Math model can help fight HIV

A new mathematical model may help scientists develop effective drugs to not only treat, but actually cure HIV. HIV is Human Immunodeficiency Virus, and it causes AIDS—Acquired Immune Deficiency Syndrome.

Current antiretroviral medicines attack cells that act as active virus factories to mass produce and spread the virus so it can infect more cells. However, any cure for HIV must deal with latently-infected cells.

AIDS orphans from Cambodia. By Cambodia4kids.org, Beth Kanter from Massachusetts, USA (HIV Kids) [CC-BY-2.0 (http://creativecommons.org/licenses/by/2.0)], via Wikimedia Commons.

AIDS orphans from Cambodia. By Cambodia4kids.org, Beth Kanter from Massachusetts, USA (HIV Kids) [CC-BY-2.0 (http://creativecommons.org/licenses/by/2.0)%5D, via Wikimedia Commons.

Instead of actively reproducing, the virus in these long-lived CD4+T cells is basically resting. And virus in those cells can survive, even after patients have been taking HIV medicines for years. Think of the latently-infected cells as sitting on the bench and waiting at some point to get into the game, as it were.

Unfortunately, HIV and AIDS are no game. Roughly 35 million people are living with HIV, reports the Joint United Nations Programme on HIV/AIDS (UNAIDS). AIDS-related causes killed about 1.5 million people last year, and the total death toll since the 1980s is 39 million.

Research is underway on latency-reversing agents, or LRAs. Until now, though, it’s been hard to say how strong those drugs would have to be to have a real cure.

“For HIV, a cure means being able to stop taking all drugs, without a risk of the virus growing back to high levels,” says Alison Hill, a researcher in evolutionary dynamics at Harvard University.

Now Hill and other researchers have developed a computer model to gauge how effective a medicine must be to really tackle those latently-infected cells. The team includes scientists from Harvard, Columbia, and Johns Hopkins universities in the United States, the Howard Hughes Medical Center, and the Institute of Integrative Biology in Zurich, Switzerland. PNAS, Proceedings of the National Academy of Sciences, is publishing the research.

As with any computer model, the researchers use math to see what might happen under different scenarios. Programming includes detailed algorithms—sets of instructions that tell the computer what to do with data.

The team found that a latency-reversing agent would have to reduce the number of infected cells by about 2,000-fold in order to let a majority of patients skip antiretroviral therapy, or ART, for one year. After that time, however, rebound could occur suddenly.

“We were able to determine that a 90%, 99%, or even 99.9% reduction in the latent pool is unlikely to lead to a cure,” notes Hill. “We predicted that if patients stop their drug cocktails after this type of reduction, they may appear to be cured for many months, but the virus is very likely to eventually reappear.”

“This means we likely need drugs much stronger than anything tested so far in the lab,” Hill continues. In order to prevent rebound altogether, the research team concluded, treatments would have to reduce infected cells by more than 10,000-fold, the team found.

That sounds like a daunting task, and it is. Moreover, the team’s results predict there would be large variation in when patients would rebound.

Nonetheless, the model can ultimately help speed up the search for a cure.

“This study was important because using math, we could help answer an important medical question that cannot yet be answered experimentally,” Hill says. “It may hopefully save researchers and patients from clinical trials that are unlikely to be successful.”

The research also helps explain why some apparent cures, such as treatment immediately after birth or bone marrow transplants, were not in fact permanent, Hill notes.

The more scientists can understand about HIV and what the challenges in fighting it are, the closer we all are to winning the battle against AIDS.

 

 

It’s All Happening at the Zoo

See how solar energy is a start at the Cincinnati Zoo & Botanical Garden. Check out my latest post at Midwest Energy News:

Cincinnati Zoo solar array

Note to Facebook: Non-apology Apologies Don’t Count

Earlier this week, Facebook COO Sheryl Sandberg offered a half-hearted apology after it became clear that data collected by the online social network was used in a social science study. Sandberg didn’t say the company was sorry for collecting the data without its users’ informed consent—only that it had been “poorly communicated.”

“We never meant to upset you,” Sandberg said.

As Time’s Jared Newman has pointed out, her words were basically a “corporate non-apology.” In other words, Facebook wasn’t sorry for what it did—only that it got caught and that people were upset.

The study in question set out to manipulate emotions based on the types of posts people saw in their Facebook Newsfeeds. In general, people whose Newsfeeds showed less positive posts were more likely to use negative words in their own status updates. Fewer negative posts produced an opposite pattern.

“The results show emotional contagion,” report study authors Adam Kramer, Jamie Guillory, and Jeffrey Hancock in PNAS, the Proceedings for the National Academy of Sciences, which published the study last month.

Now PNAS has issued an “Editorial Expression of Concern.” Because Facebook collected the data based on its internal policies, the Cornell researchers had determined they were not subject to the “Common Rule.” That’s the general federal policy for the protection of human subjects. Despite that, the editors note:

It is nevertheless a matter of concern that the collection of the data by Facebook may have involved practices that were not fully consistent with the principles of obtaining informed consent and allowing participants to opt out.

This may be more than the half-hearted apology Facebook offered, but it leaves a lot of open questions.

A primary reason for requiring informed consent is to protect potential test subjects. The Common Rule also establishes a level playing field for conducting scientific research.

The researchers in this case may have had good motives in using the Facebook data. But should any researchers be able to evade the Common Rule’s requirements just because their data comes from a corporation, rather than the laboratory?

It’s times like this that I wish Facebook had a “dislike” button.

 

What Happens in Vegas….

Las Vegas is hosting two notable conferences this month, and the groups couldn’t be more different.

Next Monday through Wednesday, the Heartland Institute will present its 9th Annual Conference on Climate Change at the Mandalay Bay Resort and Casino. However, it’s unlikely the conference will offer practical solutions to the impacts identified in the U.S. Global Change Research Program’s Third National Climate Assessment, which was released this spring. Rather, the Heartland Institute’s website promises that its conference will be “the largest gathering of global warming ‘skeptics’ in the world.”

Mandalay Bay Hotel. Image by Sascha Brück from Wikimedia.

Mandalay Bay Hotel. Image by Sascha Brück from Wikimedia.

A 2011 editorial in the journal Nature notes that there’s a big difference between asking legitimate questions to fill gaps in knowledge and seizing on any degree of uncertainty to reject sound science. “[T]he Heartland Institute and its ilk are not trying to build a theory of anything,” says the editorial. “They have set the bar much lower, and are happy muddying the waters.”

The Center for Media and Democracy has noted close ties between the Heartland Institute and ALEC, the American Legislative Exchange Council. ALEC actively opposes laws that promote renewable energy technologies and set energy efficiency goals through enforceable standards. ALEC’s board members include Ohio State Senator Bill Seitz, who championed Ohio’s recent “freeze” and substantial cutbacks to the state’s standards for energy efficiency and renewable energy.

Two weeks later, the NAACP will hold its annual convention at Mandalay Bay. Part of the organization’s work on civil and human rights includes its Climate Justice Initiative. “Global climate change has a disproportionate impact on communities of color in the United States and around the world,” explains the organization’s website.

Toward this end, the NAACP particularly opposes coal-powered electric generation. Its reports include “Coal-Blooded: Putting Profits Before People.” Another report released last December is “Just Energy Policies: Reducing Pollution and Creating Jobs.”

Both reports note that coal-fired power plants tend to be located in or close to poor communities whose residents often include substantial numbers of people of color. Pollution from the plants contributes to health problems, including lung disease, note the reports. “Therefore, many will die early from exposure to pollution if we do not change now,” said Alabama NAACP President Bernard Simelton when the “Just Energy Policies” report was released.

Contrary to the host city’s long-running ad campaign, neither organization wants what happens in Vegas to stay there. Both groups hope to influence public policy—in dramatically different ways.

The topic of climate change continues to be hot. And Las Vegas this July will be very hot–in more ways than one.

 

 

Ready, Set, Sample!

MBL, Woods Hole, MA. Image (c) Kathiann M. Kowalski.

MBL, Woods Hole, MA.  Image (c) Kathiann M. Kowalski.

 

Heading to the beach on a Saturday isn’t that unusual. After all, it’s summer. But having scientists head to beaches around the world on the same day is indeed something unusual.

Last Saturday, marine scientists collected seawater samples from more than 170 locations from Iceland to Antarctica. It’s all part of Ocean Sampling Day.

The sampling snapshots will provide important baseline knowledge about microorganisms in the world’s oceans. Jacobs University in Germany and the University of Oxford in the United Kingdome coordinate the effort, which was launched by the Micro B3 Project. Micro B3 stands for “Marine Microbial Biodiversity, Bioinformatics, Biotechnology.”

Scientists at each place collected five or six liters of seawater around midday local time. Yet while the sampling is now done, the scientists’ work has just started.

“If you sample from the environment, you’re going to have all kinds of things in that water,” notes Will Melvin. Melvin is a visiting scientist at MBL’s Josephine Bay Paul Center. He took samples near the squid gate at MBL in Woods Hole, Massachusetts.

After scientists collect the samples, fine filters strain out the biological material. That material then goes into a solution. The solution breaks open the cell walls, which lets scientists get to DNA and other material inside.

The solution also makes it easier to freeze material for future research projects. “A lot of that study will focus on bacteria,” notes Melvin.

Such studies will expand basic scientific knowledge about cell functions. It can also let scientists study particular types of bacteria.

Beyond that, scientists are interested in the overall profile of the oceans’ microbial communities. They want to know what it looks like know. And they want to see how it will change over time. After all, what looks like “just” a bottle of seawater holds clues to the health of the whole planet.

“Microbes are the most numerous inhabitants in the ocean, and it is important to the biosphere and the health of our planet that they continue to deliver the ecosystem services that they provide, including half of the oxygen we breathe,” notes Linda Amaral Zettler, also at MBL’s Josephine Bay Paul Center. She helped coordinate sample collections at the Atlantic Ocean’s Azorean Islands.

Tracking changes in microbial populations “may provide clues to ocean health and ultimately the health of the planet,” Amaral Zettler adds.

And, of course, a day at the beach beats at day in the office any time!

 

Super Stiff Stuff

Last week I wrote about flexible transistors. Within a few years, we might be wearing wrap-around phones or other bendy devices that use the organic components from Plastic Logic, a Cambridge, UK company.

This week brings something almost the opposite: ultrastiff metamaterials.

 Lawrence Livermore National Laboratory (LLNL) research team members and co-authors Eric Duoss, Julie Jackson, Chris Spadaccini, Xiaoyu “Rayne” Zheng, and Todd Weisgraber (left to right) in the lab holding larger versions of the architected materials that are highlighted in their June 19 Science  article. (Courtesy Lawrence Livermore National Laboratory.)

Lawrence Livermore National Laboratory (LLNL) research team members and co-authors Eric Duoss, Julie Jackson, Chris Spadaccini, Xiaoyu “Rayne” Zheng, and Todd Weisgraber (left to right) in the lab holding larger versions of the architected materials that are highlighted in their June 19 Science article. (Courtesy Lawrence Livermore National Laboratory.)

Sure, the world has lots of very stiff materials, ranging from uncooked pasta to glass, wooden boards, and tempered steel.

But metamaterials are engineered to have properties that wouldn’t occur in nature. And these materials are designed to be not only very stiff, but also ultralight and ultrastrong.

Researchers report on engineering the materials in this week’s issue of Science. Engineers at Lawrence Livermore National Laboratory (LLNL) and the Massachusetts Institute of Technology (MIT) worked on the team.

“These lightweight materials can withstand a load of at least 160,000 times their own weight,” LLNL Engineer Xiaoyu “Rayne” Zheng notes in the press release announcing the development.

The materials get their strength not so much from their chemical make-up, but from their structure at the microscale. As LLNL Engineer Chris Spadaccini explains in the release, that means they’re “governed by their geometric layout.”

In this case, the materials are built to make tiny lattices—structures of crossed tubes. That building takes place one tiny layer at a time with a special 3-D printing process.

Basically, the printer builds lattices of polymers and coats them with metals or ceramics. Afterward, heat melts away the polymers, leaving hollow metal or ceramic tubes.

The 3-D lattice of tubes is still very strong because of its geometric design. But removing the polymer leaves it extremely light.

Lawrence Livermore National Laboratory (LLNL) Engineer Xiaoyu “Rayne” Zheng -- lead author of the Science article -- studies a macroscale version of the unit cell which constitutes the ultralight, ultrastiff material described in the article (Courtesy Lawrence Livermore National Laboratory.)

Lawrence Livermore National Laboratory (LLNL) Engineer Xiaoyu “Rayne” Zheng — lead author of the Science article — studies a macroscale version of the unit cell which constitutes the ultralight, ultrastiff material described in the article (Courtesy Lawrence Livermore National Laboratory.)

The press release notes that the new materials could be very useful for the transportation and aerospace industries. Indeed, one can easily envision energy-efficient cars that also provide good crash protection. Lightweight, more durable planes and spacecraft would be great too.

But I expect people will also find uses for the materials that engineers aren’t even thinking of yet. For years now, for example, people have talked about aerogel’s potential aerospace applications. Yet now the bendy “frozen smoke” is also used for things like fast-charging supercapacitors.

I haven’t yet seen aerogel used for stage props, however. That was something my daughter and her high school ExploraVision team thought up when the group was brainstorming about future technology for stage crew. An aerogel sofa might have looked really cool for the right surrealistic play too.

But who knows? Maybe the new metamaterials will find their way into all sorts of creative uses.

Thanks to engineering, there’s always something new and challenging in this material world.

Efficiency matters!

My article today at Midwest Energy News:

Ohio’s rollback of efficiency law could cost ratepayers

(Photo by Carlos Lowry via Creative Commons)

While energy-saving efforts have been keeping costs down for Ohio ratepayers, a legislative “freeze” to the state’s efficiency standard raises questions about whether that will continue, particularly with new EPA carbon regulations on the horizon.

READ MORE…

 

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