Research explores why C. difficile infection continues to spread despite increased sanitation practices and intervention methods

February 10th, 2020News

Work underscores C. difficile infection is not a common hospital transmission CAMBRIDGE, MA – New research from MIT suggests the risk of becoming colonized by Clostridium difficile (C. difficile) increases immediately following gastrointestinal (GI) disturbances that result in diarrhea. Once widely considered an antibiotic and hospital associated pathogen, recent research into C. difficile has shown the infection is more frequently acquired outside of hospitals. Now, a team of researchers in MIT’s Department of Civil and Environmental Engineering (CEE) have shown that GI disturbances, such as those caused by food poisoning and laxative abuse, trigger susceptibility to colonization by C. [...]

Work underscores C. difficile infection is not a common hospital transmission

CAMBRIDGE, MA – New research from MIT suggests the risk of becoming colonized by Clostridium difficile (C. difficile) increases immediately following gastrointestinal (GI) disturbances that result in diarrhea. Once widely considered an antibiotic and hospital associated pathogen, recent research into C. difficile has shown the infection is more frequently acquired outside of hospitals. Now, a team of researchers in MIT’s Department of Civil and Environmental Engineering (CEE) have shown that GI disturbances, such as those caused by food poisoning and laxative abuse, trigger susceptibility to colonization by C. difficile, and carriers remain C. difficile positive for a year or longer.

“Our work helps show why the hospital and antibiotic association of C. difficile infections is an over-simplification of the risks and transmission patterns, and helps reconcile a lot of the observations that have followed the more recent revelation that transmission within hospitals is uncommon,” said David VanInsberghe, PhD, lead author of the study, ‘Diarrheal events can trigger long-term Clostridium difficile colonization with recurrent blooms’ in Nature Microbiology, published on February 10.

The researchers analyzed human gut microbiome time series studies conducted on individuals who had diarrhea illnesses and were not treated with antibiotics. Observing the colonization of C. difficile soon after the illnesses were acquired, they tested this association directly by feeding mice increasing quantities of laxatives while exposing them to non-pathogenic C. difficile spores. Their results suggest that GI disturbances create a window of susceptibility to C. difficile colonization during recovery.

Further, the researchers found that carriers shed C. difficile in highly variable amounts day-to-day; the number of C. difficile cells shed in a carrier’s stool can increase by over 1,000 times in one day. These recurrent blooms likely influence the transmissibility of C. difficile outside of hospitals and their unpredictability questions the reliability of single time-point diagnostics for detecting carriers.

“In our study, two of the people we followed with high temporal resolution became carriers outside of the hospital,” said VanInsberghe, now a post-doctoral researcher in the Department of Pathology at Emory University. “The observations we made from their data helped us understand how people become susceptible to colonization and what the short- and long-term patterns in C. difficile abundance in carriers look like. Those patterns told us a lot about how C. difficile can spread between people outside of hospitals.”

The research team included Joseph A. Elsherbini, MIT graduate student; Bernard Varian, MIT’s Division of Comparative Medicine; Theofilos Poutahidis Department of Pathology, College of Veterinary Medicine, Aristotle University, Greece; Susan Erdman, MIT’s Division of Comparative Medicine; Martin Polz, visiting professor, MIT’s Parsons Laboratory for Environmental Science and Engineering.

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MIT CEE Awarded Gift to Use Artificial Intelligence in Biomedical Device Design

January 22nd, 2020News

Researchers in the Department of Civil and Environmental Engineering at Massachusetts Institute of Technology (MIT) have received a gift to advance their work on a device designed to position living cells for growing human organs using acoustic waves. The Acoustofluidic Device Design with Deep Learning is being supported by Natick-based MathWorks, the leading developer of mathematical computing software. “One of the fundamental problems in growing cells is how to move and position them without damage,” said John R. Williams a professor in MIT’s Department of Civil and Environmental Engineering. “The devices we’ve designed are like acoustic tweezers.” Inspired by the [...]

Researchers in the Department of Civil and Environmental Engineering at Massachusetts Institute of Technology (MIT) have received a gift to advance their work on a device designed to position living cells for growing human organs using acoustic waves. The Acoustofluidic Device Design with Deep Learning is being supported by Natick-based MathWorks, the leading developer of mathematical computing software.

“One of the fundamental problems in growing cells is how to move and position them without damage,” said John R. Williams a professor in MIT’s Department of Civil and Environmental Engineering. “The devices we’ve designed are like acoustic tweezers.”

Inspired by the complex and beautiful patterns in the sand made by waves, our approach is to use sound waves controlled by machine learning to design complex cell patterns. The pressure waves generated by acoustics in a fluid gently move and position the cells without damaging them.

The engineers developed a computer simulator to create a variety of device designs, which were then fed to an AI platform to understand the relationship between device design and cell positions.

“Our hope is that, in time, this AI platform will create devices that we couldn’t have imagined with traditional approaches,” said Sam Raymond, PhD. Raymond recently earned his doctorate working with Williams on this project. Raymond’s thesis title, Combining Numerical Simulation and Machine Learning, explored the application of machine learning in computational engineering.

“MathWorks and MIT have a 30-year long relationship that centers on advancing innovations in engineering and science,” said P.J. Boardman, director at MathWorks. “We are pleased to support Dr. Williams and his team as they use new methodologies in simulation and deep learning to realize significant scientific breakthroughs.”

Williams and Raymond collaborated with researchers at the University of Melbourne and the Singapore University of Technology and Design on this project.

 

News Media Contact:  Maria Iacobo miacobo@mit.edu

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Mohamad Sindi ’19 PhD awarded MIT Shoji Award for Innovation

November 15th, 2019Uncategorized

Mohamad Sindi CEE alumnus Mohamad Sindi was recently honored by the Massachusetts Institute of Technology (MIT) for his PhD work. He was awarded the MIT Shoji Award for Innovation for his thesis addressing the issue of fault-tolerance for large-scale High Performance Computing (HPC) workloads. The award was presented on Oct 22 by Dr. Mikio Shoji, a longtime supporter of MIT. Dr. Sindi’s PhD work has previously won the IEEE Innovative Paper Award, as well as research grants and support from Amazon, Schlumberger, and Sandia National Laboratories (SNL).

Mohamad Sindi CEE alumnus Mohamad Sindi was recently honored by the Massachusetts Institute of Technology (MIT) for his PhD work. He was awarded the MIT Shoji Award for Innovation for his thesis addressing the issue of fault-tolerance for large-scale High Performance Computing (HPC) workloads. The award was presented on Oct 22 by Dr. Mikio Shoji, a longtime supporter of MIT. Dr. Sindi’s PhD work has previously won the IEEE Innovative Paper Award, as well as research grants and support from Amazon, Schlumberger, and Sandia National Laboratories (SNL).

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Professor John R. Williams, Mohamad Sindi, PhD ‘19 win IEEE Innovative Paper Award

October 22nd, 2019Uncategorized

Professor John R. Williams and PhD  alumnus Mohamad Sindi recently won the IEEE Innovative Paper Award for their paper titled "Using Container Migration for HPC Workloads Resilience". The award was presented during the IEEE High Performance Extreme Computing Conference (HPEC'19) on September 25 in Waltham, MA. The paper was competing against numerous submissions from some top academic institutions such as MIT, Harvard, Stanford, Georgia Tech, Duke, and Carnegie Mellon. The paper introduces an innovative method to address a global challenge in the domain of High Performance Computing (HPC), which is fault-tolerance for large scale HPC workloads. The work was rated [...]

Professor John R. Williams and PhD  alumnus Mohamad Sindi recently won the IEEE Innovative Paper Award for their paper titled “Using Container Migration for HPC Workloads Resilience”. The award was presented during the IEEE High Performance Extreme Computing Conference (HPEC’19) on September 25 in Waltham, MA. The paper was competing against numerous submissions from some top academic institutions such as MIT, Harvard, Stanford, Georgia Tech, Duke, and Carnegie Mellon. The paper introduces an innovative method to address a global challenge in the domain of High Performance Computing (HPC), which is fault-tolerance for large scale HPC workloads. The work was rated as “Outstandingly Novel” in terms of novelty. Their invention uses a machine learning algorithm that is highly accurate in detecting sick machines with a low false positive rate. Upon detection, the container running on the sick machine is frozen, a memory snapshot is taken, and the container is migrated to a healthy machine where the computation is resumed. The whole process is automated and occurs in around 60 seconds on average.

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Rising Ninth grader at Concord-Carlisle High School Naomi Miller part of the MIT-Concord Research Team presents findings at 2019 International Microscopy and Microanalysis Conference

September 13th, 20192019 News in Brief

On August 7, 2019, rising Ninth grader at Concord-Carlisle High School (CCHS) Naomi Miller, part of the MIT-Concord Research Team, presented their findings at the 2019 International Microscopy and Microanalysis Conference in Portland, Oregon. Miller and her colleagues have been working with the Laboratory for Atomistic and Molecular Mechanics (LAMM) and research scientist Dr. Kunal Kupwade-Patil since October 2018 on a NASA Challenge to research methods of making concrete by using synthetic Martian soil in order to print 3D print dwellings on Mars. This summer, the students also spent six weeks working with Concord Middle School science teacher and MIT [...]

On August 7, 2019, rising Ninth grader at Concord-Carlisle High School (CCHS) Naomi Miller, part of the MIT-Concord Research Team, presented their findings at the 2019 International Microscopy and Microanalysis Conference in Portland, Oregon. Miller and her colleagues have been working with the Laboratory for Atomistic and Molecular Mechanics (LAMM) and research scientist Dr. Kunal Kupwade-Patil since October 2018 on a NASA Challenge to research methods of making concrete by using synthetic Martian soil in order to print 3D print dwellings on Mars. This summer, the students also spent six weeks working with Concord Middle School science teacher and MIT visiting scholar Doug Shattuck at MIT furthering their research to develop a solar collector in order to melt Martian sand to form structural glass material. Read more here.

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Former postdoc Wenbo Shi in Professor Desiree Plata’s lab and colleagues from Yale University research featured on cover of Advanced Functional Materials

September 12th, 20192019 News in Brief

Former postdoc Wenbo Shi in Gilbert W. Winslow Career Development Assistant Professor Desiree Plata’s lab and colleagues from Yale University research is featured on the cover of Advanced Functional Materials. Their paper titled, “Engineering carbon nanotube forest superstructure for robust thermal desalination membranes,” can provide insight into an effective strategy to engineer carbon nanotubes to elucidate the structure-property-performance relationship of the nanocomposite membranes and to guide the design of robust thermal desalination membranes. Read more here.

Former postdoc Wenbo Shi in Gilbert W. Winslow Career Development Assistant Professor Desiree Plata’s lab and colleagues from Yale University research is featured on the cover of Advanced Functional Materials. Their paper titled, “Engineering carbon nanotube forest superstructure for robust thermal desalination membranes,” can provide insight into an effective strategy to engineer carbon nanotubes to elucidate the structure-property-performance relationship of the nanocomposite membranes and to guide the design of robust thermal desalination membranes. Read more here.

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