Open-Source LAMP Instrument Aimed At Clinicians And Biohackers Alike

Over the last few years, we’ve all been given a valuable lesson in both the promise and limitations of advanced molecular biology methods for clinical diagnostics. Polymerase chain reaction (PCR) was held up as the “gold standard” of COVID-19 testing, but the cost, complexity, and need for advanced instrumentation and operators with specialized training made PCR difficult to scale to the levels demanded by a pandemic.

There are other diagnostic methods, of course, some of which don’t have all the baggage of PCR. RT-LAMP, or reverse transcriptase loop-mediated amplification, is one method with a lot of promise, especially when it can be done on a cheap open-source instrument like qLAMP. For about 50€, qLAMP makes amplification and detection of nucleic acids, like the RNA genome of the SARS-CoV-2 virus, a benchtop operation that can be performed by anyone. LAMP is an isothermal process; it can be done at one single temperature, meaning that no bulky thermal cycler is required. Detection is via the fluorescent dye SYTO 9, which layers into the base pairs inside the amplified DNA strands, using a 470-nm LED for excitation and a photodiode with a filter to detect the emission. Heating is provided by a PCB heater and a 3D-printed aluminum block that holds tubes for eight separate reactions. Everything lives in a 3D-printed case, including the ESP32 which takes care of all the housekeeping and data analysis duties.

With the proper test kits, which cost just a couple of bucks each, qLAMP would be useful for diagnosing a wide range of diseases, and under less-than-ideal conditions. It could also be a boon to biohackers, who could use it for their own citizen science efforts. We saw a LAMP setup at the height of the pandemic that used the Mark 1 eyeball as a detector; this one is far more quantitative.

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Hackaday Links: October 23, 2022

There were strange doings this week as Dallas-Forth Worth Airport in Texas experienced two consecutive days of GPS outages. The problem first cropped up on the 17th, as the Federal Aviation Administration sent out an automated notice that GPS reception was “unreliable” within 40 nautical miles of DFW, an area that includes at least ten other airports. One runway at DFW, runway 35R, was actually closed for a while because of the anomaly. According to GPSjam.org — because of course someone built a global mapping app to track GPS coverage — the outage only got worse the next day, both spreading geographically and worsening in some areas. Some have noted that the area of the outage abuts Fort Hood, one of the largest military installations in the country, but there doesn’t appear to be any connection to military operations. The outage ended abruptly at around 11:00 PM local time on the 19th, and there’s still no word about what caused it. Loss of GPS isn’t exactly a “game over” problem for modern aviation, but it certainly is a problem, and at the very least it points out how easy the system is to break, either accidentally or intentionally.

In other air travel news, almost as quickly as Lufthansa appeared to ban the use of Apple AirTags in checked baggage, the airline reversed course on the decision. The original decision was supposed to have been based on “an abundance of caution” regarding the potential for disaster from its low-power transmitters, or should a stowed AirTag’s CR2032 battery explode. But as it turns out, the Luftfahrt-Bundesamt, the German civil aviation authority, agreed with the company’s further assessment that the tags pose little risk, green-lighting their return to the cargo compartment. What luck! The original ban totally didn’t have anything to do with the fact that passengers were shaming Lufthansa online by tracking their bags with AirTags while the company claimed they couldn’t locate them, and the sudden reversal is unrelated to the bad taste this left in passengers’ mouths. Of course, the reversal only opened the door to more adventures in AirTag luggage tracking, so that’s fun.

Energy prices are much on everyone’s mind these days, but the scale of the problem is somewhat a matter of perspective. Take, for instance, the European Organization for Nuclear Research (CERN), which runs a little thing known as the Large Hadron Collider, a 27-kilometer-long machine that smashes atoms together to delve into the mysteries of physics. In an average year, CERN uses 1.3 terawatt-hours of electricity to run the LHC and its associated equipment. Technically, this is what’s known as a hell of a lot of electricity, and given the current energy issues in Europe, CERN has agreed to shut down the LHC a bit early this year, shutting down in late November instead of the usual mid-December halt. What’s more, CERN has agreed to reduce usage by 20% next year, which will increase scientific competition for beamtime on the LHC. There’s only so much CERN can do to reduce the LHC’s usage, though — the cryogenic plant to cool the superconducting magnets draws a whopping 27 megawatts, and has to be kept going to prevent the magnets from quenching.

And finally, as if the COVID-19 pandemic hasn’t been weird enough, the fact that it has left in its wake survivors whose sense of smell is compromised is alarming. Our daily ritual during the height of the pandemic was to open up a jar of peanut butter and take a whiff, figuring that even the slightest attenuation of the smell would serve as an early warning system for symptom onset. Thankfully, the alarm hasn’t been tripped, but we know more than a few people who now suffer from what appears to be permanent anosmia. It’s no joke — losing one’s sense of smell can be downright dangerous; think “gas leak” or “spoiled food.” So it was with interest that we spied an article about a neuroprosthetic nose that might one day let the nasally challenged smell again. The idea is to use an array of chemical sensors to stimulate an array of electrodes implanted near the olfactory bulb. It’s an interesting idea, and the article provides a lot of fascinating details on how the olfactory sense actually works.

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Hackaday Links: June 12, 2022

“Don’t worry, that’ll buff right out.” Alarming news this week as the James Webb Space Telescope team announced that a meteoroid had hit the space observatory’s massive primary mirror. While far from unexpected, the strike on mirror segment C3 (the sixth mirror from the top going clockwise, roughly in the “south southeast” position) that occurred back in late May was larger than any of the simulations or test strikes performed on Earth prior to launch. It was also not part of any known meteoroid storm in the telescope’s orbit; if it had been, controllers would have been able to maneuver the spacecraft to protect the gold-plated beryllium segments. The rogue space rock apparently did enough damage to be noticeable in the data coming back from the telescope and to require adjustment to the position of the mirror segment. While it certainly won’t be the last time this happens, it would have been nice to see one picture from Webb before it started accumulating hits.

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Remoticon 2021 // Vaibhav Chhabra And The M19 Collective Make One Million Faceshields

[Vaibhav Chhabra], the co-founder of Maker’s Asylum hackerspace in Mumbai, India, starts his Remoticon talk by telling a short story about how the hackerspace rose to its current status. Born out of frustration with a collapsed office ceiling, having gone through eight years of moving and reorganizations, it accumulated a loyal participant base – not unusual with hackerspaces that are managed well. This setting provided a perfect breeding ground for the M19 effort when COVID-19 reached India, mixing “what can we do” and “what should we do” inquiries into a perfect storm and starting the 49 day work session that swiftly outgrew the hackerspace, both physically and organizationally.

When the very first two weeks of the Infinite Two Week Quarantine Of 2020 were announced in India, a group of people decided to wait it out at the hackerspace instead of confining themselves to their homes. As various aspects of our society started crashing after the direct impact of COVID-19, news came through – that of a personal protective equipment shortage, especially important for frontline workers. Countries generally were not prepared when it came to PPE, and India was no different. Thus, folks in Maker’s Asylum stepped up, finding themselves in a perfect position to manufacture protective equipment when nobody else was prepared to help.

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flow chart for Assessment of the Feasibility of Using Noninvasive Wearable Biometric Monitoring Sensors to Detect Influenza and the Common Cold Before Symptom Onset paper

Wearables Can Detect The Flu? Well…Maybe…

Surprisingly there are no pre-symptomatic screening methods for the common cold or the flu, allowing these viruses to spread unbeknownst to the infected. However, if we could detect when infected people will get sick even before they were showing symptoms, we could do a lot more to contain the flu or common cold and possibly save lives. Well, that’s what this group of researchers in this highly collaborative study set out to accomplish using data from wearable devices.

Participants of the study were given an E4 wristband, a research-grade wearable that measures heart rate, skin temperature, electrodermal activity, and movement. They then wore the E4 before and after inoculation of either influenza or rhinovirus. The researchers used 25 binary, random forest classification models to predict whether or not participants were infected based on the physiological data reported by the E4 sensor. Their results are pretty lengthy, so I’ll only highlight a few major discussion points. In one particular analysis, they found that at 36 hours after inoculation their model had an accuracy of 89% with a 100% sensitivity and a 67% specificity. Those aren’t exactly world-shaking numbers, but something the researchers thought was pretty promising nonetheless.

One major consideration for the accuracy of their model is the quality of the data reported by the wearable. Namely, if the data reported by the wearable isn’t reliable itself, no model derived from such data can be trustworthy either. We’ve discussed those points here at Hackaday before. Another major consideration is the lack of a control group. You definitely need to know if the model is simply tagging everyone as “infected” (which specificity does give us an idea of, to be fair) and a control group of participants who have not been inoculated with either virus would be one possible way to answer that question. Fortunately, the researchers admit this limitation of their work and we hope they will remedy this in future studies.

Studies like this are becoming increasingly common and the ongoing pandemic has motivated these physiological monitoring studies even further. It seems like wearables are here to stay as the academic research involving these devices seems to intensify each day. We’d love to see what kind of data could be obtained by a community-developed device, as we’ve seen some pretty impressive DIY biosensor projects over the years.

ETH0 Autumn 2021: Tiny Camp Manages COVID Precautions Indoors

It’s tempting despite news of stubbornly higher-than-ideal COVID infection figures, to imagine that just maybe the world might be returning to some semblance of pre-pandemic normality. Where this is being written we’re a largely vaccinated population long out of lockdown, and though perhaps some of the pandemic pronouncements of our politicians are a bit suspect we’re cautiously able to enjoy most of life’s essentials. Visiting the supermarket and having a beer might be one thing, but the effect of the pandemic is still being felt in our community’s gatherings. BornHack went ahead this summer, but the headline MCH hacker camp was put off until 2022 and the upcoming CCC Congress in Germany is once more to be a virtual event.

But some events manage to put together the right mix of precaution and size. Such was the case with ETH0, a hacker camp which I was happy to attend last weekend.

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Electronic Covid Test Tear Down Shows Frustrating Example Of 1-Time-Use Waste

The latest video from [TheSignalPath] is a result of his purchase of a home COVID-19 test. He found an electronic version that connects to your cell phone and displays the results on the phone. The device is an antigen test and, internally, works like the home tests that show the results using lines similar to a pregnancy test. So, somehow, the phone version reads the lines and communicates with the phone. But how? That’s the point of the video, which you can see below.

In a traditional test, there’s a control line that has to appear to show that the test was done correctly. Then a line under that indicates detection of the virus. The circuit board inside the electronic test has a plastic unit onboard that contains a similar strip and has optical sensors for both the reference line and the detection line. Since it is essentially an optical device — there are some lenses in the strip assembly that look like they are detecting the dye as it moves through the strip with LEDs onboard to shed light on the situation.

Under the microscope, the CPU is a typical Bluetooth-capable ARM chip from Nordic. The board did power up, but the device is made to only operate once because of the test strip. The video notes — and we agree — it seems wasteful to create an entire Bluetooth-enabled microcontroller board with optical components just to read a strip one time that is pretty easy to read to start with. We’ll stick with the simple test strip. Still, it is interesting to see the insides.

If you want to read more about antigen tests, we covered that. We also talked about PCR testing.

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