Tagged: research

Here’s how West Virginia University researchers caught VW cheating

WVU test rig

This photo shows how researchers caught VW cheating on its emissions tests

Revelations that as many as 11 million Volkswagen cars have been cheating on their emissions tests have become big news this week. But the research that demonstrated that VW’s diesel vehicles were generating excessive pollution has been publicly available for more than a year — ever since a team at West Virginia University published their findings in the spring of 2014.

Volkswagen reportedly programmed its vehicles to behave differently during emissions testing than in real-world driving conditions. To detect this, the West Virginia researchers developed a method for measuring a vehicle’s emissions performance as it drove down the highway…

This equipment rode around in the back of the vehicles they were testing, collecting gas from the exhaust pipe and analyzing it. The gear included an onboard generator, to make sure that the power demands of the testing equipment didn’t change the performance of the engine.

Then they drove the vehicles up and down the West Coast, testing their performance in a variety of real-world driving conditions, from city streets to mountain roads. They found that one of the vehicles they tested (we now know it was a VW Jetta) was emitting 15 to 35 times the legal limit of nitrous oxide, while another (a VW Passat) was emitting five to 20 times the limit.

At this point, the researchers didn’t know why the cars were emitting so much pollution. But when they presented their results at a 2014 conference in San Diego, there were EPA officials in the audience. They picked up the investigation from there and eventually forced Volkswagen to admit that they had programmed the vehicles to cheat on emissions tests.

Gotta love all the directions capable of basic science. Catching corporate crooks is just one avenue – but, surely, important enough to deserve applause from ordinary consumers, recognition from bureaucrats who didn’t catch on to the crime until these folks at WVU pointed out discrepancies.

Your body is surrounded by farticles


Everywhere you go, in everything you do, you are surrounded by an aura of microbes. They drift down from your hair when you scratch your head, they fly off your hand when you wave to your friend, they spew out of your mouth when you talk. Even when you sit around doing nothing, you’re sitting in your own, personal microbial bubble.

Made up of millions, billions, trillions of bacteria, yeast, cells, and cell parts, this bubble is actually more like a cloud — a cloud, new research suggests, that is unique to you. And as gross as it is to imagine everyone around you shedding microbial bits and pieces into the air, studying those clouds can be useful for people like doctors tracking down disease outbreaks and cops tracking down criminals.

The gut microbiome, often invoked in expensive probiotic-heavy diets, is probably the hottest microscopic community right now. It’s the collection of microbiota, living inside you, that helps you break down food, fight disease, and control your hunger.

But your outer body has its own microbiome, too. Your body is covered in skin, and that skin is like a vast savannah populated with millions of exotic critters. They feed on the oils seeping from your skin, dead cells, bits of organic matter, and each other. “In a single centimeter of skin, you can find thousands of bacteria,” says James Meadow, former University of Oregon researcher and co-author of a microbiome paper published…in the journal PeerJ.

Combined, the non-you cells in your body outnumber the you cells by about 10 to one. And if some sadistic scientist were to grind up and sequence all the DNA in every cell in and on your body, only about 2 percent of the genetic material would be human. The rest is microbes

So how different could individuals’ microbial clouds really be? The two trials showed that, at least in these 11 people, microbial clouds varied significantly from person to person. They also found that different people shed microbes at different rates…

That knowledge will help shape microbiome cloud research in fields like contagious disease and forensics. In hospitals, nobody really knows how germs spread. Since leaving Oregon State University, Meadow has joined a biotech company in San Francisco that wants to use the understanding of microbial clouds to help hospitals prevent things like MRSA outbreaks.

Cops see other opportunities for the microbial cloud. Gilbert has been helping crime scene investigators use microbial residue to track down criminals. He says people pick up microbes from the soil, the air, the food they eat, and the water they wash and drink with. So an individual’s unique microbial signature could put them at the scene of a crime—or exonerate them if the microbes in their cloud match their alibi.

Any guess as to who gets the most funding, first?

Cattle virus is linked to breast cancer

Can you tell if I have leukemia?

Researchers were surprised to find in a new study that a significant number of breast cancer cells from more than 200 women had evidence of exposure to bovine leukemia virus, or BLV.

BLV infects dairy and beef cattle’s blood cells and mammary tissues, and was for a long time thought not to be able to infect humans.

Nearly all bulk milk tanks at large factory farms are infected with BLV, but only about 5 percent of cows get sick if they have the virus, according to the U.S. Department of Agriculture. The same group of researchers at the University of California Berkeley involved in the new study also found last year that BLV could be transmitted to humans.

“The association between BLV infection and breast cancer was surprising to many previous reviewers of the study, but it’s important to note that our results do not prove that the virus causes cancer,” said Dr. Gertrude Buehring, a professor of virology in the University of California Berkeley, in a press release. “However, this is the most important first step. We still need to confirm that the infection with the virus happened before, not after, breast cancer developed, and if so, how.”

Using donated tissue from the Cooperative Human Tissue Network, the researchers compared breast tissue from 239 women who either had breast cancer or did not.

They found that 59 percent of breast cancer cells had evidence of exposure to BLV based on the presence of viral DNA in the cells. Cells from women who had not had breast cancer only had evidence of exposure 29 percent of the time.

When researchers further analyzed the data, they found the risk of developing breast cancer was 3.1 times higher if BLV was present in a woman than if it was not. Buehring said the odds ratio is higher than other well known risk factors for breast cancer, including obesity, alcohol consumption and hormones.

And a chill went through the hearts and minds of dairy agribusiness managers. Probably already on the phone to lobbyists to get votes lined up in the USDA/FDA to prevent any further studies accepted if they even hint at a link.

Does research on obesity go better with Coke?

Larry Husten is a medical journalist covering cardiiology

The New York Times reports that Coca-Cola gives financial support to scientists and a new foundation in order to help promote the message that the obesity epidemic is fueled not by too many calories or too much sugar but by not enough physical activity. The Times piece is well worth a read but the issue it takes up is not new.

Last year I wrote a long post which included an interview with a scientist, Carl “Chip” Lavie, a Louisiana cardiologist who is a frequent co-author of Steven Blair, another researcher who is the main focus of the Times story.

[The interview is included in this article]

First let me add one interesting detail that the Times neglected to report. In 2012 Steven Blair was chosen by Coca-Cola, a sponsor of the Olympics, to be a torchbearer for the London summer games.

Lavie writes that his views are “not for sale.” I do not want to suggest anything so stark, but I also think it is fair – and studies have demonstrated – that gifts, even very small gifts, can exert strong unconscious effects. When combined with the flattery and attention of being designated a “key opinion leader” an unconscious alignment with a company can easily occur.

Moreover, as I wrote last year [2013], in a recent paper in PLOS Medicine researchers conducted a systematic review of systematic reviews examining the association between sugar-sweetened beverages and weight gain and obesity. For the papers in which the authors reported no conflict of interest, 10 out of the 12 findings supported the association between sugar-sweetened beverages and weight gain or obesity. In stark contrast, 5 out of the 6 papers with industry support failed to find evidence for any such association. In other words, systematic reviews with industry support were 5 times more likely to find no significant association.”Our results,” wrote the authors, “confirm the hypothesis that authors of systematic reviews may draw their conclusions in ways consistent with their sponsors’ interests.”

Lavie defends Coke’s funding of research by saying that “pharma does this all the time.” This analogy represents a stretch of logic. Although pharma-funded research is often criticized, and there are many active battles over the precise role for pharma in research, it is widely agreed that pharmaceutical companies must play a vital and important role in medical research. No one would seriously argue that Coca-Cola has medicinal value. The only active question is exactly how bad an effect Coke has on public health. A much better analogy, though still imperfect, is the tobacco industry…

I think it is naive to believe with Lavie that Coke’s main interest in providing financial support to researchers in this field is “to provide a public service.” For-profit companies like Coke and Pepsi don’t spend enormous sums of money just to provide a public service. They expect a significant return on their investment, though this may be difficult to quantify. In any case, it is more than obvious why Coke would be interested in supporting scientists who maintain that sugar does not play an important role in the obesity epidemic…

Readers should be aware of a much larger context here. This is not an isolated incident. Large food and beverage companies have been insinuating their way into the healthcare discussion for many years. In the last few years I’ve noted a number of attempts, subtle and not-so-subtle, by industry to influence health policy. Earlier this year [2014] I reported that the newly elected president of the Institute of Medicine, cardiologist Victor Dzau, was a member of the Pepsico board of directors. In 2012 the president of the American College of Cardiology was chosen by the Coca-Cola Company to carry the Olympic Flame. (Steven Blair, another co-author of the JACC paper, was also chosen by Coke to be a torch-bearer.) Coke also pays a lot of money to the National Heart Lung and Blood Institute to put a red dress logo on the Diet Coke label, while the American Heart Association has struck deals with, among others, Cheetos and Subway.

I am sure that these represent just the tip of a very large iceberg.

There’s even more meat in the article. And less sugar. :)

Definitely worth a read – not one you’re likely to come across in the news-as-entertainment free press.

Researchers find no benefit from chemotherapy at end of life

Chemotherapy near death failed to improve quality of life (QOL) for patients with cancer, even those who otherwise were in good health, a review of end-of-life care showed.

Quality of life near death (QOD) deteriorated in patients who had good performance status when they started chemotherapy. Palliative chemotherapy had no impact on QOL among sicker patients, Holly Prigerson, PhD,…and colleagues reported online in JAMA Oncology.

…”Thus, chemotherapy appears to contribute directly to worse QOD, presumably through adverse and toxic effects that impair the QOL of those who are initially feelling well.”

Organizations that have clinical guidelines addressing end-of-life chemotherapy, such as the American Society of Clinical Oncology (ASCO), might need to rethink their recommendations, Prigerson and colleagues added.

Even an accompanying editorial expressing some disagreement…acknowledged that “if an oncologist suspects the death of a patient in the next 6 months, the default should be no active treatment.”…

Three years ago, ASCO’s expert panel for the “Choosing Wisely” campaign identified use of chemotherapy in patients for whom no proven benefit existed as one of the most widespread, wasteful, and unnecessary practices in oncology. ASCO recommends against the use of chemotherapy for patients who have not benefited from prior therapy…

Prigerson and colleagues examined the association among ECOG performance status, chemotherapy, and QOL in the last week of life…They hypothesized that patients with good performance status would have worse QOL if they received additional chemotherapy, and that patients with poor performance status would not have an improvement in quality of life with chemotherapy…

Beyond the data, the study suggests that “equating treatment with hope is inappropriate,” Blanke and Fromme said.

“Even when oncologists communicate clearly about prognosis and are honest about the limitations of treatment, many patients feel immense pressure to continue treatment,” they said. “Patients with end-stage cancer are encouraged by friends and family to keep fighting, but the battle analogy itself can portray the dying patient as a loser and should be discouraged. Costs aside, we fell the last 6 months of life are not best spent in an oncology traetment unit or at home suffering the toxic effects of largely ineffectual therapies for the majority of patients.”

Time to turn away from the greed-centric portion of the medical-industrial complex, folks. Pay attention to the folks who say, as did these researchers, “This is a clarion call…to take the lead in curtailing the use of ineffective therapy and ensuring a focus on palliative care and relief of symptoms throughout the course of illness.


Babble is on about “mini ice age” coming — and of course it’s not true

Ignore this crud – talk about sunspots!

“Scientists warn the sun will ‘go to sleep’ in 2030 and could cause temperatures to plummet,” blared one headline from this weekend.

“Earth heading for ‘mini ice age’ within 15 years,” warned another.

By Sunday evening, news that the Earth could be headed for period of bitter cold was trending on Facebook and whizzing across Twitter. The story — which has been reported everywhere from conservative blogs to the British press to the Weather Channel to the Huffington Post — was based on a recent presentation at the Royal Astronomical Society’s national meeting. Researchers studying sunspots found that solar activity is due to decline dramatically in the next few decades, reaching levels not seen since the 17th century, during a period known as the Maunder minimum. Back then, the decline coincided with what’s called the “Little Ice Age,” when Europe’s winters turned brutally cold, crops failed and rivers froze over. Could another one be on its way?

Not really.

Though University of Northumbria mathematics professor Valentina Zharkova, who led the sunspot research, did find that the magnetic waves that produce sunspots…are expected to counteract one another in an unusual way in the coming years, the press release about her research mentions nothing about how that will affect the Earth’s climate. Zharkova never even used the phrase “mini ice age.” Meanwhile, several other recent studies of a possible solar minimum have concluded that whatever climate effects the phenomenon may have will be dwarfed by the warming caused by greenhouse gas emissions.

Besides, that “Little Ice Age” that occurred during the Maunder minimum, it wasn’t so much a global ice age as a cold spell in Europe, and it may have been caused more by clouds of ash from volcanic eruptions than by fluctuations in solar activity.

BTW…Zharkova’s findings have not yet been published in a peer-reviewed journal, so her conclusions haven’t been vetted and refined.

But those nuances were totally lost as stories about Zharkova’s research made the rounds on social media and in the press. Instead, we got 300-year-old engravings of Londoners cavorting on the frozen River Thames accompanied by predictions of food shortages and brutal cold — plus snarky tweets about not worrying about global warming anymore…

Nope. Climate change-deniers have resorted to clutching at journalistic straws. Paying off professional skeptics doesn’t have the return it used to. Thugs like the Koch Bros. and their peers in the oil side of fossil fuel profiteering have to content themselves with the tiny, exclusive anti-science brigade contained within conservative political parties and fundamentalist religions locked into creationism.

Sad, but, true. Capable only of mustering the gullible, obedient and hopelessly ignorant.

How do toddlers use tablets? — a limited survey

Can babies use iPads?

If you’ve ever viewed YouTube videos of infants and toddlers using iPads, then you know the answer is a resounding “Yes.”

But how are they using them?

To answer that question and others, a team of University of Iowa researchers set out to study more than 200 YouTube videos. Their paper is published in the proceedings of the CHI 2015 conference, the most prestigious in the field of human-computer interaction.

In the paper they write that their goal was to “provide a window into how these children are using tablets through an analysis of relevant YouTube videos.”

What they found was information that supports “opportunities for research and starting points for design.”

“By age two, 90 percent of the children in the videos had a moderate ability to use a tablet,” says Juan Pablo Hourcade, associate professor of computer science in the UI College of Liberal Arts and Sciences and lead author of the study. “Just over 50 percent of 12-to-17-month-old children in the videos had a moderate ability…”

He says that to his knowledge, other researchers have conducted surveys of the prevalence of tablet use by young children, however, the UI study is the first to study how infants and toddlers are actually using the devices…

Hourcade acknowledged the drawbacks of using unsolicited YouTube videos, such as not knowing the exact ages of the children pictured and that the children pictured were selected by their caregivers and may not be representative of the larger society. However, he says the researchers were able to estimate the ages of the children (two-thirds of the videos included the age) and observe a clear progression of successful performance linked to age that is consistent with developmental milestones

He says he hopes that the study and others that follow will influence the development of apps that encourage interactive education for infants and toddlers. The apps he envisions might be similar to the social and interactive-like children’s programs currently found on public television.

Interesting stuff. I almost always end up supporting any sort of investigation that encourages early education.

My parents taught both my sister and me to read by the time we each were 4 years old. And we had plenty of reading material available for the following age group – and beyond. Speaking subjectively, it was a great advantage throughout school for each of us.

Analysis of party affiliation — which continues to decline


Democrats hold advantages in party identification among blacks, Asians, Hispanics, well-educated adults and Millennials. Republicans have leads among whites – particularly white men, those with less education and evangelical Protestants – as well as members of the Silent Generation…

The share of independents in the public, which long ago surpassed the percentages of either Democrats or Republicans, continues to increase. Based on 2014 data, 39% identify as independents, 32% as Democrats and 23% as Republicans. This is the highest percentage of independents in more than 75 years of public opinion polling…

When the partisan leanings of independents are taken into account, 48% either identify as Democrats or lean Democratic; 39% identify as Republicans or lean Republican. The gap in leaned party affiliation has held fairly steady since 2009, when Democrats held a 13-point advantage…

Race and ethnicity. Republicans hold a 49%-40% lead over the Democrats in leaned party identification among whites. The GOP’s advantage widens to 21 points among white men who have not completed college…and white southerners… The Democrats hold an 80%-11% advantage among blacks, lead by close to three-to-one among Asian Americans…and by more than two-to-one among Hispanics…

Gender. Women lean Democratic by 52%-36%; men are evenly divided…Gender differences are evident in nearly all subgroups: For instance, Republicans lead among married men…while married women are evenly divided…Democrats hold a substantial advantage among all unmarried adults, but their lead in leaned partisan identification is greater among unmarried women…than among unmarried men…

Education. Democrats lead by 22 points…in leaned party identification among adults with post-graduate degrees. The Democrats’ edge is narrower among those with college degrees or some post-graduate experience…and those with less education…Across all educational categories, women are more likely than men to affiliate with the Democratic Party or lean Democratic. The Democrats’ advantage is 35 points…among women with post-graduate degrees, but only eight points…among post-grad men.

Generations. Millennials continue to be the most Democratic age cohort; 51% identify as Democrats or lean Democratic, compared with 35% who identify with the GOP or lean Republican. There are only slight differences in partisan affiliation between older and younger millennials. Republicans have a four-point lead among the Silent Generation…the most Republican age cohort.

Religion. Republicans lead in leaned party identification by 48 points among Mormons and 46 points among white evangelical Protestants. Younger white evangelicals…are about as likely older white evangelicals to identify as Republicans or lean Republican. Adults who have no religious affiliation lean Democratic by a wide margins…Jews lean Democratic by roughly two-to-one…The balance of leaned partisan affiliation among white Catholics and white mainline Protestants closely resembles that of all whites.

The biggest change in partisan affiliation in recent years is the growing share of Americans who decline to affiliate with either party: 39% call themselves independents, 32% identify as Democrats and 23% as Republicans…

The rise in the share of independents has been particularly dramatic over the past decade…

I was a founding member of the Young Republicans Chapter in my home town. That lasted about six weeks.

I was the chairman of the COPE Committee in a couple of UAW Locals. Like just about everyone in any Local 1199 of hospital workers I was a political activist.

I thoroughly resent the fact that New Mexico hasn’t open primaries. I have to register as a Democrat to have a voice in choosing who I get to vote for when elections roll around. There is no likelihood the Republican Party will offer anyone I could vote for. Today.

Go back to the first sentence in this commentary – and that was in New England in the 1950’s. In the small town I lived in, then, there were honest differences in policy, priorities. Both parties in that town opposed racism, supported my kind of activism in civil rights, civil liberties. Both rejected any serious activism for peace. I became a Progressive Independent.

Democrats have lost most of their backbone since then. Republicans have walked away from any concern for equal rights, opportunity, environment, honest government. I’ll usually settle for a Democrat candidate vs. a Republican thug in my neck of the prairie. The Greens haven’t a clue. Unfortunately.

Apple’s ResearchKit offers scientists access to millions of volunteers

Jeff Williams introduces Apple’s medical research kitReuters/Robert Galbraith

Apple just released ResearchKit, an open-source software tool designed to give scientists a new way to gather information on patients by using their iPhones.

Several top research institutions have already developed applications to work on the ResearchKit platform, including those pursuing clinical studies on asthma, breast cancer, heart disease, diabetes and Parkinson’s disease. They include Stanford University School of Medicine and Weill Cornell Medical College.

The format will allow users to decide if they want to participate in a study and decide how their data is to be shared with researchers…

The ResearchKit platform is designed to work hand in hand with Apple’s HealthKit software, which allows iPhones to work with health and fitness apps that gather information on weight, blood pressure, glucose levels and asthma inhaler use.

The ResearchKit also allows researchers access to accelerometer, microphone, gyroscope and GPS sensors in the iPhone to gain insight into a patient’s gait, motor impairment, fitness, speech and memory.

The software is also designed to help researchers build more diverse study populations, which traditionally have been limited by physical proximity to large academic medical centres.

My wife teases me – calls me her personal emoticon. And I admit I cried a little when Tim Cook and Jeff Williams were introducing ResearchKit.

The primary cause of my mom’s death was Parkinson’s. She devoted a lot of her life to the American Heart Association. I’ve done some similar things; but, the best was being able to volunteer as a human test subject for one ailment that, right now, still affects millions of people. Shingles. My mom suffered through some painful episodes and it pleased me much to be in the final test cycle of the Shingles vaccine before it was approved.

That was a big deal because it included several thousand volunteers nationwide. With ResearchKit, computational analysis of everything from day-by-day, minute-by-minute tracking of symptoms, response, exercise, a great deal of information previously only available from small groups, narrow demographics – can now be collated from millions of volunteers.

Doctors, researchers, universities worldwide can develop apps to fit their particular needs. And you decide what you wish to participate in – if at all.

You decide whether or not you are anonymous. You decide the boundaries for your participation. Apple sees none of the information. It’s all up to you.

Tim Cook and the designers at Apple feel the potential for this concept is so important — they’re making the SDK open source and developers can proceed on any platform they wish. You won’t have to own Apple products to participate.

Reprogramming plants for drought tolerance

Transgenic Arabidopsis on the right survived drought vs non-transgenic on the left

Crops and other plants are constantly faced with adverse environmental conditions, such as rising temperatures (2014 was the warmest year on record) and lessening fresh water supplies, which lower yield and cost farmers billions of dollars annually.

Drought is a major environmental stress factor affecting plant growth and development. When plants encounter drought, they naturally produce abscisic acid (ABA), a stress hormone that inhibits plant growth and reduces water consumption. Specifically, the hormone turns on a receptor (special protein) in plants when it binds to the receptor like a hand fitting into a glove, resulting in beneficial changes — such as the closing of guard cells on leaves, called stomata, to reduce water loss — that help the plants survive.

While it is true that crops could be sprayed with ABA to assist their survival during drought, ABA is costly to make, rapidly inactivated inside plant cells and light-sensitive, and has therefore failed to find much direct use in agriculture. Several research groups are working to develop synthetic ABA mimics to modulate drought tolerance, but once discovered these mimics are expected to face lengthy and costly development processes.

The agrochemical mandipropamid, however, is already widely used in agricultural production to control late blight of fruit and vegetable crops. Could drought-threatened crops be engineered to respond to mandipropamid as if it were ABA, and thus enhance their survival during drought?

Yes, according to a team of scientists, led by Sean Cutler at the University of California, Riverside.

The researchers worked with Arabidopsis, a model plant used widely in plant biology labs, and the tomato plant. In the lab, they used synthetic biological methods to develop a new version of these plants’ abscisic acid receptors, engineered to be activated by mandipropamid instead of ABA. The researchers showed that when the reprogrammed plants were sprayed with mandipropamid, the plants effectively survived drought conditions by turning on the abscisic acid pathway, which closed the stomata on their leaves to prevent water loss.

The finding illustrates the power of synthetic biological approaches for manipulating crops and opens new doors for crop improvement that could benefit a growing world population.

One of the growing areas of research wherein scientists work to adapt plants to conditions not otherwise considered arable or useful for cropping. Drought-tolerance is only one of the areas. There are folks working to encourage food crops in both high-salt and high-alkaline environments.

Farmers have historically followed the roads that lead to simplest and easiest profits – once agriculture evolved beyond sustenance family farming. That generally put the focus on the most arable land, good water access, etc.. Opening up new lands, new climates, broader soil chemistry and temperature permits growing food for more.

Hopefully, common sense prevails over religion, culture and dirt-poor economics while family size continues to diminish – along with demand.