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Pioneering simulations focus on HIV-1 virus

When is a container not just a container? Credit: Bryer et al. When is a container not just a container? For the HIV-1 virus, a double layer of fatty molecules…

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When is a container not just a container?

Credit: Bryer et al.

When is a container not just a container?

For the HIV-1 virus, a double layer of fatty molecules called lipids not only serves as its container, but also plays a key role in the virus’s replication and infectivity. Scientists have used supercomputers to complete the first-ever biologically authentic computer model of the HIV-1 virus liposome, its complete spherical lipid bilayer.

What’s more, this study comes fresh off the heels of a new atomistic model of the HIV-1 capsid, which contains its genetic material. The scientists are hopeful this basic research into viral envelopes can help efforts to develop new HIV-1 therapeutics, as well as laying a foundation for study of other enveloped viruses such as the novel coronavirus, SARS-CoV-2.

“This work represents an investigation of the HIV-1 liposome at full-scale, and with an unprecedented level of chemical complexity,” said Alex Bryer, a PhD student in the Perilla Laboratory, Department of Chemistry and Biochemistry, University of Delaware. Bryer is the lead author of the liposome-modeling research, published January 2022 in the journal PLOS Computational Biology.

The science team developed a complex chemical model of the HIV-1 liposome that revealed key characteristics of the liposome’s asymmetry. Most such models assume a geometrically uniform structure and don’t capture the asymmetry inherent in such biological containers.

Lipid Flip-Flop
Bryer and his co-authors investigated a mechanism that’s known colloquially as “lipid flip-flop,” which is when lipids in one of the leaflets of the bilayer are moved or transported to the other leaflet. The leaflets flip-flop the lipids and exchange the molecules for various purposes such as achieving a dynamic equilibrium.

“For the spherical vesicle model of the liposome, our simulations show that asymmetry occurs spontaneously even without embedded proteins, and the vesicle can flip-flop to maintain an asymmetric composition within tight tolerances – even over biological timescales in excess of five microseconds,” Bryer said.

Interestingly, the science team did not observe incidence of flip-flop in a flat membrane system, which suggests that curvature of the envelope is intimately related to this biological process.

“Nothing like this has ever been simulated before.” said study co-author Juan R. Perilla, an assistant professor in the Department of Chemistry and Biochemistry, University of Delaware.

“What was surprising for us is this dynamic equilibrium that the vesicle shows,” Perilla added. “Lipids are moving in and out, but the overall composition is not changing – that was surprising.”

Key Asymmetry
This key finding shows that the complex, asymmetric membrane composition of the HIV-1 virus can lead to macroscopic properties such as the differential displacement between leaflets and lipid microdomain formation.

That formation might have implications in how membrane proteins, which often localize within specific lipid microdomains, interact with the membrane and carry out functions such as binding to host cells and allowing the virus to enter them.

For HIV-1, it’s known that microdomains form and act as a target for the localization of membrane proteins. One protein in particular, gp41, is critical for membrane fusion, which is the process of HIV-1 joining with the host cell membrane and ultimately infecting it.

“It’s thought that gp41 localizes to these domains,” Bryer said. “What we showed was that these microdomains can form in the vesicle without the aid of proteins. They seem to emerge spontaneously.”

This finding might also explain the preferential budding behavior in HIV-1 viral replication, without the need of embedded proteins in mediating the formation of the microdomains that enable budding.

Supercomputer Simulations
The computer model Bryer and colleagues developed is 150 nm in diameter and consists of 24 different chemical constituents. There are more than 300,000 total lipid molecules, solvated in water and ionized with sodium chloride, to represent a biological environment. The science team employed a coarse-grained model known as MARTINI, which allowed them to reduce the degrees of freedom in the molecular system and achieve simulation sampling over microsecond timescales.

The scientists were awarded supercomputer allocations and training by XSEDE funded by the National Science Foundation. Through XSEDE, they used the Stampede2 system at the Texas Advanced Computing Center (TACC) and Bridges-2 at the Pittsburgh Supercomputing Center (PSC). Additionally, they used Grizzly at the Los Alamos National Laboratory; Blue Waters at the National Center for Supercomputing Applications; and the Frontera system at TACC.

“Our study wouldn’t have been possible without XSEDE resources,” Bryer said. “We can achieve some very high sampling efficiencies using Stampede2 Skylake nodes, both to run the simulations and perform analyses.”

“I was able to perform calculations, and without needing to transfer data, I could set up a visualization session through the TACC portal and analyze and work with my data directly on Stampede2. That’s amazing,” added Bryer. He found that not having to transfer terabytes of data into a separate visualization computer node was “just huge in terms of productivity.”
“We also used quite a bit of the high memory nodes on Bridges-2 of PSC,” Perilla said. They helped power simulations that compared the control, a flat HIV-1 viral membrane, to the curved one in dynamic equilibrium.

What’s more, the Perilla Lab has transferred the simulation work to their local cluster, the XSEDE-allocated DARWIN system of the University of Delaware.

“It’s important to highlight the fact that XSEDE does not just provide resources, which are extremely valuable. There’s training and other opportunities such as workshops,” Perilla said.

“When I joined the group, I had never logged into a supercomputer,” Bryer said. He recalled valuable training in XSEDE workshops on OpenMP, MPI, and OpenACC, which assist scientists in parallelizing their computer code.

Frontera Work
Bryer also highlighted the analysis work run on TACC’s Frontera, the fastest academic supercomputer in the world. “Parallel I/O via Luster is what made a lot of the analyses possible in the manuscript,” Bryer said. “On Frontera we were able to classify the volume surrounding the vesicle quickly and process our data in minutes. We estimated it might take about three weeks if we were to run the analysis in a serial naive implementation.”

The Perilla Lab has focused all of this computing power and expertise into learning more about the mysteries of what happens to the HIV-1 viral envelope during infection.

“While this study does not provide the whole answer, it’s getting there in what the lipids are doing and what integral membrane proteins are doing or could be doing; and not only how proteins like gp41 interact with human receptors but also how they transmit their signals and how that is related to lipid composition,” Perilla said.

“This computational study provides an opportunity for drug development research,” Perilla added.

Since lipid symmetry is maintained by the curvature of the envelope, a promising possibility yet unexplored is development of small molecules that affect the symmetry and potentially yield a therapeutic target.

HIV-1 Capsid
Just prior to the liposome research, Perilla and colleagues also broke new ground in using supercomputers to build the first-ever atomistic model of the HIV-1 capsid, the envelope for its genetic material, in the presence of the metabolite IP6. The work was published November 2021 in the journal Science Advances. It also used the Bridges-2 and Stampede2 supercomputers allocated through XSEDE.

The simulations, validated by cryo-electron tomography data, showed that IP6 was able to bind in two locations to the capsid, instead of just one as previously thought. This finding is important because during infection, the capsid is exposed to the cytoplasm and has to go through the nuclear import mechanism, namely the nuclear pore complex. All these pieces together point to the capsid being able to “sense” in an as yet unknown way the concentration of IP6.

Said Perilla: “Computationally, these are very unique simulations because of the number of degrees of freedom involved. Nobody’s ever walked this path before. We’re walking through the dark. And we’re making tools that can help us see beyond where we are.”


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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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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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The Coming Of The Police State In America

The Coming Of The Police State In America

Authored by Jeffrey Tucker via The Epoch Times,

The National Guard and the State Police are now…

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The Coming Of The Police State In America

Authored by Jeffrey Tucker via The Epoch Times,

The National Guard and the State Police are now patrolling the New York City subway system in an attempt to do something about the explosion of crime. As part of this, there are bag checks and new surveillance of all passengers. No legislation, no debate, just an edict from the mayor.

Many citizens who rely on this system for transportation might welcome this. It’s a city of strict gun control, and no one knows for sure if they have the right to defend themselves. Merchants have been harassed and even arrested for trying to stop looting and pillaging in their own shops.

The message has been sent: Only the police can do this job. Whether they do it or not is another matter.

Things on the subway system have gotten crazy. If you know it well, you can manage to travel safely, but visitors to the city who take the wrong train at the wrong time are taking grave risks.

In actual fact, it’s guaranteed that this will only end in confiscating knives and other things that people carry in order to protect themselves while leaving the actual criminals even more free to prey on citizens.

The law-abiding will suffer and the criminals will grow more numerous. It will not end well.

When you step back from the details, what we have is the dawning of a genuine police state in the United States. It only starts in New York City. Where is the Guard going to be deployed next? Anywhere is possible.

If the crime is bad enough, citizens will welcome it. It must have been this way in most times and places that when the police state arrives, the people cheer.

We will all have our own stories of how this came to be. Some might begin with the passage of the Patriot Act and the establishment of the Department of Homeland Security in 2001. Some will focus on gun control and the taking away of citizens’ rights to defend themselves.

My own version of events is closer in time. It began four years ago this month with lockdowns. That’s what shattered the capacity of civil society to function in the United States. Everything that has happened since follows like one domino tumbling after another.

It goes like this:

1) lockdown,

2) loss of moral compass and spreading of loneliness and nihilism,

3) rioting resulting from citizen frustration, 4) police absent because of ideological hectoring,

5) a rise in uncontrolled immigration/refugees,

6) an epidemic of ill health from substance abuse and otherwise,

7) businesses flee the city

8) cities fall into decay, and that results in

9) more surveillance and police state.

The 10th stage is the sacking of liberty and civilization itself.

It doesn’t fall out this way at every point in history, but this seems like a solid outline of what happened in this case. Four years is a very short period of time to see all of this unfold. But it is a fact that New York City was more-or-less civilized only four years ago. No one could have predicted that it would come to this so quickly.

But once the lockdowns happened, all bets were off. Here we had a policy that most directly trampled on all freedoms that we had taken for granted. Schools, businesses, and churches were slammed shut, with various levels of enforcement. The entire workforce was divided between essential and nonessential, and there was widespread confusion about who precisely was in charge of designating and enforcing this.

It felt like martial law at the time, as if all normal civilian law had been displaced by something else. That something had to do with public health, but there was clearly more going on, because suddenly our social media posts were censored and we were being asked to do things that made no sense, such as mask up for a virus that evaded mask protection and walk in only one direction in grocery aisles.

Vast amounts of the white-collar workforce stayed home—and their kids, too—until it became too much to bear. The city became a ghost town. Most U.S. cities were the same.

As the months of disaster rolled on, the captives were let out of their houses for the summer in order to protest racism but no other reason. As a way of excusing this, the same public health authorities said that racism was a virus as bad as COVID-19, so therefore it was permitted.

The protests had turned to riots in many cities, and the police were being defunded and discouraged to do anything about the problem. Citizens watched in horror as downtowns burned and drug-crazed freaks took over whole sections of cities. It was like every standard of decency had been zapped out of an entire swath of the population.

Meanwhile, large checks were arriving in people’s bank accounts, defying every normal economic expectation. How could people not be working and get their bank accounts more flush with cash than ever? There was a new law that didn’t even require that people pay rent. How weird was that? Even student loans didn’t need to be paid.

By the fall, recess from lockdown was over and everyone was told to go home again. But this time they had a job to do: They were supposed to vote. Not at the polling places, because going there would only spread germs, or so the media said. When the voting results finally came in, it was the absentee ballots that swung the election in favor of the opposition party that actually wanted more lockdowns and eventually pushed vaccine mandates on the whole population.

The new party in control took note of the large population movements out of cities and states that they controlled. This would have a large effect on voting patterns in the future. But they had a plan. They would open the borders to millions of people in the guise of caring for refugees. These new warm bodies would become voters in time and certainly count on the census when it came time to reapportion political power.

Meanwhile, the native population had begun to swim in ill health from substance abuse, widespread depression, and demoralization, plus vaccine injury. This increased dependency on the very institutions that had caused the problem in the first place: the medical/scientific establishment.

The rise of crime drove the small businesses out of the city. They had barely survived the lockdowns, but they certainly could not survive the crime epidemic. This undermined the tax base of the city and allowed the criminals to take further control.

The same cities became sanctuaries for the waves of migrants sacking the country, and partisan mayors actually used tax dollars to house these invaders in high-end hotels in the name of having compassion for the stranger. Citizens were pushed out to make way for rampaging migrant hordes, as incredible as this seems.

But with that, of course, crime rose ever further, inciting citizen anger and providing a pretext to bring in the police state in the form of the National Guard, now tasked with cracking down on crime in the transportation system.

What’s the next step? It’s probably already here: mass surveillance and censorship, plus ever-expanding police power. This will be accompanied by further population movements, as those with the means to do so flee the city and even the country and leave it for everyone else to suffer.

As I tell the story, all of this seems inevitable. It is not. It could have been stopped at any point. A wise and prudent political leadership could have admitted the error from the beginning and called on the country to rediscover freedom, decency, and the difference between right and wrong. But ego and pride stopped that from happening, and we are left with the consequences.

The government grows ever bigger and civil society ever less capable of managing itself in large urban centers. Disaster is unfolding in real time, mitigated only by a rising stock market and a financial system that has yet to fall apart completely.

Are we at the middle stages of total collapse, or at the point where the population and people in leadership positions wise up and decide to put an end to the downward slide? It’s hard to know. But this much we do know: There is a growing pocket of resistance out there that is fed up and refuses to sit by and watch this great country be sacked and taken over by everything it was set up to prevent.

Tyler Durden Sat, 03/09/2024 - 16:20

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