Tag Archives: Massachusetts Institute of Technology. MIT

Breakthrough with Alpaca nanobodies

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Caption: Bryson and Sanchez, two alpacas who produce unusually small antibodies. These ‘nanobodies’ could help highly promising CAR T-cell therapies kill solid tumors, where right now they work only in blood cancers. Credit: Courtesy of Boston Children’s Hospital

Bryson and Sanchez are not the first camelids to grace this blog. ‘Llam’ me lend you some antibodies—antibody particles extracted from camels and llamas, a June 12, 2014 posting, and Llama-derived nanobodies are good for solving crystal structure, a December 14, 2017 posting, both feature news about medical breakthroughs with regard to the antibodies found in Llamas, camels, and other camelids (including alpacas) could enable.

The latest camelid-oriented medical research story is in an April 11, 2019 news item on phys.org (Note: A link has been removed),

In 1989, two undergraduate students at the Free University of Brussels were asked to test frozen blood serum from camels, and stumbled on a previously unknown kind of antibody. It was a miniaturized version of a human antibody, made up only of two heavy protein chains, rather than two light and two heavy chains. As they eventually reported, the antibodies’ presence was confirmed not only in camels, but also in llamas and alpacas.

Fast forward 30 years. In the journal PNAS [Proceedings of the National Academy of Science] this week [April 8 – 12, 2019], researchers at Boston Children’s Hospital and MIT [Massachusetts Institute of Technology] show that these mini-antibodies, shrunk further to create so-called nanobodies, may help solve a problem in the cancer field: making CAR T-cell therapies work in solid tumors.

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An April 11, 2019 Boston Children’s Hospital news release on EurekAlert, which originated the news item, explores the technology,

Highly promising for blood cancers, chimeric antigen receptor (CAR) T-cell therapy genetically engineers a patient’s own T cells to make them better at attacking cancer cells. The Dana-Farber/Boston Children’s Cancer and Blood Disorders Center is currently using CAR T-cell therapy for relapsed acute lymphocytic leukemia (ALL), for example.

But CAR T cells haven’t been good at eliminating solid tumors. It’s been hard to find cancer-specific proteins on solid tumors that could serve as safe targets. Solid tumors are also protected by an extracellular matrix, a supportive web of proteins that acts as a barrier, as well as immunosuppressive molecules that weaken the T-cell attack.

Rethinking CAR T cells

That’s where nanobodies come in. For two decades, they largely remained in the hands of the Belgian team. But that changed after the patent expired in 2013. [emphases mine]

“A lot of people got into the game and began to appreciate nanobodies’ unique properties,” says Hidde Ploegh, PhD, an immunologist in the Program in Cellular and Molecular Medicine at Boston Children’s and senior investigator on the PNAS study.

One useful attribute is their enhanced targeting abilities. Ploegh and his team at Boston Children’s, in collaboration with Noo Jalikhani, PhD, and Richard Hynes, PhD at MIT’s Koch Institute for Integrative Cancer Research, have harnessed nanobodies to carry imaging agents, allowing precise visualization of metastatic cancers.

The Hynes team targeted the nanobodies to the tumors’ extracellular matrix, or ECM — aiming imaging agents not at the cancer cells themselves, but at the environment that surrounds them. Such markers are common to many tumors, but don’t typically appear on normal cells.

“Our lab and the Hynes lab are among the few actively pursuing this approach of targeting the tumor micro-environment,” says Ploegh. “Most labs are looking for tumor-specific antigens.”

Targeting tumor protectors

Ploegh’s lab took this idea to CAR T-cell therapy. His team, including members of the Hynes lab, took aim at the very factors that make solid tumors difficult to treat.

The CAR T cells they created were studded with nanobodies that recognize specific proteins in the tumor environment, bearing signals directing them to kill any cell they bound to. One protein, EIIIB, a variant of fibronectin, is found only on newly formed blood vessels that supply tumors with nutrients. Another, PD-L1, is an immunosuppressive protein that most cancers use to silence approaching T cells.

Biochemist Jessica Ingram, PhD of the Dana-Farber Cancer Institute, Ploegh’s partner and a coauthor on the paper, led the manufacturing pipeline. She would drive to Amherst, Mass., to gather T cells from two alpacas, Bryson and Sanchez, inject them with the antigen of interest and harvest their blood for further processing back in Boston to generate mini-antibodies.

Taking down melanoma and colon cancer

Tested in two separate melanoma mouse models, as well as a colon adenocarcinoma model in mice, the nanobody-based CAR T cells killed tumor cells, significantly slowed tumor growth and improved the animals’ survival, with no readily apparent side effects.

Ploegh thinks that the engineered T cells work through a combination of factors. They caused damage to tumor tissue, which tends to stimulate inflammatory immune responses. Targeting EIIIB may damage blood vessels in a way that decreases blood supply to tumors, while making them more permeable to cancer drugs.

“If you destroy the local blood supply and cause vascular leakage, you could perhaps improve the delivery of other things that might have a harder time getting in,” says Ploegh. “I think we should look at this as part of a combination therapy.”

Future directions

Ploegh thinks his team’s approach could be useful in many solid tumors. He’s particularly interested in testing nanobody-based CAR T cells in models of pancreatic cancer and cholangiocarcinoma, a bile duct cancer from which Ingram passed away in 2018.

The technology itself can be pushed even further, says Ploegh.

“Nanobodies could potentially carry a cytokine to boost the immune response to the tumor, toxic molecules that kill tumor and radioisotopes to irradiate the tumor at close range,” he says. “CAR T cells are the battering ram that would come in to open the door; the other elements would finish the job. In theory, you could equip a single T cell with multiple chimeric antigen receptors and achieve even more precision. That’s something we would like to pursue.”

So, the Belgian researchers have a patent for two decades and, after it expires, more researchers could help to take the work further. Hmm …

Moving on, here’s a link to and a citation for the paper,

Nanobody-based CAR T cells that target the tumor microenvironment inhibit the growth of solid tumors in immunocompetent mice by Yushu Joy Xie, Michael Dougan, Noor Jailkhani, Jessica Ingram, Tao Fang, Laura Kummer, Noor Momin, Novalia Pishesha, Steffen Rickelt, Richard O. Hynes, and Hidde Ploegh. PNAS DOI: https://doi.org/10.1073/pnas.1817147116
First published April 1, 2019

This paper is behind a paywall

How the technology of writing shaped Roman thought

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I have two bits about the Romans: the first is noted in the head for this posting and the second is about a chance to experience a Roman style classroom.

Empire of Letters

This January 8, 2019 news item on phys.org announces a book about how the technology of writing influenced how ancient Romans saw the world and provides a counterpoint to the notion that the ancient world (in Europe) was relentlessly oral in nature,

The Roman poet Lucretius’ epic work “De rerum natura,” or “On the Nature of Things,” is the oldest surviving scientific treatise written in Latin. Composed around 55 B.C.E., the text is a lengthy piece of contrarianism. Lucreutius was in the Epicurean school of philosophy: He wanted an account of the world rooted in earthly matter, rather than explanations based on the Gods and religion

Among other things, Lucretius believed in atomism, the idea that the world and cosmos consisted of minute pieces of matter, rather than four essential elements. To explain this point, Lucretius asked readers to think of bits of matter as being like letters of the alphabet. Indeed, both atoms and letters are called “elementa” in Latin—probably derived from the grouping of L,M, and N in the alphabet

To learn these elements of writing, students would copy out tables of letters and syllables, which Lucretius thought also served as a model for understanding the world, since matter and letters could be rearranged in parallel ways. For instance, Lucretius wrote, wood could be turned into fire by adding a little heat, while the word for wood, “lingum,” could be turned into the world for fire, “ignes,” by altering a few letters.

Students taking this analogy to heart would thus learn “the combinatory potential of nature and language,” says Stephanie Frampton, an associate professor of literature at MIT [Massachusetts Institute of Technology], in a new book on writing in the Roman world.

Moreover, Frampton emphasizes, the fact that students were learning all this specifically through writing exercises is a significant and underappreciated point in our understanding of ancient Rome: Writing, and the tools of writing, helped shape the Roman world.

A January 3, 2019 MIT news release, which originated the news item, expands on the theme,

“Everyone says the ancients are really into spoken and performed poetry, and don’t care about the written word,” Frampton says. “But look at Lucretius, who’s the first person writing a scientific text in Latin — the way that he explains his scientific insight is through this metaphor founded upon the written word.”

Frampton explores this and other connections between writing and Roman society in her new work, “Empire of Letters,” published last week by Oxford University Press [according to their webpage, the paper version will be published on February 4, 2019; the e-book is now available for purchase].

The book is a history of technology itself, as Frampton examines the particulars of Roman books — which often existed as scrolls back then — and their evolution over time. But a central focus of the work is how those technologies influenced how the Romans “thought about thought,” as she says.

Moreover, as Frampton notes, she is studying the history of Romans as “literate creatures,” which means studying the tools of writing used not just in completed works, but in education, too. The letter tables detailed by Lucretius are just one example of this. Romans also learned to read and write using wax tablets that they could wipe clean after exercises.

The need to wipe such tablets clean drove the Roman emphasis on learning the art of memory — including the “memory palace” method, which uses visualized locations for items to remember them, and which is still around today. For this reason Cicero, among other Roman writers, called memory and writing “most similar, though in a different medium.”
As Frampton writes in the book, such tablets also produced “an intimate and complex relationship with memory” in the Roman world, and meant that “memory was a fundamental part of literary composition.”  

Tablets also became a common Roman metaphor for how our brains work: They thought “the mind is like a wax tablet where you can write and erase and rewrite,” Frampton says. Understanding this kind of relationship between technology and the intellect, she thinks, helps us get that much closer to life as the Romans lived it

“I think it’s analagous to early computing,” Frampton says. “The way we talk about the mind now is that it’s a computer. … We think about the computer in the same way that [intellectuals] in Rome were thinking about writing on wax tablets.”

As Frampton discusses in the book, she believes the Romans did produce a number of physical innovations to the typical scroll-based back of the classic world, including changes in layout, format, coloring pigments, and possibly even book covers and the materials used as scroll handles, including ivory.

“The Romans were engineers, that’s [one thing] they were famous for,” Frampton says. “They are quite interesting and innovative in material culture.”

Looking beyond “Empire of Letters” itself, Frampton will co-teach an MIT undergraduate course in 2019, “Making Books,” that looks at the history of the book and gets students to use old technologies to produce books as they were once made. While that course has previously focused on printing-press technology, Frampton will help students go back even further in time, to the days of the scroll and codex, if they wish. All these reading devices, after all, were important innovations in their day.

“I’m working on old media,” Frampton says, “But those old media were once new.” [emphasis mine]

While the technologies Carolyn Marvin was writing about were not quite as old Frampton’s, she too noted the point about old and new technology in her 1990 book “When Old Technologies Were New” published by the Oxford University Press in 1990.

Getting back to Frampton, she has founded an organization known as the Materia Network, which is focused on (from @materianetwork’s Twitter description) “New Approaches to Material Text in the Roman World is a conference series and network for scholars of books and writing in Classical antiquity.”

You can find Materia here. They do have a Call for Proposals but I believe the deadline should read: December 20, 2018 (not 2019) since the conference will be held in April 2019).

Also, you can purchase the ebook or print version of Frampton’s Empire of Letters from the Oxford University Press here.

I have a couple of final comments. (1) The grand daddy of oral and literate culture discussion is Walter J. Ong and I’m referring specifically to his 1982 book, Orality and Literacy. BTW, in addition to being a English Literature professor, the man was a Jesuit priest.

Reading Ancient Schoolroom

(2) The University of Reading (UK) has organized over the last few years, although they skipped in 2018, a series of events known as Reading Ancient Schoolroom (my August 9, 2018 posting features the ‘schoolroom’). The 2019 event is taking place January 23 – 25, 2019. You can find out more about the 2019 opportunity here. For anyone who can’t get to the UK easily, here’s a video of the Reading Ancient Schoolroom,

According to the description on YouTube,

UniofReading

Published on Feb 22, 2018

The Reading Ancient Schoolroom is a historically accurate reconstruction of an ancient schoolroom. It gives modern children an immersive experience of antiquity, acting the part of ancient children, wearing their clothes and using their writing equipment. It was developed by Eleanor Dickey at the University of Reading. Find out more at: www.readingancientschoolroom.com

There you have it.

Xenotransplantation—organs for transplantation in human patients—it’s a business and a science

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The last time (June 18, 2018 post) I mentioned xenotransplantation (transplanting organs from one species into another species; see more here), it was in the context of an art/sci (or sciart) event coming to Vancouver (Canada).,

Patricia Piccinini’s Curious Imaginings Courtesy: Vancouver Biennale [downloaded from http://dailyhive.com/vancouver/vancouver-biennale-unsual-public-art-2018/]

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The latest edition of the Vancouver Biennale was featured in a June 6, 2018 news item on the Daily Hive (Vancouver),

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Melbourne artist Patricia Piccinini’s Curious Imaginings is expected to be one of the most talked about installations of the exhibit. Her style of “oddly captivating, somewhat grotesque, human-animal hybrid creature” is meant to be shocking and thought-provoking.

Piccinini’s interactive [emphasis mine] experience will “challenge us to explore the social impacts of emerging biotechnology and our ethical limits in an age where genetic engineering and digital technologies are already pushing the boundaries of humanity.”

Piccinini’s work will be displayed in the 105-year-old Patricia Hotel in Vancouver’s Strathcona neighbourhood. The 90-day ticketed exhibition [emphasis mine] is scheduled to open this September [2018].

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(The show opens on Sept. 14, 2018.)

At the time, I had yet to stumble across Ingfei Chen’s thoughtful dive into the topic in her May 9, 2018 article for Slate.com,

In the United States, the clock is ticking for more than 114,700 adults and children waiting for a donated kidney or other lifesaving organ, and each day, nearly 20 of them die. Researchers are devising a new way to grow human organs inside other animals, but the method raises potentially thorny ethical issues. Other conceivable futuristic techniques sound like dystopian science fiction. As we envision an era of regenerative medicine decades from now, how far is society willing to go to solve the organ shortage crisis?

I found myself pondering this question after a discussion about the promises of stem cell technologies veered from the intriguing into the bizarre. I was interviewing bioengineer Zev Gartner, co-director and research coordinator of the Center for Cellular Construction at the University of California, San Francisco, about so-called organoids, tiny clumps of organlike tissue that can self-assemble from human stem cells in a Petri dish. These tissue bits are lending new insights into how our organs form and diseases take root. Some researchers even hope they can nurture organoids into full-size human kidneys, pancreases, and other organs for transplantation.

Certain organoid experiments have recently set off alarm bells, but when I asked Gartner about it, his radar for moral concerns was focused elsewhere. For him, the “really, really thought-provoking” scenarios involve other emerging stem cell–based techniques for engineering replacement organs for people, he told me. “Like blastocyst complementation,” he said.

Never heard of it? Neither had I. Turns out it’s a powerful new genetic engineering trick that researchers hope to use for growing human organs inside pigs or sheep—organs that could be genetically personalized for transplant patients, in theory avoiding immune-system rejection problems. The science still has many years to go, but if it pans out, it could be one solution to the organ shortage crisis. However, the prospect of creating hybrid animals with human parts and killing them to harvest organs has already raised a slew of ethical questions. In 2015, the National Institutes of Health placed a moratorium on federal funding of this nascent research area while it evaluated and discussed the issues.

As Gartner sees it, the debate over blastocyst complementation research—work that he finds promising—is just one of many conversations that society needs to have about the ethical and social costs and benefits of future technologies for making lifesaving transplant organs. “There’s all these weird ways that we could go about doing this,” he said, with a spectrum of imaginable approaches that includes organoids, interspecies organ farming, and building organs from scratch using 3D bioprinters. But even if it turns out we can produce human organs in these novel ways, the bigger issue, in each technological instance, may be whether we should.

Gartner crystallized things with a downright creepy example: “We know that the best bioreactor for tissues and organs for humans are human beings,” he said. Hypothetically, “the best way to get you a new heart would be to clone you, grow up a copy of yourself, and take the heart out.” [emphasis mine] Scientists could probably produce a cloned person with the technologies we already have, if money and ethics were of no concern. “But we don’t want to go there, right?” he added in the next breath. “The ethics involved in doing it are not compatible with who we want to be as a society.”

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This sounds like Gartner may have been reading some science fiction, specifically, Lois McMaster Bujold and her Barrayar series where she often explored the ethics and possibilities of bioengineering. At this point, some of her work seems eerily prescient.

As for Chen’s article, I strongly encourage you to read it in its entirety if you have the time.

Medicine, healing, and big money

At about the same time, there was a May 31, 2018 news item on phys.org offering a perspective from some of the leaders in the science and the business (Note: Links have been removed),

Over the past few years, researchers led by George Church have made important strides toward engineering the genomes of pigs to make their cells compatible with the human body. So many think that it’s possible that, with the help of CRISPR technology, a healthy heart for a patient in desperate need might one day come from a pig.

“It’s relatively feasible to change one gene in a pig, but to change many dozens—which is quite clear is the minimum here—benefits from CRISPR,” an acronym for clustered regularly interspaced short palindromic repeats, said Church, the Robert Winthrop Professor of Genetics at Harvard Medical School (HMS) and a core faculty member of Harvard’s Wyss Institute for Biologically Inspired Engineering. Xenotransplantation is “one of few” big challenges (along with gene drives and de-extinction, he said) “that really requires the ‘oomph’ of CRISPR.”

To facilitate the development of safe and effective cells, tissues, and organs for future medical transplantation into human patients, Harvard’s Office of Technology Development has granted a technology license to the Cambridge biotech startup eGenesis.

Co-founded by Church and former HMS doctoral student Luhan Yang in 2015, eGenesis announced last year that it had raised $38 million to advance its research and development work. At least eight former members of the Church lab—interns, doctoral students, postdocs, and visiting researchers—have continued their scientific careers as employees there.

“The Church Lab is well known for its relentless pursuit of scientific achievements so ambitious they seem improbable—and, indeed, [for] its track record of success,” said Isaac Kohlberg, Harvard’s chief technology development officer and senior associate provost. “George deserves recognition too for his ability to inspire passion and cultivate a strong entrepreneurial drive among his talented research team.”

The license from Harvard OTD covers a powerful set of genome-engineering technologies developed at HMS and the Wyss Institute, including access to foundational intellectual property relating to the Church Lab’s 2012 breakthrough use of CRISPR, led by Yang and Prashant Mali, to edit the genome of human cells. Subsequent innovations that enabled efficient and accurate editing of numerous genes simultaneously are also included. The license is exclusive to eGenesis but limited to the field of xenotransplantation.

A May 30, 2018 Harvard University news release by Caroline Petty, which originated the news item, explores some of the issues associated with incubating humans organs in other species,

The prospect of using living, nonhuman organs, and concerns over the infectiousness of pathogens either present in the tissues or possibly formed in combination with human genetic material, have prompted the Food and Drug Administration to issue detailed guidance on xenotransplantation research and development since the mid-1990s. In pigs, a primary concern has been that porcine endogenous retroviruses (PERVs), strands of potentially pathogenic DNA in the animals’ genomes, might infect human patients and eventually cause disease. [emphases mine]

That’s where the Church lab’s CRISPR expertise has enabled significant advances. In 2015, the lab published important results in the journal Science, successfully demonstrating the use of genome engineering to eliminate all 62 PERVs in porcine cells. Science later called it “the most widespread CRISPR editing feat to date.”

In 2017, with collaborators at Harvard, other universities, and eGenesis, Church and Yang went further. Publishing again in Science, they first confirmed earlier researchers’ fears: Porcine cells can, in fact, transmit PERVs into human cells, and those human cells can pass them on to other, unexposed human cells. (It is still unknown under what circumstances those PERVs might cause disease.) In the same paper, they corrected the problem, announcing the embryogenesis and birth of 37 PERV-free pigs. [Note: My July 17, 2018 post features research which suggests CRISPR-Cas9 gene editing may cause greater genetic damage than had been thought.]

“Taken together, those innovations were stunning,” said Vivian Berlin, director of business development in OTD, who manages the commercialization strategy for much of Harvard’s intellectual property in the life sciences. “That was the foundation they needed, to convince both the scientific community and the investment community that xenotransplantation might become a reality.”

“After hundreds of tests, this was a critical milestone for eGenesis — and the entire field — and represented a key step toward safe organ transplantation from pigs,” said Julie Sunderland, interim CEO of eGenesis. “Building on this study, we hope to continue to advance the science and potential of making xenotransplantation a safe and routine medical procedure.”

Genetic engineering may undercut human diseases, but also could help restore extinct species, researcher says. [Shades of the Jurassic Park movies!]

It’s not, however, the end of the story: An immunological challenge remains, which eGenesis will need to address. The potential for a patient’s body to outright reject transplanted tissue has stymied many previous attempts at xenotransplantation. Church said numerous genetic changes must be achieved to make porcine organs fully compatible with human patients. Among these are edits to several immune functions, coagulation functions, complements, and sugars, as well as the PERVs.

“Trying the straight transplant failed almost immediately, within hours, because there’s a huge mismatch in the carbohydrates on the surface of the cells, in particular alpha-1-3-galactose, and so that was a showstopper,” Church explained. “When you delete that gene, which you can do with conventional methods, you still get pretty fast rejection, because there are a lot of other aspects that are incompatible. You have to take care of each of them, and not all of them are just about removing things — some of them you have to humanize. There’s a great deal of subtlety involved so that you get normal pig embryogenesis but not rejection.

“Putting it all together into one package is challenging,” he concluded.

In short, it’s the next big challenge for CRISPR.

Not unexpectedly, there is no mention of the CRISPR patent fight between Harvard/MIT’s (Massachusetts Institute of Technology) Broad Institute and the University of California at Berkeley (UC Berkeley). My March 15, 2017 posting featured an outcome where the Broad Institute won the first round of the fight. As I recall, it was a decision based on the principles associated with King Solomon, i.e., the US Patent Office, divided the baby and UCBerkeley got the less important part of the baby. As you might expect the decision has been appealed. In an April 30, 2018 piece, Scientific American reprinted an article about the latest round in the fight written by Sharon Begley for STAT (Note: Links have been removed),

All You Need to Know for Round 2 of the CRISPR Patent Fight

It’s baaaaack, that reputation-shredding, stock-moving fight to the death over key CRISPR patents. On Monday morning in Washington, D.C., the U.S. Court of Appeals for the Federal Circuit will hear oral arguments in University of California v. Broad Institute. Questions?

How did we get here? The patent office ruled in February 2017 that the Broad’s 2014 CRISPR patent on using CRISPR-Cas9 to edit genomes, based on discoveries by Feng Zhang, did not “interfere” with a patent application by UC based on the work of UC Berkeley’s Jennifer Doudna. In plain English, that meant the Broad’s patent, on using CRISPR-Cas9 to edit genomes in eukaryotic cells (all animals and plants, but not bacteria), was different from UC’s, which described Doudna’s experiments using CRISPR-Cas9 to edit DNA in a test tube—and it was therefore valid. The Patent Trial and Appeal Board concluded that when Zhang got CRISPR-Cas9 to work in human and mouse cells in 2012, it was not an obvious extension of Doudna’s earlier research, and that he had no “reasonable expectation of success.” UC appealed, and here we are.

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For anyone who may not realize what the stakes are for these institutions, Linda Williams in a March 16, 1999 article for the LA Times had this to say about universities, patents, and money,

The University of Florida made about $2 million last year in royalties on a patent for Gatorade Thirst Quencher, a sports drink that generates some $500 million to $600 million a year in revenue for Quaker Oats Co.

The payments place the university among the top five in the nation in income from patent royalties.

Oh, but if some people on the Gainesville, Fla., campus could just turn back the clock. “If we had done Gatorade right, we would be getting $5 or $6 million (a year),” laments Donald Price, director of the university’s office of corporate programs. “It is a classic example of how not to handle a patent idea,” he added.

Gatorade was developed in 1965 when many universities were ill equipped to judge the commercial potential of ideas emerging from their research labs. Officials blew the university’s chance to control the Gatorade royalties when they declined to develop a professor’s idea.

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The Gatorade story does not stop there and, even though it’s almost 20 years old, this article stands the test of time. I strongly encourage you to read it if the business end of patents and academia interest you or if you would like to develop more insight into the Broad Institute/UC Berkeley situation.

Getting back to the science, there is that pesky matter of diseases crossing over from one species to another. While, Harvard and eGenesis claim a victory in this area, it seems more work needs to be done.

Infections from pigs

An August 29, 2018 University of Alabama at Birmingham news release (also on EurekAlert) by Jeff Hansen, describes the latest chapter in the quest to provide more organs for transplantion,

A shortage of organs for transplantation — including kidneys and hearts — means that many patients die while still on waiting lists. So, research at the University of Alabama at Birmingham and other sites has turned to pig organs as an alternative. [emphasis mine]

Using gene-editing, researchers have modified such organs to prevent rejection, and research with primates shows the modified pig organs are well-tolerated.

An added step is needed to ensure the safety of these inter-species transplants — sensitive, quantitative assays for viruses and other infectious microorganisms in donor pigs that potentially could gain access to humans during transplantation.

The U.S. Food and Drug Administration requires such testing, prior to implantation, of tissues used for xenotransplantation from animals to humans. It is possible — though very unlikely — that an infectious agent in transplanted tissues could become an emerging infectious disease in humans.

In a paper published in Xenotransplantation, Mark Prichard, Ph.D., and colleagues at UAB have described the development and testing of 30 quantitative assays for pig infectious agents. These assays had sensitivities similar to clinical lab assays for viral loads in human patients. After validation, the UAB team also used the assays on nine sows and 22 piglets delivered from the sows through caesarian section.

“Going forward, ensuring the safety of these organs is of paramount importance,” Prichard said. “The use of highly sensitive techniques to detect potential pathogens will help to minimize adverse events in xenotransplantation.”

“The assays hold promise as part of the screening program to identify suitable donor animals, validate and release transplantable organs for research purposes, and monitor transplant recipients,” said Prichard, a professor in the UAB Department of Pediatrics and director of the Department of Pediatrics Molecular Diagnostics Laboratory.

The UAB researchers developed quantitative polymerase chain reaction, or qPCR, assays for 28 viruses sometimes found in pigs and two groups of mycoplasmas. They established reproducibility, sensitivity, specificity and lower limit of detection for each assay. All but three showed features of good quantitative assays, and the lower limit of detection values ranged between one and 16 copies of the viral or bacterial genetic material.

Also, the pig virus assays did not give false positives for some closely related human viruses.

As a start to understanding the infectious disease load in normal healthy animals and ensuring the safety of pig tissues used in xenotransplantation research, the researchers then screened blood, nasal swab and stool specimens from nine adult sows and 22 of their piglets delivered by caesarian section.

Mycoplasma species and two distinct herpesviruses were the most commonly detected microorganisms. Yet 14 piglets that were delivered from three sows infected with either or both herpesviruses were not infected with the herpesviruses, showing that transmission of these viruses from sow to the caesarian-delivery piglet was inefficient.

Prichard says the assays promise to enhance the safety of pig tissues for xenotransplantation, and they will also aid evaluation of human specimens after xenotransplantation.

The UAB researchers say they subsequently have evaluated more than 300 additional specimens, and that resulted in the detection of most of the targets. “The detection of these targets in pig specimens provides reassurance that the analytical methods are functioning as designed,” said Prichard, “and there is no a priori reason some targets might be more difficult to detect than others with the methods described here.”

As is my custom, here’s a link to and a citation for the paper,

Xenotransplantation panel for the detection of infectious agents in pigs by Caroll B. Hartline, Ra’Shun L. Conner, Scott H. James, Jennifer Potter, Edward Gray, Jose Estrada, Mathew Tector, A. Joseph Tector, Mark N. Prichard. Xenotransplantaion Volume 25, Issue 4 July/August 2018 e12427 DOI: https://doi.org/10.1111/xen.12427 First published: 18 August 2018

This paper is open access.

All this leads to questions about chimeras. If a pig is incubating organs with human cells it’s a chimera but then means the human receiving the organ becomes a chimera too. (For an example, see my Dec. 22, 2013 posting where there’s mention of a woman who received a trachea from a pig. Scroll down about 30% of the way.)

What is it to be human?

A question much beloved of philosophers and others, the question seems particularly timely with xenotransplantion and other developments such neuroprosthetics (cyborgs) and neuromorphic computing (brainlike computing).

As I’ve noted before, although not recently, popular culture offers a discourse on these issues. Take a look at the superhero movies and the way in which enhanced humans and aliens are presented. For example, X-Men comics and movies present mutants (humans with enhanced abilities) as despised and rejected. Video games (not really my thing but there is the Deus Ex series which has as its hero, a cyborg also offer insight into these issues.

Other than popular culture and in the ‘bleeding edge’ arts community, I can’t recall any public discussion on these matters arising from the extraordinary set of technologies which are being deployed or prepared for deployment in the foreseeable future.

(If you’re in Vancouver (Canada) from September 14 – December 15, 2018, you may want to check out Piccinini’s work. Also, there’s ” NCSU [North Carolina State University] Libraries, NC State’s Genetic Engineering and Society (GES) Center, and the Gregg Museum of Art & Design have issued a public call for art for the upcoming exhibition Art’s Work in the Age of Biotechnology: Shaping our Genetic Futures.” from my Sept. 6, 2018 posting. Deadline: Oct. 1, 2018.)

At a guess, there will be pushback from people who have no interest in debating what it is to be human as they already know, and will find these developments, when they learn about them, to be horrifying and unnatural.

AI (artificial intelligence) for Good Global Summit from May 15 – 17, 2018 in Geneva, Switzerland: details and an interview with Frederic Werner

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With all the talk about artificial intelligence (AI), a lot more attention seems to be paid to apocalyptic scenarios: loss of jobs, financial hardship, loss of personal agency and privacy, and more with all of these impacts being described as global. Still, there are some folks who are considering and working on ‘AI for good’.

If you’d asked me, the International Telecommunications Union (ITU) would not have been my first guess (my choice would have been United Nations Educational, Scientific and Cultural Organization [UNESCO]) as an agency likely to host the 2018 AI for Good Global Summit. But, it turns out the ITU is a UN (United Nations agency) and, according to its Wikipedia entry, it’s an intergovernmental public-private partnership, which may explain the nature of the participants in the upcoming summit.

The news

First, there’s a May 4, 2018 ITU media advisory (received via email or you can find the full media advisory here) about the upcoming summit,

Artificial Intelligence (AI) is now widely identified as being able to address the greatest challenges facing humanity – supporting innovation in fields ranging from crisis management and healthcare to smart cities and communications networking.

The second annual ‘AI for Good Global Summit’ will take place 15-17 May [2018] in Geneva, and seeks to leverage AI to accelerate progress towards the United Nations’ Sustainable Development Goals and ultimately benefit humanity.

WHAT: Global event to advance ‘AI for Good’ with the participation of internationally recognized AI experts. The programme will include interactive high-level panels, while ‘AI Breakthrough Teams’ will propose AI strategies able to create impact in the near term, guided by an expert audience of mentors representing government, industry, academia and civil society – through interactive sessions. The summit will connect AI innovators with public and private-sector decision-makers, building collaboration to take promising strategies forward.

A special demo & exhibit track will feature innovative applications of AI designed to: protect women from sexual violence, avoid infant crib deaths, end child abuse, predict oral cancer, and improve mental health treatments for depression – as well as interactive robots including: Alice, a Dutch invention designed to support the aged; iCub, an open-source robot; and Sophia, the humanoid AI robot.

WHEN: 15-17 May 2018, beginning daily at 9 AM

WHERE: ITU Headquarters, 2 Rue de Varembé, Geneva, Switzerland (Please note: entrance to ITU is now limited for all visitors to the Montbrillant building entrance only on rue Varembé).

WHO: Confirmed participants to date include expert representatives from: Association for Computing Machinery, Bill and Melinda Gates Foundation, Cambridge University, Carnegie Mellon, Chan Zuckerberg Initiative, Consumer Trade Association, Facebook, Fraunhofer, Google, Harvard University, IBM Watson, IEEE, Intellectual Ventures, ITU, Microsoft, Massachusetts Institute of Technology (MIT), Partnership on AI, Planet Labs, Shenzhen Open Innovation Lab, University of California at Berkeley, University of Tokyo, XPRIZE Foundation, Yale University – and the participation of “Sophia” the humanoid robot and “iCub” the EU open source robotcub.

The interview

Frederic Werner, Senior Communications Officer at the International Telecommunication Union and** one of the organizers of the AI for Good Global Summit 2018 kindly took the time to speak to me and provide a few more details about the upcoming event.

Werner noted that the 2018 event grew out of a much smaller 2017 ‘workshop’ and first of its kind, about beneficial AI which this year has ballooned in size to 91 countries (about 15 participants are expected from Canada), 32 UN agencies, and substantive representation from the private sector. The 2017 event featured Dr. Yoshua Bengio of the University of Montreal  (Université de Montréal) was a featured speaker.

“This year, we’re focused on action-oriented projects that will help us reach our Sustainable Development Goals (SDGs) by 2030. We’re looking at near-term practical AI applications,” says Werner. “We’re matchmaking problem-owners and solution-owners.”

Academics, industry professionals, government officials, and representatives from UN agencies are gathering  to work on four tracks/themes:

  • ​AI and satellite imagery
  • AI and health
  • AI ​and smart cities & communities
  • Trust in AI

In advance of this meeting, the group launched an AI repository (an action item from the 2017 meeting) on April 25, 2018 inviting people to list their AI projects (from the ITU’s April 25, 2018? AI repository news announcement),

ITU has just launched an AI Repository where anyone working in the field of artificial intelligence (AI) can contribute key information about how to leverage AI to help solve humanity’s greatest challenges.

This is the only global repository that identifies AI-related projects, research initiatives, think-tanks and organizations that aim to accelerate progress on the 17 United Nations’ Sustainable Development Goals (SDGs).

To submit a project, just press ‘Submit’ on the AI Repository site and fill in the online questionnaire, providing all relevant details of your project. You will also be asked to map your project to the relevant World Summit on the Information Society (WSIS) action lines and the SDGs. Approved projects will be officially registered in the repository database.

Benefits of participation on the AI Repository include:

WSIS Prizes recognize individuals, governments, civil society, local, regional and international agencies, research institutions and private-sector companies for outstanding success in implementing development oriented strategies that leverage the power of AI and ICTs.

Creating the AI Repository was one of the action items of last year’s AI for Good Global Summit.

We are looking forward to your submissions.

If you have any questions, please send an email to: ai@itu.int

“Your project won’t be visible immediately as we have to vet the submissions to weed out spam-type material and projects that are not in line with our goals,” says Werner. That said, there are already 29 projects in the repository. As you might expect, the UK, China, and US are in the repository but also represented are Egypt, Uganda, Belarus, Serbia, Peru, Italy, and other countries not commonly cited when discussing AI research.

Werner also pointed out in response to my surprise over the ITU’s role with regard to this AI initiative that the ITU is the only UN agency which has 192* member states (countries), 150 universities, and over 700 industry members as well as other member entities, which gives them tremendous breadth of reach. As well, the organization, founded originally in 1865 as the International Telegraph Convention, has extensive experience with global standardization in the information technology and telecommunications industries. (See more in their Wikipedia entry.)

Finally

There is a bit more about the summit on the ITU’s AI for Good Global Summit 2018 webpage,

The 2nd edition of the AI for Good Global Summit will be organized by ITU in Geneva on 15-17 May 2018, in partnership with XPRIZE Foundation, the global leader in incentivized prize competitions, the Association for Computing Machinery (ACM) and sister United Nations agencies including UNESCO, UNICEF, UNCTAD, UNIDO, Global Pulse, UNICRI, UNODA, UNIDIR, UNODC, WFP, IFAD, UNAIDS, WIPO, ILO, UNITAR, UNOPS, OHCHR, UN University, WHO, UNEP, ICAO, UNDP, The World Bank, UN DESA, CTBTO, UNISDR, UNOG, UNOOSA, UNFPA, UNECE, UNDPA, and UNHCR.

The AI for Good series is the leading United Nations platform for dialogue on AI. The action​​-oriented 2018 summit will identify practical applications of AI and supporting strategies to improve the quality and sustainability of life on our planet. The summit will continue to formulate strategies to ensure trusted, safe and inclusive development of AI technologies and equitable access to their benefits.

While the 2017 summit sparked the first ever inclusive global dialogue on beneficial AI, the action-oriented 2018 summit will focus on impactful AI solutions able to yield long-term benefits and help achieve the Sustainable Development Goals. ‘Breakthrough teams’ will demonstrate the potential of AI to map poverty and aid with natural disasters using satellite imagery, how AI could assist the delivery of citizen-centric services in smart cities, and new opportunities for AI to help achieve Universal Health Coverage, and finally to help achieve transparency and explainability in AI algorithms.

Teams will propose impactful AI strategies able to be enacted in the near term, guided by an expert audience of mentors representing government, industry, academia and civil society. Strategies will be evaluated by the mentors according to their feasibility and scalability, potential to address truly global challenges, degree of supporting advocacy, and applicability to market failures beyond the scope of government and industry. The exercise will connect AI innovators with public and private-sector decision-makers, building collaboration to take promising strategies forward.

“As the UN specialized agency for information and communication technologies, ITU is well placed to guide AI innovation towards the achievement of the UN Sustainable Development ​Goals. We are providing a neutral close quotation markplatform for international dialogue aimed at ​building a ​common understanding of the capabilities of emerging AI technologies.​​” Houlin Zhao, Secretary General ​of ITU​

Should you be close to Geneva, it seems that registration is still open. Just go to the ITU’s AI for Good Global Summit 2018 webpage, scroll the page down to ‘Documentation’ and you will find a link to the invitation and a link to online registration. Participation is free but I expect that you are responsible for your travel and accommodation costs.

For anyone unable to attend in person, the summit will be livestreamed (webcast in real time) and you can watch the sessions by following the link below,

https://www.itu.int/en/ITU-T/AI/2018/Pages/webcast.aspx

For those of us on the West Coast of Canada and other parts distant to Geneva, you will want to take the nine hour difference between Geneva (Switzerland) and here into account when viewing the proceedings. If you can’t manage the time difference, the sessions are being recorded and will be posted at a later date.

*’132 member states’ corrected to ‘192 member states’ on May 11, 2018 at 1500 hours PDT.

*Redundant ‘and’ removed on July 19, 2018.

Understanding how carbon nanotubes grow and self-organize is key to better production

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This research may help to commercialize use of carbon nanotubes (CNTs), a  ‘magical’ nanoscale material with great promise and great difficulties (standardizing production being one of the main difficulties). A Feb. 10, 2017 news item on phys.org describes how researchers at the Lawrence Livermore National Laboratory (LLNL) and other collaborators have recorded carbon nanotubes self-organizing,

For the first time, Lawrence Livermore National Laboratory scientists and collaborators have captured a movie of how large populations of carbon nanotubes grow and align themselves.

Understanding how carbon nanotubes (CNT) nucleate, grow and self-organize to form macroscale materials is critical for application-oriented design of next-generation supercapacitors, electronic interconnects, separation membranes and advanced yarns and fabrics.

A Feb. 9, 2017 LLNL news release, which originated the news item, provides more information about the research (Note: Links have been removed),

New research by LLNL scientist Eric Meshot and colleagues from Brookhaven National Laboratory (link is external) (BNL) and Massachusetts Institute of Technology (link is external) (MIT) has demonstrated direct visualization of collective nucleation and self-organization of aligned carbon nanotube films inside of an environmental transmission electron microscope (ETEM).

In a pair of studies reported in recent issues of Chemistry of Materials (link is external) and ACS Nano (link is external), the researchers leveraged a state-of-the-art kilohertz camera in an aberration-correction ETEM at BNL to capture the inherently rapid processes that govern the growth of these exciting nanostructures.

Among other phenomena discovered, the researchers are the first to provide direct proof of how mechanical competition among neighboring carbon nanotubes can simultaneously promote self-alignment while also frustrating and limiting growth.

“This knowledge may enable new pathways toward mitigating self-termination and promoting growth of ultra-dense and aligned carbon nanotube materials, which would directly impact several application spaces, some of which are being pursued here at the Laboratory,” Meshot said.

Meshot has led the CNT synthesis development at LLNL for several projects, including those supported by the Laboratory Directed Research and Development (LDRD) program and the Defense Threat Reduction Agency (link is external) (DTRA) that use CNTs as fluidic nanochannels for applications ranging from single-molecule detection to macroscale membranes for breathable and protective garments.

Here’s a link to and a citation for the both of the papers mentioned in the news release,

Measurement of the Dewetting, Nucleation, and Deactivation Kinetics of Carbon Nanotube Population Growth by Environmental Transmission Electron Microscopy by Mostafa Bedewy, B. Viswanath, Eric R. Meshot, Dmitri N. Zakharov, Eric A. Stach, and A. John Hart. Chem. Mater., 2016, 28 (11), pp 3804–3813 DOI: 10.1021/acs.chemmater.6b00798 Publication Date (Web): May 23, 2016

Copyright © 2016 American Chemical Society

Real-Time Imaging of Self-Organization and Mechanical Competition in Carbon Nanotube Forest Growth by Viswanath Balakrishnan, Mostafa Bedewy, Eric R. Meshot, Sebastian W. Pattinson, Erik S. Polsen, Fabrice Laye, Dmitri N. Zakharov, Eric A. Stach, and A. John Hart. ACS Nano, 2016, 10 (12), pp 11496–11504 DOI: 10.1021/acsnano.6b07251 Publication Date (Web): November 23, 2016

Copyright © 2016 American Chemical Society

Both papers are behind a paywall.

The researchers have also provided this image which allows you to appreciate the difference between a ‘scientific’ version of the work and an artistic version,

This transmission electron microscope image shows growth of a dense carbon nanotube population. Courtesy: LLNL

“Breaking Me Softly” at the nanoscale

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“Breaking Me Softly” sounds like a song title but in this case the phrase as been coined to describe a new technique for controlling materials at the nanoscale according to a June 6, 2016 news item on ScienceDaily,

A finding by a University of Central Florida researcher that unlocks a means of controlling materials at the nanoscale and opens the door to a new generation of manufacturing is featured online in the journal Nature.

Using a pair of pliers in each hand and gradually pulling taut a piece of glass fiber coated in plastic, associate professor Ayman Abouraddy found that something unexpected and never before documented occurred — the inner fiber fragmented in an orderly fashion.

“What we expected to see happen is NOT what happened,” he said. “While we thought the core material would snap into two large pieces, instead it broke into many equal-sized pieces.”

He referred to the technique in the Nature article title as “Breaking Me Softly.”

A June 6, 2016 University of Central Florida (UCF) news release (also on EurekAlert) by Barbara Abney, which originated the news item, expands on the theme,

The process of pulling fibers to force the realignment of the molecules that hold them together, known as cold drawing, has been the standard for mass production of flexible fibers like plastic and nylon for most of the last century.

Abouraddy and his team have shown that the process may also be applicable to multi-layered materials, a finding that could lead to the manufacturing of a new generation of materials with futuristic attributes.

“Advanced fibers are going to be pursuing the limits of anything a single material can endure today,” Abouraddy said.

For example, packaging together materials with optical and mechanical properties along with sensors that could monitor such vital sign as blood pressure and heart rate would make it possible to make clothing capable of transmitting vital data to a doctor’s office via the Internet.

The ability to control breakage in a material is critical to developing computerized processes for potential manufacturing, said Yuanli Bai, a fracture mechanics specialist in UCF’s College of Engineering and Computer Science.

Abouraddy contacted Bai, who is a co-author on the paper, about three years ago and asked him to analyze the test results on a wide variety of materials, including silicon, silk, gold and even ice.

He also contacted Robert S. Hoy, a University of South Florida physicist who specializes in the properties of materials like glass and plastic, for a better understanding of what he found.

Hoy said he had never seen the phenomena Abouraddy was describing, but that it made great sense in retrospect.

The research takes what has traditionally been a problem in materials manufacturing and turned it into an asset, Hoy said.

“Dr. Abouraddy has found a new application of necking” –  a process that occurs when cold drawing causes non-uniform strain in a material, Hoy said.  “Usually you try to prevent necking, but he exploited it to do something potentially groundbreaking.”

The necking phenomenon was discovered decades ago at DuPont and ushered in the age of textiles and garments made of synthetic fibers.

Abouraddy said that cold-drawing is what makes synthetic fibers like nylon and polyester useful. While those fibers are initially brittle, once cold-drawn, the fibers toughen up and become useful in everyday commodities. This discovery at DuPont at the end of the 1920s ushered in the age of textiles and garments made of synthetic fibers.

Only recently have fibers made of multiple materials become possible, he said.  That research will be the centerpiece of a $317 Million U.S. Department of Defense program focused on smart fibers that Abouraddy and UCF will assist with.   The Revolutionary Fibers and Textiles Manufacturing Innovation Institute (RFT-MII), led by the Massachusetts Institute of Technology, will incorporate research findings published in the Nature paper, Abouraddy said.

The implications for manufacturing of the smart materials of the future are vast.

By controlling the mechanical force used to pull the fiber and therefore controlling the breakage patterns, materials can be developed with customized properties allowing them to interact with each other and eternal forces such as the sun (for harvesting energy) and the internet in customizable ways.

A co-author on the paper, Ali P. Gordon, an associate professor in the Department of Mechanical & Aerospace Engineering and director of UCF’s Mechanics of Materials Research Group said that the finding is significant because it shows that by carefully controlling the loading condition imparted to the fiber, materials can be developed with tailored performance attributes.

“Processing-structure-property relationships need to be strategically characterized for complex material systems. By combining experiments, microscopy, and computational mechanics, the physical mechanisms of the fragmentation process were more deeply understood,” Gordon said.

Abouraddy teamed up with seven UCF scientists from the College of Optics & Photonics and the College of Engineering & Computer Science (CECS) to write the paper.   Additional authors include one researcher each from the Massachusetts Institute of Technology, Nanyang Technological University in Singapore and the University of South Florida.

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

Controlled fragmentation of multimaterial fibres and films via polymer cold-drawing by Soroush Shabahang, Guangming Tao, Joshua J. Kaufman, Yangyang Qiao, Lei Wei, Thomas Bouchenot, Ali P. Gordon, Yoel Fink, Yuanli Bai, Robert S. Hoy & Ayman F. Abouraddy. Nature (2016) doi:10.1038/nature17980 Published online  06 June 2016

This paper is behind a paywall.

Fermionic atoms and the microscopes that can see them

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The new fermionic microscope built at the Massachusetts Institute of Technology (MIT) allows you to image 1000 or more fermionic atoms according to a May 13, 2015 news item on ScienceDaily,

Fermions are the building blocks of matter, interacting in a multitude of permutations to give rise to the elements of the periodic table. Without fermions, the physical world would not exist.

Examples of fermions are electrons, protons, neutrons, quarks, and atoms consisting of an odd number of these elementary particles. Because of their fermionic nature, electrons and nuclear matter are difficult to understand theoretically, so researchers are trying to use ultracold gases of fermionic atoms as stand-ins for other fermions.

But atoms are extremely sensitive to light: When a single photon hits an atom, it can knock the particle out of place — an effect that has made imaging individual fermionic atoms devilishly hard.

Now a team of MIT physicists has built a microscope that is able to see up to 1,000 individual fermionic atoms. The researchers devised a laser-based technique to trap and freeze fermions in place, and image the particles simultaneously.

A May 13, 2015 MIT news release, which originated the news item, provides intriguing detail about the microscope and fascinating insight into fermions (for those who are interested but not expert and sufficiently brave to endure certain failure to understand everything in this piece),

The new imaging technique uses two laser beams trained on a cloud of fermionic atoms in an optical lattice. The two beams, each of a different wavelength, cool the cloud, causing individual fermions to drop down an energy level, eventually bringing them to their lowest energy states — cool and stable enough to stay in place. At the same time, each fermion releases light, which is captured by the microscope and used to image the fermion’s exact position in the lattice — to an accuracy better than the wavelength of light.

With the new technique, the researchers are able to cool and image over 95 percent of the fermionic atoms making up a cloud of potassium gas. Martin Zwierlein, a professor of physics at MIT, says an intriguing result from the technique appears to be that it can keep fermions cold even after imaging.

“That means I know where they are, and I can maybe move them around with a little tweezer to any location, and arrange them in any pattern I’d like,” Zwierlein says.

Zwierlein and his colleagues, including first author and graduate student Lawrence Cheuk, have published their results today in the journal Physical Review Letters.

Seeing fermions from bosons

For the past two decades, experimental physicists have studied ultracold atomic gases of the two classes of particles: fermions and bosons — particles such as photons that, unlike fermions, can occupy the same quantum state in limitless numbers. In 2009, physicist Markus Greiner at Harvard University devised a microscope that successfully imaged individual bosons in a tightly spaced optical lattice. This milestone was followed, in 2010, by a second boson microscope, developed by Immanuel Bloch’s group at the Max Planck Institute of Quantum Optics.

These microscopes revealed, in unprecedented detail, the behavior of bosons under strong interactions. However, no one had yet developed a comparable microscope for fermionic atoms.

“We wanted to do what these groups had done for bosons, but for fermions,” Zwierlein says. “And it turned out it was much harder for fermions, because the atoms we use are not so easily cooled. So we had to find a new way to cool them while looking at them.”

Techniques to cool atoms ever closer to absolute zero have been devised in recent decades. Carl Wieman, Eric Cornell, and MIT’s Wolfgang Ketterle were able to achieve Bose-Einstein condensation in 1995, a milestone for which they were awarded the 2001 Nobel Prize in physics. Other techniques include a process using lasers to cool atoms from 300 degrees Celsius to a few ten-thousandths of a degree above absolute zero.

A clever cooling technique

And yet, to see individual fermionic atoms, the particles need to be cooled further still. To do this, Zwierlein’s group created an optical lattice using laser beams, forming a structure resembling an egg carton, each well of which could potentially trap a single fermion. Through various stages of laser cooling, magnetic trapping, and further evaporative cooling of the gas, the atoms were prepared at temperatures just above absolute zero — cold enough for individual fermions to settle onto the underlying optical lattice. The team placed the lattice a mere 7 microns from an imaging lens, through which they hoped to see individual fermions.

However, seeing fermions requires shining light on them, causing a photon to essentially knock a fermionic atom out of its well, and potentially out of the system entirely.

“We needed a clever technique to keep the atoms cool while looking at them,” Zwierlein says.

His team decided to use a two-laser approach to further cool the atoms; the technique manipulates an atom’s particular energy level, or vibrational energy. Each atom occupies a certain energy state — the higher that state, the more active the particle is. The team shone two laser beams of differing frequencies at the lattice. The difference in frequencies corresponded to the energy between a fermion’s energy levels. As a result, when both beams were directed at a fermion, the particle would absorb the smaller frequency, and emit a photon from the larger-frequency beam, in turn dropping one energy level to a cooler, more inert state. The lens above the lattice collects the emitted photon, recording its precise position, and that of the fermion.

Zwierlein says such high-resolution imaging of more than 1,000 fermionic atoms simultaneously would enhance our understanding of the behavior of other fermions in nature — particularly the behavior of electrons. This knowledge may one day advance our understanding of high-temperature superconductors, which enable lossless energy transport, as well as quantum systems such as solid-state systems or nuclear matter.

“The Fermi gas microscope, together with the ability to position atoms at will, might be an important step toward the realization of a quantum computer based on fermions,” Zwierlein says. “One would thus harness the power of the very same intricate quantum rules that so far hamper our understanding of electronic systems.”

Zwierlein says it is a good time for Fermi gas microscopists: Around the same time his group first reported its results, teams from Harvard and the University of Strathclyde in Glasgow also reported imaging individual fermionic atoms in optical lattices, indicating a promising future for such microscopes.

Zoran Hadzibabic, a professor of physics at Trinity College [University of Cambridge, UK], says the group’s microscope is able to detect individual atoms “with almost perfect fidelity.”

“They detect them reliably, and do so without affecting their positions — that’s all you want,” says Hadzibabic, who did not contribute to the research. “So far they demonstrated the technique, but we know from the experience with bosons that that’s the hardest step, and I expect the scientific results to start pouring out.”

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

Quantum-Gas Microscope for Fermionic Atoms by Lawrence W. Cheuk, Matthew A. Nichols, Melih Okan, Thomas Gersdorf, Vinay V. Ramasesh, Waseem S. Bakr, Thomas Lompe, and Martin W. Zwierlein. Phys. Rev. Lett. 114, 193001 – Published 13 May 2015 (print: Vol. 114, Iss. 19 — 15 May 2015) DOI: http://dx.doi.org/10.1103/PhysRevLett.114.193001

I believe this paper is behind a paywall.

There is an earlier version available on arXiv.org,

A Quantum Gas Microscope for Fermionic Atoms by Lawrence W. Cheuk, Matthew A. Nichols, Melih Okan, Thomas Gersdorf, Vinay V. Ramasesh, Waseem S. Bakr, Thomas Lompe, Martin W. Zwierlein. (Submitted on 9 Mar 2015 (v1), last revised 10 Mar 2015 (this version, v2))

This an open access website.