Tag Archives: test

New, fast and high-accuracy test developed for COVID-19 infections

Researchers at the University of Washington have developed a new COVID-19 test that has the speed of over-the-counter antigen tests and the accuracy of medical-grade PCR tests.

Image credits Nuttada Panpradist et al., (2022), Science Advances.

Dubbed the ‘Harmony’ test, this diagnostic tool looks for the genetic material of the SARS-CoV-2 virus in test samples. However, unlike PCR tests, which can take several hours to produce a result, the Harmony kit can provide a diagnosis in under 20 minutes with high accuracy.

The test was designed to be low-cost and straightforward to use, according to the authors, in a bid to help everyone, from doctors to the public, to better detect and track coronavirus infections.

New tools

“We designed the test to be low-cost and simple enough that it could be used anywhere,” said Barry Lutz, a UW associate professor of bioengineering, an investigator with the Brotman Baty Institute for Precision Medicine, and senior author of the paper. “We hope that the low cost will make high-performance testing more accessible locally and around the world.”

The Harmony test uses a “PCR-like” approach to detecting the virus — samples are obtained using a nasal swab and processed with ready-to-use reagents using a series of simple steps. The kit is meant to be used with a low-cost detector that can be operated using a smartphone, which provides the results. Each detector can handle up to four samples at a time.

The team explains that one of their main reasons for designing this test kit was the need for affordable and easy-to-use COVID-19 tests that provide reliable accuracy. Many at-home antigen kits available today test for pieces of the virus, not traces of its genetic material, and are only about 80-85% accurate and may be less accurate with the Omicron strain. PCR (polymerase chain reaction) tests are much better — providing around 95% accuracy — but are slow and cannot be carried out at home, as they require specialized devices and training to process. The Harmony kit is meant to combine the strengths of both of these types of tests.

Preliminary results show that Harmony is 97% accurate for nasal swabs. The test detects three different regions of the virus’ genome to help keep it effective against new strains: if a new variant of the virus develops many mutations in one region, the test can still detect the other two. The Harmony kit can detect the Omicron strain.

The step that makes PCR tests so time- and technology-intensive is a series of a few dozen heating and cooling cycles. Temperatures need to be very accurately controlled during these cycles to maintain the integrity of the sample. The Harmony test uses a similar method, known as RT-LAMP (reverse transcription loop-mediated isothermal amplification), with the key difference being that this doesn’t require the same temperature cycling.

“This test operates at a constant temperature, so it eliminates the time to heat and cool and gives results in about 30 minutes,” said Lutz.

Together with two of his colleagues, Lutz set up a new company for the UW — Anavasi Diagnostics — which will take the Harmony kit from an experimental device to a commercially-available product. The team believes that the kit will first be available for clinics and other medical institutions, then in settings where monitoring for infections is required, such as workplaces or schools. After these needs are met, they will adapt the test for home use.

“For a long time, the options have been either a PCR test that is expensive and typically takes a day or more to get a result, or a rapid antigen test that gives fast results and is low cost, but typically has lower accuracy than a lab PCR test,” said Lutz. “From the first day, we designed our test to be manufacturable at low cost and high volume, while delivering fast results with PCR-like performance.”

“We plan to make our test accessible and affordable throughout the world,” he adds.

The paper “Harmony COVID-19: A ready-to-use kit, low-cost detector, and smartphone app for point-of-care SARS-CoV-2 RNA detection” has been published in the journal Science Advances.

A novel blood test can detect the presence of cancer, and whether it’s metastasized

A candidate for a cheap and simple blood test for cancer has shown promise in early tests. The findings point the way towards such a procedure which, in the future, could become a widely available method of screening patients at risk of various types of cancer.

Image credits Fernando Zhiminaicela.

The test is non-specific — it can be used to detect the presence of a wide range of cancer types — and provides doctors with quick and reliable information on whether it has metastasized (spread) throughout the patient’s body.

Quick and easy

“Cancer cells have unique metabolomic fingerprints due to their different metabolic processes. We are only now starting to understand how metabolites produced by tumors can be used as biomarkers to accurately detect cancer” says Dr. James Larkin from the University of Oxford, first author of the study.

“We have already demonstrated that this technology can successfully identify if patients with multiple sclerosis are progressing to the later stages of disease, even before trained clinicians could tell. It is very exciting that the same technology is now showing promise in other diseases, like cancer.”

The study worked with samples harvested from 300 patients that were showing non-specific cancer symptoms, including fatigue and weight loss. All participants were recruited through the Oxfordshire Suspected CANcer (SCAN) Diagnostic Pathway. It involved the researchers assessing whether their test could tell apart patients with a range of solid tumors from those who were cancer-free.

All in all, the test correctly detected the disease in 19 out of every 20 patients with cancer. Apart from this, the test identified the metastatic phase of the disease with an overall accuracy of 94%.

This is the first method to be developed that can determine metastatic cancer from a simple blood test without previous knowledge of the type of cancer the patient is suffering from, the authors explain.

Unlike many other blood tests for cancer, which look for genetic material from tumorous cells, the current test relies on a technique called NMR metabolomics. This involves the use of magnetic fields and radio waves to measure metabolite levels in the patient’s blood.

Patients with localized cancer, those with metastatic cancer, and healthy individuals all have different metabolite profiles in their blood, the authors explain. Raw data from the test is then run through an algorithm that distinguishes between these states and offers a diagnosis.

The authors are hopeful that their test can help doctors detect and assess cancer much more quickly and cheaply than ever before. Although the test itself cannot accurately pinpoint the particular type of cancer in question, it still is a very powerful tool in determining who needs further tests, and who’s in the clear.

Early detection of cancer improves a patient’s chances of a successful outcome. Being rapid and cheap to administer, this test could help improve the overall rate of successful cancer treatments, especially in patients who only show non-specific symptoms (for whom a diagnosis generally takes longer).

“This work describes a new way of identifying cancer. The goal is to produce a test for cancer that any GP can request,” says Dr. Fay Probert, lead researcher of the study from the University of Oxford. “We envisage that metabolomic analysis of the blood will allow accurate, timely and cost-effective triaging of patients with suspected cancer, and could allow better prioritization of patients based on the additional early information this test provides on their disease.”

For now, the test is still in its early testing stages. Further research with larger cohorts of patients will be needed to give us a better and more reliable understanding of it, its capabilities, and its limitations.

The paper “Metabolomic Biomarkers in Blood Samples Identify Cancers in a Mixed Population of Patients with Nonspecific Symptoms,” has been published in the journal Clinical Cancer Research.

How to tell if eggs are bad — according to science

Every once in a while, you come across an egg and you’re not exactly sure if it’s still good anymore. Maybe it smells a bit funny, maybe it’s past its due date, or it’s just been in the fridge for a few days and you wanna be sure. But due dates can be misleading, and smell alone is not a reliable indicator. So how can you tell if the eggs are still good?

We’ve looked at some of the methods and found what really works.

Why it matters

Every year, the average person on the globe consumes 197 eggs. In many countries (like the US) that figure is much higher, at almost 300 per year. But many eggs are also thrown away. In the UK alone, 720 million eggs are wasted every year and worldwide, and while global estimates are scarce, wasted eggs probably number in the billions every year.

Granted, some of this waste happens due to restaurants or producers, but consumers can also play their part and not throw away eggs unless they have gone bad. At the same time, you really don’t want to consume bad eggs, as this would increase the risk of Salmonella or E. coli infection — which can cause diarrhea, fever, and vomiting.

To reduce the risk of bacterial infection from eggs, you can keep eggs refrigerated (which keeps them fresh for a longer time), and cook them thoroughly. A 2011 research project has found that keeping eggs at steady, low temperatures can help their natural defenses against bacteria.

Generally speaking, you shouldn’t eat eggs past their expiration date. However, some eggs have sell-by dates, others have eat-by (or expiration dates), which can get confusing. Also, those dates aren’t absolute. Most health and food organizations note that eggs are usually good for several weeks past the stamped date, but they can also get bad quicker, if stored improperly.

This is why it’s important to have a reliable method to check if your eggs are still good.

How to tell if eggs are bad: the floating test

The most common (and probably most reliable) test to check if an egg is bad is the floating test. You take a glass (or a pot, or any container really), and fill it with room temperature water. Place your egg (or eggs, just one at a time) in the water. If the egg floats, it’s not good anymore — simple as that.

Good eggs are heavier than water, which is why they sink. But when an egg starts to decompose, it becomes lighter by giving off gases. This creates pockets of air, especially at the bottom of the egg. But if the egg was a perfectly isolated system, it wouldn’t float. After all, even when solid or liquid mass changes into gas, it has the same mass.

This common method is not a myth, it actually works, and there’s some interesting science as to why it does.

Why it works

There’s a common misconception about the egg float test. The reason why bad eggs float has to do with pockets of air forming, but that’s only half of the story.

Good eggs are heavier than water, which is why they sink. But when an egg starts to decompose, it becomes lighter. When an egg starts to decompose, it gives off gases. This creates pockets of air, especially at the bottom of the egg. But if the egg was a perfectly isolated system, it wouldn’t float. After all, even when solid or liquid mass changes into gas, it has the same mass.

However, eggs aren’t perfectly isolated, they have pores and gases can escape. These gases, light as they may be, still have mass, and when they escape, they make the egg lighter. At some point, when the egg becomes lighter than water, it floats — and it’s not good for consumption anymore. This is probably the best test to employ to see if eggs are still good.

The shake test

A less reliable but still useful test is to take an egg and shake it gently by your ear. Listen carefully; is there a sloshing sound and feel? If not, you’ve probably got a fresh egg. If you do hear it, you may be dealing with an egg that has gone bad.

Keep in mind that if you shake them hard enough, even fresh eggs can make a sloshing sound, so shake them gently.

Why it works

As an egg gets older, the yolk becomes more alkaline and runny. It’s hard to say exactly where exactly the point of no return is, but as a rule of thumb, if the yolk seems too runny, it’s a bad egg.

There’s a bit of art to this test, and it’s best to complement it with another.

The good old smell test

A good cracked egg.

We’ve mentioned before that smell alone is not a reliable indicator — and it’s not. But if you crack an egg and it just smells bad, you should throw it away (they don’t call them rotten eggs for nothing). There’s a good chance the egg may actually be bad, but even if it’s not, you probably won’t be able to enjoy it, so better not to take any risks.

Why it works

The smell from bad eggs is a mixture of things, but a key component is hydrogen sulfide (H2S) — a heavy and pungent gas. If you feel any sulfur-type smell coming from the eggs, that’s a sign of decomposition.

Fresh eggs don’t emit a smell, but keep in mind that eggs can “suck” up smells from your fridge (which is why you should keep them covered and in a carton that can absorb any unwanted smells).

The visual test

If you crack open an egg and you see a discolored yolk, it’s likely bad. The same thing goes for eggs with white parts that are cloudy. But if you’ve reached that point, the odds are the egg is stinky already.

Why it works

It’s not just decomposition and bacteria, there’s also some chemistry that changes the color (and smell) of the eggs. Eggs contain carbonic acid — an acid that forms when carbon dioxide reacts with water. Carbonic acid slowly turns into CO2 (and other gases), and leaves the egg; this is why the floating egg test works. But at the same time, this makes the remaining egg more alkaline, and more chemically capable of interacting with hydrogen.

This changing chemistry is a big part of why the inside of the egg looks different, and also a big part of why it smells differently.

The “not sure” test

Are you unsure if an egg is safe to eat? Just don’t eat it — that’s the “not sure” test.

We all want to play our part and fight food waste, and that’s a very noble goal. But if you’ve done the test and still have doubts about it, it’s best to just play it safe and not take any risks.

Egg tips

Boiling eggs and then storing them in the fridge for a few days can be useful for salads, sandwiches, etc.

Always cook eggs properly. Cooking isn’t just something we do to make food edible or tastier, it’s also something we do to kill off pathogens.

If you’ve got eggs and want to cook them but not consume them right away, the best thing to do is boil them. Boiled eggs don’t last as long as fresh eggs in the fridge, but hard-boiling eggs is a good way of giving them a couple of extra days. Boiled eggs can last up to a week when stored in the fridge, so if you’ve got a bunch of eggs you need to eat in a few days, you can use this for dressing or sandwiches or whatever else you like.

To give your eggs the most fridge life, store them in the coldest part of the fridge where they won’t freeze. It’s common to store eggs on the door, but that’s actually the least cold part of the fridge. Go deep and put them where it’s cold.

If you take eggs out, either put them back in quickly or cook them. When you take cold eggs out of the fridge, they “sweat” as the water condenses, creating an environment well-suited for bacterial growth. Avoid leaving eggs out for more than an hour, and if you do, it’s safest to cook them.

You can also freeze eggs (after cracking them), but if you don’t know what you’re doing, it’s best to avoid this.

As mentioned, leave eggs in their original carton. If you don’t have one, store them in something covered. Eggs can absorb smells and pick up unpleasant odors from your fridge.

Some countries (most notably in Western Europe) don’t store supermarket eggs in the fridge — but the fridge is still the best place to store them at home.

New blood test can determine who’s at risk of Alzheimer’s years before symptoms begin

A newly-developed blood test could help tell who’s at risk of developing Alzheimer’s before the onset of symptoms.

Image credits Mohamed Hassan.

The research focused on patients who were clinically diagnosed as not having Alzheimer’s, but perceived themselves as being cognitively impaired — a condition known as Subjective Cognitive Decline, SCD. The goal was to see whether a new type of test could tell which of these patients were at risk of developing Alzheimer’s later on.

So far, the findings are very encouraging: the test managed to pinpoint during the study all 22 subjects who developed Alzheimer’s dementia, thus the clinical symptoms, within six years. It further identified those participants who were at very low risk of developing it as well.

Testing for the future

The authors, a joint German-Dutch research team worked with 203 participants, taking samples of their blood and analyzing these through an immuno-infrared sensor for misfolding of the amyloid-beta (Aβ) peptides — a known biomarker for Alzheimer’s disease. They were also extensively tested for Alzheimer’s, proving that none of the participants had developed the condition at the study’s onset.

However, testing revealed misfolded Aβ peptides at this point in 22 participants, all of whom developed clinical Alzheimer’s in the six years after the study. For patients with mild misfolding, onset of clinical Alzheimer’s took longer on average (3.4 years) than for subjects with severe Aβ misfolding (2.2 years).

The researchers used these figures to predict the risk of each participant developing clinical Alzheimer’s disease using a statistical model. This suggested that participants with SCD and mild misfolding have an 11-fold higher risk of developing the condition, while those with SCD and severe misfolding were 19 times as likely to develop clinical Alzheimer’s than the other participants.

“Misfolding of Aβ is therefore a very precise prognostic plasma biomarker,” concludes  biophysics Professor Klaus Gerwert from the Bochum Research Center for Protein Diagnostics, lead researcher of the paper.

They further checked whether their predictions could be improved by looking at the combination of two different measurement methods for Alzhimer’s biomarkers — the level of misfolding of all Aβ isoforms alongside the ratio of Aβ42 to Aβ40 in plasma. This did increase the accuracy of the predictions statistically, the team explains.

“We can now very accurately predict the risk of developing clinical Alzheimer’s disease in the future, with a simple blood test on symptom-free individuals with subjective concerns,” explains Gerwert. “However, we can just as confidently give the all-clear for SCD patients who have a very low probability of developing Alzheimer’s disease in the next six years.”

The test can also be used to “monitor disease progression over 14 years”, starting frim the asymptomatic stage all the way to clinical onset, says Julia Stockmann of the Bochum Research Center for Protein Diagnostics, co-lead author of the paper.

Such a test is an essential half of a working strategy against Alzheimer’s. Once we’re able to actually treat the condition (there are some drugs in the works that may serve this purpose, such as aducanumab, still in testing with the U.S. Food and Drug Administration), such a test can be used to tell who is most in need of treatment, potentially saving thousands of lives from a debilitating condition.

“Our results indicate that Alzheimer’s drugs should be applied as early as possible in a non-clinical stage to improve therapy response,” Gerwert said.

The paper “Amyloid-β misfolding as a plasma biomarker indicates risk for future clinical Alzheimer’s disease in individuals with subjective cognitive decline” has been published in the journal Alzheimer’s Research & Therapy.

NASA tests its new spacesuits underwater, finds them “acceptable”

NASA personnel are taking a bath for a good cause — they’re testing the agency’s new space suits.

The suits being tested underwater. Image credits NASA.

The iconic white suits that put a man on the moon are a bit outdated, so NASA is hard at work tailoring the space suit of the modern age. However, launching people into orbit is expensive and, with untested suits, probably not a good idea. So NASA is testing its new wardrobe using an underwater laboratory.

A bath and the beyond

NASA’s old suits carry the fancy name Extravehicular Mobility Units (or EMUs, to the delight of every Australian out there), but they’re starting to show their age, design-wise. They were introduced over 40 years ago and, as such, they don’t readily lend themselves to being kitted out with the latest technology and gadgets. These suits will likely take astronauts back to the moon, maybe even to Mars.

In order to make sure they’re working as intended, researchers at the Johnson Space Center’s Neutral Buoyancy Lab (NBL) performed underwater tests using the xEMUs. This facility houses a massive basin that’s almost 10 times larger than an Olympic swimming pool, which is meant to simulate low-gravity environments. NASA says these underwater tests are essential because they can replicate the limited mobility of a real mission. 

The suits were also tested in the “rock yard” at Johnson Space Center, an area boasting several types of simulated landscapes that one might find beyond Earth. This yard is generally used to test the capabilities of rovers and space suits in practical applications, to make sure they won’t break in the field. While we don’t have the exact results of the test just yet, NASA’s Aerospace Safety Council says the suits are performing as intended so far, and that their development is running according to schedule.

“Preliminary feedback from astronauts who have completed the test series evaluate the xEMU Demo architecture as acceptable to complete a demonstration mission on the ISS,” a NASA blog post explains.

South Korea reports a startling number of COVID-19 reinfections

The question of how we gain immunity to the novel coronavirus remains a very pressing one, and one to which the answer is still somewhat elusive. Surely, people who defeat the virus must develop some type of antibodies — that’s what defeating the virus means in the first place.

These antibodies also don’t just go away immediately (they might fade after a few months or years, but that’s a different matter). So then why are people testing positive again, days after they were cleared?

South Korea has been wildly hailed as one of the role models in dealing with the novel COVID-19 pandemic. Although it was one of the first countries to report an outbreak, and despite initial uncontrolled spread, South Korea managed to handle the outbreak without imposing draconic measures. Right now, the country doesn’t have a major lockdown, and yet only reports 20-30 new cases every day.

However, a startling number emerged from Korea recently: at least 116 people initially cleared of the new coronavirus had tested positive again.

What this means

First of all, there is a strong case to say that some type of immunity is developed in the vast majority of people. But given the low number of new cases in Korea, 116 reinfections doesn’t sound like a small number at all — unless, it’s not reinfections we’re dealing with.

There are two likely explanations for this (which are not mutually exclusive). The first is that we are simply seeing false positives. No test is perfect, especially for a disease as novel as COVID-19. It could also be that the test is picking up a low amount of virus that is inactive. This is very likely and has been highlighted as a possibility before. However, this does not explain the full picture, as some people who initially test negative start developing visible symptoms and clearly have an ongoing infection.

Which brings us to the second possibility: false negatives. RT-PCR testing is most useful when it is positive, but when it is negative, it doesn’t necessarily mean that the person doesn’t have the disease.

In a brief statement, the World Health Organization has said that they working with Korean experts to get to the bottom of this problem.

“We are aware of these reports of individuals who have tested negative for COVID-19 using PCR (polymerase chain reaction) testing and then after some days testing positive again,” the statement said.

“We are closely liaising with our clinical experts and working hard to get more information on those individual cases. It is important to make sure that when samples are collected for testing on suspected patients, procedures are followed properly . “

Figuring out how immunity for the novel coronavirus works is essential for our long-term strategy against it. Previous research has shown that the virus has a relatively low mutation rate, which could indicate that a vaccine effect would be long-lasting, but this is far from proven at this moment.

Up to one-in-five COVID-19 patients in a new analysis co-infected with another respiratory virus

Roughly 20%, or one in every five, patients who test positive for COVID-19 are also infected with other respiratory viruses, according to an analysis led by Ian Brown, MD, a clinical associate professor of emergency medicine at the Stanford School of Medicine.

Pennsylvania Commonwealth microbiologist Kerry Pollard performs a manual extraction of the coronavirus inside at the Pennsylvania Department of Health Bureau of Laboratories on March 6th.
Image credits Governor Tom Wolf / Flickr.

According to the authors, the findings challenge the assumption that patients with another type of viral respiratory disease can’t be infected with COVID-19.

Co-threats

“Currently, if a patient tests positive for a different respiratory virus, we believe that they don’t have COVID-19,” said Nigam Shah, MBBS, Ph.D., associate professor of medicine and of biomedical data science at the medical school. “However, given the co-infection rates we’ve observed in this sample, that is an incorrect assumption.”

Since hospitals have a limited capacity to test for SARS-CoV-2, doctors tend to test patients coming in with respiratory symptoms for other viruses. If the patient tests positive for influenza, rhinovirus (common cold), or another respiratory virus, they may be sent home without being tested for COVID-19, and it is assumed that the alternative diagnosis is the source of the symptoms, Brown explains.

Given how important accurate and rapid tests are for containing the virus and saving lives, we need to know how likely co-infection is for SARS-CoV-2 and other viruses that produce respiratory symptoms. In order to find out, Brown and his colleagues analyzed 562 people who were recently tested for COVID-19 at Stanford Health Care’s Marc and Laura Andreessen Emergency Department. Forty-nine of these patients initially tested positive for SARS-CoV-2, and 517 were also tested for the presence of other common respiratory viruses, such as influenza A and B, respiratory syncytial virus, rhinovirus, adenovirus and several types of pneumonia, with 127 testing positive.

The team reports that 11 patients who were tested for both SARS-CoV-2 and other respiratory viruses were found to be co-infected with both kinds of viruses. This would mean that 22% of all the COVID-19 patients tested and 8.7% of people with other respiratory virus infections were co-infected.

While the findings are based on a relatively small sample, they do point to the need for a more thorough screening of potential COVID-19 patients. However, the reality on the ground is that many hospitals are struggling to supply the necessary equipment to test everyone who comes in. The USA is still lacking adequate testing data for the virus.

The findings were published on the platform Medium.

MIT develops new, cheap, fast Covid-19 test, is awaiting approval from FDA

A new startup created by members from the Massachusetts Institute of Technology (MIT) is preparing to submit a new and fast Covid-19 test for “emergency use authorization” by the FDA.

SARS-CoV-2 as seen under the transmission electron microscope.
Image credits NIH Image Gallery.

The new test is based on technology developed at MIT’s Institute for Medical Engineering and Science (IMES), reports MIT News. It can provide reliable diagnostics in about 20 minutes, which is extremely fast. The E25Bio startup plans to make the test — which works similarly to a pregnancy test — commercially available as soon as possible in order to help fight the current outbreak under the FDA’s “emergency use authorization” model.

Speed testing

“Our hope is that, similar to other tests that we’ve developed, this will be usable on the day that symptoms develop,” says Lee Gehrke, the Hermann L.F. von Helmholtz Professor at IMES, who led the development of the test.

“We don’t have to wait for antibodies to the virus to come up.”

The team behind the new test has years of experience working on similar diagnostic devices. They used a technology known as lateral flow technology, which is similar to the ones used by pregnancy tests but aimed at identifying viral proteins, to create tests for Ebola, dengue fever, and Zika virus, among other infectious diseases.

The test itself consists of small strips of paper coated with antibodies that bind to specific viral proteins. A solution of gold nanoparticles, a different antibody, and samples harvested from the patient is then mixed, and the test dipped into it. In case the virus is present, its marker protein will attach to the antibodies on the strip of paper together with nanoparticles and antibodies in the solution, creating a colored line on the test. The whole thing takes around 20 minutes, the team explains.

There are two types of Covid-19 tests available so far. One involves testing blood for antibodies against the virus — however, this can be unreliable as antibodies only become detectable a few days after onset of the symptoms — while the other checks for viral DNA in saliva or mucus samples. The latter is more reliable and can be used to detect the virus earlier in the infection, but relies on polymerase chain reaction (PCR), a technique that ‘amplifies’ traces of DNA but takes several hours and specialized equipment to perform.

E25Bio is awaiting FDA approval of the test so that they may begin trials using patient samples. If that proves successful, the next step would involve using it for clinical diagnosis.

One advantage of the study, the team notes, is that it is simple and cheap to produce, making it ideal for quick manufacturing in large quantities.

Fuel meter.

Duo of engineers are working on a kit to test your stress levels at home

Feeling stressed? A new test kit can help you see just how stressed you are — and whether you should seek help with handling it.

Fuel meter.

Image via Pixabay.

Researchers at the University of Cincinnati have developed a new test that can measure common stress hormones in sweat, blood, urine, or saliva. The test was designed to be as simple and straightforward as possible, and the team hopes to further develop it for use at home.

Spotting stress 101

“Stress harms us in so many ways. And it sneaks up on you. You don’t know how devastating a short or long duration of stress can be,” says UC graduate Prajokta Ray, the study’s first author.

“So many physical ailments such as diabetes, high blood pressure and neurological or psychological disorders are attributed to stress the patient has gone through. That’s what interested me.”

Andrew Steckl, an Ohio Eminent Scholar and professor of electrical engineering in UC’s College of Engineering and Applied Science and the other co-author of the paper, says their test was born from the desire to make “something that’s simple and easy to interpret.” Steckl has personal experience helping his father handle medical care, who often needed help getting “to the lab or doctor to have tests done to adjust his medication.” Having an easy-to-use stress test that they could run at home to determine whether they needed to make the trip would have saved them both a lot of time and effort, not to mention helping them worry less.

Steckl has a background in biosensors, and he drew upon that expertise to create the very product he lacked — and needed — when caring for his father. The result isn’t perfect, but it’s more than enough to give you a rough idea of your state of stress and to help you determine whether or not you should see a specialist.

The technology, in its current state, involves blasting a sample of fluid (sweat, blood, urine, or saliva) with UV light, which the can then be read to determine the concentration of stress hormones and biomarkers it contains (a technique known as UV spectroscopy). The team says it “primarily focused” on cortisol, serotonin, dopamine, norepinephrine, and neuropeptide Y for now. The concentrations of each of these compounds vary across different bodily fluids, but the team reports that so far, they’ve been able to reliably measure them in all samples.

“This [test] doesn’t replace laboratory tests, but it could tell patients more or less where they are,” he explains. “This may not give you all the information, but it tells you whether you need a professional who can take over.”

“It measures not just one biomarker but multiple biomarkers. And it can be applied to different bodily fluids. That’s what’s unique,” he adds.

The project was, in part, funded by a grant from the National Science Foundation and the U.S. Air Force Research Lab, as stress levels are a particular area of interest for the military. US armed forces are engaged in active research regarding acute stress in personnel that operate at the fringes of human resistance, such as fighter pilots.

“Pilots are placed under enormous stress during missions. The ground controller would like to know when the pilot is reaching the end of his or her ability to control the mission properly and pull them out before a catastrophic ending,” Steckl said.

The resulting device, however, needn’t be only used by the military — Steckl’s lab is currently working through commercial applications for the test. It’s not going to “replace a full-panel laboratory blood test,” he says, but it would be very useful as a quick indicator to let patients know how much their medical state has changed.

The paper “Label-Free Optical Detection of Multiple Biomarkers in Sweat, Plasma, Urine, and Saliva” has been published in the journal ACS Sensors.

Rubics.

Smart on a budget: researchers design free IQ test that takes 10 minutes to complete

Researchers from the University of California (UC) Riverside and UC Irvine have developed a new IQ test kit. The test is reliable, takes only 10 minutes, and it’s completely free.

Rubics.

This is the customary cliche for ‘intelligent’, right?
Image credits Urh Kočar.

The most commonly-used IQ measuring tool used today is the Advanced Progressive Matrices, or APM, developed by John C. Raven in 1936. It’s a cross-referenced tool that has stood the test of time, making it a benchmark in its field. It’s not without flaws, however: it takes between 40 to 60 minutes to complete an APM test. Furthermore, a single kit and its answer sheets can cost up to hundreds of dollars — which is quite pricey.

That’s why a team of UC researchers set out to make their own test.

I’m you, but shorter (and free)

The new test, christened the University of California Matrix Reasoning Task (UCMRT), is actually highly comparable to the APM. However, it’s much shorter, taking only 10 minutes to complete. The UCMRT measures “fluid intelligence” — intelligence that is not dependent on pre-existing knowledge and is linked to reasoning and problem solving– and works on tablets and other mobile devices. Most importantly, it’s a reliable tool for measuring nonverbal problem-solving skills, the team says, which is a good predictor of academic proficiency.

The UCMRT offers three alternate versions, allowing the test to be used three times by the same user. The APM only has a single version.

“Performance on UCMRT correlated with a math test, college GPA, as well as college admissions test scores,” said Anja Pahor, a postdoctoral researcher who designed UCMRT’s problems and works at both UC campuses.

“Perhaps the greatest advantage of UCMRT is its short administration time. Further, it is self-administrable, allowing for remote testing. Log files instantly provide the number of problems solved correctly, incorrectly, or skipped, which is easily understandable for researchers, clinicians, and users. Unlike standard paper and pencil tests, UCMRT provides insight into problem-solving patterns and reaction times.”

Raven’s APM, while reliable, is often more of a liability in studies. It’s much too expensive, requires a lot of time to complete (which puts many volunteers off), and provides the same set of questions each time — meaning it isn’t very useful for repeat testing. However, there simply weren’t any viable cross-validated alternatives to the APM. Pahor and her co-authors decided to develop the UCMRT following their experience with the test. The test’s design is largely based on matrix problems generated by Sandia National Laboratories. The UCR Brain Game Center wrote the code for the problems.

UCMRT screenshot.

UCMRT screenshot.
Image credits UCR Brain Game Center.

The test only has 23 problems for individuals to tackle, whereas the APM has 36. Still, the team’s testing revealed that both work equally well. UCMRT was tested on 713 students, of whom about 230 took both tests. The UCMRT results correlated with “APM about as well as APM correlates with itself,” Pahor said. In fact, there’s one area where the new test takes the cake:

“UCMRT predicts standardized test scores better than Raven’s APM,” said Aaron Seitz, a professor of psychology at UCR and paper co-author. “Intelligence tests are big-money operations. Companies that create the tests often levy a hefty charge for their use, an impediment to doing research.”

“Our test, available for free, levels the playing field for a vast number of researchers interested in using it.”

The design of the UCMRT allows the inclusion of variants that can be used for different age segments of the population, the team adds. Visual appeal was also prioritized when designing the problems, to help keep participants motivated during each task. The UCMRT also comes with a few practice problems to get everybody into the groove before the actual testing begins.

“We are motivated by helping the scientific community and want to create versions of UCMRT for different age groups and abilities,” Seitz added. “This test could help with early intervention programs. We are already working on a project with California State University at San Bernardino to move forward with that.”

Among other future plans, the team also wants to design non-English versions of the UCMRT.

The paper “Validation of a matrix reasoning task for mobile devices” has been published in the journal Behavior Research Methods.

The $2 testing device, about the size of a soda can, does not require electricity or technical expertise to use. Credits: University of Pennsylvania.

Penn engineers develop $2 portable Zika test

Researchers from the University of Pennsylvania have developed a cheap and quick test for the Zika virus. The patient needs to provide only a saliva test which turns blue in the presence of the virus — and it only costs $2.

The $2 testing device, about the size of a soda can, does not require electricity or technical expertise to use. Credits: University of Pennsylvania.

The $2 testing device, about the size of a soda can, does not require electricity or technical expertise to use. Credits: University of Pennsylvania.

Rapid, accurate diagnosis of Zika is vital, especially for pregnant women. While the disease is not typically life-threatening for adults, it can cause microcephaly (underdevelopment of the brain and head) and other devastating birth defects. It is estimated that 1.5 million people have been infected by Zika in Brazil, with over 3,500 cases of microcephaly reported between October 2015 and January 2016.

Having a test which could quickly identify the disease is no easy feat. The genetic material from the Zika itself is considered the golden standard for disease detection because other, indirect methods (like detecting Zika-fighting antibodies) can create false positives from people who are infected but haven’t yet produced enough antibodies, or false positives from people who have antibodies for a different disease that is similar enough to trigger the test. But genetic tests are generally time-consuming and require specific lab equipment (which also costs a lot).

“The CDC has approved, on an emergency basis, only these kinds of laboratory-based molecular tests for the Zika virus,” said Research Assistant Professor Changchun Liu. “Generally, lateral flow tests, which directly change the color of a test strip based on the presence of Zika antibodies, suffer from low sensitivity. And since antibodies to the Zika virus cross-react with other similar viruses prevalent in Zika-endemic areas, lateral flow tests for Zika also suffer from low specificity.”

This is where this research steps in. They developed a procedure which provides a genetic test without requiring the very specific lab processes. Their solution involves a thermos bottle, a self-contained heating element that uses a chemical reaction from portable military rations and a wax-like material that absorbs excess heat by melting. A 3-D printed lid fits on top of the thermos and holds all of the test’s components in place.

“In parallel,” Liu said, “we engineered a low-cost, point-of-care system that consists of a diagnostic cassette and a processor. The cassette isolates, concentrates and purifies nucleic acids and carries out enzymatic amplification. The test results are indicated by the change in the color of a dye, which can be inspected visually.”

All you need to do is insert the saliva into the cartridge and wait for 40 minutes. So far, initial tests have proven to be very promising and researchers want to test them at a much greater scale.

“Our work represents a proof of concept at this stage,” said Professor Haim Bau of the Department of Mechanical Engineering and Applied Mechanics in Penn’s School of Engineering and Applied Science. “Before the assay can be adapted for medical use, we must experiment with patients’ samples and make assure that our assay and system match the performance of the gold standard and operate reproducibly and reliably. We are fortunate to have dedicated colleagues in endemic regions ready to assist us in this task.”

As it stands at the moment, the virus has created an epidemic throughout South America, with no end in sight. The outbreak began in April 2015 in Brazil, and has spread to other countries in South America, Central America, Mexico, and the Caribbean. In January 2016, the WHO said the virus was likely to spread throughout most of the Americas by the end of the year.

New technique can identify any known virus in a blood sample – without fail

Ian Lipkin, a virus hunter from Columbia University, along with fellow professors Thomas Briese and Amit Kapoor have designed a new system, known as VirCapSeq-VERT, that they claim can detect any known human virus in a blood sample.

Image via rna-seqblog

“When people analyze samples from people who are ill, they have some idea in mind. This is probably an enterovirus, or maybe it’s a herpesvirues. They then do a specific assay for that particular agent. They don’t usually have the capacity to look broadly.”

The team recently received a blood sample from the National Institutes of Health. They were taken from a man who had received a bone-marrow transplant and had fallen mysteriously ill, with evidence of severely inflamed blood vessels.A few years back, working on a similar case, Lipkin discovered a new polyomavirus — part of a family that can cause disease in people with compromised immune systems — so he jumped at the chance; perhaps this was his chance to discover yet another virus.

Lipkin’s team ran the sample through a system that they had devised to detect human viruses, and found that the man was infected with dengue virus. In hindsight, that made sense—he had recently returned from Vietnam, where dengue is prevalent. The team wasn’t looking for dengue virus, but it still showed up — and as regular blood tests can find if a particular virus is present or not in a sample, their new system could save thousand of hours in the lab, trying to guess the right virus to test for, and thousands of lives.

“It wasn’t what we anticipated, but we didn’t have to make a priori decisions about what we planned to find,” Lipkin says.

In the 120 or so years since viruses were first discovered, our ability to identify them, and diagnose the diseases they cause, has improved enormously. But even the most cutting-edge of techniques have limitations. Sequencing technologies allow scientists to unambiguously decipher the genetic material of viruses in a sample, but they suffer from poor sensitivity — sometimes they just miss detecting the genes they’re looking for, as they are usually swamped by the genetic material of heir host.

One way to solve this is to use a method of DNA amplification known as PCR. This solves the problem by making lots and lots of copies of the analyzed genes beforehand. It allows for exquisitely sensitive results but it’s also hard to do in bulk, and you need to have some idea of what you’re looking for in the first place.

VirCapSeq-VERT takes the best features of these techniques, and the team threw a few improvements of their own in the mix. They compare the method to a massive exercise in fishing for viruses. The hooks are made of distinctive stretches of DNA from the genomes of every group of virus known to affect humans and other vertebrates, that the team identified and synthesized — netting them two million such virus-hooks, each tailored to catch a specific virus. If you throw the hooks in a blood sample, wiggle them a bit, then take them out and sequence everything that they caught, you get the full genome of every virus in the sample.

The team tested the system using tissue samples spiked with genes from many infamous viruses, including those responsible for Ebola, dengue, flu, and MERS. They also tried analyzing a nasal swab from a patient and a stool sample from a bat. VirCapSeq-VERT successfully identified all the viruses in these samples, even when they were present at miniscule amounts.

And since the technique offers up the full genomes of the virus it detects, it’s impossible to fool.

“If you get a genome, you know what it is. It’s unequivocal,” says Lipkin. “It also allows you to find mutations that would circumvent traditional diagnostics, or that might would affect resistance to drugs or vaccines.”

And it can analyze many patients at once. To do that, they fuse a unique barcode sequence to the viral DNA from each individual sample, before mixing them together and running them through VirCapSeq-VERT. After the system does its thing, the team can check the barcodes to work out which sample each virus came from.

“We can do up to 21 at a time, which makes it financially viable,” says Lipkin.

Finally, the system is flexible. It should pull out any virus that’s even a modest fit to the baited hooks, which includes mutant strains and, potentially, previously unknown viruses.

“We probably won’t find anything entirely new, but we’ll be able to find anything that’s within 60 percent similarity to something represented in our library,” says Lipkin, whose team has discovered over 700 viruses. Already, they have used VirCapSeq-VERT to identify a new virus in tilapia, an economically important fish that is being increasingly farmed in aquaculture.

“The results look very promising,” says Nick Loman from the University of Birmingham, who was not involved in the study.

“Going forward, we can combine techniques like this with portable sequencing and have a diagnostic device which provides incredibly rich data for clinicians and epidemiologists. Ultimately what we would like is an entirely unbiased method that captured all pathogens—known and unknown—with exquisite sensitivity.”

Your smartphone will be able to tell if you have blood parasites

Scientists have managed to use a simple smartphone to test for blood parasites; the device and app was successful in small trials in Cameroon.

Image credits: BBC.

Parasitic worms cause many problems in several areas of Africa, especially in central Africa, where tropical diseases are running rampant. There are many issues with detecting and treating these diseases, especially diagnosing infections in the early stages, while treatment can still be effective. With this new app, with only a finger prick, you can find if your blood is infected with a worm. But it gets even better.

Among the problems in dealing with such diseases is the fact that some people react well to treatment, while for others, the treatment can be fatal. This app can also detect who will react well and who won’t.

“With one touch of the screen, the device moves the sample, captures video and automatically analyses the images,” said one of the researchers, Prof Daniel Fletcher.

The trick is that the app doesn’t try to actually detect the worm, but it focuses on detecting movement within the blood. The whole system is very efficient and it was praised by experts in the field.

“This is a very important technology,” said Baylor College of Medicine’s Dr. Peter Hotez, a well-known specialist in neglected tropical diseases who wasn’t involved in the new research. “It’s very practical,” by eliminating the need for specially trained health workers and pricey equipment in remote villages, he added.

Now, researchers are wondering if a similar system could be used to detect other diseases, including TB, malaria and soil-transmitted parasitic worms. Considering other recent advancements in using smartphones to detect diseases, there’s reasons to be optimistic – Columbia University scientists created a device that can detect HIV or syphilis and are pilot testing it in Rwanda, while at the Massachusetts General Hospital, doctors are researching a tool that clips over a smartphone camera to detect cancer in blood or tissue samples. To me, using advanced, yet commonly accessible technology to detect such serious diseases is a spectacular achievement.

Prof Simon Brooker from the London School of Hygiene & Tropical Medicine, commented:

“I think it’s one of the most fundamental advances in neglected tropical diseases in a long time. In the 21st Century we are using 20th Century technology to diagnose these infections, this brings us into the modern world. It really is exciting; when you see it you just go ‘wow’; hopefully it will transform efforts to eliminate diseases,” he added.

At home test for colon cancer screening receives unanimous support from FDA advisors (10-0)

Improving colon cancer detection is crucial; it can prevent colon-related cancer deaths by as much as 60 percent in adults who are at least 50-years old – simply through routine scanning. However, traditional screening methods are associated with significant discomfort; this at home test solves this issue, and provides many advantages.

colon-cancer

This screens for colon cancer using DNA, so you don’t have to wait until you get a lesion or cancer for the doctor to notice – you can find it before any of this happens. Also, it uses a stool sample, as opposed to a blood sample, and it eliminates all the discomfort associated with a colonoscopy.

In order to take a colonoscopy, the patient has to follow a low fiber or clear-liquid only diet for 1-3 days – you’re essentially drinking lots of liquids which will give you diarrhea. The day before the colonoscopy, the patient is given a laxative preparation, and the procedure itself is… let’s just say it’s unpleasant. It’s nowhere nearly as bad as it used to be years ago and you are sedated during the procedure, but people still tend to avoid it, even though they shouldn’t, as the disease poses a major threat.

But this development could change things significantly. Cologuard, a colon cancer screening test that analyzes DNA found in the stool is set for approval – it hasn’t been approved yet by the FDA, but they almost always follow the advisors.

“Exact Sciences Corp. (Nasdaq: EXAS) today announced that the U.S. Food and Drug Administration’s (FDA) Molecular and Clinical Genetics Panel of the Medical Devices Advisory Committee determined by a unanimous vote of 10 to zero that Exact Sciences has demonstrated safety, effectiveness and a favorable risk benefit profile of Cologuard, the company’s stool-based DNA (sDNA), non-invasive colorectal cancer screening test,” Exact Sciences announced on its website.

Symptoms of colon cancer do not often show up until the disease is already in its later stage. Health experts recommend screening so the disease can be detected in its early stages, when it still have a very good chance of being cured. The disease is one of the leading causes of cancer-related deaths in the United States.