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Startup detects COVID-19 using spit, light, and a computer built to analyze patterns

A Seattle-area startup called Pattern Computer is developing a rapid COVID-19 test based on patterns in light from spit, one of several projects moving…

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Pattern Computer’s ProSpectral device for detecting COVID-19. (Pattern Computer Photo)

A Seattle-area startup called Pattern Computer is developing a rapid COVID-19 test based on patterns in light from spit, one of several projects moving ahead from the 7-year-old company that designed its own computer from scratch.

The company’s “Pattern Discovery Engine” was created specifically to discover and analyze patterns and excels at the task, said CEO and co-founder Mark Anderson.

Pattern Computer CEO Mark Anderson. (Pattern Photo)

Pattern Computer keeps the workings of its system closely guarded, and has not published its AI models in peer-reviewed journals. Outside researchers say it’s hard to know what’s under the hood.

But its approach has attracted seasoned computer science talent and biotech heavyweights to the startup.

The company’s chief technology officer, co-founder Ty Carlson, previously managed the Amazon team that launched products such as the Amazon Echo. Its advisory board includes Leroy Hood, a co-founder of the Institute for Systems Biology, genome pioneer Craig Venter, and serial biotech startup founder George Church, a Harvard professor.

Anderson is founder and CEO of technology newsletter Strategic News Service, read by Bill Gates, Jeff Bezos, Michael Dell and Elon Musk, he said. He’s known as a “tech prognosticator” and each year brings together an eclectic mix of tech leaders and scientists at his “Future in Review” conference (he also co-founded the Whale Museum in Friday Harbor, Wash., where he lives).

At his 2015 conference, Anderson hosted a “chief technology officer challenge,” where participants designed a desktop supercomputer. The resulting system formed the seed for Pattern Computer. Participants included the other company co-founders, entrepreneur Brad Holtz and Michael Riddle, who previously co-founded Autodesk, makers of AutoCAD and other industrial software.

Leroy Hood
Genetics pioneer Leroy Hood. (Institute for Systems Biology Photo)

Pattern Computer focuses on biomedicine. But it also addresses problems in materials design, veterinary medicine, finance, mathematics, and aerospace with its partners, such as an analysis of ways to reduce flight delays.

Pattern Computer has raised $26 million to date, all from individual investors, including Venter and Ken Goldman, former chief financial officer of Yahoo and Pattern’s consulting CFO. The startup is now seeking to raise $40 million with a valuation of $1.2 billion, said Anderson.

“It’s a company that is taking an intriguing new approach to manipulate and analyze big data,” said Hood. And when the pandemic hit, it “thought deeply about the COVID problem,” said Hood.

Gearing up a spit test

Pattern Computer takes a unique approach to COVID-19 testing. The company analyzes patterns of light that pass through and are absorbed by spit.

The test takes only two drops of saliva and reads off a result from the company’s “ProSpectral” device within three seconds. The device harnesses an approach called hyperspectral sensing, which involves the analysis of light across all spectrums.

Instead of measuring the virus directly, the test captures the jumbled immune and metabolic response to disease. “There’s a fingerprint for that in light,” said Anderson.

Company researchers trained and assessed their model using spit from 470 samples roughly equally divided between those that were COVID-19 positive and negative on a PCR test, a conventional way to detect the disease.

Fred Hutch associate professor Taran Gujral. (Fred Hutch Photo)

Pattern’s test could detect 100% of people with the disease, with 8% of individuals without the disease showing a false-positive result, Anderson reported at the Life Sciences Innovation Northwest meeting this April. Shifting the test’s parameters enabled some COVID-19 cases to slip through undetected but yielded fewer false-positive results.

The test is also inexpensive: the in-house cost of running it is about 50 cents.

The testing approach is “very smart,” said Taran Gujral, a systems biologist and associate professor at Fred Hutchinson Cancer Center. Gujral, who does not have a financial or collaboration relationship with the company, said the method also holds promise for detecting other diseases, potentially enabling rapid testing in airports, hospitals, and in the field.

“We think it will change diagnostics,” said Anderson.

Pattern Computer’s COVID-19 test. (Pattern Computer Image)

Keeping company secrets

Other outside researchers said they need more information to assess the company’s approach to COVID-19 testing.

The company does not divulge whether it captures data using a standard type of spectrophotometer that measures light in biological samples, or another instrument. “They are not sharing any information on how the signal is generated,” said Dan Fu, an assistant professor of chemistry at the University of Washington.

University of Washington microbiology professor Evgeni Sokurenko, who is developing a rapid test for COVID-19 variants as co-founder of ID Genomics, said it’s important to look closely at Pattern Computer’s data — in particular, the PCR data it used to train and test its models.

PCR tests work by replicating viral DNA through multiple cycles to detect a signal. Different labs use different cycle numbers for COVID-19 testing, he said. Higher cycle numbers detect lower levels of virus.

Evgeni Sokurenko, co-founder of ID Genomics and University of Washington professor. (UW Photo)

The majority of Pattern Computer’s COVID-19 positive samples had a cycle threshold below 30, said company researcher Matt Keener — whereas the typical threshold is set higher, said Sokurenko (generally at 35-40).

That raises the possibility that the company’s models may not be geared to pick up low levels of the virus, and could therefore miss some people with asymptomatic infections, said Sokurenko.

Keener countered that the company’s data are consistent across all PCR thresholds. The results “don’t show any statistical sensitivity to the PCR value,” said Keener. “Our accuracy holds no matter what the PCR value for an individual test sample is.” In addition, the accuracy of the company’s test held true whether the samples came from asymptomatic or symptomatic individuals, he said.

The U.S. Food and Drug Administration will be the final judge of the company’s COVID-19 test.

Pattern Computer has applied to the agency for emergency use authorization. It’s also identified four other countries for potential launch and has arranged for partners to help it scale up and produce the test.

“We’re looking forward to being able to discuss more once we are comfortably down the road to regulatory approvals and such,” said Keener.

Pattern Computer’s other bioscience projects include mining databases on gene activity in cancer cells to identify potential treatments, based on drugs already approved for other diseases — though how the company’s approach to this and other data-mining problems compares to others is hard to tell, said Gujral, who does similar research on patient tumor samples.

The company has identified two drug combinations that kill breast cancer cell lines in culture, and is moving them through animal testing for hard-to-treat “triple-negative” tumors. It also is investigating treatments for ovarian cancer and other tumor types.

Speaking at an investor presentation earlier this year, Omid Moghadam, CEO of diagnostics startup Namida Lab, said Pattern’s discovery engine substantially increased the predictive accuracy of an experimental test for breast cancer based on tear samples. Moghadam is a Pattern Computer customer and advisor.

And while Pattern has not published its bioscience projects in peer-reviewed journals, “their first priority has been to get everything going, which they’ve really had to put an enormous amount of time into,” said Hood. “I suspect they will be publishing comparative papers in the future.”

The team has been refining its system and mathematical tools over the last several years, with a lean crew of 21 employees. “We’ve been very heads down,” said Anderson.

Next generation computing

Pattern Computer is following the path of other groups, from academic labs to tech companies like Alphabet, that are changing how computers are constructed and programmed. The advent of artificial intelligence is spurring a surge of innovation.

AI models need to process vast numbers of calculations simultaneously. And current computing architecture designs are becoming a bottleneck for “computing speed, infrastructure cost, and power consumption,” said University of Chicago assistant professor of molecular engineering Sihong Wang.

“People working on the hardware side have started to develop a completely different type of computing platform that processes information by emulating the operation of neurons in the brain,” said Wang, who recently developed a flexible computing chip for wearable health tech, and is not familiar with Pattern Computer’s system.

University of Chicago professor Sihong Wang with his new chip. (Univ. Chicago Photo)

Anderson said Pattern Computer’s approach is unique. The company created an AI system that is distinct from the neural network approached leveraged by others, he said. “This is qualitatively very different from where someone has a neural network and they’re pushing it and modifying it,” he said.

Pattern Computer’s “explainable AI” enables it to counteract bias that can be baked into more conventional machine learning models by skewed training datasets, said Anderson.

“It allows us to see how and why the system was successful in getting high prediction rates,” he said. “Knowing how and why the system works provides the type of knowledge required to make major pattern discoveries, improve research, and solve real business problems.”

Building that new way to make sense of patterns is “a challenging problem,” said Neeraj Kumar, a senior data scientist at Pacific Northwest National Laboratory.

In a recent preprint with outside researchers, company researchers published their view of how explainable AI could be applied to health data.

The publication does not dive into the details of how the company’s system works, said Vijay Janap Reddi, a Harvard associate professor who directs the university’s Edge Computing Lab. “It is hard to glean much” about the startup from the preprint, said Reddi, who was not familiar with the company.

But Kumar has seen enough to be convinced.

“Pattern Computer’s computational approach is very robust,” said Kumar, an author on the paper. And it is “the first step for developing an explainable AI by extracting novel patterns in complex data that cannot be discovered using conventional analytical techniques and algorithms,” he said.

Meanwhile, the company is turning its attention to securing regulatory approval for its COVID-19 test and planning for scale up.

“We’ve created a different kind of company,” said Anderson. “We’ve done it in a different way.”

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Veterans Affairs Kept COVID-19 Vaccine Mandate In Place Without Evidence

Veterans Affairs Kept COVID-19 Vaccine Mandate In Place Without Evidence

Authored by Zachary Stieber via The Epoch Times (emphasis ours),

The…

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Veterans Affairs Kept COVID-19 Vaccine Mandate In Place Without Evidence

Authored by Zachary Stieber via The Epoch Times (emphasis ours),

The U.S. Department of Veterans Affairs (VA) reviewed no data when deciding in 2023 to keep its COVID-19 vaccine mandate in place.

Doses of a COVID-19 vaccine in Washington in a file image. (Jacquelyn Martin/Pool/AFP via Getty Images)

VA Secretary Denis McDonough said on May 1, 2023, that the end of many other federal mandates “will not impact current policies at the Department of Veterans Affairs.”

He said the mandate was remaining for VA health care personnel “to ensure the safety of veterans and our colleagues.”

Mr. McDonough did not cite any studies or other data. A VA spokesperson declined to provide any data that was reviewed when deciding not to rescind the mandate. The Epoch Times submitted a Freedom of Information Act for “all documents outlining which data was relied upon when establishing the mandate when deciding to keep the mandate in place.”

The agency searched for such data and did not find any.

The VA does not even attempt to justify its policies with science, because it can’t,” Leslie Manookian, president and founder of the Health Freedom Defense Fund, told The Epoch Times.

“The VA just trusts that the process and cost of challenging its unfounded policies is so onerous, most people are dissuaded from even trying,” she added.

The VA’s mandate remains in place to this day.

The VA’s website claims that vaccines “help protect you from getting severe illness” and “offer good protection against most COVID-19 variants,” pointing in part to observational data from the U.S. Centers for Disease Control and Prevention (CDC) that estimate the vaccines provide poor protection against symptomatic infection and transient shielding against hospitalization.

There have also been increasing concerns among outside scientists about confirmed side effects like heart inflammation—the VA hid a safety signal it detected for the inflammation—and possible side effects such as tinnitus, which shift the benefit-risk calculus.

President Joe Biden imposed a slate of COVID-19 vaccine mandates in 2021. The VA was the first federal agency to implement a mandate.

President Biden rescinded the mandates in May 2023, citing a drop in COVID-19 cases and hospitalizations. His administration maintains the choice to require vaccines was the right one and saved lives.

“Our administration’s vaccination requirements helped ensure the safety of workers in critical workforces including those in the healthcare and education sectors, protecting themselves and the populations they serve, and strengthening their ability to provide services without disruptions to operations,” the White House said.

Some experts said requiring vaccination meant many younger people were forced to get a vaccine despite the risks potentially outweighing the benefits, leaving fewer doses for older adults.

By mandating the vaccines to younger people and those with natural immunity from having had COVID, older people in the U.S. and other countries did not have access to them, and many people might have died because of that,” Martin Kulldorff, a professor of medicine on leave from Harvard Medical School, told The Epoch Times previously.

The VA was one of just a handful of agencies to keep its mandate in place following the removal of many federal mandates.

“At this time, the vaccine requirement will remain in effect for VA health care personnel, including VA psychologists, pharmacists, social workers, nursing assistants, physical therapists, respiratory therapists, peer specialists, medical support assistants, engineers, housekeepers, and other clinical, administrative, and infrastructure support employees,” Mr. McDonough wrote to VA employees at the time.

This also includes VA volunteers and contractors. Effectively, this means that any Veterans Health Administration (VHA) employee, volunteer, or contractor who works in VHA facilities, visits VHA facilities, or provides direct care to those we serve will still be subject to the vaccine requirement at this time,” he said. “We continue to monitor and discuss this requirement, and we will provide more information about the vaccination requirements for VA health care employees soon. As always, we will process requests for vaccination exceptions in accordance with applicable laws, regulations, and policies.”

The version of the shots cleared in the fall of 2022, and available through the fall of 2023, did not have any clinical trial data supporting them.

A new version was approved in the fall of 2023 because there were indications that the shots not only offered temporary protection but also that the level of protection was lower than what was observed during earlier stages of the pandemic.

Ms. Manookian, whose group has challenged several of the federal mandates, said that the mandate “illustrates the dangers of the administrative state and how these federal agencies have become a law unto themselves.”

Tyler Durden Sat, 03/09/2024 - 22:10

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Are Voters Recoiling Against Disorder?

Are Voters Recoiling Against Disorder?

Authored by Michael Barone via The Epoch Times (emphasis ours),

The headlines coming out of the Super…

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Are Voters Recoiling Against Disorder?

Authored by Michael Barone via The Epoch Times (emphasis ours),

The headlines coming out of the Super Tuesday primaries have got it right. Barring cataclysmic changes, Donald Trump and Joe Biden will be the Republican and Democratic nominees for president in 2024.

(Left) President Joe Biden delivers remarks on canceling student debt at Culver City Julian Dixon Library in Culver City, Calif., on Feb. 21, 2024. (Right) Republican presidential candidate and former U.S. President Donald Trump stands on stage during a campaign event at Big League Dreams Las Vegas in Las Vegas, Nev., on Jan. 27, 2024. (Mario Tama/Getty Images; David Becker/Getty Images)

With Nikki Haley’s withdrawal, there will be no more significantly contested primaries or caucuses—the earliest both parties’ races have been over since something like the current primary-dominated system was put in place in 1972.

The primary results have spotlighted some of both nominees’ weaknesses.

Donald Trump lost high-income, high-educated constituencies, including the entire metro area—aka the Swamp. Many but by no means all Haley votes there were cast by Biden Democrats. Mr. Trump can’t afford to lose too many of the others in target states like Pennsylvania and Michigan.

Majorities and large minorities of voters in overwhelmingly Latino counties in Texas’s Rio Grande Valley and some in Houston voted against Joe Biden, and even more against Senate nominee Rep. Colin Allred (D-Texas).

Returns from Hispanic precincts in New Hampshire and Massachusetts show the same thing. Mr. Biden can’t afford to lose too many Latino votes in target states like Arizona and Georgia.

When Mr. Trump rode down that escalator in 2015, commentators assumed he’d repel Latinos. Instead, Latino voters nationally, and especially the closest eyewitnesses of Biden’s open-border policy, have been trending heavily Republican.

High-income liberal Democrats may sport lawn signs proclaiming, “In this house, we believe ... no human is illegal.” The logical consequence of that belief is an open border. But modest-income folks in border counties know that flows of illegal immigrants result in disorder, disease, and crime.

There is plenty of impatience with increased disorder in election returns below the presidential level. Consider Los Angeles County, America’s largest county, with nearly 10 million people, more people than 40 of the 50 states. It voted 71 percent for Mr. Biden in 2020.

Current returns show county District Attorney George Gascon winning only 21 percent of the vote in the nonpartisan primary. He’ll apparently face Republican Nathan Hochman, a critic of his liberal policies, in November.

Gascon, elected after the May 2020 death of counterfeit-passing suspect George Floyd in Minneapolis, is one of many county prosecutors supported by billionaire George Soros. His policies include not charging juveniles as adults, not seeking higher penalties for gang membership or use of firearms, and bringing fewer misdemeanor cases.

The predictable result has been increased car thefts, burglaries, and personal robberies. Some 120 assistant district attorneys have left the office, and there’s a backlog of 10,000 unprosecuted cases.

More than a dozen other Soros-backed and similarly liberal prosecutors have faced strong opposition or have left office.

St. Louis prosecutor Kim Gardner resigned last May amid lawsuits seeking her removal, Milwaukee’s John Chisholm retired in January, and Baltimore’s Marilyn Mosby was defeated in July 2022 and convicted of perjury in September 2023. Last November, Loudoun County, Virginia, voters (62 percent Biden) ousted liberal Buta Biberaj, who declined to prosecute a transgender student for assault, and in June 2022 voters in San Francisco (85 percent Biden) recalled famed radical Chesa Boudin.

Similarly, this Tuesday, voters in San Francisco passed ballot measures strengthening police powers and requiring treatment of drug-addicted welfare recipients.

In retrospect, it appears the Floyd video, appearing after three months of COVID-19 confinement, sparked a frenzied, even crazed reaction, especially among the highly educated and articulate. One fatal incident was seen as proof that America’s “systemic racism” was worse than ever and that police forces should be defunded and perhaps abolished.

2020 was “the year America went crazy,” I wrote in January 2021, a year in which police funding was actually cut by Democrats in New York, Los Angeles, San Francisco, Seattle, and Denver. A year in which young New York Times (NYT) staffers claimed they were endangered by the publication of Sen. Tom Cotton’s (R-Ark.) opinion article advocating calling in military forces if necessary to stop rioting, as had been done in Detroit in 1967 and Los Angeles in 1992. A craven NYT publisher even fired the editorial page editor for running the article.

Evidence of visible and tangible discontent with increasing violence and its consequences—barren and locked shelves in Manhattan chain drugstores, skyrocketing carjackings in Washington, D.C.—is as unmistakable in polls and election results as it is in daily life in large metropolitan areas. Maybe 2024 will turn out to be the year even liberal America stopped acting crazy.

Chaos and disorder work against incumbents, as they did in 1968 when Democrats saw their party’s popular vote fall from 61 percent to 43 percent.

Views expressed in this article are opinions of the author and do not necessarily reflect the views of The Epoch Times or ZeroHedge.

Tyler Durden Sat, 03/09/2024 - 23:20

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Low Iron Levels In Blood Could Trigger Long COVID: Study

Low Iron Levels In Blood Could Trigger Long COVID: Study

Authored by Amie Dahnke via The Epoch Times (emphasis ours),

People with inadequate…

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Low Iron Levels In Blood Could Trigger Long COVID: Study

Authored by Amie Dahnke via The Epoch Times (emphasis ours),

People with inadequate iron levels in their blood due to a COVID-19 infection could be at greater risk of long COVID.

(Shutterstock)

A new study indicates that problems with iron levels in the bloodstream likely trigger chronic inflammation and other conditions associated with the post-COVID phenomenon. The findings, published on March 1 in Nature Immunology, could offer new ways to treat or prevent the condition.

Long COVID Patients Have Low Iron Levels

Researchers at the University of Cambridge pinpointed low iron as a potential link to long-COVID symptoms thanks to a study they initiated shortly after the start of the pandemic. They recruited people who tested positive for the virus to provide blood samples for analysis over a year, which allowed the researchers to look for post-infection changes in the blood. The researchers looked at 214 samples and found that 45 percent of patients reported symptoms of long COVID that lasted between three and 10 months.

In analyzing the blood samples, the research team noticed that people experiencing long COVID had low iron levels, contributing to anemia and low red blood cell production, just two weeks after they were diagnosed with COVID-19. This was true for patients regardless of age, sex, or the initial severity of their infection.

According to one of the study co-authors, the removal of iron from the bloodstream is a natural process and defense mechanism of the body.

But it can jeopardize a person’s recovery.

When the body has an infection, it responds by removing iron from the bloodstream. This protects us from potentially lethal bacteria that capture the iron in the bloodstream and grow rapidly. It’s an evolutionary response that redistributes iron in the body, and the blood plasma becomes an iron desert,” University of Oxford professor Hal Drakesmith said in a press release. “However, if this goes on for a long time, there is less iron for red blood cells, so oxygen is transported less efficiently affecting metabolism and energy production, and for white blood cells, which need iron to work properly. The protective mechanism ends up becoming a problem.”

The research team believes that consistently low iron levels could explain why individuals with long COVID continue to experience fatigue and difficulty exercising. As such, the researchers suggested iron supplementation to help regulate and prevent the often debilitating symptoms associated with long COVID.

It isn’t necessarily the case that individuals don’t have enough iron in their body, it’s just that it’s trapped in the wrong place,” Aimee Hanson, a postdoctoral researcher at the University of Cambridge who worked on the study, said in the press release. “What we need is a way to remobilize the iron and pull it back into the bloodstream, where it becomes more useful to the red blood cells.”

The research team pointed out that iron supplementation isn’t always straightforward. Achieving the right level of iron varies from person to person. Too much iron can cause stomach issues, ranging from constipation, nausea, and abdominal pain to gastritis and gastric lesions.

1 in 5 Still Affected by Long COVID

COVID-19 has affected nearly 40 percent of Americans, with one in five of those still suffering from symptoms of long COVID, according to the U.S. Centers for Disease Control and Prevention (CDC). Long COVID is marked by health issues that continue at least four weeks after an individual was initially diagnosed with COVID-19. Symptoms can last for days, weeks, months, or years and may include fatigue, cough or chest pain, headache, brain fog, depression or anxiety, digestive issues, and joint or muscle pain.

Tyler Durden Sat, 03/09/2024 - 12:50

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