Suramya's Blog : Welcome to my crazy life…

June 14, 2021

New technique Lets Users Preview Files Stored in DNA Data Storage

Filed under: Computer Hardware,Emerging Tech,Science Related,Tech Related — Suramya @ 7:45 AM

Using DNA for storage is an idea that has been around for a while with the initial idea of DNA storage being postulated by Richard P. Feynman in 1959. It was mostly a theoretical exercise till 1988, when researchers from Harvard and the artist Joe Davis stored an image of an ancient Germanic rune representing life and the female Earth in the DNA sequence of E.coli. After that In November 2016 (Lot more stuff happened between the two dates and you can read it all on the Wiki page), a company called Catalog encoded 144 words from Robert Frost’s famous poem, “The Road Not Taken” into strands of DNA. Pretty soon after that in June 2019, scientists reported that all 16 GB of text from Wikipedia’s English-language version have been encoded into synthetic DNA.

DNA storage has been becoming easier and cheaper as time goes on with more and more companies getting on the bandwagon. Even Microsoft has a DNA Storage Research project. However, even with all the advances so far there is a lot more work required before this becomes stable, cheap and reliable enough to be a commercial product. One of the problems that we faced with the storage in the past was that it wasn’t possible to preview the data stored in DNA. You had to open the entire file if you wanted to know what was in it. Think of trying to browse an image gallery without thumbnails, you would have to open each file to see what it was when trying to find a particular file.

Researchers from North Carolina State University have developed a way to provide previews of a stored data file similar to how a thumbnail works for image files. Basically they used the fact that when files have similar file names then the system will copy pieces of multiple data files. Till now this was a problem but the researchers figured out how to use this behavior to allow them to either open the entire file or a subset.

“The advantage to our technique is that it is more efficient in terms of time and money,” says Kyle Tomek, lead author of a paper on the work and a Ph.D. student at NC State. “If you are not sure which file has the data you want, you don’t have to sequence all of the DNA in all of the potential files. Instead, you can sequence much smaller portions of the DNA files to serve as previews.”

Here’s a quick overview of how this works.

Users “name” their data files by attaching sequences of DNA called primer-binding sequences to the ends of DNA strands that are storing information. To identify and extract a given file, most systems use polymerase chain reaction (PCR). Specifically, they use a small DNA primer that matches the corresponding primer-binding sequence to identify the DNA strands containing the file you want. The system then uses PCR to make lots of copies of the relevant DNA strands, then sequences the entire sample. Because the process makes numerous copies of the targeted DNA strands, the signal of the targeted strands is stronger than the rest of the sample, making it possible to identify the targeted DNA sequence and read the file.

However, one challenge that DNA data storage researchers have grappled with is that if two or more files have similar file names, the PCR will inadvertently copy pieces of multiple data files. As a result, users have to give files very distinct names to avoid getting messy data.

“At some point it occurred to us that we might be able to use these non-specific interactions as a tool, rather than viewing it as a problem,” says Albert Keung, co-corresponding author of a paper on the work and an assistant professor of chemical and biomolecular engineering at NC State.

Specifically, the researchers developed a technique that makes use of similar file names to let them open either an entire file or a specific subset of that file. This works by using a specific naming convention when naming a file and a given subset of the file. They can choose whether to open the entire file, or just the “preview” version, by manipulating several parameters of the PCR process: the temperature, the concentration of DNA in the sample, and the types and concentrations of reagents in the sample.

The new technique is compatible with the DNA Enrichment and Nested Separation (DENSe) system that enables us to make DNA storage systems more scalable. The researchers are looking for industry partners to explore commercial viability. If things work out then maybe in the near future we could start storing data in biological samples (like spit). Although, it does sound gross to be handling spit and other bio matter when searching for saved data.

Source: New Twist on DNA Data Storage Lets Users Preview Stored Files
Paper: Nature.com: Promiscuous molecules for smarter file operations in DNA-based data storage

– Suramya

May 16, 2021

Tiny, Wireless, Injectable Chips created to monitor body functions

Filed under: Emerging Tech,Science Related — Suramya @ 9:10 PM

Injectable chips have long been the boogyman for Anti-Vaxers as they think that people (like Bill Gates) are injecting them with tracking chips to track them and modify their behavior. However, till now this was mostly in the realm of Science Fiction as the smallest chips we had were still quite visible and difficult to power or inject (which is why they were implanted). Now, Researchers at Columbia Engineering have created the world’s smallest single chip system that is small enough that it is only visible under a microscope and is powered using Ultrasonic sound.

This is a great achievement because having injectable chips brings us closer to functioning nano-tech and these chips can be used to monitor physiological conditions, such as temperature, blood pressure, glucose levels, and respiration etc.

These devices could be used to monitor physiological conditions, such as temperature, blood pressure, glucose, and respiration for both diagnostic and therapeutic procedures. To date, conventional implanted electronics have been highly volume-inefficient — they generally require multiple chips, packaging, wires, and external transducers, and batteries are often needed for energy storage… Researchers at Columbia Engineering report that they have built what they say is the world’s smallest single-chip system, consuming a total volume of less than 0.1 mm cubed. The system is as small as a dust mite and visible only under a microscope…

“We wanted to see how far we could push the limits on how small a functioning chip we could make,” said the study’s leader Ken Shepard, Lau Family professor of electrical engineering and professor of biomedical engineering. “This is a new idea of ‘chip as system’ — this is a chip that alone, with nothing else, is a complete functioning electronic system. This should be revolutionary for developing wireless, miniaturized implantable medical devices that can sense different things, be used in clinical applications, and eventually approved for human use….”

The chip, which is the entire implantable/injectable mote with no additional packaging, was fabricated at the Taiwan Semiconductor Manufacturing Company with additional process modifications performed in the Columbia Nano Initiative cleanroom and the City University of New York Advanced Science Research Center (ASRC) Nanofabrication Facility. Shepard commented, “This is a nice example of ‘more than Moore’ technology—we introduced new materials onto standard complementary metal-oxide-semiconductor to provide new function. In this case, we added piezoelectric materials directly onto the integrated circuit to transducer acoustic energy to electrical energy….” The team’s goal is to develop chips that can be injected into the body with a hypodermic needle and then communicate back out of the body using ultrasound, providing information about something they measure locally.

The current devices measure body temperature, but there are many more possibilities the team is working on.

The only downside is that the anti-vaxers are going to use this as proof that the ‘Government’ is controlling their brains or tracking them. Never mind the fact that they can track you much more easily using the phone you carry everywhere or using the camera’s that are now almost everywhere.

The study was published online in Science Advances: Application of a sub–0.1-mm3 implantable mote for in vivo real-time wireless temperature sensing.

Thanks to Slashdot for the link.

– Suramya

May 15, 2021

Providing Oxygen through the intestines in Mammals is now possible as per research

Filed under: My Thoughts,News/Articles,Science Related — Suramya @ 11:53 PM

It takes a certain kind of mind to decide that today I am going to experiment if mammals can absorb oxygen through their intestines. Apparently a some of the aquatic animals like sea cucumbers and catfish, breathe through their intestines and since humans can absorb medicines through their intestines Takanori Takebe, a gastroenterologist from Cincinnati Children’s Hospital decided to do a study to see if they can absorb oxygen as well. So to test this out they basically injected pure pressurized oxygen into the rectums of the scrubbed mice (the mucus layer was thinned) and four of the seven unscrubbed ones. There was an immediate improvement in the O2 levels of the mice, with 75% the scrubbed mice surviving the procedure.

Obviously that is not a great survival rate and the scrubbing procedure is dangerous/involved but it did prove that mammals can absorb o2 with their intestines. So they looked at using perfluorocarbons which have a high O2 level and giving the rats & pigs an enema of the fluid. They saw an almost 15% improvement in the blood oxygen saturation allowing the subjects to recover from hypoxia.

These two tests prove that mammals can breath through their intestine but there is still a lot of study that needs to be done to check for the safety of this procedure. But if things go smoothly we can be looking at a new way to provide oxygen to patients when O2 canisters are in limited supply like the case currently in India due to the Covid crises.

But this doesn’t mean that mouth to mouth CPR will be replaced with mouth to ass CPR. (I can hear the sigh of relief from medical professional/emergency care folks).

More details on the study: ScienceMag: Mammals can breathe through their intestines
Full Paper: Mammalian enteral ventilation ameliorates respiratory failure

– Suramya

May 12, 2021

Using a centrifuge to improve a compressor

Filed under: My Thoughts,Science Related — Suramya @ 11:19 PM

A compressor is such a standard piece of equipment that we no longer think about it and it is used everywhere from pumps to air conditioners. If we can improve the design then it can lead to a huge power savings. A California company (Carnot) has come up with a new design that reduces the noise output, lasts longer and reduces the cost of ownership by 20 percent while using no oil. The new design uses a Trompe and combines it with a centrifuge to get it to work more efficiently.

A Trompe is an ancient technology which uses falling water to compress air. It was used extensively till fossil fuels made it less desirable by producing more power. Historically, miners have used large-scale trompes to power their mining equipment and provided ventilation. In fact a 350-feet-deep trompe was setup in Michigan which was able to produce 5,000 horsepower.

A trompe, often placed in a river, has a simple design. Flowing water falls into an intake pipe which has an air cone (or some other aerating device) on top. The water falling around the cone creates suction, pulling the air down with it. Air bubbles travel down the pipe with the water until reaching an air chamber.

At the air chamber (also called a plenum or reservoir), the bubbles escape from the water. In the process, the air has been compressed, dehumidified, and cooled to the same temperature as the water. The pressurized air can now be put to use.

Meanwhile, the water leaves through the outtake pipe. Air pressure from the reservoir pushes the water upwards, nearly to the same height it originally fell from, and the water returns to the river.

The issue with Trompe is that it needs a large setup if we want to generate enough compression and that is obviously not possible in all places. So the Carnot team explored options to accelerate the water movement and arrived at using a centrifuge. In their setup the compressor sucks in air through a filter at the top and mixes it with water on top of a fast moving drum, this outward force compresses the air and the mixture of air & water is forced out at that bottom where they are separated into air and water as they pass through the exit channel. The image below gives a good overview of how the technology would work:


Model of Carnot compressor

The resultant compressor is very quiet since the only moving parts are the spinning drum powered by an electric motor and an exhaust fan. In lab tests the system was found to operate indoors at below 70 dB. Obviously the technology is still quite new and needs to mature a lot before bulk deployment, but it is very interesting and I see a great future for it if it works as advertised.

Source: Carnot puts a centrifugal spin on a 500-year-old air compressor design
The Trompe: A Basic Overview

– Suramya

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