Tag Archives: Carnegie Mellon University

I sing the body cyber: two projects funded by the US National Science Foundation

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Points to anyone who recognized the reference to Walt Whitman’s poem, “I sing the body electric,” from his classic collection, Leaves of Grass (1867 edition; h/t Wikipedia entry). I wonder if the cyber physical systems (CPS) work being funded by the US National Science Foundation (NSF) in the US will occasion poetry too.

More practically, a May 15, 2015 news item on Nanowerk, describes two cyber physical systems (CPS) research projects newly funded by the NSF,

Today [May 12, 2015] the National Science Foundation (NSF) announced two, five-year, center-scale awards totaling $8.75 million to advance the state-of-the-art in medical and cyber-physical systems (CPS).

One project will develop “Cyberheart”–a platform for virtual, patient-specific human heart models and associated device therapies that can be used to improve and accelerate medical-device development and testing. The other project will combine teams of microrobots with synthetic cells to perform functions that may one day lead to tissue and organ re-generation.

CPS are engineered systems that are built from, and depend upon, the seamless integration of computation and physical components. Often called the “Internet of Things,” CPS enable capabilities that go beyond the embedded systems of today.

“NSF has been a leader in supporting research in cyber-physical systems, which has provided a foundation for putting the ‘smart’ in health, transportation, energy and infrastructure systems,” said Jim Kurose, head of Computer & Information Science & Engineering at NSF. “We look forward to the results of these two new awards, which paint a new and compelling vision for what’s possible for smart health.”

Cyber-physical systems have the potential to benefit many sectors of our society, including healthcare. While advances in sensors and wearable devices have the capacity to improve aspects of medical care, from disease prevention to emergency response, and synthetic biology and robotics hold the promise of regenerating and maintaining the body in radical new ways, little is known about how advances in CPS can integrate these technologies to improve health outcomes.

These new NSF-funded projects will investigate two very different ways that CPS can be used in the biological and medical realms.

A May 12, 2015 NSF news release (also on EurekAlert), which originated the news item, describes the two CPS projects,

Bio-CPS for engineering living cells

A team of leading computer scientists, roboticists and biologists from Boston University, the University of Pennsylvania and MIT have come together to develop a system that combines the capabilities of nano-scale robots with specially designed synthetic organisms. Together, they believe this hybrid “bio-CPS” will be capable of performing heretofore impossible functions, from microscopic assembly to cell sensing within the body.

“We bring together synthetic biology and micron-scale robotics to engineer the emergence of desired behaviors in populations of bacterial and mammalian cells,” said Calin Belta, a professor of mechanical engineering, systems engineering and bioinformatics at Boston University and principal investigator on the project. “This project will impact several application areas ranging from tissue engineering to drug development.”

The project builds on previous research by each team member in diverse disciplines and early proof-of-concept designs of bio-CPS. According to the team, the research is also driven by recent advances in the emerging field of synthetic biology, in particular the ability to rapidly incorporate new capabilities into simple cells. Researchers so far have not been able to control and coordinate the behavior of synthetic cells in isolation, but the introduction of microrobots that can be externally controlled may be transformative.

In this new project, the team will focus on bio-CPS with the ability to sense, transport and work together. As a demonstration of their idea, they will develop teams of synthetic cell/microrobot hybrids capable of constructing a complex, fabric-like surface.

Vijay Kumar (University of Pennsylvania), Ron Weiss (MIT), and Douglas Densmore (BU) are co-investigators of the project.

Medical-CPS and the ‘Cyberheart’

CPS such as wearable sensors and implantable devices are already being used to assess health, improve quality of life, provide cost-effective care and potentially speed up disease diagnosis and prevention. [emphasis mine]

Extending these efforts, researchers from seven leading universities and centers are working together to develop far more realistic cardiac and device models than currently exist. This so-called “Cyberheart” platform can be used to test and validate medical devices faster and at a far lower cost than existing methods. CyberHeart also can be used to design safe, patient-specific device therapies, thereby lowering the risk to the patient.

“Innovative ‘virtual’ design methodologies for implantable cardiac medical devices will speed device development and yield safer, more effective devices and device-based therapies, than is currently possible,” said Scott Smolka, a professor of computer science at Stony Brook University and one of the principal investigators on the award.

The group’s approach combines patient-specific computational models of heart dynamics with advanced mathematical techniques for analyzing how these models interact with medical devices. The analytical techniques can be used to detect potential flaws in device behavior early on during the device-design phase, before animal and human trials begin. They also can be used in a clinical setting to optimize device settings on a patient-by-patient basis before devices are implanted.

“We believe that our coordinated, multi-disciplinary approach, which balances theoretical, experimental and practical concerns, will yield transformational results in medical-device design and foundations of cyber-physical system verification,” Smolka said.

The team will develop virtual device models which can be coupled together with virtual heart models to realize a full virtual development platform that can be subjected to computational analysis and simulation techniques. Moreover, they are working with experimentalists who will study the behavior of virtual and actual devices on animals’ hearts.

Co-investigators on the project include Edmund Clarke (Carnegie Mellon University), Elizabeth Cherry (Rochester Institute of Technology), W. Rance Cleaveland (University of Maryland), Flavio Fenton (Georgia Tech), Rahul Mangharam (University of Pennsylvania), Arnab Ray (Fraunhofer Center for Experimental Software Engineering [Germany]) and James Glimm and Radu Grosu (Stony Brook University). Richard A. Gray of the U.S. Food and Drug Administration is another key contributor.

It is fascinating to observe how terminology is shifting from pacemakers and deep brain stimulators as implants to “CPS such as wearable sensors and implantable devices … .” A new category has been created, CPS, which conjoins medical devices with other sensing devices such as wearable fitness monitors found in the consumer market. I imagine it’s an attempt to quell fears about injecting strange things into or adding strange things to your body—microrobots and nanorobots partially derived from synthetic biology research which are “… capable of performing heretofore impossible functions, from microscopic assembly to cell sensing within the body.” They’ve also sneaked in a reference to synthetic biology, an area of research where some concerns have been expressed, from my March 19, 2013 post about a poll and synthetic biology concerns,

In our latest survey, conducted in January 2013, three-fourths of respondents say they have heard little or nothing about synthetic biology, a level consistent with that measured in 2010. While initial impressions about the science are largely undefined, these feelings do not necessarily become more positive as respondents learn more. The public has mixed reactions to specific synthetic biology applications, and almost one-third of respondents favor a ban “on synthetic biology research until we better understand its implications and risks,” while 61 percent think the science should move forward.

I imagine that for scientists, 61% in favour of more research is not particularly comforting given how easily and quickly public opinion can shift.

Centralized depot (Wikipedia style) for data on neurons

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The decades worth of data that has been collected about the billions of neurons in the brain is astounding. To help scientists make sense of this “brain big data,” researchers at Carnegie Mellon University have used data mining to create http://www.neuroelectro.org, a publicly available website that acts like Wikipedia, indexing physiological information about neurons.

opens a March 30, 2015 news item on ScienceDaily (Note: A link has been removed),

The site will help to accelerate the advance of neuroscience research by providing a centralized resource for collecting and comparing data on neuronal function. A description of the data available and some of the analyses that can be performed using the site are published online by the Journal of Neurophysiology

A March 30, 2015 Carnegie Mellon University news release on EurekAlert, which originated the news item, describes, in more detail,  the endeavour and what the scientists hope to achieve,

The neurons in the brain can be divided into approximately 300 different types based on their physical and functional properties. Researchers have been studying the function and properties of many different types of neurons for decades. The resulting data is scattered across tens of thousands of papers in the scientific literature. Researchers at Carnegie Mellon turned to data mining to collect and organize these data in a way that will make possible, for the first time, new methods of analysis.

“If we want to think about building a brain or re-engineering the brain, we need to know what parts we’re working with,” said Nathan Urban, interim provost and director of Carnegie Mellon’s BrainHubSM neuroscience initiative. “We know a lot about neurons in some areas of the brain, but very little about neurons in others. To accelerate our understanding of neurons and their functions, we need to be able to easily determine whether what we already know about some neurons can be applied to others we know less about.”

Shreejoy J. Tripathy, who worked in Urban’s lab when he was a graduate student in the joint Carnegie Mellon/University of Pittsburgh Center for the Neural Basis of Cognition (CNBC) Program in Neural Computation, selected more than 10,000 published papers that contained physiological data describing how neurons responded to various inputs. He used text mining algorithms to “read” each of the papers. The text mining software found the portions of each paper that identified the type of neuron studied and then isolated the electrophysiological data related to the properties of that neuronal type. It also retrieved information about how each of the experiments in the literature was completed, and corrected the data to account for any differences that might be caused by the format of the experiment. Overall, Tripathy, who is now a postdoc at the University of British Columbia, was able to collect and standardize data for approximately 100 different types of neurons, which he published on the website http://www.neuroelectro.org.

Since the data on the website was collected using text mining, the researchers realized that it was likely to contain errors related to extraction and standardization. Urban and his group validated much of the data, but they also created a mechanism that allows site users to flag data for further evaluation. Users also can contribute new data with minimal intervention from site administrators, similar to Wikipedia.

“It’s a dynamic environment in which people can collect, refine and add data,” said Urban, who is the Dr. Frederick A. Schwertz Distinguished Professor of Life Sciences and a member of the CNBC. “It will be a useful resource to people doing neuroscience research all over the world.”

Ultimately, the website will help researchers find groups of neurons that share the same physiological properties, which could provide a better understanding of how a neuron functions. For example, if a researcher finds that a type of neuron in the brain’s neocortex fires spontaneously, they can look up other neurons that fire spontaneously and access research papers that address this type of neuron. Using that information, they can quickly form hypotheses about whether or not the same mechanisms are at play in both the newly discovered and previously studied neurons.

To demonstrate how neuroelectro.org could be used, the researchers compared the electrophysiological data from more than 30 neuron types that had been most heavily studied in the literature. These included pyramidal neurons in the hippocampus, which are responsible for memory, and dopamine neurons in the midbrain, thought to be responsible for reward-seeking behaviors and addiction, among others. The site was able to find many expected similarities between the different types of neurons, and some similarities that were a surprise to researchers. Those surprises represent promising areas for future research.

In ongoing work, the Carnegie Mellon researchers are comparing the data on neuroelectro.org with other kinds of data, including data on neurons’ patterns of gene expression. For example, Urban’s group is using another publicly available resource, the Allen Brain Atlas, to find whether groups of neurons with similar electrical function have similar gene expression.

“It would take a lot of time, effort and money to determine both the physiological properties of a neuron and its gene expression,” Urban said. “Our website will help guide this research, making it much more efficient.”

The researchers have produced a brief video describing neurons and their project,

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

Brain-wide analysis of electrophysiological diversity yields novel categorization of mammalian neuron types by Shreejoy J Tripathy, Shawn D. Burton, Matthew Geramita, Richard C. Gerkin, and Nathaniel N. Urban. Journal of Neurophysiology Published 25 March 2015 DOI: 10.1152/jn.00237.2015

This paper is behind a paywall.

Think of your skin as a smartphone

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A March 5, 2015 news item on Azonano highlights work on flexible, transparent electronics designed to adhere to your skin,

Someone wearing a smartwatch can look at a calendar or receive e-mails without having to reach further than their wrist. However, the interaction area offered by the watch face is both fixed and small, making it difficult to actually hit individual buttons with adequate precision. A method currently being developed by a team of computer scientists from Saarbrücken in collaboration with researchers from Carnegie Mellon University in the USA may provide a solution to this problem. They have developed touch-sensitive stickers made from flexible silicone and electrically conducting sensors that can be worn on the skin.

Here’s what the sticker looks like,

Caption: The stickers are skin-friendly and are attached to the skin with a biocompatible, medical-grade adhesive. Credit: Oliver Dietze

Caption: The stickers are skin-friendly and are attached to the skin with a biocompatible, medical-grade adhesive. Credit: Oliver Dietze Courtesy: Saarland University

A March 4, 2015 University of Saarland press release on EurekAlert, which originated the news item, expands on the theme on connecting technology to the body,

… The stickers can act as an input space that receives and executes commands and thus controls mobile devices. Depending on the type of skin sticker used, applying pressure to the sticker could, for example, answer an incoming call or adjust the volume of a music player. ‘The stickers allow us to enlarge the input space accessible to the user as they can be attached practically anywhere on the body,’ explains Martin Weigel, a PhD student in the team led by Jürgen Steimle at the Cluster of Excellence at Saarland University. The ‘iSkin’ approach enables the human body to become more closely connected to technology. [emphasis mine]

Users can also design their iSkin patches on a computer beforehand to suit their individual tastes. ‘A simple graphics program is all you need,’ says Weigel. One sticker, for instance, is based on musical notation, another is circular in shape like an LP. The silicone used to fabricate the sensor patches makes them flexible and stretchable. ‘This makes them easier to use in an everyday environment. The music player can simply be rolled up and put in a pocket,’ explains Jürgen Steimle, who heads the ‘Embodied Interaction Group’ in which Weigel is doing his research. ‘They are also skin-friendly, as they are attached to the skin with a biocompatible, medical-grade adhesive. Users can therefore decide where they want to position the sensor patch and how long they want to wear it.’

In addition to controlling music or phone calls, the iSkin technology could be used for many other applications. For example, a keyboard sticker could be used to type and send messages. Currently the sensor stickers are connected via cable to a computer system. According to Steimle, in-built microchips may in future allow the skin-worn sensor patches to communicate wirelessly with other mobile devices.

The publication about ‘iSkin’ won the ‘Best Paper Award’ at the SIGCHI conference, which ranks among the most important conferences within the research area of human computer interaction. The researchers will present their project at the SIGCHI conference in April [2015] in Seoul, Korea, and beforehand at the computer expo Cebit, which takes place from the 16th until the 20th of March [2015] in Hannover (hall 9, booth E13).

Hopefully, you’ll have a chance to catch researchers’ presentation at the SIGCHI or Cebit events.

That quote about enabling “the human body to become more closely connected to technology” reminds me of a tag (machine/flesh) I created to categorize research of this nature. I explained the idea being explored in a May 9, 2012 posting titled: Everything becomes part machine,

Machine/flesh. That’s what I’ve taken to calling this process of integrating machinery into our and, as I newly realized, other animals’ flesh.

I think my latest previous post on this topic was a Jan. 10, 2014 post titled: Chemistry of Cyborgs: review of the state of the art by German researchers.

Nanomaterials and safety: Europe’s non-governmental agencies make recommendations; (US) Arizona State University initiative; and Japan’s voluntary carbon nanotube management

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I have three news items which have one thing in common, they concern nanomaterials and safety. Two of these of items are fairly recent; the one about Japan has been sitting in my drafts folder for months and I’m including it here because if I don’t do it now, I never will.

First, there’s an April 7, 2014 news item on Nanowerk (h/t) about European non-governmental agencies (CIEL; the Center for International Environmental Law and its partners) and their recommendations regarding nanomaterials and safety. From the CIEL April 2014 news release,

CIEL and European partners* publish position paper on the regulation of nanomaterials at a meeting of EU competent authorities

*ClientEarth, The European Environmental Bureau, European citizen’s Organization for Standardisation, The European consumer voice in Standardisation –ANEC, and Health Care Without Harm, Bureau of European Consumers

… Current EU legislation does not guarantee that all nanomaterials on the market are safe by being assessed separately from the bulk form of the substance. Therefore, we ask the European Commission to come forward with concrete proposals for a comprehensive revision of the existing legal framework addressing the potential risks of nanomaterials.

1. Nanomaterials are different from other substances.

We are concerned that EU law does not take account of the fact that nano forms of a substance are different and have different intrinsic properties from their bulk counterpart. Therefore, we call for this principle to be explicitly established in the REACH, and Classification Labeling and Packaging (CLP) regulations, as well as in all other relevant legislation. To ensure adequate consideration, the submission of comprehensive substance identity and characterization data for all nanomaterials on the market, as defined by the Commission’s proposal for a nanomaterial definition, should be required.

Similarly, we call on the European Commission and EU Member States to ensure that nanomaterials do not benefit from the delays granted under REACH to phase-in substances, on the basis of information collected on their bulk form.

Further, nanomaterials, due to their properties, are generally much more reactive than their bulk counterpart, thereby increasing the risk of harmful impact of nanomaterials compared to an equivalent mass of bulk material. Therefore, the present REACH thresholds for the registration of nanomaterials should be lowered.

Before 2018, all nanomaterials on the market produced in amounts of over 10kg/year must be registered with ECHA on the basis of a full registration dossier specific to the nanoform.

2. Risk from nanomaterials must be assessed

Six years after the entry into force of the REACH registration requirements, only nine substances have been registered as nanomaterials despite the much wider number of substances already on the EU market, as demonstrated by existing inventories. Furthermore, the poor quality of those few nano registration dossiers does not enable their risks to be properly assessed. To confirm the conclusions of the Commission’s nano regulatory review assuming that not all nanomaterials are toxic, relevant EU legislation should be amended to ensure that all nanomaterials are adequately assessed for their hazardous properties.

Given the concerns about novel properties of nanomaterials, under REACH, all registration dossiers of nanomaterials must include a chemical safety assessment and must comply with the same information submission requirements currently required for substances classified as Carcinogenic, Mutagenic or Reprotoxic (CMRs).

3. Nanomaterials should be thoroughly evaluated

Pending the thorough risk assessment of nanomaterials demonstrated by comprehensive and up-to-date registration dossiers for all nanoforms on the market, we call on ECHA to systematically check compliance for all nanoforms, as well as check the compliance of all dossiers which, due to uncertainties in the description of their identity and characterization, are suspected of including substances in the nanoform. Further, the Community Roling Action Plan (CoRAP) list should include all identified substances in the nanoform and evaluation should be carried out without delay.

4. Information on nanomaterials must be collected and disseminated

All EU citizens have the right to know which products contain nanomaterials as well as the right to know about their risks to health and environment and overall level of exposure. Given the uncertainties surrounding nanomaterials, the Commission must guarantee that members of the public are in a position to exercise their right to know and to make informed choices pending thorough risk assessments of nanomaterials on the market.

Therefore, a publicly accessible inventory of nanomaterials and consumer products containing nanomaterials must be established at European level. Moreover, specific nano-labelling or declaration requirements must be established for all nano-containing products (detergents, aerosols, sprays, paints, medical devices, etc.) in addition to those applicable to food, cosmetics and biocides which are required under existing obligations.

5. REACH enforcement activities should tackle nanomaterials

REACH’s fundamental principle of “no data, no market” should be thoroughly implemented. Therefore, nanomaterials that are on the market without a meaningful minimum set of data to allow the assessment of their hazards and risks should be denied market access through enforcement activities. In the meantime, we ask the EU Member States and manufacturers to use a precautionary approach in the assessment, production, use and disposal of nanomaterials

This comes on the heels of CIEL’s March 2014 news release announcing a new three-year joint project concerning nanomaterials and safety and responsible development,

…

Supported by the VELUX foundations, CIEL and ECOS (the European Citizen’s Organization for Standardization) are launching a three-year project aiming to ensure that risk assessment methodologies and risk management tools help guide regulators towards the adoption of a precaution-based regulatory framework for the responsible development of nanomaterials in the EU and beyond.

Together with our project partner the German Öko-Institut, CIEL and ECOS will participate in the work of the standardization organizations Comité Européen de Normalisation and International Standards Organization, and this work of the OECD [Organization for Economic Cooperation and Development], especially related to health, environmental and safety aspects of nanomaterials and exposure and risk assessment. We will translate progress into understandable information and issue policy recommendations to guide regulators and support environmental NGOs in their campaigns for the safe and sustainable production and use of nanomaterials.

The VILLUM FOUNDATION and the VELUX FOUNDATION are non-profit foundations created by Villum Kann Rasmussen, the founder of the VELUX Group and other entities in the VKR Group, whose mission it is to bring daylight, fresh air and a better environment into people’s everyday lives.

Meanwhile in the US, an April 6, 2014 news item on Nanowerk announces a new research network, based at Arizona State University (ASU), devoted to studying health and environmental risks of nanomaterials,

Arizona State University researchers will lead a multi-university project to aid industry in understanding and predicting the potential health and environmental risks from nanomaterials.

Nanoparticles, which are approximately 1 to 100 nanometers in size, are used in an increasing number of consumer products to provide texture, resiliency and, in some cases, antibacterial protection.

The U.S. Environmental Protection Agency (EPA) has awarded a grant of $5 million over the next four years to support the LCnano Network as part of the Life Cycle of Nanomaterials project, which will focus on helping to ensure the safety of nanomaterials throughout their life cycles – from the manufacture to the use and disposal of the products that contain these engineered materials.

An April 1, 2014 ASU news release, which originated the news item, provides more details and includes information about project partners which I’m happy to note include nanoHUB and the Nanoscale Informal Science Education Network (NISENet) in addition to the other universities,

Paul Westerhoff is the LCnano Network director, as well as the associate dean of research for ASU’s Ira A. Fulton Schools of Engineering and a professor in the School of Sustainable Engineering and the Built Environment.

The project will team engineers, chemists, toxicologists and social scientists from ASU, Johns Hopkins, Duke, Carnegie Mellon, Purdue, Yale, Oregon’s state universities, the Colorado School of Mines and the University of Illinois-Chicago.

Engineered nanomaterials of silver, titanium, silica and carbon are among the most commonly used. They are dispersed in common liquids and food products, embedded in the polymers from which many products are made and attached to textiles, including clothing.

Nanomaterials provide clear benefits for many products, Westerhoff says, but there remains “a big knowledge gap” about how, or if, nanomaterials are released from consumer products into the environment as they move through their life cycles, eventually ending up in soils and water systems.

“We hope to help industry make sure that the kinds of products that engineered nanomaterials enable them to create are safe for the environment,” Westerhoff says.

“We will develop molecular-level fundamental theories to ensure the manufacturing processes for these products is safer,” he explains, “and provide databases of measurements of the properties and behavior of nanomaterials before, during and after their use in consumer products.”

Among the bigger questions the LCnano Network will investigate are whether nanomaterials can become toxic through exposure to other materials or the biological environs they come in contact with over the course of their life cycles, Westerhoff says.

The researchers will collaborate with industry – both large and small companies – and government laboratories to find ways of reducing such uncertainties.

Among the objectives is to provide a framework for product design and manufacturing that preserves the commercial value of the products using nanomaterials, but minimizes potentially adverse environmental and health hazards.

In pursuing that goal, the network team will also be developing technologies to better detect and predict potential nanomaterial impacts.

Beyond that, the LCnano Network also plans to increase awareness about efforts to protect public safety as engineered nanomaterials in products become more prevalent.

The grant will enable the project team to develop educational programs, including a museum exhibit about nanomaterials based on the LCnano Network project. The exhibit will be deployed through a partnership with the Arizona Science Center and researchers who have worked with the Nanoscale Informal Science Education Network.

The team also plans to make information about its research progress available on the nanotechnology industry website Nanohub.org.

“We hope to use Nanohub both as an internal virtual networking tool for the research team, and as a portal to post the outcomes and products of our research for public access,” Westerhoff says.

The grant will also support the participation of graduate students in the Science Outside the Lab program, which educates students on how science and engineering research can help shape public policy.

Other ASU faculty members involved in the LCnano Network project are:

• Pierre Herckes, associate professor, Department of Chemistry and Biochemistry, College of Liberal Arts and Sciences
• Kiril Hristovski, assistant professor, Department of Engineering, College of Technology and Innovation
• Thomas Seager, associate professor, School of Sustainable Engineering and the Built Environment
• David Guston, professor and director, Consortium for Science, Policy and Outcomes
• Ira Bennett, assistant research professor, Consortium for Science, Policy and Outcomes
• Jameson Wetmore, associate professor, Consortium for Science, Policy and Outcomes, and School of Human Evolution and Social Change

I hope to hear more about the LCnano Network as it progresses.

Finally, there was this Nov. 12, 2013 news item on Nanowerk about instituting  voluntary safety protocols for carbon nanotubes in Japan,

Technology Research Association for Single Wall Carbon Nanotubes (TASC)—a consortium of nine companies and the National Institute of Advanced Industrial Science and Technology (AIST) — is developing voluntary safety management techniques for carbon nanotubes (CNTs) under the project (no. P10024) “Innovative carbon nanotubes composite materials project toward achieving a low-carbon society,” which is sponsored by the New Energy and Industrial Technology Development Organization (NEDO).

Lynn Bergeson’s Nov. 15, 2013 posting on nanotech.lawbc.com provides a few more details abut the TASC/AIST carbon nanotube project (Note: A link has been removed),

Japan’s National Institute of Advanced Industrial Science and Technology (AIST) announced in October 2013 a voluntary guidance document on measuring airborne carbon nanotubes (CNT) in workplaces. … The guidance summarizes the available practical methods for measuring airborne CNTs:  (1) on-line aerosol measurement; (2) off-line quantitative analysis (e.g., thermal carbon analysis); and (3) sample collection for electron microscope observation. …

You can  download two protocol documents (Guide to measuring airborne carbon nanotubes in workplaces and/or The protocols of preparation, characterization and in vitro cell based assays for safety testing of carbon nanotubes), another has been published since Nov. 2013, from the AIST’s Developing voluntary safety management techniques for carbon nanotubes (CNTs): Protocol and Guide webpage., Both documents are also available in Japanese and you can link to the Japanese language version of the site from the webpage.

Duke University’s (North Carolina, US) Center for Environmental Implications of NanoTechnology (CEINT) wins $15M grant

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A Nov. 13, 2013 news item on Azonano announces that the Center for Environmental Implications of Nanotechnology (CEINT) at Duke University has been awarded $15M,

A pioneering, multi-institution research center headquartered at Duke’s Pratt School of Engineering has just won $15-million grant renewal from the National Science Foundation and the US Environmental Protection Agency to continue learning more about where nanoparticles accumulate, how they interact with other chemicals and how they affect the environment.

Founded in 2008, the Center for Environmental Implications of NanoTechnology (CEINT) has been evaluating the effect of long-term nanomaterial exposure on organisms and ecosystems.

“The previous focus has been on studying simple, uniform nanomaterials in simple environments,” said Mark Wiesner, James L. Meriam Professor of Civil & Environmental Engineering and director of CEINT. “As we look to the next five years, we envision a dramatically different landscape. We will be evaluating more complex nanomaterials in more realistic natural environments such as agricultural lands and water treatment systems where these materials are likely to be found.”

The Nov. 11, 2013 Duke University news release by Karyn Hede, which originated the news item, provides some history and context for CEINT (Note: Links have been removed),

When CEINT formed, little research had been done on how materials manufactured at the nanoscale—about 1/10,000th the diameter of a human hair—enter the environment and whether their size and unique properties render them a new category of environmental risk. For example, nanoparticles can be highly reactive with other chemicals in the environment and had been shown to disrupt activities in living organisms. Indeed, nanosilver is used in clothing precisely because it effectively kills odor-causing bacteria.

To tackle this expansive research agenda, CEINT leadership assembled a multi-institutional research team encompassing expertise in ecosystems biology, chemistry, geology, materials science, computational science, mathematical modeling and other specialties, to complement its engineering expertise. The Center has 29 faculty collaborators, as well as 76 graduate and undergraduate students participating in research. Over its first five years, CEINT has answered some of the most pressing questions about environmental risk and has learned where to focus future research.

The center also pioneered the use of a new test chamber, called a mesocosm, that replicates a small wetland environment. “Over the long term, we want to evaluate how nanoparticles bioaccumulate in complex food webs,” said Emily Bernhardt, an associate professor of biology at Duke and ecosystem ecologist who helped design the simulated ecosystems. “The additional funding will allow us to study the subtle effect of low-dose exposure on ecosystems over time, as well as complex interactions among nanoparticles and other environmental contaminants.”

Looking forward, the investigators at CEINT plan to expand the use of systems modeling and to create a “knowledge commons,” a place to store various kinds of data that can then be analyzed as a whole, said CEINT Executive Director Christine Hendren.

“Our investigators and collaborators are located across the globe,” Hendren added. “We are committed to disseminating information that can be translated into responsible regulatory frameworks and that will be available to compare with results of future research.”

…

Key findings from CEINT’s first five years include:

Naturally occurring nanomaterials far outnumber engineered particles. CEINT scientist Michael Hochella, a geoscientist at Virginia Tech, inventoried nanoparticles and concluded that natural nanoparticles are found everywhere, from dust in the atmosphere to sea spray to volcanoes. The environmental risks of these natural nanomaterials are difficult to separate from engineered nanomaterials.

Engineered nanoparticles change once they enter the environment. Gregory V. Lowry, deputy director of CEINT and professor at Carnegie Mellon University, Pittsburgh, along with colleagues from the University of Birmingham, U.K. and the University of South Carolina found that the relatively large surface area of nanoparticles makes them highly reactive once they enter the environment. These transformations will alter their movement and toxicity and must be considered when studying nanomaterials. Their review article on this topic was named the best feature article of 2012 by the journal Environmental Science and Technology.

Nanoparticles can be visualized, even in complex environmental samples. A research team led by CEINT investigators Jie Liu, associate professor of chemistry at Duke, and CEINT Director Mark Wiesner showed that more than a dozen types of engineered nanoparticles, including silver, gold, and titanium dioxide, along with carbon nanotubes, can be surveyed using a technique called hyperspectral imaging, which measures light scattering caused by different types of nanoparticles. The new technique, co-developed by postdoctoral researcher Appala Raju Badireddy, is sensitive enough to analyze nanoparticles found in water samples ranging from ultrapurified to wastewater. It will be used in future long-term studies of how nanoparticles move and accumulate in ecological systems.

It is possible to estimate current and future volume of engineered nanomaterials. Understanding the volume of nanomaterials being produced and released into the environment is a crucial factor in risk assessment. CEINT researchers led by Christine Hendren measured the upper- and lower-bound annual U.S. production of five classes of nanomaterials, totaling as much as a combined 40,000 metric tons annually as of 2011.

Silver nanoparticles caused environmental stress in a simulated wetland environment. CEINT has developed  “mesocosms,”  open-air terrarium-like structures that simulate wetland ecosystems that can be evaluated over time. Even low doses of silver nanoparticles used in many consumer products produced about a third less biomass in a mesocosm. The researchers will now  look at how nanomaterials are transferred between organisms in a mesocosm.

I have written about CEINT and its work, including the mesocosm, many times. My August 15, 2011 posting offers an introduction to the CEINT mesocosm.

RNA (ribonucleic acid) video game

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I am a great fan of  Foldit, a protein-folding game I have mentioned several times here (my first posting about Foldit was Aug. 6, 2010) and now via the Foresight Insitute’s July 16, 2012 blog posting, I have discovered an RNA video game (Note: I have removed links),

As we pointed out a few months ago, the greater complexity of folding rules for RNA compared to its chemical cousin DNA gives RNA a greater variety of compact, three-dimensional shapes and a different set of potential functions than is the case with DNA, and this gives RNA nanotechnology a different set of advantages compared to DNA nanotechnology … Proteins have even more complex folding rules and an even greater variety of structures and functions. We also noted here that online gamers playing Foldit topped scientists in redesigning a protein to achieve a novel enzymatic activity that might be especially useful in developing molecular building blocks for molecular manufacturing. Now KurzweilAI.net brings news of an online game that allows players to design RNA molecules …

Here’s more from the KurzwelAI.net June 26, 3012 posting about the new RNA game EteRNA,

EteRNA, an online game with more than 38,000 registered users, allows players to design molecules of ribonucleic acid — RNA — that have the power to build proteins or regulate genes.

EteRNA players manipulate nucleotides, the fundamental building blocks of RNA, to coax molecules into shapes specified by the game.

Those shapes represent how RNA appears in nature while it goes about its work as one of life’s most essential ingredients.

EteRNA was developed by scientists at Stanford and Carnegie Mellon universities, who use the designs created by players to decipher how real RNA works. The game is a direct descendant of Foldit — another science crowdsourcing tool disguised as entertainment — which gets players to help figure out the folding structures of proteins.

Here’s how the EteRNA folks describe this game (from the About EteRNA page),

By playing EteRNA, you will participate in creating the first large-scale library of synthetic RNA designs. Your efforts will help reveal new principles for designing RNA-based switches and nanomachines — new systems for seeking and eventually controlling living cells and disease-causing viruses. By interacting with thousands of players and learning from real experimental feedback, you will be pioneering a completely new way to do science. Join the global laboratory!

The About EteRNA webpage also offers a discussion about RNA,

RNA is often called the “Dark Matter of Biology.” While originally thought to be an unstable cousin of DNA, recent discoveries have shown that RNA can do amazing things. They play key roles in the fundamental processes of life and disease, from protein synthesis and HIV replication, to cellular control. However, the full biological and medical implications of these discoveries is still being worked out.

…

RNA is made of four nucleotides (A, C,G,and U, which stand for adenine, cytosine, guanine, and uracil). Chemically, each of these building blocks is made of atoms of carbon, oxygen, nitrogen, phosphorus, and hydrogen. When you design RNAs with EteRNA, you’re really creating a chain of these nucleotides.

RNA Nucleotides (from the About EteRNA webpage)

…

Scientists do not yet understand all of RNA’s roles, but we already know about a large collection of RNAs that are critical for life: (see the Thermus Thermophilus image representing following points)

  1. mRNAs are short copies of a cell’s DNA genome that gets cut up, pasted, spliced, and otherwise remixed before getting translated into proteins.
  1. rRNA forms the core machinery of an ancient machine, the ribosome. This machine synthesizes the proteins of your cells and all living cells, and is the target of most antibiotics.
  2. miRNAs (microRNAs) are short molecules (about 22-letters) that are used by all complex cells as commands for silencing genes and appear to have roles in cancer, heart disease, and other medical problems.
  3. Riboswitches are ubiquitous in bacteria. They sense all sorts of small molecules that could be food or signals from other bacteria, and turn on or off genes by changing their shapes. These are interesting targets for new antibiotics.
  4. Ribozymes are RNAs that can act as enzymes. They catalyze chemical reactions like protein synthesis and RNA splicing, and provide evidence of RNA’s dominance in a primordial stage of Life’s evolution.
  5. Retroviruses, like Hepatitis C, poliovirus, and HIV, are very large RNAs coated with proteins.
  6. And much much more… shRNA, piRNA, snRNA, and other new classes of important RNAs are being discovered every year.

Thermus Thermophilus – Large Subunit Ribosomal RNA
Source: Center for Molecular Biology (downloaded from the About EteRNA webpage)

I do wonder about the wordplay EteRNA/eternal. Are these scientists trying to tell us something?

Nearby Nature GigaBlitz—Summer Solstice 2012—get your science out

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The June 20 – 26, 2012 GigaBlitz event is an international citizen science project focused on biodiversity. From the June 13, 2012 news item on physorg.com,

A high-resolution image of a palm tree in Brazil, which under close examination shows bees, wasps and flies feasting on nectars and pollens, was the top jury selection among the images captured during last December’s Nearby Nature GigaBlitz. It’s also an example of what organizers hope participants will produce for the next GigaBlitz, June 20-26 [2012].

Here’s a close up from the Brazilian palm tree image,

Bee close up from Palmeira em flor, by Eduardo Frick (http://gigapan.com/gigapans/95168/)

This bee close up does not convey the full impact of an image that you can zoom from a standard size to extreme closeups of insects, other animals, portions of palm fronds, etc. To get the full impact go here.

Here’s more about the Nearby Nature GigaBlitz events from the June 13, 2012 Carnegie Mellon University news release,

The Nearby Nature GigaBlitz events are citizen science projects in which people use gigapixel imagery technology to document biodiversity in their backyards — if not literally in their backyards, then in a nearby woodlot or vacant field. These images are then shared and made available for analysis via the GigaPan website. The events are organized by a trio of biologists and their partners at Carnegie Mellon University’s CREATE Lab.

…

December’s GigaBlitz included contributors from the United States, Canada, Spain, Japan, South Africa, Brazil, Singapore, Indonesia and Australia. Ten of the best images are featured in the June issue of GigaPan Magazine, an online publication of CMU’s CREATE Lab.

The issue was guest-edited by the organizers of the GigaBlitz: Ken Tamminga, professor of landscape architecture at Penn State University; Dennis vanEngelsdorp, research scientist at the University of Maryland’s Department of Entomology; and M. Alex Smith, assistant professor of integrative biology at the University of Guelph, Ontario.

The inspiration for the gigablitz comes from the world of ornithology (bird watching), from the Carnegie Mellon University June 13, 2012 news release,

Tamminga, vanEngelsdorp and Smith envisioned something akin to a BioBlitz, an intensive survey of a park or nature preserve that attempts to identify all living species within an area at a given time, and citizen science efforts such as the Audubon Society’s Christmas Bird Count.

“We imagined using these widely separated, but nearby, panoramas as a way of collecting biodiversity data – similar to the Christmas bird count – where citizen scientists surveyed their world, then distributed and shared that data with the world through public GigaPans,” they wrote. “The plus of the GigaPan approach was that the sharing was bi-directional – not merely ‘This is what I saw,’ but also hearing someone say, ‘This is what I found in your GigaPan.'”

Here’s an excerpt from the Nearby Nature gigablitz June 20 -26, 2012 Call for Entries,

The challenge: Gigapixel imaging can reveal a surprising range of animal and plant species in the ordinary and sometimes extraordinary settings in which we live, learn, and work. Your challenge is to capture panoramas of Nearby Nature and share them with your peers at gigapan.org for further exploration. We hope that shared panoramas and snapshotting will help the GigaPan community more deeply explore, document, and celebrate the diversity of life forms in their local habitats.

Gigablitz timing: The event will take place over a 7-day period – a gigablitz – that aligns with the June solstice. Please capture and upload your images to the gigapan.org website between 6am, June 20 and 11pm, June 26 (your local time).

Juried selections:    Panoramas that meet the criteria below are eligible for inclusion in the science.gigapan.org Nearby Nature collection. The best panoramas will be selected by a jury for publication in an issue of GigaPan Magazine dedicated to the Nearby Nature collection.  Selection criteria are as follows:

  • Biodiversity: the image is species rich.
  • Uniqueness: the image contains particularly interesting or unique species, or the image captures a sense of the resilience of life-forms in human-dominated settings.
  • Nearby Nature context: image habitat is part of, or very near, the everyday places that people inhabit.
  • Image quality: the image is of high quality and is visually captivating.

Subjects and locations: The gigablitz subject may be any “nearby” location in which you have a personal interest:  schoolyard garden, backyard habitat, balcony planter, village grove, nearby remnant woods, vacant lot meadow next door and others.  Panoramas with high species richness (the range of different species in a given area) that are part of everyday places are especially encouraged.  It is the process of making and sharing gigapans that will transform the ordinary into the extraordinary.

Here are 3 things to keep in mind when choosing a place:

  • The panorama should focus on organisms in a habitat near your home, school or place of work.
  • Any life-forms are acceptable, such as plants, insects, and other animals.
  • Rich, sharp detail will encourage snapshotters to help identify organisms in your panorama.  Thus, your gigapan unit should be positioned close to the subject habitat – within 100 feet (30 meters) away, and preferably much closer.  Up close mini-habitats in the near-macro range are welcome.

Please do check the Call for Entries for additional information about the submissions.

As for the website which hosts the contest, I checked the About GigaPan page and found this,

What is a GigaPan?

Gigapans are gigapixel panoramas, digital images with billions of pixels. They are huge panoramas with fascinating detail, all captured in the context of a single brilliant photo. Phenomenally large, yet remarkably crisp and vivid, gigapans are available to be explored at GigaPan.com. Zoom in and discover the detail of over 50,000 panoramas from around the world.

A New Dimension for Photography

GigaPan gives experienced and novice photographers the technology to create high-resolution panorama images more easily than ever before, and the resulting GigaPan images offer viewers a new, unique perspective on the world.

GigaPan offers the first solution for shooting, viewing and exploring high-resolution panoramic images in a single system: EPIC series of robotic camera mounts capture photos using almost any digital camera; GigaPan Stitch Software automatically combines the thousands of images taken into a single image; and GigaPan.com enables the unique mega-high resolution viewing experience.

GigaPan EPIC

GigaPan EPIC robotic mounts empower cameras to take hundreds, even thousands of photos, which are combined to create one highly detailed image with amazing depth and clarity.

The GigaPan EPIC and EPIC 100 are compatible with a broad range of point-and-shoot cameras and small DSLRs to capture gigapans, quickly and accurately. Light and compact, they are easy-to-use, and remarkably efficient. The EPIC Pro is designed to work with DSLR cameras and larger lenses, features advanced technology, and delivers stunning performance and precision. Strong enough to hold a camera and lens combination of up to 10 lbs, the EPIC Pro enables users to capture enormous panoramas with crisp, vivid detail.

Bringing Mars Rover Technology to Earth

The GigaPan EPIC series is based on the same technology employed by the Mars Rovers, Spirit and Opportunity, to capture the incredible images of the red planet. Now everyone has the opportunity to use technology developed for Mars to take their own incredible images.

GigaPan was formed in 2008 as a commercial spin-off of a successful research collaboration between a team of researchers at NASA and Carnegie Mellon University. The company’s mission is to bring this powerful, high-resolution imaging capability to a broad audience.

The original GigaPan prototype and related software were devised by a team led by Randy Sargent, a senior systems scientist at Carnegie Mellon West and the NASA Ames Research Center in Moffett Field, Calif., and Illah Nourbakhsh, an associate professor of robotics at Carnegie Mellon in Pittsburgh.

If I understand this rightly, this commercial enterprise (GigaPan), which offers hardware and software,  also supports a community-sharing platform for the types of images made possible by the equipment they sell.

Science communication at the US National Academy of Sciences

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I guess it’s going to be a science communication kind of day on this blog. Dr. Andrew Maynard on his 2020 Science blog posted a May 22, 2012 piece about a recent two-day science communication event at the US National Academy of Sciences in Washington, DC.

Titled The Science of Science Communication and held May 21 – 22, 2012, I was a little concerned about the content since it suggests a dedication to metrics (which are useful but I find often misused) and the possibility of a predetermined result for science communication. After watching a webcast of the first session (Introduction and Overviews offered by Baruch Fischhof [Carnegie Mellon University] and Dietram Scheufele [University of Wisconsin at Madison], 55:35 mins.), I’m relieved to say that the first two presenters mostly avoided those pitfalls.

You can go here to watch any of the sessions held during that two days, although I will warn you that these are not TED talks. The shortest are roughly 27 mins. with most running over 1 hour, while a couple  of them run over two hours.

Getting back to Andrew and his take on the proceedings, excerpted from his May 22, 2012 posting,

It’s important that the National Academies of Science are taking the study of science communication (and its practice) seriously.  Inviting a bunch of social scientists into the National Academies – and into a high profile colloquium like this – was a big deal.  And irrespective of the meeting’s content, it flags a commitment to work closely with researchers studying science communication and decision analysis to better ensure informed and effective communication strategies and practice.  Given the substantial interest in the colloquium – on the web as well as at the meeting itself – I hope that the National Academies build on this and continue to engage fully in this area.

Moving forward, there needs to be more engagement between science communication researchers and practitioners.  Practitioners of science communication – and the practical insight they bring – were notable by their absence (in the main) from the colloquium program.  If the conversation around empirical research is to connect with effective practice, there must be better integration of these two communities.

It’s interesting to read about the colloquia (the science communication event was one of a series events known as the Arthur M. Sackler Colloquia) from the perspective of a someone who was present in real time.

Sometimes when we touch: Touché, a sensing project from Disnery Research and Carnegie Mellon

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Researchers at Carnegie Mellon University and Disney Research, Pittsburgh (Philadelphia, US) have taken capacitive sensing, used for touchscreens such as smartphones, and added new capabilities. From the May 4, 2012 news item on Nanowerk,

A doorknob that knows whether to lock or unlock based on how it is grasped, a smartphone that silences itself if the user holds a finger to her lips and a chair that adjusts room lighting based on recognizing if a user is reclining or leaning forward are among the many possible applications of Touché, a new sensing technique developed by a team at Disney Research, Pittsburgh, and Carnegie Mellon University.

Touché is a form of capacitive touch sensing, the same principle underlying the types of touchscreens used in most smartphones. But instead of sensing electrical signals at a single frequency, like the typical touchscreen, Touché monitors capacitive signals across a broad range of frequencies.

This Swept Frequency Capacitive Sensing (SFCS) makes it possible to not only detect a “touch event,” but to recognize complex configurations of the hand or body that is doing the touching. An object thus could sense how it is being touched, or might sense the body configuration of the person doing the touching.

Disney Research, Pittsburgh made this video describing the technology and speculating on some of the possible applications (this is a research-oriented video, not your standard Disney fare),

Here’s a bit  more about the technology (from the May 4, 2012 news item),

Both Touché and smartphone touchscreens are based on the phenomenon known as capacitive coupling. In a capacitive touchscreen, the surface is coated with a transparent conductor that carries an electrical signal. That signal is altered when a person’s finger touches it, providing an alternative path for the electrical charge.

By monitoring the change in the signal, the device can determine if a touch occurs. By monitoring a range of signal frequencies, however, Touché can derive much more information. Different body tissues have different capacitive properties, so monitoring a range of frequencies can detect a number of different paths that the electrical charge takes through the body.

Making sense of all of that SFCS information, however, requires analyzing hundreds of data points. As microprocessors have become steadily faster and less expensive, it now is feasible to use SFCS in touch interfaces, the researchers said.

“Devices keep getting smaller and increasingly are embedded throughout the environment, which has made it necessary for us to find ways to control or interact with them, and that is where Touché could really shine,” Harrison [Chris Harrison, a Ph.D. student in Carnegie Mellon’s Human-Computer Interaction Institute] said. Sato [Munehiko Sato, a Disney intern and a Ph.D. student in engineering at the University of Tokyo] said Touché could make computer interfaces as invisible to users as the embedded computers themselves. “This might enable us to one day do away with keyboards, mice and perhaps even conventional touchscreens for many applications,” he said.

We’re seeing more of these automatic responses to a gesture or movement. For example, common spelling errors are corrected as you key in (type) text in wordprocessing packages and in search engines. In fact, there are times when an applications insists on its own correction and I have to insist (and I don’t always manage to override the system) if I have something which is nonstandard. As I watch these videos and read about these new technical possibilities, I keep asking myself, Where is the override?

Wetware, nanoelectronics and fuel cells

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Some of the computer engineers I worked with years ago used to ‘jokingly’ refer to people as wetware putting us on a continuum with hardware, software, and firmware. Clearly they knew something I didn’t as it seems we’re getting closer to making that joke a reality with the term wetware expanding to include biological systems. Michael Berger in his July 19, 2011 Nanowerk Spotlight essay, Squishy electronics, takes a look at some of the developments in biocompatible electronics [Mar.7.12: duplicate paragraph removed from essay excerpt],

There is a physical and electrical disconnect between the world of electronics and the world of biology. Electronics tend to be rigid, operate using electrons, and are inherently two-dimensional. The brain, as a basis for comparison, is soft, operates using ions, and is three-dimensional. Researchers have therefore been looking to find different routes to create biocompatible devices that work well in wet environments like biological systems.

Berger goes on to highlight some research in North Carolina,

The device fabricated by the NC State team (that included graduate students Ju-Hee So and Hyung-Jun Koo, who also first-authored the paper [research team was led by Orlin Velev and Michael Dickey]) is composed primarily of water-based gels that are, in principle, compatible with biological species including cells, enzymes, proteins, and tissues and thus hold promise for interfacing electronics with biological systems. [emphasis mine]

The novelty of this work is the operating mechanism of the memory device combined with the fact that it is built entirely from materials with properties similar to Jell-O. The memristor-like devices are simple to fabricate and basically consist of two liquid-metal electrodes that sandwich a slab of hydrogel.

This line of work fits in nicely with ‘vampire’ batteries (my latest posting on this topic, July 18k 3011) which can, theoretically, run on blood. Coincidentally, The Scientist  published a June 23, 2011 article,  by Megan Scudellari which focuses on biological fuel cells that can run on bacteria,

This tiny biological fuel cell, the smallest of its kind with a total volume of just 0.3 microliters, was built using microfluidics and relies on bacteria to produce energy. Bacteria colonize the anode, the negatively charged end of the system, and through their natural metabolism produce electrons that flow to the cathode, creating a circuit. Together, the anode and cathode are only a few human hairs wide, but the tiny circuit generates a consistent flow of electricity.

An undated news item on the Carnegie Mellon University website offers this information,

Carnegie Mellon University’s Kelvin B. Gregory and Philip R. LeDuc have created the world’s smallest fuel cell — powered by bacteria.

Future versions of it could be used for self-powered sensing devices in remote locations where batteries are impractical, such as deep ocean or geological environments.

“We have developed a biological fuel cell which uses microbial electricity generation enabled by microfluidic flow control to produce power,” said Gregory, an assistant professor of civil and environmental engineering at CMU.

No bigger than a human hair, the fuel cell generates energy from the metabolism of bacteria on thin gold plates in micro-manufactured channels.

Those injunctions about not mixing liquids with electricity may soon seem a trifle old-fashioned.