Tag Archives: Johns Hopkins University

New director for TRIUMF, Canada’s national laboratory for particle and nuclear physics starts

Here’s the announcement, straight from the March 18, 2014 TRIUMF news release,

After a seven month, highly competitive, international search for TRIUMF’s next director, the laboratory’s Board of Management announced today that Dr. Jonathan Bagger, Krieger-Eisenhower Professor, Vice Provost, and former Interim Provost at the Johns Hopkins University, will join TRIUMF this summer as the laboratory’s next director.

TRIUMF is Canada’s national laboratory for particle and nuclear physics, focusing on probing the structure and origins of matter and advancing isotopes for science and medicine.  Located on the campus of the University of British Columbia, TRIUMF is owned and operated by a consortium of 18 leading Canadian universities and supported by the federal and provincial governments.

Bagger was attracted to TRIUMF because, “Its collaborative, interdisciplinary model represents the future for much of science.  TRIUMF helps Canada connect fundamental research to important societal goals, ranging from health and safety to education and innovation.”  Noting TRIUMF’s new strategic plan that recently secured five years of core funding from the Government of Canada, he added, “It is an exciting time to lead the
laboratory.”

Bagger brings extensive experience to the job.  Professor Paul Young, Chair of TRIUMF’s Board of Management and Vice-President of Research and Innovation at the University of Toronto, said, “Jon is an outstanding, internationally renowned physicist with a wealth of leadership experience and a track record of excellence.  He is a welcome addition to Canada and I am confident that under his tenure, TRIUMF will continue to flourish.”

Jim Hanlon, Interim CEO/Chief Administrator Officer of TRIUMF and President and CEO of Advanced Applied Physics Solutions Inc., welcomed the news.  He said, “The laboratory has been shaped and served greatly by its past directors.  Today the need continues for an extraordinary combination of vision, leadership, and excellence.  Jon will bring all of this and more to TRIUMF.  On behalf of the staff, we’re excited about moving forward with Jon
at the helm.”

Bagger expressed his enthusiasm in moving across the border to join TRIUMF as the next director. “TRIUMF is known internationally for its impressive capabilities in science and engineering, ranging from rare-isotope studies on its Vancouver campus to its essential contributions to the Higgs boson discovery at CERN.  All rest on the legendary dedication and commitment of TRIUMF’s researchers and staff.  I look forward to working with this
terrific team to advance innovation and discovery in Vancouver, in Canada, and on the international stage.”

Bagger will lead the laboratory for a six-year term beginning July 1 [2014].  He reports he is ready to go:  “I have installed a metric speedometer in my car, downloaded the Air Canada app, and cleansed my home of all Washington Capitals gear.”

Nice of Bagger to start his new job on Canada Day. From a symbolic perspective, it’s an interesting start date. As for his metric speedometer and Air Canada app, bravo! Perhaps though he might have wanted the last clause to feature the Vancouver Canucks, e.g., ‘and set aside money/have set aside space for Vancouver Canucks gear’. You can find out more about TRIUMF here.

Does education kill the ability to do algebra?

Apparently, the ability to perform basic algebra is innate in humans, mice, fish, and others. Researchers at Johns Hopkins describe some of their findings about algebra and innate abilities in this video,

While the researchers don’t accuse the education system of destroying or damaging one’s ability to perform algebra, I will make the suggestion, the gut level instinct the researchers are describing is educated out of most of us. Here’s more from the March 6, 2014 news item on ScienceDaily describing the research,

Millions of high school and college algebra students are united in a shared agony over solving for x and y, and for those to whom the answers don’t come easily, it gets worse: Most preschoolers and kindergarteners can do some algebra before even entering a math class.

In a just-published study in the journal Developmental Science, lead author and post-doctoral fellow Melissa Kibbe and Lisa Feigenson, associate professor of psychological and brain sciences at Johns Hopkins University’s Krieger School of Arts and Sciences, find that most preschoolers and kindergarteners, or children between 4 and 6, can do basic algebra naturally.

“These very young children, some of whom are just learning to count, and few of whom have even gone to school yet, are doing basic algebra and with little effort,” Kibbe said. “They do it by using what we call their ‘Approximate Number System:’ their gut-level, inborn sense of quantity and number.”

A Johns Hopkins University March 7, 2014 news piece by Latarsha Gatlin describes the research further,

The “Approximate Number System,” or ANS, is also called “number sense,” and describes humans’ and animals’ ability to quickly size up the quantity of objects in their everyday environments. We’re born with this ability, which is probably an evolutionary adaptation to help human and animal ancestors survive in the wild, scientists say.

Previous research has revealed some interesting facts about number sense, including that adolescents with better math abilities also had superior number sense when they were preschoolers, and that number sense peaks at age 35.

Kibbe, who works in Feigenson’s lab, wondered whether preschool-age children could harness that intuitive mathematical ability to solve for a hidden variable. In other words, could they do something akin to basic algebra before they ever received formal classroom mathematics instruction? The answer was “yes,” at least when the algebra problem was acted out by two furry stuffed animals—Gator and Cheetah—using “magic cups” filled with objects like buttons, plastic doll shoes, and pennies.

In the study, children sat down individually with an examiner who introduced them to the two characters, each of which had a cup filled with an unknown quantity of items. Children were told that each character’s cup would “magically” add more items to a pile of objects already sitting on a table. But children were not allowed to see the number of objects in either cup: they only saw the pile before it was added to, and after, so they had to infer approximately how many objects Gator’s cup and Cheetah’s cup contained.

At the end, the examiner pretended that she had mixed up the cups, and asked the children—after showing them what was in one of the cups—to help her figure out whose cup it was. The majority of the children knew whose cup it was, a finding that revealed for the researchers that the pint-sized participants had been solving for a missing quantity. In essence, this is the same as doing basic algebra.

“What was in the cup was the x and y variable, and children nailed it,” said Feigenson, director of the Johns Hopkins Laboratory for Child Development. “Gator’s cup was the x variable and Cheetah’s cup was the y variable. We found out that young children are very, very good at this. It appears that they are harnessing their gut level number sense to solve this task.”

If this kind of basic algebraic reasoning is so simple and natural for 4, 5, and 6-year-olds, then why it is so difficult for teens and others?

“One possibility is that formal algebra relies on memorized rules and symbols that seem to trip many people up,” Feigenson said. “So one of the exciting future directions for this research is to ask whether telling teachers that children have this gut level ability—long before they master the symbols—might help in encouraging students to harness these skills. Teachers may be able to help children master these kind of computations earlier, and more easily, giving them a wedge into the system.”

While number sense helps children in solving basic algebra, more sophisticated concepts and reasoning are needed to master the complex algebra problems that are taught later in the school age years.

Another finding from the research was that an ANS aptitude does not follow gender lines. Boys and girls answered questions correctly in equal proportions during the experiments, the researchers said. Although other research shows that even young children can be influenced by gender stereotypes about girls’ versus boys’ math prowess, “we see no evidence for gender differences in our work on basic number sense,” Feigenson said.

Parents with numerically challenged kids shouldn’t worry that their child will be bad at math. The psychologists say it’s more important to nurture and support young children’s use of their number sense in solving problems that will later be introduced more formally in school.

“We find links at all ages between the precision of people’s Approximate Number System and their formal math ability,” Feigenson said. “But this does not necessarily mean that children with poorer precision grow up to be bad at math. For example, children with poorer number sense may need to rely on other strategies, besides their gut sense of number, to solve math problems. But this is an area where much future research is needed.”

Here’s a link to and a citation for the paper,

Young children ‘solve for x’ using the Approximate Number System by Melissa M. Kibbe and Lisa Feigenson. Article first published online: 3 MAR 2014 DOI: 10.1111/desc.12177

© 2014 John Wiley & Sons Ltd

This paper is behind a paywall.

2013 International Science & Engineering Visualization Challenge Winners

Thanks to a RT from @coreyspowell I stumbled across a Feb. 7, 2014 article in Science (magazine) describing the 2013 International Science & Engineering Visualization Challenge Winners. I am highlighting a few of the entries here but there are more images in the article and a slideshow.

First Place: Illustration

Credit: Greg Dunn and Brian Edwards, Greg Dunn Design, Philadelphia, Pennsylvania; Marty Saggese, Society for Neuroscience, Washington, D.C.; Tracy Bale, University of Pennsylvania, Philadelphia; Rick Huganir, Johns Hopkins University, Baltimore, Maryland

Cortex in Metallic Pastels. Credit: Greg Dunn and Brian Edwards, Greg Dunn Design, Philadelphia, Pennsylvania; Marty Saggese, Society for Neuroscience, Washington, D.C.; Tracy Bale, University of Pennsylvania, Philadelphia; Rick Huganir, Johns Hopkins University, Baltimore, Maryland

From the article, a description of Greg Dunn and his work,

With a Ph.D. in neuroscience and a love of Asian art, it may have been inevitable that Greg Dunn would combine them to create sparse, striking illustrations of the brain. “It was a perfect synthesis of my interests,” Dunn says.

Cortex in Metallic Pastels represents a stylized section of the cerebral cortex, in which axons, dendrites, and other features create a scene reminiscent of a copse of silver birch at twilight. An accurate depiction of a slice of cerebral cortex would be a confusing mess, Dunn says, so he thins out the forest of cells, revealing the delicate branching structure of each neuron.

Dunn blows pigments across the canvas to create the neurons and highlights some of them in gold leaf and palladium, a technique he is keen to develop further.

“My eventual goal is to start an art-science lab,” he says. It would bring students of art and science together to develop new artistic techniques. He is already using lithography to give each neuron in his paintings a different angle of reflectance. “As you walk around, different neurons appear and disappear, so you can pack it with information,” he says.

People’s Choice:  Games & Apps

Meta!Blast: The Leaf. Credit: Eve Syrkin Wurtele, William Schneller, Paul Klippel, Greg Hanes, Andrew Navratil, and Diane Bassham, Iowa State University, Ames

Meta!Blast: The Leaf. Credit: Eve Syrkin Wurtele, William Schneller, Paul Klippel, Greg Hanes, Andrew Navratil, and Diane Bassham, Iowa State University, Ames

More from the article,

“Most people don’t expect a whole ecosystem right on the leaf surface,” says Eve Syrkin Wurtele, a plant biologist at Iowa State University. Meta!Blast: The Leaf, the game that Wurtele and her team created, lets high school students pilot a miniature bioship across this strange landscape, which features nematodes and a lumbering tardigrade. They can dive into individual cells and zoom around a chloroplast, activating photosynthesis with their ship’s search lamp. Pilots can also scan each organelle they encounter to bring up more information about it from the ship’s BioLog—a neat way to put plant biology at the heart of an interactive gaming environment.

This is a second recognition for Meta!Blast, which won an Honorable Mention in the 2011 visualization challenge for a version limited to the inside of a plant cell.

The Metablast website homepage describes the game,

The last remaining plant cell in existence is dying. An expert team of plant scientists have inexplicably disappeared. Can you rescue the lost team, discover what is killing the plant, and save the world?

Meta!Blast is a real-time 3D action-adventure game that puts you in the pilot’s seat. Shrink down to microscopic size and explore the vivid, dynamic world of a soybean plant cell spinning out of control. Interact with numerous characters, fight off plant pathogens, and discover how important plants are to the survival of the human race.

Enjoy!

Squishy knees and tissue engineering at Johns Hopkins

Researchers at Johns Hopkins University School of Medicine’s Translational Tissue Engineering Center (TTEC) have developed a material (a kind of hydrogel) which they use with a new technique they’ve developed for growing new tissue and cartilage in knees. From the Jan. 15, 2013 news release on EurekAlert,

Proof-of-concept clinical trial in 18 patients shows improved tissue growth

In a small study, researchers reported increased healthy tissue growth after surgical repair of damaged cartilage if they put a “hydrogel” scaffolding into the wound to support and nourish the healing process. The squishy hydrogel material was implanted in 15 patients during standard microfracture surgery, in which tiny holes are punched in a bone near the injured cartilage. The holes stimulate patients’ own specialized stem cells to emerge from bone marrow and grow new cartilage atop the bone.

“Our pilot study indicates that the new implant works as well in patients as it does in the lab, so we hope it will become a routine part of care and improve healing,” says Jennifer Elisseeff, Ph.D., Jules Stein Professor of Ophthalmology and director of the Johns Hopkins University School of Medicine’s Translational Tissue Engineering Center (TTEC). Damage to cartilage, the tough-yet-flexible material that gives shape to ears and noses and lines the surface of joints so they can move easily, can be caused by injury, disease or faulty genes. Microfracture is a standard of care for cartilage repair, but for holes in cartilage caused by injury, it often either fails to stimulate new cartilage growth or grows cartilage that is less hardy than the original tissue.

Here are more details from the Johns Hopkins Jan. 15, 2013 news release,

Tissue engineering researchers, including Elisseeff, theorized that the specialized stem cells needed a nourishing scaffold on which to grow, but demonstrating the clinical value of hydrogels has “taken a lot of time,” Elisseeff says. By experimenting with various materials, her group eventually developed a promising hydrogel, and then an adhesive that could bind it to the bone.

After testing the combination for several years in the lab and in goats, with promising results, she says, the group and their surgeon collaborators conducted their first clinical study, in which 15 patients with holes in the cartilage of their knees received a hydrogel and adhesive implant along with microfracture. For comparative purposes, another three patients were treated with microfracture alone. After six months, the researchers reported that the implants had caused no major problems, and MRIs showed that patients with implants had new cartilage filling an average 86 percent of the defect in their knees, while patients with only microfracture had an average of 64 percent of the tissue replaced. Patients with the implant also reported a greater decrease in knee pain in the six months following surgery, according to the investigators.

The trial continues, has enrolled more patients and is now being managed by a company called Biomet. The trial is part of efforts to win European regulatory approval for the device.

In the meantime, Elisseeff says her team has begun developing a next-generation implant, one in which the hydrogel and adhesive will be combined in a single material. In addition, they are working on technologies to lubricate joints and reduce inflammation.

The study has been published in the AAAS’s (American Association for the Advancement of Science) Science Translational Medicine journal,

Human Cartilage Repair with a Photoreactive Adhesive-Hydrogel Composite

Surgical options for cartilage resurfacing may be significantly improved by advances and application of biomaterials that direct tissue repair. A poly(ethylene glycol) diacrylate (PEGDA) hydrogel was designed to support cartilage matrix production, with easy surgical application. A model in vitro system demonstrated deposition of cartilage-specific extracellular matrix in the hydrogel

Sci Transl Med 9 January 2013:
Vol. 5 no. 167 pp. 167ra6DOI:10.1126/scitranslmed.3004838

This article is behind a paywall and for some reason the authors are listed only in the news release,

Jennifer Elisseeff, Blanka Sharma, Sara Fermanian, Matthew Gibson, Shimon Unterman, Daniel A. Herzka, Jeannine Coburn and Alexander Y. Hui of the Johns Hopkins School of Medicine; Brett Cascio of Lake Charles Memorial Hospital; Norman Marcus, a private practice orthopedic surgeon; and Garry E. Gold of Stanford University

Repairing joints with nanoscale scaffolds and stem cells

Cartilage damage is a major problem for millions of people and chondroitin supplements are widely used to counteract the pain and damage since cartilage does not regrow. Until now.

Researchers at Johns Hopkins University have used chondroitin sulfate to create nanoscaffolds for growing new cartilage. From the July 17, 2012 news release on EurekAlert,

Unlike skin, cartilage can’t repair itself when damaged. For the last decade, Elisseeff’s [Jennifer Elisseeff, Ph.D., Jules Stein Professor of Ophthalmology and director of the Translational Tissue Engineering Center at the Johns Hopkins University School of Medicine] team has been trying to better understand the development and growth of cartilage cells called chondrocytes, while also trying to build scaffolding that mimics the cartilage cell environment and generates new cartilage tissue. This environment is a 3-dimensional mix of protein fibers and gel that provides support to connective tissue throughout the body, as well as physical and biological cues for cells to grow and differentiate.

In the laboratory, the researchers created a nanofiber-based network using a process called electrospinning, which entails shooting a polymer stream onto a charged platform, and added chondroitin sulfate—a compound commonly found in many joint supplements—to serve as a growth trigger. After characterizing the fibers, they made a number of different scaffolds from either spun polymer or spun polymer plus chondroitin. They then used goat bone marrow-derived stem cells (a widely used model) and seeded them in various scaffolds to see how stem cells responded to the material.

Elisseeff  and her team watched the cells grow and found that compared to cells growing without scaffold, these cells developed into more voluminous, cartilage-like tissue. “The nanofibers provided a platform where a larger volume of tissue could be produced,” says Elisseeff, adding that 3-dimensional nanofiber scaffolds were more useful than the more common nanofiber sheets for studying cartilage defects in humans.

They’ve also experimented with animal models,

The investigators then tested their system in an animal model. They implanted the nanofiber scaffolds into damaged cartilage in the knees of rats, and compared the results to damaged cartilage in knees left alone.

They found that the use of the nanofiber scaffolds improved tissue development and repair as measured by the production of collagen, a component of cartilage. The nanofiber scaffolds resulted in greater production of a more durable type of collagen, which is usually lacking in surgically repaired cartilage tissue. In rats, for example, they found that the limbs with damaged cartilage treated with nanofiber scaffolds generated a higher percentage of the more durable collagen (type 2) than those damaged areas that were left untreated.

“Whereas scaffolds are generally pretty good at regenerating cartilage protein components in cartilage repair, there is often a lot of scar tissue-related type 1 collagen produced, which isn’t as strong,” says Elisseeff. “We found that our system generated more type 2 collagen, which ensures that cartilage lasts longer.”

“Creating a nanofiber network that enables us to more equally distribute cells and more closely mirror the actual cartilage extracellular environment are important advances in our work and in the field. These results are very promising,” she says.

I wouldn’t rush out yet for new cartilage . It’s likely to be several years before this is available to people.

Small boxes in your bloodstream

The boxes in question self-assemble although why anyone would consider the image of small boxes in one’s bloodstream appealing escapes me. Well, we are talking about engineers and mathematicians so perhaps it’s understandable. From the April 23, 2012 news item on Nanowerk,

… now, interdisciplinary research by engineers at Johns Hopkins University in Baltimore, Md., and mathematicians at Brown University in Providence, R.I., has led to a breakthrough showing that higher order polyhedra can indeed fold up and assemble themselves.

“What is remarkable here is not just that a structure folds up on its own, but that it folds into a very precise, three-dimensional shape, and it happens without any tweezers or human intervention,” says David Gracias, a chemical and biomolecular engineer at Johns Hopkins. “Much like nature assembles everything from sea shells to gem stones from the bottom up, the idea of self-assembly promises a new way to manufacture objects from the bottom up.”

Here’s a video from the US National Science Foundation about the work being done by David Gracias and his colleague at Brown University, mathematician Govind Menon,

Miles O’Brien of the NSF’s Science Nation magazine notes in his April 23, 2012 article that there are many applications for these structures,

Imagine thousands of precisely structured, tiny, biodegradable, boxes rushing through the bloodstream en route to a sick organ. Once they arrive at their destination, they can release medicine with pinpoint accuracy. That’s the vision for the future. For now, the more immediate concern is getting the design of the structures just right so that they can be manufactured with high yields.

“Our process is also compatible with integrated circuit fabrication, so we envision that we can use it to put silicon-based logic and memory chips onto the faces of 3-D polyhedra. Our methodology opens the door to the creation of truly three-dimensional ‘smart’ and multi-functional particles on both micro- and nano- length scales,” says Gracias.

Here’s more about the structures themselves, as mentioned in the video and in O’Brien’s article,

Menon’s team at Brown began designing these tiny 3-D structures by first flattening them out. They worked with a number of shapes, such as 12-sided interconnected panels, which can potentially fold into a dodecahedron shaped container. “Imagine cutting it up and flattening out the faces as you go along,” says Menon. “It’s a two-dimensional unfolding of the polyhedron.”

And not all flat shapes are created equal; some fold better than others. “The best ones are the ones which are most compact. There are 43,380 ways to fold a dodecahedron,” notes Menon.

The researchers developed an algorithm to sift through all of the possible choices, narrowing the field to a few compact shapes that easily fold into 3-D structures. Menon’s team sent those designs to Gracias and his team at Johns Hopkins who built the shapes, and validated the hypothesis.

“We deposit a material in between the faces and the edges, and then heat them up, which creates surface tension and pulls the edges together, fusing the structure shut,” explains Gracias. “The angle between adjacent panels in a dodecahedron is 116.6 degrees and in our process, pentagonal panels precisely align at these remarkably precise angles and seal themselves; all on their own.”

As noted earlier, I’m not thrilled with the idea of tiny boxes in my bloodstream but, analogy aside, the medical applications are appealing. As for Gracias’ smart and multifunctional particles, I look forward to hearing more about them.

3-D and self-assembly

Here’s an intriguing approach to self-assembly for manufacturing purposes from scientists at Brown and Johns Hopkins Universities, respectively. From the Dec. 7, 2011 news item on Nanowerk,

In a paper published in the Proceedings of National Academy of Sciences (“Algorithmic design of self-folding polyhedra”), researchers from Brown and Johns Hopkins University determined the best 2-D arrangements, called planar nets, to create self-folding polyhedra with dimensions of a few hundred microns, the size of a small dust particle. The strength of the analysis lies in the combination of theory and experiment. The team at Brown devised algorithms to cut through the myriad possibilities and identify the best planar nets to yield the self-folding 3-D structures. Researchers at Johns Hopkins then confirmed the nets’ design principles with experiments.

Here’s the magnitude of the problem these scientists were solving (from the news item),

Material chemists and engineers would love to figure out how to create self-assembling shells, containers or structures that could be used as tiny drug-carrying containers or to build 3-D sensors and electronic devices.

There have been some successes with simple 3-D shapes such as cubes, but the list of possible starting points that could yield the ideal self-assembly for more complex geometric configurations gets long fast. For example, while there are 11 2-D arrangements for a cube, there are 43,380 for a dodecahedron (12 equal pentagonal faces). Creating a truncated octahedron (14 total faces – six squares and eight hexagons) has 2.3 million possibilities.

Associate professor of applied mathematics at Brown University, Govind Menon, says (from the news item),

“The issue is that one runs into a combinatorial explosion. … How do we search efficiently for the best solution within such a large dataset? This is where math can contribute to the problem.”

Here’s how they solved the problem (from the news item),

 

“Using a combination of theory and experiments, we uncovered design principles for optimum nets which self-assemble with high yields,” said David Gracias, associate professor in of chemical and biomolecular engineering at Johns Hopkins and a co-corresponding author on the paper.

“In doing so, we uncovered striking geometric analogies between natural assembly of proteins and viruses and these polyhedra, which could provide insight into naturally occurring self-assembling processes and is a step toward the development of self-assembly as a viable manufacturing paradigm.”

“This is about creating basic tools in nanotechnology,” said Menon, co-corresponding author on the paper. “It’s important to explore what shapes you can build. The bigger your toolbox, the better off you are.” While the approach has been used elsewhere to create smaller particles at the nanoscale, the researchers at Brown and Johns Hopkins used larger sizes to better understand the principles that govern self-folding polyhedra.

The news item on Nanowerk features more details, a video of a self-assembling dodecahedron, and an image of various options for 2-D nets that can be used to create 3-D shapes.

“Using a combination of theory and experiments, we uncovered design principles for optimum nets which self-assemble with high yields,” said David Gracias, associate professor in of chemical and biomolecular engineering at Johns Hopkins and a co-corresponding author on the paper. “In doing so, we uncovered striking geometric analogies between natural assembly of proteins and viruses and these polyhedra, which could provide insight into naturally occurring self-assembling processes and is a step toward the development of self-assembly as a viable manufacturing paradigm.”
“This is about creating basic tools in nanotechnology,” said Menon, co-corresponding author on the paper. “It’s important to explore what shapes you can build. The bigger your toolbox, the better off you are.”
While the approach has been used elsewhere to create smaller particles at the nanoscale, the researchers at Brown and Johns Hopkins used larger sizes to better understand the principles that govern self-folding polyhedra.