Category Archives: graduate

Mitochondria expose tumors’ misbehavior

Mitochondria cancer researchMitochondria are able to change function and shape, according to the needs of the cell. When these mitochondrial dynamics go wrong, though, they can contribute to a number of human diseases. Early detection of these abnormalities can lead to faster diagnosis and treatment. A team of researchers, including engineers from the Tufts Department of Biomedical Engineering, has shown that these signs of mitochondrial dysfunction can be seen in living human skin by monitoring the mitochondrial metabolic coenzyme NADH. This represents a significant step from current techniques, which rely on mitochondria-specific dyes or are invasive.

With this new technique allowing for near real-time assessments of mitochondrial organization, researchers were able to differentiate healthy skin from melonoma and basal cell carcinoma.

Read the full paper in Science Translational Medicine.

Authors included Dimitra Pouli, Carlo Alonzo, Zhiyi Liu, Kyle Quinn, and Associate Professor Irene Georgakoudi from the Tufts Department of Biomedical Engineering, working alongside colleagues from the University of Malaga and the University of California, Irvine.

M.S. candidate wins student poster competition

M.S. candidate Sam Gaeth receives the award.

M.S. candidate Sam Gaeth receives the award.

Civil and environmental engineering M.S. candidate Sam Gaeth won first place in a student poster competition for his research titled “Syngeristic Effects of Utilizing Abiotic and Biotic Degradation Pathways Simultaneously for Chlorinated Solvents Remediation,” conducted with his advisors, Research Assistant Professor Natalie Cápiro and Professor and Chair Kurt Pennell.

Gaeth presented the research at the Association for Environmental Health and Sciences (AEHS) Foundation’s 32nd Annual International Conference on Soils, Sediments, Water, and Energy, on October 17-20 in Amherst, Massachusetts.

Tissue healing after a heart attack

Tufts University engineers have developed new, non-destructive techniques to evaluate tissue healing following a heart attack. These techniques, described in a paper recently published in Nature Scientific Reports, could be used to evaluate current treatments for aiding cardiac repair and to provide a basis for evaluating heart disease progression.

Every year, about 735,000 Americans have a heart attack. Of these cases, 525,000 are a first heart attack.* After a heart attack, or myocardial infarction, the body quickly attempts to replace damaged cardiac tissue with new collagen scaffolding to provide support to withstand the forces associated with a normal heartbeat. The body can sometimes overbuild this scaffolding, or extracellular matrix (ECM), or expand the remodeled ECM into heart tissue not initially adversely affected by the heart attack. The altered heart tissue resulting from ECM remodeling is often responsible for functional deterioration, leading to heart failure.

Though scientists have studied some elements of how remodeled tissue structure affects function following heart attack, little is understood about the relationship between ECM composition of the scar tissue and its mechanical properties in the earliest stages of remodeling. By using a process called decellularization—the removal of cells from the heart tissue structure—and pairing this with 3D multi-photon microscopy, the tissue’s mechanical properties and structure remains intact and can be studied. As a result, the Tufts biomedical engineering team has uniquely identified structure-function relationships specific to the myocardial ECM. Specifically they have found that the ECM that is newly remodeled/deposited, following infarction, is weaker than healthy tissues, most likely due to alterations in the chemical connections within and between fibers called“crosslinks.” This weaker ECM may be contributing to the expanding scar by adversely signaling cells in the remodeling tissue to continue to make more ECM.

The team of Tufts researchers included Kyle Quinn, Kelly Sullivan, Zhiyi Liu, Zachary Ballard, Christos Siokatas, Associate Professor Irene Georgakoudi, and Associate Professor Lauren Black.

Read the full paper in Nature Scientific Reports.

* Source:

Mechanical engineers receive best poster award

Xiao and Barlow pose with their winning poster.

Xiao and Barlow pose with their winning poster.

On October 29, mechanical engineering major Stan Barlow, E17, and Ph.D. candidate Xiao Xiao attended the American Society for Gravitational and Space Research Conference in Cleveland, Ohio. They received the Best Poster – Young Investigator Award from the NASA Center for the Advancement of Science in Space (CASIS).

Xiao and Barlow won the award for their poster titled “Density Measurement for Industrial Turbine Blade Superalloys,” which they worked on with Associate Professor Douglas Matson and Ph.D. candidate Justin Rodriguez.


Tufts attends Grace Hopper Celebration

The 2016 Grace Hopper Celebration kicks off in Houston. Photo courtesy of Sara Amr Amin.

The 2016 Grace Hopper Celebration kicks off in Houston. Photo courtesy of Sara Amr Amin.

In late October, a group of Tufts students and faculty attended the annual Grace Hopper Celebration of Women in Computing (GHC) in Houston, Texas. GHC is the world’s largest technical conference for women in computing, where women technologists and leaders in computing convene to highlight the contributions of women to computing. Named in honor of Admiral Grace Murray Hopper, GHC is co-presented by the Anita Borg Institute and the Association of Computing Machinery (ACM).

This year, Tufts attendees included 16 undergraduates, two graduate students, and one faculty member. Students were able to make connections across the industry, from engineers at Otto, Uber’s self-driving semi-truck company, to Google X project leads, computer science Ph.D. students, and recruiters hiring for open positions.

“Most valuable was meeting people on specific teams at companies I’m interested in, because that’s how I want to think about potential,” says Alice Lee, a senior who’s interested in programming languages and embedded systems. “I was inspired by the women who are actively breaking glass ceilings and ready to talk about just how they did it.”

Tufts team wins international computational biology competition

A team of Tufts computer scientists and mathematicians won top prize in the Disease Module Identification DREAM Challenge, which is an “open community effort to: (1) Systematically assess module identification methods on a panel of state-of-the-art genomic networks, and (2) discover novel network modules/pathways underlying complex diseases.” The competition is driven by the interconnected nature of multiple genes interacting within molecular pathways to drive physiological and disease processes.

Out of 42 teams from across the globe, Team Tusk won first place with its response, “A Double Spectral Approach to DREAM 11 Subchallenge.” Team members included, from the Department of Computer Science, Professor Lenore Cowen, Professor Donna Slonim, Assistant Professor Ben Hescott, and master’s student Jake Crawford; and, from the Department of Mathematics, Assistant Professor Xiaozhe Hu and Ph.D. student Joanne Lin.

$1 million grant to support low-income engineering students

Professor Laurie Baise and engineering students visit a construction site.  (Alonso Nichols/Tufts University)

Professor Laurie Baise and engineering students visit a construction site. (Alonso Nichols/Tufts University)

The new FAST-TRAC program will provide scholarships and support to low-income students who are earning a B.S. and an M.S. in Tufts’ five-year combined degree program. Thanks to a $1 million grant from the National Science Foundation (NSF), Tufts can fund FAST-TRAC through at least 2020. Engineering undergraduates starting their junior year this fall will be the first class eligible for FAST-TRAC. The program applies to all majors within the School of Engineering.

The effort is led by Associate Dean for Graduate Education Karen Panetta, Associate Dean for Undergraduate Education Darryl Williams, and Kristin Finch, Associate Director of the Center for STEM Diversity.

“The landscape for entry-level engineering jobs is changing significantly,” Williams says. “The more competitive applicants are those who have master’s degrees.” FAST-TRAC will bring a master’s degree within reach for more engineering students.

Communicating health risks with visualizations

Associate Professor Remco Chang creates visualizations to help communicate health risks to patients.

Associate Professor Remco Chang creates visualizations to help communicate health risks to patients.

Associate Professor Remco Chang, students, and collaborators at Maine Medical Center (MMC) created a project to investigate how older men with prostate cancer use visualizations to better understand their own health risk information. Chang, master’s student Anzu Hakone, E16, recent graduate Nate Winters, E16, doctoral recipient Alvitta Ottley, EG16, postdoctoral researcher Lane Harrison, and MCC collaborators Dr. Paul Han and Caitlin Gutheil have a paper entitled “PROACT: Iterative Design of a Patient-Centered Visualization for Effective Prostate Cancer Health Risk Communication” appearing at the 2016 IEEE InfoVis conference. The web-based visualization prototype, PROACT, supports patients to learn about their cancer risk and the possible side effects of different treatment options.

Combining cloud and internet to support VR

Doctoral student Osama Haq and Assistant Professor Fahad Dogar work on improving virtual reality applications.

Doctoral student Osama Haq and Assistant Professor Fahad Dogar work on improving virtual reality applications.

Assistant Professor Fahad Dogar and doctoral student Osama Haq are working on providing a suitable network support for emerging real-time applications (e.g., virtual reality). They are exploring how the highly reliable, but expensive, cloud network infrastructure could be combined with the best-effort, but cheaper, Internet paths. The goal is to provide guaranteed bandwidth and low-latency for such applications. The preliminary idea and feasibility of this work appeared in ACM HotNets 2015. The ongoing research in this project also involves collaborators from Boston University’s Department of Computer Science.

Driving the Autobahn

Professor Kathleen Fisher, Remy Wang, and Diogenes Nunez worked on a Haskell program called AUTOBAHN.

Professor Kathleen Fisher, Remy Wang, and Diogenes Nunez created a Haskell program called AUTOBAHN.

A paper by doctoral student Diogenes Nunez, senior Remy Wang, and Professor and Chair Kathleen Fisher, entitled “AUTOBAHN: Using Genetic Algorithms to Infer Strictness Annotations,” will appear at the 2016 Haskell Symposium. This work, which started as a project in Associate Professor Norman Ramsey’s functional programming class, tackles the long-standing problem of how to improve the performance of Haskell programs by telling the compiler which program fragments should be evaluated eagerly. Currently, inserting the appropriate annotations is a black art, known only to expert Haskell programmers. The Autobahn tool developed by Nunez and Wang automatically suggests appropriate places to put annotations to improve a number of performance metrics.