It’s possible that I shall make an ass of myself. But in that case one can always get out of it with a little dialectic. I have, of course, so worded my proposition as to be right either way (K.Marx, Letter to F.Engels on the Indian Mutiny)
Saturday, October 28, 2023
Community-developed guidelines for publishing images help address reproducibility problem in science
Images created by a plethora of high-tech instruments are widely found in scientific research as both illustrations and sources of data. Recent advancements in light (or optical) microscopy in particular have enabled sensitive, fast, and high-resolution imaging of diverse samples, making image use in scientific papers more popular than ever.
And yet there are no common standards for the publication of images. This causes major snags in an essential element of the scientific process: reproducibility. Any researcher looking to replicate the results of a study without full information on how images key to those results were produced has an impossible task before them.
“A lot of imaging scientists around the world have been very concerned by the reproducibility crisis,” says Alison North, senior director of the Bio-Imaging Resource Center (BIRC) at Rockefeller University. “People publish so little information about how they acquire their images and how they analyze them.”
That’s why an international consortium of experts, including North and BIRC image analyst Ved Sharma, recently put together easy-to-follow guidelines for publishing images and image analyses born of their collective knowledge of best practices. These guidelines were recently published in an open-access study in Nature Methods.
The guidelines were assembled in a two-year project involving dozens of imaging scientists from QUAREP-LiMi (Quality Assessment and Reproducibility for Instruments & Images in Light Microscopy), a group that includes 554 members from 39 countries.
They include practical checklists for scientists to follow with the goal of publishing fully understandable and interpretable images.
Each checklist is divided into three levels: minimal, which describes essential requirements for reproducible images; recommended, which bolsters image comprehensibility; and ideal, which includes top-tier best practices.
For example, the checklist includes standards for formatting, color handling, and annotation. Indicating the origin of an inset from an image is minimal; providing intensity scales for grayscale, color, and pseudocolor is recommended; and annotating image details such as pixel size and exposure time are ideal.
North says, “We advise everyone to publish their images in black and white rather than color, because your eye is much more sensitive to details in monochrome. Many investigators like color images because they’re pretty and they look impressive. But they don’t realize they’re actually throwing away a lot of information.”
The image-analysis checklists cover three different kinds of workflows: established, new, and machine-learning. Citing each step is a minimal requirement of an established workflow, for example, while providing a screen recording of or tutorial for a new workflow is ideal.
This is especially relevant because NIH-funded researchers now have to include data management protocols to meet the requirements of the new NIH data management policy, North says. “People have been saying, ‘What are we supposed to write in that?’ This paper gives them those guidelines.”
That scientists have a clearly articulated image-analysis workflow is important for scientific journals as well; as the primary disseminators of scientific knowledge, journals have a vested interest in ensuring that the papers they publish are transparent about how results were produced. To that end, journal editors took part in discussion with the study authors.
The guidelines can only increase accessibility to the data in a paper, Sharma says. “There is so much information that could be included for each image in a paper, but most of the time it’s not available, or the reader has to dig deep into the paper to find out where the information is in order to make sense of the image,” Sharma says. “If scientists start adopting even the minimal standard for image publication, reproducibility would be so much easier for everyone.”
Fukuoka, Japan—In the continued effort to move humanity away from fossil fuels and towards more environmentally friendly energy sources, researchers in Japan have developed a new material capable storing hydrogen energy in a more efficient and cheaper manner. The new hydrogen energy carrier can even store said energy for up to three months at room temperature. Moreover, since the material is nickel based, its cost is relatively cheap. The results were reported in Chemistry—A European Journal.
As humanity combats the ongoing climate crisis, one avenue researchers focus on is the transition into alternative sources of energy such as hydrogen. For several decades now Kyushu University has been investigating ways to more efficiently use and store hydrogen energy in the effort to realize a carbon neutral society.
"We have been working on developing new materials that can store and transport hydrogen energy," explains Professor Seiji Ogo of Kyushu University's International Institute for Carbon-Neutral Energy Research who led the research team. "Transporting it in its gaseous state requires significant energy. An alternative way of storing and transporting it would be to 'split-up' the hydrogen atoms into its base components, electrons and protons."
Many candidates have been considered as possible hydrogen energy carries such as ammonia, formic acid, and metal hydrides. However, the final energy carrier had not yet been established.
"So, we looked to nature for hints. There are a series of enzymes called hydrogenases that catalyze hydrogen into protons and electrons and can store that energy for later use, even at room temperature," continues Ogo. "By studying these enzymes our team was able to develop a new compound that does exactly that."
Not only was their new compound able to extract and store electrons at room temperature, further investigations showed that it can be its own catalyst to extract said electron, something that had not been possible with previous hydrogen energy carriers. The team also showed that the energy could be stored for up the three months.
Ogo also highlights the fact that the compound uses an inexpensive element: nickel. Until now, similar catalysts have used expensive metals like platinum, rhodium, or iridium. Now that nickel is a viable option for hydrogen energy storage, it can potentially reduce the cost of future compounds.
The team intends to collaborate with the industrial sector to transfer their new findings into more practical applications.
"We would also like to work on improving storage time and efficiency as well as investigate the viability of cheaper metals for such compounds, " concludes Ogo. "Hopefully our findings will contribute to the goal of decarbonization so that we can build a greener and environmentally friendly future."
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For more information about this research, see "Single-Step Synthesis of NiI from NiII with H2," Chiaki Takahashi, Takeshi Yatabe, Hidetaka Nakai, and Seiji Ogo, Chemistry—A European Journal, https://doi.org/10.1002/chem.202302297
About Kyushu University Kyushu University is one of Japan's leading research-oriented institutes of higher education since its founding in 1911. Home to around 19,000 students and 8,000 faculty and staff, Kyushu U's world-class research centers cover a wide range of study areas and research fields, from the humanities and arts to engineering and medical sciences. Its multiple campuses—including one of the largest in Japan—are located around Fukuoka City, a coastal metropolis on the southwestern Japanese island of Kyushu that is frequently ranked among the world's most livable cities and historically known as Japan's gateway to Asia. Through its Vision 2030, Kyushu U will 'Drive Social Change with Integrative Knowledge.' Its synergistic application of knowledge will encompass all of academia and solve issues in society while innovating new systems for a better future.
Researchers at the Department of Energy’s Oak Ridge National Laboratory have improved flaw detection to increase confidence in metal parts that are 3D-printed using laser powder bed fusion. This type of additive manufacturing offers the energy, aerospace, nuclear and defense industries the ability to create highly specialized parts with complex shapes from a broad range of materials. However, the technology isn’t more widely used because it’s challenging to check the product thoroughly and accurately; conventional inspection methods may not find flaws embedded deep in the layers of a printed part.
ORNL researchers developed a method that combines inspection of the printed part after it is built with information collected from sensors during the printing process. The combined data then teaches a machine-learning algorithm to identify flaws in the product. Even more significantly, this framework allows operators to know the probability of accurate flaw detection just as reliably as traditional evaluation methods that demand more time and labor.
“We can detect flaw sizes of about half a millimeter — about the thickness of a business card – 90% of the time,” said ORNL researcher Luke Scime. “We’re the first to put a number value on the level of confidence possible for in situ (in process) flaw detection.” By extension, that reflects confidence in the product’s safety and reliability.
Laser powder bed fusion, the most common metal 3D-printing process, uses a high-energy laser to selectively melt metal powder that has been spread across a build plate. Then the build plate lowers before the system spreads and melts another layer, slowly building up the designed product.
Engineers know there will be flaws in the material.
“For regular manufacturing we know what those are and where and how to find them,” said ORNL researcher Zackary Snow. “(Operators) know the probability that they can detect flaws of a certain size, so they know how often to inspect to get a representative sample.”
3D printing has not benefited from the same confidence.
“Not having a number makes it hard to qualify and certify parts,” Snow said. “It’s one of the biggest hurdles in additive manufacturing.”
A paper by ORNL researchers and partner RTX, recently published in Additive Manufacturing, explains the process they developed to arrive at a 90% detection rate while reducing the probability of false positives, which can lead to scrapping good products.
For the first research step, aerospace and defense company RTX designed a part similar to one it already produces, providing opportunities to see realistic-looking flaws. Then, RTX 3D-printed the part multiple times monitoring during the build with a standard near-infrared camera and an added visible-light camera. Both RTX and ORNL researchers conducted quality inspections afterward using X-ray computed tomography, commonly called CT scans.
With consultation from RTX, ORNL additive manufacturing experts aligned the data into a layered stack of images, which essentially became the textbook for the machine-learning algorithm. During training, the algorithm took a first pass at labeling flaws using the CT scan images. Then a human operator annotated the rest based on visual cues in data collected during the printing process. Human feedback continues to train the software, so the algorithm recognizes flaws more accurately each time. Previous ORNL advances in in-situ monitoring and deep-learning frameworks were used as tools in this novel approach. Over time, this will reduce the need for human involvement in manufacturing inspection.
“This allows CT-level confidence without CT,” Snow said. A common method for checking some 3D-printed parts, CT imaging and analysis drives up costs because it requires extra time and expertise. Plus, CT cannot effectively penetrate dense metals, limiting its application.
When the algorithm is applied to a single design consistently manufactured with the same material and process, it can learn to provide consistent quality analysis within days, Scime said. At the same time, the software incorporates all that it learns from different designs and constructions, so it will eventually be able to accurately check products with unfamiliar designs.
The ORNL-developed inspection framework could help in expanding additive manufacturing applications. With statistically verified quality control, additive manufacturing could become viable for mass-producing products like car parts, Snow said.
It could also diversify the types of parts that can be 3D printed. Certainty about the smallest detectable flaw size allows more design freedom. This is important because the industry is already headed toward larger print volumes and faster print rates – meaning more lasers interacting to create bigger parts with different types of flaws, said Brian Fisher, senior principal engineer for additive manufacturing at RTX’s Raytheon Technologies Research Center.
“You can really start to save time and money and make a business case when printing larger assemblies – except those are also the hardest to inspect today,” Fisher said. “The vision is with additive, we can make large, highly-complex parts in very dense materials, which traditionally would be very difficult and expensive to thoroughly inspect.”
Next, the ORNL team will train the deep-learning algorithm to better differentiate between types of irregularities and to categorize flaws that have multiple causes.
Additional ORNL researchers who contributed to the project also include Amir Ziabari and Vincent Paquit. The research was sponsored by DOE's Advanced Materials and Manufacturing Technologies Office, or AMMTO, with support from RTX and took place at DOE's Manufacturing Demonstration Facility.
UT-Battelle manages ORNL for the Department of Energy’s Office of Science, the single largest supporter of basic research in the physical sciences in the United States. The Office of Science is working to address some of the most pressing challenges of our time. For more information, please visit energy.gov/science.
AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE (AAAS)
The Science and Science Careers’ 2023 Top Employers Survey polled employees in biotechnology, biopharmaceutical, pharmaceutical, and related industries to determine the 20 best employers as well as their driving characteristics. Respondents to the web-based survey were asked to rate companies based on 24 characteristics, including innovative leadership, respect for employees, and social responsibility.
Insmed, Bridgewater, New Jersey, receives the top honor in a ranking of the world’s most respected employers. The rankings, determined from a study conducted by an independent research firm commissioned by the Science/AAAS Office of Publishing, will appear in the October 27, 2023, print issue of Science and online at ScienceCareers.org.
Like Science and Science Careers’2022 ranking of biopharma employers (https://www.science.org/content/article/2022-s-top-employers-provide-safety-support-and-success-scientists), the 2023 survey sought to identify the companies with the best reputations as employers. The findings are based on more than 6,800 completed surveys from readers of Science,and other survey invitees. Survey respondents came from North America (59%), Europe (18%), Asia/Pacific Rim (16%), and other locations (7%). A vast majority (96%) of the respondents worked in biotechnology, biopharmaceutical, and pharmaceutical companies.
Survey responses were analyzed by The Brighton Consulting Group, which used a mathematical process to determine the driving characteristics of a top employer and to assign a unique score to rate each company’s employer reputation. Each company received a ranking, for example, on the basis of whether it is an innovative leader in the industry, and whether it treats employees with respect.
The American Association for the Advancement of Science (AAAS) is the world’s largest general scientific society and publisher of the journal Science, as well as Science Translational Medicine; Science Signaling; a digital, open-access journal, Science Advances; Science Immunology; and Science Robotics. AAAS was founded in 1848, and includes more than 250 affiliated societies and academies of science, serving 10 million individuals. The nonprofit AAAS is open to all and fulfills its mission to “advance science and serve society” through initiatives in science policy, international programs, science education, public engagement, and more.
Shape-shifting fiber can produce morphing fabrics
The low-cost FibeRobo, which is compatible with existing textile manufacturing techniques, could be used in adaptive performance wear or compression garments.
CAMBRIDGE, Mass. -- Instead of needing a coat for each season, imagine having a jacket that would dynamically change shape so it becomes more insulating to keep you warm as the temperature drops.
A programmable, actuating fiber developed by an interdisciplinary team of MIT researchers could someday make this vision a reality. Known as FibeRobo, the fiber contracts in response to an increase in temperature, then self-reverses when the temperature decreases, without any embedded sensors or other hard components.
The low-cost fiber is fully compatible with textile manufacturing techniques, including weaving looms, embroidery, and industrial knitting machines, and can be produced continuously by the kilometer. This could enable designers to easily incorporate actuation and sensing capabilities into a wide range of fabrics for myriad applications, such as programmable compression garments that could aid in post-surgery recovery.
The fibers can also be combined with conductive thread, which acts as a heating element when electric current runs through it. In this way, the fibers actuate using electricity, which offers a user digital control over a textile’s form. For instance, a fabric could change shape based on any piece of digital information, such as readings from a heart rate sensor.
“We use textiles for everything. We make planes with fiber-reinforced composites, we cover the International Space Station with a radiation-shielding fabric, we use them for personal expression and performance wear. So much of our environment is adaptive and responsive, but the one thing that needs to be the most adaptive and responsive — textiles — is completely inert,” says Jack Forman, a graduate student in the Tangible Media Group and the Center for Bits and Atoms in the MIT Media Lab, and lead author of a paper on the actuating fiber.
He is joined on the paper by 11 other researchers at MIT and Northeastern University, including his advisors, Professor Neil Gershenfeld, who leads the Center for Bits and Atoms, and Hiroshi Ishii, the Jerome B. Wiesner Professor of Media Arts and Sciences and director of the Tangible Media Group. The research will be presented at the ACM Symposium on User Interface Software and Technology.
Morphing materials
Current shape-changing fibers have pitfalls that have largely prevented them from being incorporated into textiles beyond laboratory settings.
One fiber, known as a shape-changing alloy, only contracts by about 5 percent, doesn’t self-reverse, and often stops working after a handful of actuations. Another, called a McKibben actuator, is pneumatically driven and requires an air compressor to actuate.
The MIT researchers wanted a fiber that could actuate silently and change its shape dramatically, while being compatible with common textile manufacturing procedures. To achieve this, they used a material known as liquid crystal elastomer (LCE).
A liquid crystal is a series of molecules that can flow like liquid, but when they’re allowed to settle, they stack into a periodic crystal arrangement. The researchers incorporate these crystal structures into an elastomer network, which is stretchy like a rubber band.
As the LCE material heats up, the crystal molecules fall out of alignment and pull the elastomer network together, causing the fiber to contract. When the heat is removed, the molecules return to their original alignment, and the material to its original length, Forman explains.
By carefully mixing chemicals to synthesize the LCE, the researchers can control the final properties of the fiber, such as its thickness or the temperature at which it actuates.
They perfected a preparation technique that creates LCE fiber which can actuate at skin-safe temperatures, making it suitable for wearable fabrics. Researchers had been unable to accomplish this with other LCE fibers, Forman says.
“There are a lot of knobs we can turn. It was a lot of work to come up with this process from scratch, but ultimately it gives us a lot of freedom for the resulting fiber,” he adds.
However, the researchers discovered that making fiber from LCE resin is a finicky process. Existing techniques often result in a fused mass that is impossible to unspool.
Forman built a machine using 3D-printed and laser-cut parts and basic electronics to overcome the fabrication challenges. He initially built the machine as part of the graduate-level course MAS.865 (Rapid-Prototyping of Rapid-Prototyping Machines: How to Make Something that Makes (almost) Anything).
To begin, the thick and viscous LCE resin is heated, and then slowly squeezed through a nozzle like that of a glue gun. As the resin comes out, it is cured carefully using UV lights that shine on both sides of the slowly extruding fiber.
If the light is too dim, the material will separate and drip out of the machine, but if it is too bright, clumps can form, which yields bumpy fibers.
Then the fiber is dipped in oil to give it a slippery coating and cured again, this time with UV lights turned up to full blast, creating a strong and smooth fiber. Finally, it is collected into a top spool and dipped in powder so it will slide easily into machines for textile manufacturing.
From chemical synthesis to finished spool, the process takes about a day and produces approximately a kilometer of ready-to-use fiber.
“At the end of the day, you don’t want a diva fiber. You want a fiber that, when you are working with it, falls into the ensemble of materials — one that you can work with just like any other fiber material, but then it has a lot of exciting new capabilities,” Forman says.
Creating such a fiber took a great deal of trial and error, as well as the collaboration of researchers with expertise in many disciplines, from chemistry to mechanical engineering to electronics to design.
The resulting fiber, called FibeRobo, can contract up to 40 percent without bending, actuate at skin-safe temperatures, and be produced with a low-cost setup for 20 cents per meter, which is about 60 times cheaper than commercially available shape-changing fibers.
The fiber can be incorporated into industrial sewing and knitting machines, as well as nonindustrial processes like hand looms or manual crocheting, without the need for any process modifications.
The MIT researchers used FibeRobo to demonstrate several applications, including an adaptive sports bra made by embroidery that tightens when the user begins exercising.
They also used an industrial knitting machine to create a compression jacket for Forman’s dog, whose name is Professor. The jacket would actuate and “hug” the dog based on a Bluetooth signal from Forman’s smartphone. Compression jackets are commonly used to alleviate the separation anxiety a dog can feel while its owner is away.
In the future, the researchers want to adjust the fiber’s chemical components so it can be recyclable or biodegradable. They also want to streamline the polymer synthesis process so users without wet lab expertise could make it on their own.
Forman is excited to see the FibeRobo applications other research groups identify as they build on these early results. In the long run, he hopes FibeRobo can become something a maker could buy in a craft store, just like a ball of yarn, and use to easily produce morphing fabrics.
This research was supported, in part, by the William Asbjornsen Albert Memorial Fellowship, the Dr. Martin Luther King Jr. Visiting Professor Program, Toppan Printing Co., Honda Research, Chinese Scholarship Council, and Shima Seiki. The team included Ozgun Kilic Afsar, Sarah Nicita, Rosalie (Hsin-Ju) Lin, Liu Yang, Akshay Kothakonda, Zachary Gordon, and Cedric Honnet at MIT; and Megan Hofmann and Kristen Dorsey at Northeastern University.
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Written by Adam Zewe, MIT News
Paper: “FibeRobo: Fabricating 4D Fiber Interfaces by Continuous Drawing of Temperature Tunable Liquid Crystal Elastomers”
* Multimodal means the process by which information is exchanged through various sensory interfaces such as visual sensation and auditory sensation.
The joint research team led by Principal Researcher Soongeun Kwon of the Department of Nano Manufacturing Technology of the Korea Institute of Machinery and Materials (President Sang-jin Park, hereinafter referred to as KIMM), an institute under the jurisdiction of the Ministry of Science and ICT, and Professor Young-Jin Kim of the Department of Mechanical Engineering of the Korea Advanced Institute of Science and Engineering (President Kwang-hyung Lee, hereinafter referred to as KAIST) developed graphene-based, customized e-textiles for the first time in the world, and published the findings in “ACS Nano (IF = 18.027),” a renowned scientific journal.
*Title of publication: “Multimodal E-Textile Enabled by One-Step Maskless Patterning of Femtosecond-Laser-Induced Graphene on Nonwoven, Knit, and Woven Textiles (2023.10.10.)”
Instead of using toxic chemicals or optical masks for patterning, the joint research team used the laser direct patterning technology* to form laser-induced graphene (LIG) on e-textiles and successfully manufactured graphene-based e-textiles. * Laser direct patterning technology refers to the technology used for making patterns for functional materials by irradiating laser onto the surface of the garment so that the materials of only the parts reached by the laser are converted. * When high-power laser is irradiated to the surface of a polymer film or a garment, the light energy is converted into thermal energy on the surface and a carbon material is instantly fabricated on the part where the laser is irradiated. This is called laser-induced graphene (LIG), as the crystal structure of the fabricated carbon material is similar to graphene, a two-dimensional nanomaterial.
Conventionally, e-textiles have been manufactured by coating fabrics with conductive ink to make electrically conductive textiles and then weaving them with generic fabrics, or by attaching a thin, functional layer onto generic fabrics. These methods have a low design flexibility and high process complexity. Moreover, harmful chemicals may be leaked during the manufacturing process, which places a limitation on mass production.
By using the newly developed technology, high-quality LIG materials that have world-class electrical conductivity can be manufactured simply by irradiating laser onto the surface of fabrics. A major advantage of this technology is that e-textiles can be manufactured in an environmentally friendly manner, as neither the use of chemicals nor any additional processing is required. Meanwhile, the world-class electrical conductivity of LIG electrodes has been realized by applying the femtosecond laser processing technology*. * Femtosecond laser processing technology is the technology for fabricating materials using ultrashort laser that has an extremely short pulse width and a high peak power. Compared with other lasers, this technology causes almost no damage to the materials and, therefore, is useful for making high resolution patterns.
The newly developed technology can be used in the future for manufacturing industrial and military clothes for personal health management and also for producing customized “smart” clothes in the healthcare sector.
Principal Researcher Soongeun Kwon of the KIMM was quoted as saying, “This technology has been developed by analyzing the structures of generic fabrics and realizing them as graphene-based materials that have advanced features of optimal e-textiles.” He added, “This technology is significantly meaningful in that it allows for the mass production of customized e-textiles using an environment-friendly and simple method.”
Meanwhile, this research was carried out with the support of the project for the “development of nano-based “Omni-TEX” manufacturing technologies,” one of the KIMM’s basic projects.
A cover image of the journal paper published in ACS Nano
CREDIT
Korea Institute of Machinery and Materials (KIMM)
The Korea Institute of Machinery and Materials (KIMM) is a non-profit government-funded research institute under the Ministry of Science and ICT. Since its foundation in 1976, KIMM is contributing to economic growth of the nation by performing R&D on key technologies in machinery and materials, conducting reliability test evaluation, and commercializing the developed products and technologies.
This research was carried out with the support of the project for the “development of nano-based “Omni-TEX” manufacturing technologies,” one of the KIMM’s basic projects.
An electron moving through a solid generates a polarization in its environment due to its electric charge. In his theoretical considerations, the Russian physicist Lev Landau extended the description of such particles by their interaction with the environment and spoke of quasiparticles. More than ten years ago, the team led by Rudolf Grimm at the Institute of Quantum Optics and Quantum Information (IQQOI) of the Austrian Academy of Sciences (ÖAW) and the Department of Experimental Physics of the University of Innsbruck succeeded in generating such quasiparticles for both attractive and repulsive interactions with the environment. For this purpose, the scientists use an ultracold quantum gas consisting of lithium and potassium atoms in a vacuum chamber. With the help of magnetic fields, they control the interactions between the particles, and by means of radio-frequency pulses push the potassium atoms into a state in which they attract or repel the lithium atoms surrounding them. In this way, the researchers simulate a complex state similar to the one produced in the solid state by a free electron.
A Closer Look at Solids
Now, the scientists led by Rudolf Grimm have been able to generate several such quasiparticles simultaneously in the quantum gas and observe their interactions with each other. „In a naive notion, one would assume that polarons always attract each other, regardless of whether their interaction with the environment is attractive or repulsive,” says the experimental physicist. „However, this is not the case. We see attractive interaction in bosonic polarons, repulsive interaction in fermionic polarons. Here, quantum statistics plays a crucial role.” The researchers have now been able to demonstrate this behavior, which in principle already follows as a consequence of Landau's theory, in an experiment for the first time. The theoretical calculations for this were done by colleagues from Mexico, Spain and Denmark. „High experimental skills were required to implement this in the laboratory”, explains Cosetta Baroni, first author of the study, “because even the smallest deviations could have skewed the measurements.”
“Such investigations provide us with insights into very fundamental mechanisms of nature and offer us excellent opportunities to study them in detail,” says Rudolf Grimm excitedly.