasizes interdisciplinary learning, with 72% of undergrads combining two or more areas of study. Northwestern’s full-time undergraduate and graduate programs operate on an approximately 10-week academic quarter system with the academic year beginning in late September and ending in early June. Undergraduates typically take four courses each quarter and twelve courses in an academic year and are required to complete at least twelve quarters on campus to graduate. Northwestern offers honors, accelerated, and joint degree programs in medicine, science, mathematics, engineering, and journalism. The comprehensive doctoral graduate program has high coexistence with undergraduate programs.

    Despite being a mid-sized university, Northwestern maintains a relatively low student to faculty ratio of 6:1.

    Research

    Northwestern was elected to the Association of American Universities in 1917 and is classified as an R1 university, denoting “very high” research activity. Northwestern’s schools of management, engineering, and communication are among the most academically productive in the nation. The university received $887.3 million in research funding in 2019 and houses over 90 school-based and 40 university-wide research institutes and centers. Northwestern also supports nearly 1,500 research laboratories across two campuses, predominately in the medical and biological sciences.

    Northwestern is home to the Center for Interdisciplinary Exploration and Research in Astrophysics, Northwestern Institute for Complex Systems, Nanoscale Science and Engineering Center, Materials Research Center, Center for Quantum Devices, Institute for Policy Research, International Institute for Nanotechnology, Center for Catalysis and Surface Science, Buffet Center for International and Comparative Studies, the Initiative for Sustainability and Energy at Northwestern, and the Argonne/Northwestern Solar Energy Research Center among other centers for interdisciplinary research.

    Student body

    Northwestern enrolled 8,186 full-time undergraduate, 9,904 full-time graduate, and 3,856 part-time students in the 2019–2020 academic year. The freshman retention rate for that year was 98%. 86% of students graduated after four years and 92% graduated after five years. These numbers can largely be attributed to the university’s various specialized degree programs, such as those that allow students to earn master’s degrees with a one or two year extension of their undergraduate program.

    The undergraduate population is drawn from all 50 states and over 75 foreign countries. 20% of students in the Class of 2024 were Pell Grant recipients and 12.56% were first-generation college students. Northwestern also enrolls the 9th-most National Merit Scholars of any university in the nation.

    In Fall 2014, 40.6% of undergraduate students were enrolled in the Weinberg College of Arts and Sciences, 21.3% in the McCormick School of Engineering and Applied Science, 14.3% in the School of Communication, 11.7% in the Medill School of Journalism, 5.7% in the Bienen School of Music, and 6.4% in the School of Education and Social Policy. The five most commonly awarded undergraduate degrees are economics, journalism, communication studies, psychology, and political science. The Kellogg School of Management’s MBA, the School of Law’s JD, and the Feinberg School of Medicine’s MD are the three largest professional degree programs by enrollment. With 2,446 students enrolled in science, engineering, and health fields, the largest graduate programs by enrollment include chemistry, integrated biology, material sciences, electrical and computer engineering, neuroscience, and economics.

    Athletics

    Northwestern is a charter member of the Big Ten Conference. It is the conference’s only private university and possesses the smallest undergraduate enrollment (the next-smallest member, the University of Iowa, is roughly three times as large, with almost 22,000 undergraduates).

    Northwestern fields 19 intercollegiate athletic teams (8 men’s and 11 women’s) in addition to numerous club sports. 12 of Northwestern’s varsity programs have had NCAA or bowl postseason appearances. Northwestern is one of five private AAU members to compete in NCAA Power Five conferences (the other four being Duke, Stanford, USC, and Vanderbilt) and maintains a 98% NCAA Graduation Success Rate, the highest among Football Bowl Subdivision schools.

    In 2018, the school opened the Walter Athletics Center, a $270 million state of the art lakefront facility for its athletics teams.

    Nickname and mascot

    Before 1924, Northwestern teams were known as “The Purple” and unofficially as “The Fighting Methodists.” The name Wildcats was bestowed upon the university in 1924 by Wallace Abbey, a writer for the Chicago Daily Tribune, who wrote that even in a loss to the University of Chicago, “Football players had not come down from Evanston; wildcats would be a name better suited to “[Coach Glenn] Thistletwaite’s boys.” The name was so popular that university board members made “Wildcats” the official nickname just months later. In 1972, the student body voted to change the official nickname to “Purple Haze,” but the new name never stuck.

    The mascot of Northwestern Athletics is “Willie the Wildcat”. Prior to Willie, the team mascot had been a live, caged bear cub from the Lincoln Park Zoo named Furpaw, who was brought to the playing field on game days to greet the fans. After a losing season however, the team decided that Furpaw was to blame for its misfortune and decided to select a new mascot. “Willie the Wildcat” made his debut in 1933, first as a logo and then in three dimensions in 1947, when members of the Alpha Delta fraternity dressed as wildcats during a Homecoming Parade.

    Traditions

    Northwestern’s official motto, “Quaecumque sunt vera,” was adopted by the university in 1890. The Latin phrase translates to “Whatsoever things are true” and comes from the Epistle of Paul to the Philippians (Philippians 4:8), in which St. Paul admonishes the Christians in the Greek city of Philippi. In addition to this motto, the university crest features a Greek phrase taken from the Gospel of John inscribed on the pages of an open book, ήρης χάριτος και αληθείας or “the word full of grace and truth” (John 1:14).
    Alma Mater is the Northwestern Hymn. The original Latin version of the hymn was written in 1907 by Peter Christian Lutkin, the first dean of the School of Music from 1883 to 1931. In 1953, then Director-of-Bands John Paynter recruited an undergraduate music student, Thomas Tyra (’54), to write an English version of the song, which today is performed by the Marching Band during halftime at Wildcat football games and by the orchestra during ceremonies and other special occasions.
    Purple became Northwestern’s official color in 1892, replacing black and gold after a university committee concluded that too many other universities had used these colors. Today, Northwestern’s official color is purple, although white is something of an official color as well, being mentioned in both the university’s earliest song, Alma Mater (1907) (“Hail to purple, hail to white”) and in many university guidelines.
    The Rock, a 6-foot high quartzite boulder donated by the Class of 1902, originally served as a water fountain. It was painted over by students in the 1940s as a prank and has since become a popular vehicle of self-expression on campus.
    Armadillo Day, commonly known as Dillo Day, is the largest student-run music festival in the country. The festival is hosted every Spring on Northwestern’s Lakefront.
    Primal Scream is held every quarter at 9 p.m. on the Sunday before finals week. Students lean out of windows or gather in courtyards and scream to help relieve stress.
    In the past, students would throw marshmallows during football games, but this tradition has since been discontinued.

    Philanthropy

    One of Northwestern’s most notable student charity events is Dance Marathon, the most established and largest student-run philanthropy in the nation. The annual 30-hour event is among the most widely-attended events on campus. It has raised over $1 million for charity ever year since 2011 and has donated a total of $13 million to children’s charities since its conception.

    The Northwestern Community Development Corps (NCDC) is a student-run organization that connects hundreds of student volunteers to community development projects in Evanston and Chicago throughout the year. The group also holds a number of annual community events, including Project Pumpkin, a Halloween celebration that provides over 800 local children with carnival events and a safe venue to trick-or-treat each year.

    Many Northwestern students participate in the Freshman Urban Program, an initiative for students interested in community service to work on addressing social issues facing the city of Chicago, and the university’s Global Engagement Studies Institute (GESI) programs, including group service-learning expeditions in Asia, Africa, or Latin America in conjunction with the Foundation for Sustainable Development.

    Several internationally recognized non-profit organizations were established at Northwestern, including the World Health Imaging, Informatics and Telemedicine Alliance, a spin-off from an engineering student’s honors thesis.

    Media
    Print

    Established in 1881, The Daily Northwestern is the university’s main student newspaper and is published on weekdays during the academic year. It is directed entirely by undergraduate students and owned by the Students Publishing Company. Although it serves the Northwestern community, the Daily has no business ties to the university and is supported wholly by advertisers.
    North by Northwestern is an online undergraduate magazine established in September 2006 by students at the Medill School of Journalism. Published on weekdays, it consists of updates on news stories and special events throughout the year. It also publishes a quarterly print magazine.
    Syllabus is the university’s undergraduate yearbook. It is distributed in late May and features a culmination of the year’s events at Northwestern. First published in 1885, the yearbook is published by Students Publishing Company and edited by Northwestern students.
    Northwestern Flipside is an undergraduate satirical magazine. Founded in 2009, it publishes a weekly issue both in print and online.
    Helicon is the university’s undergraduate literary magazine. Established in 1979, it is published twice a year: a web issue is released in the winter and a print issue with a web complement is released in the spring.
    The Protest is Northwestern’s quarterly social justice magazine.
    The Northwestern division of Student Multicultural Affairs supports a number of publications for particular cultural groups including Ahora, a magazine about Hispanic and Latino/a culture and campus life; Al Bayan, published by the Northwestern Muslim-cultural Student Association; BlackBoard Magazine, a magazine centered around African-American student life; and NUAsian, a magazine and blog on Asian and Asian-American culture and issues.
    The Northwestern University Law Review is a scholarly legal publication and student organization at Northwestern University School of Law. Its primary purpose is to publish a journal of broad legal scholarship. The Law Review publishes six issues each year. Student editors make the editorial and organizational decisions and select articles submitted by professors, judges, and practitioners, as well as student pieces. The Law Review also publishes scholarly pieces weekly on the Colloquy.
    The Northwestern Journal of Technology and Intellectual Property is a law review published by an independent student organization at Northwestern University School of Law.
    The Northwestern Interdisciplinary Law Review is a scholarly legal publication published annually by an editorial board of Northwestern undergraduates. Its mission is to publish interdisciplinary legal research, drawing from fields such as history, literature, economics, philosophy, and art. Founded in 2008, the journal features articles by professors, law students, practitioners, and undergraduates. It is funded by the Buffett Center for International and Comparative Studies and the Office of the Provost.

    Web-based

    Established in January 2011, Sherman Ave is a humor website that often publishes content on Northwestern student life. Most of its staff writers are current Northwestern undergraduates writing under various pseudonyms. The website is popular among students for its interviews of prominent campus figures, Freshman Guide, and live-tweeting coverage of football games. In Fall 2012, the website promoted a satiric campaign to end the Vanderbilt University football team’s custom of clubbing baby seals.
    Politics & Policy is dedicated to the analysis of current events and public policy. Established in 2010 by students at the Weinberg College of Arts and Sciences, School of Communication, and Medill School of Journalism, the publication reaches students on more than 250 college campuses around the world. Run entirely by undergraduates, it is published several times a week and features material ranging from short summaries of events to extended research pieces. The publication is financed in part by the Buffett Center.
    Northwestern Business Review is a campus source for business news. Founded in 2005, it has an online presence as well as a quarterly print schedule.
    TriQuarterly Online (formerly TriQuarterly) is a literary magazine published twice a year featuring poetry, fiction, nonfiction, drama, literary essays, reviews, blog posts, and art.
    The Queer Reader is Northwestern’s first radical feminist and LGBTQ+ publication.

    Radio, film, and television

    WNUR (89.3 FM) is a 7,200-watt radio station that broadcasts to the city of Chicago and its northern suburbs. WNUR’s programming consists of music (jazz, classical, and rock), literature, politics, current events, varsity sports (football, men’s and women’s basketball, baseball, softball, and women’s lacrosse), and breaking news on weekdays.
    Studio 22 is a student-run production company that produces roughly ten films each year. The organization financed the first film Zach Braff directed, and many of its films have featured students who would later go into professional acting, including Zach Gilford of Friday Night Lights.
    Applause for a Cause is currently the only student-run production company in the nation to create feature-length films for charity. It was founded in 2010 and has raised over $5,000 to date for various local and national organizations across the United States.
    Northwestern News Network is a student television news and sports network, serving the Northwestern and Evanston communities. Its studios and newsroom are located on the fourth floor of the McCormick Tribune Center on Northwestern’s Evanston campus. NNN is funded by the Medill School of Journalism.

     
  • richardmitnick 2:05 pm on February 1, 2021 Permalink | Reply
    Tags: "Medicine by Design researchers focus on promoting self-repair of the brain", , Bioengineering, , , , Medicine by Design-a strategic research initiative working at the convergence of engineering; medicine; science to catalyze transformative discoveries in regenerative medicine., Neurobiology, Stem Cell Biology, ,   

    From University of Toronto (CA): “Medicine by Design researchers focus on promoting self-repair of the brain” 

    U Toronto Bloc

    From University of Toronto (CA)

    January 28, 2021
    Julie Crljen

    1
    Credit: Jolygon via Getty Images.

    If you asked Freda Miller 10 years ago if stem cells could be harnessed to repair brain injuries and disease, she would have said it was too early to tell.

    Today, she describes the progress that she and other regenerative medicine experts have made in understanding what regulates populations of stem cells – cells with the potential to turn into many different cell types – and the rapid advances those discoveries have driven.

    “Science is like a playground right now,” says Miller, an adjunct scientist in the neurosciences and mental health program at The Hospital for Sick Children (SickKids) and a professor in the department of molecular genetics in the University of Toronto’s Temerty Faculty of Medicine.

    “The approaches we’re using allow us to find so much information on things we could only dream of before.”

    Miller, who is also a professor at the University of British Columbia, is leading a Medicine by Design-funded team with expertise in computational biology, neurobiology, bioengineering and stem cell biology that is investigating multiple strategies to recruit stem cells to promote self-repair in the brain and in muscle. If it succeeds, the research could improve treatments for diseases such as multiple sclerosis (MS) and cerebral palsy, as well as brain injury.

    Miller’s team is one of 11 at U of T and its partner hospitals that are sharing nearly $21 million in funding from Medicine by Design over three years. Funded by a $114-million grant from the Canada First Research Excellence Fund, Medicine by Design is a strategic research initiative that is working at the convergence of engineering, medicine and science to catalyze transformative discoveries in regenerative medicine and accelerate them toward clinical impact.

    This is the second round of large-scale, collaborative team projects that Medicine by Design has funded. The support builds on the progress made in the first round of projects (2016-2019) and is spurring further innovation to push regenerative medicine forward. It also led to a 2017 publication – by many of the same researchers on Miller’s current project – in Cell Reports that essentially provided a roadmap for how brain stem cells build the brain developmentally, and then persist to function in the adult brain.

    Miller, a neuroscientist, has always been fascinated by the brain and neurons, the network of billions of nerve cells in the brain. Around 15 years ago, when she started to take an interest in the potential regenerative capabilities of stem cells, she began to wonder if she could use stem cells to treat brain injury or disease. Though too little was known about stem cells at the time, she knew that it was a question worth investigating. But she also realized that making and integrating new nerve cells, which are the working parts of brain circuits, would be a daunting task.

    “Even if you can convince the stem cells to make more neurons, those neurons then have to survive and they have to integrate into this really complex circuitry,” says Miller. “It just made sense to me that if we’re really going to test this idea of self-repair in the brain, we should go after something that’s more achievable biologically.”

    So, Miller turned her attention to a substance called myelin, which covers nerves and allows nerve impulses to travel easily. In many nervous system diseases – MS is a well-known example – and brain injuries, damage to and loss of myelin is a main factor in debilitating symptoms. Thanks in part to the team project award from Medicine by Design, Miller leads a team that has a focus on recruiting stem cells to promote the generation of myelin.

    Miller says repairing myelin, also called remyelination, will eventually help to better understand the effects of the target disease or injury, possibly even leading scientists to discover how to reverse it. Boosting myelin is a promising area of research, she adds, because it’s not an all-or-nothing situation.

    “Even a little bit of remyelination could have a big impact. You don’t have to win the whole lottery; you don’t have to have 100 per cent remyelination to have a measurable outcome.”

    The team’s work is not limited to generating myelin to treat nervous system diseases or brain injury. They are also looking at how they could recruit stem cells to generate more muscle. They are specifically looking at muscular dystrophy, but Miller says the applications from that work can be used in other diseases or situations where damage to muscles has occurred, such as age-related disorders.

    Miller’s team includes experts from diverse fields: Gary Bader, a professor at the Donnelly Centre for Cellular and Biomolecular Research and a computational biologist; bioengineers Alison McGuigan, a professor in the department of chemical engineering and applied chemistry in the Faculty of Applied Science & Engineering, and Penney Gilbert, an associate professor at the Institute of Biomedical Engineering; Sid Goyal, a professor at the department of physics in the Faculty of Arts & Science; Professor David Kaplan and Assistant Professor Yun Li, both in the Temerty Faculty of Medicine and a senior scientist and a scientist, respectively, at SickKids; stem cell biologist Cindi Morshead, a professor and chair of the division of anatomy in the department of surgery in the Temerty Faculty of Medicine; and Peter Zandstra, a University Professor in the Faculty of Applied Science & Engineering and director of Michael Smith Laboratories at the University of British Columbia.

    Miller says Medicine by Design’s contribution in bringing teams like hers together is immeasurable.

    “There are tangible results you can measure like publications and other grants and clinical trials,” Miller says. “But there are a lot of intangible things Medicine by Design brings to the table like developing a culture of people from very diverse places and allowing them to do science together at a time when the biggest breakthroughs are going to be made by combining technological and biological approaches. It’s hard to do that if you’re on your own.”

    This large, interdisciplinary team effort combines data and computer modelling to look at individual stem cells in the brain and predict their behaviours. Through experimentation, they can then test if the cells behave the way they predicted, which Miller says they have had great success with. From there, the team casts a wide net, testing various ways to try to control cells’ behaviour with the end goal of convincing the stem cells to turn into cells that aid in healing and repair.

    One approach they use is testing already approved pharmaceuticals to see if they have the desired effect on the stem cells’ behaviour. This approach has had success. In summer 2020, Morshead, Miller and their collaborators, led by Donald Mabbott, a SickKids senior scientist and professor in the department of psychology in the Faculty of Arts & Science, published a paper in Nature Medicine that showed that metformin, a common diabetes drug, has the potential to reverse brain injury in children who had had cranial radiation as a curative therapy for brain tumours.

    Miller says that, to her knowledge, this is the first paper that demonstrates that this type of brain repair is possible in humans.

    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 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 outside the United States, the other being McGill University.
    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.

     
  • richardmitnick 9:33 am on January 25, 2021 Permalink | Reply
    Tags: "Researchers use lasers and molecular tethers to create perfectly patterned platforms for tissue engineering", A biologically compatible 3D scaffold in which cells can grow, , Bioengineering, Biomaterials, , Decorate the biologically compatible 3D scaffold with biochemical messages in the correct configuration to trigger the formation of the desired organ or tissue., , Laboratory-grown organs and tissues, , Light-based methods to modify synthetic scaffolds with protein signals, mCherry proteins, , , Protein-based biochemical messages that affect cell behavior, The signals that the team added to the hydrogels are proteins., The tethered proteins were fully functional delivering desired signals to cells., Two types of biological polymers: collagen and fibrin,   

    From University of Washington: “Researchers use lasers and molecular tethers to create perfectly patterned platforms for tissue engineering” 

    From University of Washington

    January 18, 2021
    James Urton

    1
    Top view of a collagen hydrogel that researchers decorated with immobilized mCherry proteins, which glow red under fluorescent light. The team shined UV light on the hydrogel through a mask cut out in the shape of a former University of Washington logo. Black regions were masked from the light, and so the mCherry protein did not adhere to those portions of the hydrogel. Scale bar is 50 micrometers.Batalov et al., PNAS, 2021.

    2
    Top view of two collagen hydrogels that researchers decorated with immobilized mCherry proteins, which glow red under fluorescent light. The team scanned near-infrared lasers in the shapes of a monster (left) and the Space Needle (right) to create these patterns. Black regions were not scanned with the laser, and so the mCherry protein did not adhere to those portions of the hydrogel. Scale bar is 50 micrometers.Batalov et al., PNAS, 2021.

    3
    The team used near-infrared lasers to create this intricate pattern in the shape of a human heart of immobilized mCherry proteins, which glow red under fluorescent light, within a collagen hydrogel. On the left is a composite image of 3D slices from the gel. On the right are cross-sectional views of the mCherry patterns. Scale bar is 50 micrometers.Batalov et al., PNAS, 2021.

    4
    This is a top view of a cylindrical fibrin hydrogel. By design, the right side of the hydrogel contains immobilized Delta-1 proteins, which activate Notch signaling pathways within cells. The left side does not contain immobilized Delta-1 (see insert). The team introduced human bone cancer cells, which were engineered to glow when their Notch signaling pathways are activated, into the hydrogel. The right side of the hydrogel glows brightly, indicating that cells in that region have activated their Notch signaling pathways. Cells on the left side of the hydrogel have not. Scale bar is 1 millimeter.Batalov et al., PNAS, 2021.

    Imagine going to a surgeon to have a diseased or injured organ switched out for a fully functional, laboratory-grown replacement. This remains science fiction and not reality because researchers today struggle to organize cells into the complex 3D arrangements that our bodies can master on their own.

    There are two major hurdles to overcome on the road to laboratory-grown organs and tissues. The first is to use a biologically compatible 3D scaffold in which cells can grow. The second is to decorate that scaffold with biochemical messages in the correct configuration to trigger the formation of the desired organ or tissue.

    In a major step toward transforming this hope into reality, researchers at the University of Washington have developed a technique to modify naturally occurring biological polymers with protein-based biochemical messages that affect cell behavior. Their approach, published the week of Jan. 18 in the PNAS, uses a near-infrared laser to trigger chemical adhesion of protein messages to a scaffold made from biological polymers such as collagen, a connective tissue found throughout our bodies.

    Mammalian cells responded as expected to the adhered protein signals within the 3D scaffold, according to senior author Cole DeForest, a UW associate professor of chemical engineering and of bioengineering. The proteins on these biological scaffolds triggered changes to messaging pathways within the cells that affect cell growth, signaling and other behaviors.

    These methods could form the basis of biologically based scaffolds that might one day make functional laboratory-grown tissues a reality, said DeForest, who is also a faculty member with the UW Molecular Engineering and Sciences Institute and the UW Institute for Stem Cell and Regenerative Medicine.

    “This approach provides us with the opportunities we’ve been waiting for to exert greater control over cell function and fate in naturally derived biomaterials — not just in three-dimensional space but also over time,” said DeForest. “Moreover, it makes use of exceptionally precise photochemistries that can be controlled in 4D while uniquely preserving protein function and bioactivity.”

    DeForest’s colleagues on this project are lead author Ivan Batalov, a former UW postdoctoral researcher in chemical engineering and bioengineering, and co-author Kelly Stevens, a UW assistant professor of bioengineering and of laboratory medicine and pathology.

    Their method is a first for the field, spatially controlling cell function inside naturally occurring biological materials as opposed to those that are synthetically derived. Several research groups, including DeForest’s, have developed light-based methods to modify synthetic scaffolds with protein signals. But natural biological polymers can be a more attractive scaffold for tissue engineering because they innately possess biochemical characteristics that cells rely on for structure, communication and other purposes.

    “A natural biomaterial like collagen inherently includes many of the same signaling cues as those found in native tissue,” said DeForest. “In many cases, these types of materials keep cells ‘happier’ by providing them with similar signals to those they would encounter in the body.”

    They worked with two types of biological polymers: collagen and fibrin, a protein involved in blood clotting. They assembled each into fluid-filled scaffolds known as hydrogels.

    The signals that the team added to the hydrogels are proteins, one of the main messengers for cells. Proteins come in many forms, all with their own unique chemical properties. As a result, the researchers designed their system to employ a universal mechanism to attach proteins to a hydrogel — the binding between two chemical groups, an alkoxyamine and an aldehyde. Prior to hydrogel assembly, they decorated the collagen or fibrin precursors with alkoxyamine groups, all physically blocked with a “cage” to prevent the alkoxyamines from reacting prematurely. The cage can be removed with ultraviolet light or a near-infrared laser.

    Using methods previously developed in DeForest’s laboratory, the researchers also installed aldehyde groups to one end of the proteins they wanted to attach to the hydrogels. They then combined the aldehyde-bearing proteins with the alkoxyamine-coated hydrogels, and used a brief pulse of light to remove the cage covering the alkoxyamine. The exposed alkoxyamine readily reacted with the aldehyde group on the proteins, tethering them within the hydrogel. The team used masks with patterns cut into them, as well as changes to the laser scan geometries, to create intricate patterns of protein arrangements in the hydrogel — including an old UW logo, Seattle’s Space Needle, a monster and the 3D layout of the human heart.

    The tethered proteins were fully functional, delivering desired signals to cells. Rat liver cells — when loaded onto collagen hydrogels bearing a protein called EGF, which promotes cell growth — showed signs of DNA replication and cell division. In a separate experiment, the researchers decorated a fibrin hydrogel with patterns of a protein called Delta-1, which activates a specific pathway in cells called Notch signaling. When they introduced human bone cancer cells into the hydrogel, cells in the Delta-1-patterned regions activated Notch signaling, while cells in areas without Delta-1 did not.

    These experiments with multiple biological scaffolds and protein signals indicate that their approach could work for almost any type of protein signal and biomaterial system, DeForest said.

    “Now we can start to create hydrogel scaffolds with many different signals, utilizing our understanding of cell signaling in response to specific protein combinations to modulate critical biological function in time and space,” he added.

    With more-complex signals loaded on to hydrogels, scientists could then try to control stem cell differentiation, a key step in turning science fiction into science fact.

    The research was funded by the National Science Foundation, the National Institutes of Health and Gree Real Estate.

    See the full article here .


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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    u-washington-campus
    The University of Washington 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.

     
  • richardmitnick 11:21 am on October 7, 2020 Permalink | Reply
    Tags: "How do you predict unprecedented events?", A "black swan" event is a highly unlikely but massively consequential incident., “Black swan” events, Bioengineering, Bioengineers at Stanford University are suggesting a method for forecasting these supposedly unforeseeable fluctuations., Researchers combined avalanche physics with ecosystem data to create a computational method for predicting extreme ecological events.,   

    From Stanford University Engineering: “How do you predict unprecedented events?” 

    Stanford University Name
    From Stanford University

    From Stanford University Engineering

    August 06, 2020 [Just now in social media.]
    Taylor Kubota

    Researchers combined avalanche physics with ecosystem data to create a computational method for predicting extreme ecological events.

    1
    Researchers developed a computational method for predicting unprecedented, extreme events, known as “black swan” events. Credit: Getty Images.

    A black swan event is a highly unlikely but massively consequential incident, such as the 2008 global recession and the loss of one-third of the world’s saiga antelope in a matter of days in 2015.

    Challenging the quintessentially unpredictable nature of black swan events, bioengineers at Stanford University are suggesting a method for forecasting these supposedly unforeseeable fluctuations.

    “By analyzing long-term data from three ecosystems, we were able to show that fluctuations that happen in different biological species are statistically the same across different ecosystems,” said Samuel Bray, a research assistant in the lab of Bo Wang, assistant professor of bioengineering at Stanford. “That suggests there are certain underlying universal processes that we can take advantage of in order to forecast this kind of extreme behavior.”

    The forecasting method the researchers have developed, which was detailed recently in PLOS Computational Biology, is based on natural systems and could find use in health care and environmental research. It also has potential applications in disciplines outside ecology that have their own black swan events, such as economics and politics.

    “This work is exciting because it’s a chance to take the knowledge and the computational tools that we’re building in the lab and use those to better understand — even predict or forecast — what happens in the world surrounding us,” said Wang, who is senior author of the paper. “It connects us to the bigger world.”

    From microbes to avalanches

    Over years of studying microbial communities, Bray noticed several instances where one species would undergo an unanticipated population boom, overtaking its neighbors. Discussing these events with Wang, they wondered whether this phenomenon occurred outside the lab as well and, if so, whether it could be predicted.

    In order to address this question, the researchers had to find other biological systems that experience black swan events. The researchers needed details, not only about the black swan events themselves but also the context in which they occurred. So, they specifically sought ecosystems that scientists have been closely monitoring for many years.

    “These data have to capture long periods of time and that’s hard to collect,” said Bray, who is lead author of the paper. “It’s much more than a PhD-worth of information. But that’s the only way you can see the spectra of these fluctuations at large scales.”

    Bray settled on three eclectic datasets: an eight-year study of plankton from the Baltic Sea with species levels measured twice weekly; net carbon measurements from a deciduous broadleaf forest at Harvard University, gathered every 30 minutes since 1991; and measurements of barnacles, algae and mussels on the coast of New Zealand, taken monthly for over 20 years.

    The researchers then analyzed these three datasets using theory about avalanches — physical fluctuations that, like black swan events, exhibit short-term, sudden, extreme behavior. At its core, this theory attempts to explain the physics of systems like avalanches, earthquakes, fire embers, or even crumpling candy wrappers, which all respond to external forces with discrete events of various magnitudes or sizes — a phenomenon scientists call “crackling noise.”

    Built on the analysis, the researchers developed a method for predicting black swan events, one that is designed to be flexible across species and timespans, and able to work with data that are far less detailed and more complex than those used to develop it.

    “But Sam’s method is different in that it assumes we are only seeing part of the world. It extrapolates a little about what we’re missing, and it turns out that helps tremendously in terms of prediction.”

    Forecasting in the real world

    The researchers tested their method using the three ecosystem datasets on which it was built. Using only fragments of each dataset — specifically fragments which contained the smallest fluctuations in the variable of interest — they were able to accurately predict extreme events that occurred in those systems.

    They would like to expand the application of their method to other systems in which black swan events are also present, such as in economics, epidemiology, politics and physics. At present, the researchers are hoping to collaborate with field scientists and ecologists to apply their method to real-world situations where they could make a positive difference in the lives of other people and the planet.

    This research was funded by the Volkswagen Foundation and Arnold and Mabel Beckman Foundation.

    See the full article here .

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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    Stanford Engineering has been at the forefront of innovation for nearly a century, creating pivotal technologies that have transformed the worlds of information technology, communications, health care, energy, business and beyond.

    The school’s faculty, students and alumni have established thousands of companies and laid the technological and business foundations for Silicon Valley. Today, the school educates leaders who will make an impact on global problems and seeks to define what the future of engineering will look like.
    Mission

    Our mission is to seek solutions to important global problems and educate leaders who will make the world a better place by using the power of engineering principles, techniques and systems. We believe it is essential to educate engineers who possess not only deep technical excellence, but the creativity, cultural awareness and entrepreneurial skills that come from exposure to the liberal arts, business, medicine and other disciplines that are an integral part of the Stanford experience.

    Our key goals are to:

    Conduct curiosity-driven and problem-driven research that generates new knowledge and produces discoveries that provide the foundations for future engineered systems
    Deliver world-class, research-based education to students and broad-based training to leaders in academia, industry and society
    Drive technology transfer to Silicon Valley and beyond with deeply and broadly educated people and transformative ideas that will improve our society and our world.

    The Future of Engineering

    The engineering school of the future will look very different from what it looks like today. So, in 2015, we brought together a wide range of stakeholders, including mid-career faculty, students and staff, to address two fundamental questions: In what areas can the School of Engineering make significant world‐changing impact, and how should the school be configured to address the major opportunities and challenges of the future?

    One key output of the process is a set of 10 broad, aspirational questions on areas where the School of Engineering would like to have an impact in 20 years. The committee also returned with a series of recommendations that outlined actions across three key areas — research, education and culture — where the school can deploy resources and create the conditions for Stanford Engineering to have significant impact on those challenges.

    Stanford University

    Leland and Jane Stanford founded the University to “promote the public welfare by exercising an influence on behalf of humanity and civilization.” Stanford opened its doors in 1891, and more than a century later, it remains dedicated to finding solutions to the great challenges of the day and to preparing our students for leadership in today’s complex world. Stanford, is an American private research university located in Stanford, California on an 8,180-acre (3,310 ha) campus near Palo Alto. Since 1952, more than 54 Stanford faculty, staff, and alumni have won the Nobel Prize, including 19 current faculty members

    Stanford University Seal

     
  • richardmitnick 9:26 pm on May 29, 2018 Permalink | Reply
    Tags: Bioengineering, ,   

    From Lawrence Berkeley National Lab: “New Machine Learning Approach Could Accelerate Bioengineering” 

    Berkeley Logo

    From Lawrence Berkeley National Lab

    May 29, 2018
    Dan Krotz
    dakrotz@lbl.gov
    510-486-4019

    1
    A new approach developed by Zak Costello (left) and Hector Garcia Martin brings the the speed and analytic power of machine learning to bioengineering. (Credit: Marilyn Chung, Berkeley Lab)

    Scientists from the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) have developed a way to use machine learning to dramatically accelerate the design of microbes that produce biofuel.

    Their computer algorithm starts with abundant data about the proteins and metabolites in a biofuel-producing microbial pathway, but no information about how the pathway actually works. It then uses data from previous experiments to learn how the pathway will behave. The scientists used the technique to automatically predict the amount of biofuel produced by pathways that have been added to E. coli bacterial cells.

    The new approach is much faster than the current way to predict the behavior of pathways, and promises to speed up the development of biomolecules for many applications in addition to commercially viable biofuels, such as drugs that fight antibiotic-resistant infections and crops that withstand drought.

    The research was published May 29 in the journal Nature Systems Biology and Applications.

    In biology, a pathway is a series of chemical reactions in a cell that produce a specific compound. Researchers are exploring ways to re-engineer pathways, and import them from one microbe to another, to harness nature’s toolkit to improve medicine, energy, manufacturing, and agriculture. And thanks to new synthetic biology capabilities, such as the gene-editing tool CRISPR-Cas9, scientists can conduct this research at a precision like never before.

    “But there’s a significant bottleneck in the development process,” said Hector Garcia Martin, group lead at the DOE Agile BioFoundry and director of Quantitative Metabolic Modeling at the Joint BioEnergy Institute (JBEI), a DOE Bioenergy Research Center funded by DOE’s Office of Science and led by Berkeley Lab. The research was performed by Zak Costello (also with the Agile BioFoundry and JBEI) under the direction of Garcia Martin. Both researchers are also in Berkeley Lab’s Biological Systems and Engineering Division.

    “It’s very difficult to predict how a pathway will behave when it’s re-engineered. Trouble-shooting takes up 99% of our time. Our approach could significantly shorten this step and become a new way to guide bioengineering efforts,” Garcia Martin added.

    The current way to predict a pathway’s dynamics requires a maze of differential equations that describe how the components in the system change over time. Subject-area experts develop these “kinetic models” over several months, and the resulting predictions don’t always match experimental results.

    Machine learning, however, uses data to train a computer algorithm to make predictions. The algorithm learns a system’s behavior by analyzing data from related systems. This allows scientists to quickly predict the function of a pathway even if its mechanisms are poorly understood — as long as there are enough data to work with.


    Machine learning approaches, such as the technique recently developed by Berkeley Lab scientists, are hamstrung by a lack of large quantities of quality data. New automation capabilities at JBEI and the Agile BioFoundry will be able to produce these data in a systematic fashion. This video shows a liquid handler coupled with an automated fermentation platform at JBEI, which takes samples automatically to produce data for the machine learning algorithms.

    The scientists tested their technique on pathways added to E. coli cells. One pathway is designed to produce a bio-based jet fuel called limonene; the other produces a gasoline replacement called isopentenol. Previous experiments at JBEI yielded a trove of data related to how different versions of the pathways function in various E. coli strains. Some of the strains have a pathway that produces small amounts of either limonene or isopentenol, while other strains have a version that produces large amounts of the biofuels.

    The researchers fed this data into their algorithm. Then machine learning took over: The algorithm taught itself how the concentrations of metabolites in these pathways change over time, and how much biofuel the pathways produce. It learned these dynamics by analyzing data from the two experimentally known pathways that produce small and large amounts of biofuels.

    The algorithm used this knowledge to predict the behavior of a third set of “mystery” pathways the algorithm had never seen before. It accurately predicted the biofuel-production profiles for the mystery pathways, including that the pathways produce a medium amount of fuel. In addition, the machine learning-derived prediction outperformed kinetic models.

    “And the more data we added, the more accurate the predictions became,” said Garcia Martin. “This approach could expedite the time it takes to design new biomolecules. A project that today takes ten years and a team of experts could someday be handled by a summer student.”

    The work was part of the DOE Agile BioFoundry, supported by DOE’s Office of Energy Efficiency and Renewable Energy, and the Joint BioEnergy Institute, supported by DOE’s Office of Science.

    See the full article here .


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

    stem

    Stem Education Coalition

    A U.S. Department of Energy National Laboratory Operated by the University of California

    University of California Seal

    DOE Seal

     
  • richardmitnick 8:56 am on January 2, 2015 Permalink | Reply
    Tags: , Bioengineering,   

    From NYT: “Scientists Alter Crops With Techniques Outside Regulators’ Scope” 

    New York Times

    The New York Times

    JAN. 1, 2015
    ANDREW POLLACK

    Its first attempt to develop genetically engineered grass ended disastrously for the Scotts Miracle-Gro Company. The grass escaped into the wild from test plots in Oregon in 2003, dooming the chances that the government would approve the product for commercial use.

    Yet Scotts is once again developing genetically modified grass that would need less mowing, be a deeper green and be resistant to damage from the popular weedkiller Roundup. But this time the grass will not need federal approval before it can be field-tested and marketed.

    Scotts and several other companies are developing genetically modified crops using techniques that either are outside the jurisdiction of the Agriculture Department or use new methods — like “genome editing” — that were not envisioned when the regulations were created.

    The department has said, for example, that it has no authority over a new herbicide-resistant canola, a corn that would create less pollution from livestock waste, switch grass tailored for biofuel production, and even an ornamental plant that glows in the dark.

    1
    A test plot of bioengineered grass in Gervais, Ore., is examined by a scientist for the Scotts Miracle-Gro Company. Credit Rick Bowmer/Associated Press

    The trend alarms critics of biotech crops, who say genetic modification can have unintended effects, regardless of the process.

    “They are using a technical loophole so that what are clearly genetically engineered crops and organisms are escaping regulation,” said Michael Hansen, a senior scientist at Consumers Union. He said the grass “can have all sorts of ecological impact and no one is required to look at it.”

    Even some people who say the crops are safe and the regulations overly burdensome have expressed concern that because some crops can be left unregulated, the whole oversight process is confusing and illogical, in some cases doing more harm than good.

    In November’s Nature Biotechnology, plant researchers at the University of California, Davis, wrote that the regulatory framework had become “obsolete and an obstacle to the development of new agricultural products.”

    But companies using the new techniques say that if the methods were not labeled genetic engineering, novel crops could be marketed or grown in Europe and other countries that do not readily accept genetically modified crops.

    Freedom from oversight could also open opportunities for smaller companies and university breeders and for the modification of less common crops. Until now, in part because of the costs associated with regulation, crop biotechnology has been dominated by Monsanto and a handful of other big companies working mainly on widely grown crops like corn and soybeans.

    c
    Cells from a canola leaf during processing at Cellectis Plant Sciences.

    “It enables small companies to develop products, and even university start-ups,” said Luc Mathis, chief executive of Cellectis Plant Sciences, which recently received a regulatory exemption for a potato it says will make French fries less unhealthy.

    An industry-sponsored study said that the large companies spend an average of $136 million on the development of a genetically engineered crop, including $35 million in regulatory costs. The Agriculture Department once took two to five years to review applications, though it is trying to reduce that to 13 to 16 months.

    Genetically engineered crops, popularly called genetically modified organisms or G.M.O.s, typically have genes from other organisms inserted into their DNA. The most popular ones, like Roundup-resistant soybeans and insect-resistant corn, use genes from bacteria.

    Under a framework announced in 1986, oversight of the crops is shared by the Agriculture Department, the Environmental Protection Agency and the Food and Drug Administration. Rather than enact new laws for genetically engineered crops, the government covers them under existing statutes.

    The Agriculture Department, which approves crops for commercial planting, is a case in point. Its authority stems from its responsibility for protecting American crops from plant pests, which typically are insects or pathogens.

    That responsibility extends to certain G.M.O. crops because for many of them, the foreign gene is inserted through the use of a bacterium, or the inserted DNA contains a genetic “on” switch from a plant virus.

    p
    Peter Beetham, chief executive of Cibus, which uses genome editing to modify plants. Credit Sandy Huffaker for The New York Times

    But companies can get around that oversight by avoiding components from plant pests. In Scotts’s newer grasses, for instance, the foreign genetic material comes only from other plants and is inserted with a gene gun rather than by the bacterium.

    “If you take genetic material from a plant and it’s not considered a pest, and you don’t use a transformation technology that would sort of violate the rules, there’s a bunch of stuff you can do that at least technically is unregulated,” Jim Hagedorn, Scotts chief executive, told analysts in December 2013. He said the company nearly shut its biotech program after the previous mishap, until it hit upon the new strategy and created “a stunning array of products that are not regulated.”

    The company recently started testing the grass on the lawns of its employees. But a spokesman said the grass was years from reaching the market.

    A spokeswoman for the Agriculture Department said the agency was acting within the authority given to it by Congress and that even if it did not have oversight of a particular crop, the F.D.A. or E.P.A. might still be involved.

    Other companies, including Cellectis, are using new genome-editing techniques that can change the plant’s existing DNA rather than insert foreign genes. Cibus, a privately held San Diego company, is beginning to sell herbicide-resistant canola developed this way.

    “With our technology, we can develop the same traits but in a way that’s not transgenic,” said Peter Beetham, chief executive of Cibus, using a term for a plant containing foreign genes.

    c
    At Cellectis, creating a plant from a genome-edited cell.

    Regulators around the world are now grappling with whether these techniques are even considered genetic engineering and how, if at all, they should be regulated.

    “The technology is always one step ahead of the regulators,” said Michiel van Lookeren Campagne, head of biotechnology research at Syngenta, a seed and agricultural chemical company.

    Some researchers argue that using genome editing to inactivate a gene in a plant, or to make a tiny change in an existing gene, results in a crop no different from what could be obtained through natural mutations and conventional breeding, though it is achieved more quickly.

    “Those are basically comparable to what you get from conventional breeding,” said Neal Gutterson, vice president for agricultural biotechnology at DuPont Pioneer, a seed company. “We certainly hope that the regulatory agencies recognize that and treat the products accordingly.”

    The gene editing, they argue, is also more directed and precise than the existing technique of exposing plants to radiation or chemicals to induce random mutations in hopes of generating a desirable change. This technique has been used for decades and is not regulated, even though it can potentially cause unknown and unintended changes to crops.

    But critics of biotech crops say the genome-editing techniques can make changes in plant DNA other than the intended one. Also, the gene editing is typically done on plant cells or plant tissues growing in a dish. The process of then turning those genetically altered cells or tissues into a full plant can itself induce mutations.

    Another category that some researchers say should receive less scrutiny is so-called cisgenic crops, which are developed using conventional genetic engineering but with the inserted genes from the same species as the crop.

    An example is a potato developed by the J. R. Simplot Company that resists bruising and makes a less unhealthy French fry. The Agriculture Department reviewed the Simplot potato before approving it recently.

    Jennifer Kuzma, co-director of the Genetic Engineering and Society Center at North Carolina State University, said that there would soon be a flood of crops seeking regulatory exemptions and that there needed to be a public discourse about what should be regulated, in part to allay possible consumer anxiety.

    “It’s not that I think these are risky,” she said of the crops escaping regulation. “But the very fact that this is the route we are taking without any discussion is troubling.”

    See the full article here.

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  • richardmitnick 5:18 pm on December 22, 2014 Permalink | Reply
    Tags: , Bioengineering,   

    From Brown: “New technology makes tissues, someday maybe organs” 

    Brown University
    Brown University

    December 22, 2014
    David Orenstein 401-863-1862

    A new instrument could someday build replacement human organs the way electronics are assembled today: with precise picking and placing of parts.


    Building large tissues
    A new device allows perfusion of bioengineered structures built from smaller pieces of tissue prepared in the lab. It is a first step toward someday building whole organs. Video: Mike Cohea/Brown University

    In this case, the parts are not resistors and capacitors, but 3-D microtissues containing thousands to millions of living cells that need a constant stream of fluid to bring them nutrients and to remove waste. The new device is called “BioP3” for pick, place, and perfuse. A team of researchers led by Jeffrey Morgan, a Brown University bioengineer, and Dr. Andrew Blakely, a surgery fellow at Rhode Island Hospital and the Warren Alpert Medical School, introduces BioP3 in a new paper in the journal Tissue Engineering Part C.

    Because it allows assembly of larger structures from small living microtissue components, Morgan said, future versions of BioP3 may finally make possible the manufacture of whole organs such as livers, pancreases, or kidneys.

    b
    Honeycombs of bioengineered tissue, top, can be stacked and arranged to build larger living structures.

    “For us it’s exciting because it’s a new approach to building tissues, potentially organs, layer by layer with large, complex living parts,” said Morgan, professor of molecular pharmacology, physiology and Biotechnology. “In contrast to 3-D bioprinting that prints one small drop at a time, our approach is much faster because it uses pre-assembled living building parts with functional shapes and a thousand times more cells per part.”

    Morgan’s research has long focused on making individual microtissues in various shapes such as spheres, long rods, donut rings and honeycomb slabs. He uses a novel micromolding technique to direct the cells to self-assemble and form these complex shapes. He is a founder of the Providence startup company MicroTissues Inc., which sells such culture-making technology.

    Now, the new paper shows, there is a device to build even bigger tissues by combining those living components.

    “This project was particularly interesting to me since it is a novel approach to large-scale tissue engineering that hasn’t been previously described,” Blakely said.

    The BioP3 prototype

    The BioP3, made mostly from parts available at Home Depot for less than $200, seems at first glance to be a small, clear plastic box with two chambers: one side for storing the living building parts and one side where a larger structure can be built with them. It’s what rests just above the box that really matters: a nozzle connected to some tubes and a microscope-like stage that allows an operator using knobs to precisely move it up, down, left, right, out and in.

    The plumbing in those tubes allows a peristaltic pump to create fluid suction through the nozzle’s finely perforated membrane. That suction allows the nozzle to pick up, carry and release the living microtissues without doing any damage to them, as shown in the paper.

    Once a living component has been picked, the operator can then move the head from the picking side to the placing side to deposit it precisely. In the paper, the team shows several different structures Blakely made including a stack of 16 donut rings and a stack of four honeycombs. Because these are living components, the stacked microtissues naturally fuse with each other to form a cohesive whole after a short time.

    Because each honeycomb slab had about 250,000 cells, the stack of four achieved a proof-of-concept, million-cell structure more than 2 millimeters thick.

    That’s not nearly enough cells to make an organ such as a liver (an adult’s has about 100 billion cells), Morgan said, but the stack did have a density of cells consistent with that of human organs. In 2011, Morgan’s lab reported that it could make honeycomb slabs 2 centimeters wide, with 6 million cells each. Complex stacks with many more cells are certainly attainable, Morgan said.

    If properly nurtured, stacks of these larger structures could hypothetically continue to grow, Morgan said. That’s why the BioP3 keeps a steady flow of nutrient fluid through the holes of the honeycomb slabs to perfuse nutrients and remove waste. So far, the researchers have shown that stacks survive for days.

    In the paper the team made structures with a variety of cell types including H35 liver cells, KGN ovarian cells, and even MCF-7 breast cancer cells (building large tumors could have applications for testing of chemotherapeutic drugs or radiation treatments). Different cell types can also be combined in the microtissue building parts. In 2010, for example, Morgan collaborated on the creation of an artificial human ovary unifying three cell types into a single tissue.

    Improvements underway

    Because version 1.0 of the BioP3 is manually operated, it took Blakely about 60 minutes to stack the 16 donut rings around a thin post, but he and Morgan have no intention of keeping it that way.

    In September, Morgan received a $1.4-million, three-year grant from the National Science Foundation in part to make major improvements, including automating the movement of the nozzle to speed up production.

    “Since we now have the NSF grant, the Bio-P3 will be able to be automated and updated into a complete, independent system to precisely assemble large-scale, high-density tissues,” Blakely said.

    In addition, the grant will fund more research into living building parts — how large they can be made and how they will behave in the device over longer periods of time. Those studies include how their shape will evolve and how they function as a stack.

    “We are just at the beginning of understanding what kinds of living parts we can make and how they can be used to design vascular networks within the structures,” Morgan said. “Building an organ is a grand challenge of biomedical engineering. This is a significant step in that direction.”

    Brown has sought a patent on the BioP3.

    In addition to Blakely and Morgan, the paper’s other authors are biology graduate student Kali Manning and Anubhav Tripathi, professor of engineering, who co-directs Brown’s Center for Biomedical Engineering with Morgan.

    The
    National Institutes of Health (grant T32 GM065085-09) and the NSF (grant CBET-1428092) have supported the research.

    See the full article here.

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    Welcome to Brown

    Rhode Island Hall: Rhode Island Hall’s classical exterior was recently renovated with a modern interiorRhode Island Hall: Rhode Island Hall’s classical exterior was recently renovated with a modern interior

    Located in historic Providence, Rhode Island and founded in 1764, Brown University is the seventh-oldest college in the United States. Brown is an independent, coeducational Ivy League institution comprising undergraduate and graduate programs, plus the Alpert Medical School, School of Public Health, School of Engineering, and the School of Professional Studies.

    With its talented and motivated student body and accomplished faculty, Brown is a leading research university that maintains a particular commitment to exceptional undergraduate instruction.

    Brown’s vibrant, diverse community consists of 6,000 undergraduates, 2,000 graduate students, 400 medical school students, more than 5,000 summer, visiting and online students, and nearly 700 faculty members. Brown students come from all 50 states and more than 100 countries.

    Undergraduates pursue bachelor’s degrees in more than 70 concentrations, ranging from Egyptology to cognitive neuroscience. Anything’s possible at Brown—the university’s commitment to undergraduate freedom means students must take responsibility as architects of their courses of study.

     
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