Category Archives: Academia

Fecal transplants the cure for immune disorders?


The dramatic increase in scientific studies of fecal material and the microbial components in feces in numbers per gram. (Seth Bordenstein / Vanderbilt University)

The dramatic increase in scientific studies of fecal material and the microbial components in feces in numbers per gram. (Seth Bordenstein / Vanderbilt University)

Following up on the previous post linking the populations of our gut bacteria to multiple sclerosis and a host of other diseases, another new report asks whether fecal transplants much offer hopes for a cure.

And, yes, you read that right: Fecal transplants. Kinda adds a whole new spin to the notion of “getting your shit together.”

From Vanderbilt University:

These days fecal transplantation is no joke.

Fecal transplants are increasingly being used as the treatment of last resort for certain infections in the human gut and have had remarkable success treating the nursing home and hospital-acquired scourge, Clostridium difficile colitis, an infectious diarrhea that often follows antibiotic treatment. There is also preliminary evidence that the transplantation of stool from healthy individuals can be effective in treating multiple sclerosis and Crohn’s disease.

At the same time, there has been a major increase in animal experiments involving fecal material. In one study, for example, researchers found that fecal transplants from lean mice turned sterile mice into lean mice, while fecal transplants from fat mice turned sterile mice into fat mice.

“This research is just getting started. It is driven by the new paradigm of the microbiome which recognizes that every plant and animal species harbors a collection of microbes that have significant and previously unrecognized effects on host health, evolution and behavior,” said Seth Bordenstein, associate professor of biological sciences and pathology, microbiology, and immunology at Vanderbilt University.

In an article titled “Fecal Transplants: What is Being Transferred” just published in the journal PLOS Biology, Bordenstein reviews the growing scientific literature on the subject.

“There is no doubt that poo can save lives,” said Bordenstein. Take the case of the use of fecal transplants to treat Clostridium difficile infections. According to the literature, it has a 95 percent cure rate. “Right now fecal transplants are used as the treatment of last resort, but their effectiveness raises an important question: When will doctors start prescribing them, or some derivative, first?” Bordenstein asked.

There’s more, after the jump. . . Continue reading

Big Pharma’s bribes control research, reports


Two stories summarize everything that’s wrong with corporate science, exposing the corruption at the heart of the most profitable business on earth.

First, consider this graphic, accompanying a fascinating Der Speigel interview of a British physician who has done more than anyone else to expose the infection that’s driving up drug prices and filling pharmacies with patent medicines of little or no value:

BLOG POharma

And a brief excerpt from the interview itself, via Der Spiegel:

Semi-retired British cardiologist Peter Wilmshurst — described in 2012 by the British Medical Journal as a “successful and cheerful whistleblower” — began his crusade against dishonesty in medical research in 1986. In the course of the 66-year-old’s career, he conducted studies for pharmaceutical and medical devices companies, and unlike many of his colleagues, never hesitated to publish negative results. He’s been the subject of multiple cases of legal action and risked bankruptcy and his reputation to expose misconduct in the pharmaceutical industry. Today he advises and supports other whistleblowers with the organization “Patients First.”

He sat down with SPIEGEL to discuss mistruths and fraud in medical research and why he decided to challenge the pharmaceutical industry.

SPIEGEL: In your early years as a researcher, a pharmaceutical company offered you a bribe equivalent to two years of your salary: They wanted to prevent you from publishing negative study results. Were you disappointed that you weren’t worth more?

Peter Wilmshurst: (laughs) I was just a bit surprised to be offered any money, really. I was a very junior researcher and doctor, only 33 years old, so I didn’t know that sort of thing happened. I didn’t know that you could be offered money to conceal data.

SPIEGEL: How exactly did they offer it to you? They probably didn’t say: “Here’s a bribe for you.”

Wilmshurst: No, of course not! Initially we were talking about the results that I’d obtained: That the drug that I had been testing for them did not work and had dangerous side effects. Then the company representatives asked me to leave some of the patients out of the data analysis. Without these patients, the study result would have been positive. When I said I couldn’t do that, they asked me not to publish the data. And to compensate me for the work I had done in vain, they said, they would offer me this amount of money.

SPIEGEL: What went through your head at that moment?

Wilmshurst: Well, I thought it was wrong. If you’ve got the data, you have got to publish it. That’s the imperative. I mean, that’s one of the big issues in pharmaceutical research, that the data we’re basing our treatments on are actually only part of the data, because industry conceals the unfavorable bits.

And when you can’t buy the research, buy the university

Hell, you can even buy one of the most prestigious universities on earth — or try to, until some nosy reporters ask the wrong questions.

The source of the funds in question is a foundation created and owned by Boehringer Ingelheim GmbH, a German pharmaceutical company controlling 146 affiliates.

From Science:

In a surprise move, the president of the Johannes Gutenberg University of Mainz in Germany. . .announced plans to overhaul controversial contracts governing the use of a €150 million donation from a philanthropic foundation. Critics have charged that the agreement gives the donor, the Boehringer Ingelheim Foundation in Mainz, too much control over publishing decisions and faculty appointments at the school’s Institute of Molecular Biology, which the foundation helped create in 2009.

The move, which could eventually influence similar funding arrangements at other German universities, only partly satisfies critics. They are pushing for greater transparency from universities and donors.

In a 4 July meeting with journalists, university President Georg Krausch conceded that contract provisions give the foundation the authority to veto faculty appointments made by the university, but said that was not the intent of the agreement, and that the foundation had never blocked an appointment. And he said language requiring the university to get prepublication consent from the foundation for press releases and “publications,” which could include research papers, was an “error.” The intent of such language, he said, was to ensure that research products were of good quality, not to give the funder control. Still, Krausch admitted that the provisions created a perception that the university was not free to act independently. “Throughout all these issues … you can interpret it as quality assurance or exercise of influence,” he said.

Krausch said the university will now work with foundation officials to revise the problematic language.

It’s enough to give you a headache. . .

And we’re sure they have just the prescription you need.

If you can afford it.

Rising seas may trigger atmospheric carbon rise


Map of global peatlands (black shading) lying at or below 5 m elevation.

Map of global peatlands (black shading) lying at or below 5 m elevation. From the study, link after the jump.

In life, few things are purely linear. Complications invariably arise, adding complexity.

Consider the case of rising seas induced by global climate change.

A new study from Britain reveals how those sea level rises may actually increase atmospheric carbon dioxide levels by unexpected means.

From the University of Exeter:

Rising sea-levels linked to global warming could pose a significant threat to the effectiveness of the world’s peatland areas as carbon sinks, a new study has shown.

The pioneering new study, carried out by Geographers at the University of Exeter, examined the impact that salt found in sea water has on how successfully peatland ecosystems accumulate carbon from the atmosphere.

The researchers studied an area of blanket bog – a peat bog that forms in cool regions susceptible to high rainfall – at Kentra Moss, in Northwest Scotland.

They discovered that the rate at which the peatland area accumulated carbon was significantly impacted as the concentration of salt rose.

The results indicate that rising sea levels, linked to predicted climate change, could pose a serious threat to the future security of the peatlands because they would inundate areas and deposit more salt, further inland.

The findings feature in respected scientific journal, Scientific Reports, on Wednesday, June 29 2016.

Dr Angela Gallego-Sala, co-author of the paper and a Senior Lecturer in Physical Geography at Exeter said: “Peatland areas play a crucial role in taking carbon from our atmosphere and storing it”.

“We know that rising sea levels through global warming can have catastrophic effects on many areas across the globe, and this study shows just how vulnerable some peatland areas are to the same phenomenon.

“The effects of global warming are already being observed, but the longer we wait to act, the quicker changes to our environment, which would have a devastating impact on many regions around the world, will take place.”

There’s more, and a link, after the jump. . . Continue reading

Chart of the day: European graduation divides


From Eurostat, the diploma divides in European collegiate education:

BLOG Ed divide

UC Berkeley-spawned Amyris shares collapse


The decline and fall of Amyris share prices, via NASDAQ.

The decline and fall of Amyris share prices, via NASDAQ.

Amyris Inc. [previously], the company started by UC Berkeley “bioengineer” Jay Keasling to create affordable fuels from using technology created to genetically engineer yeast to produce the most widely used antimalarial drug, hit an all-time low of forty-one cents per share today, down from the post-IPO high of $33.85.

Part of the reason is contained in a 20 June filing lodged by the company with the Security and Exchange Commission:

On June 14, 2016, Amyris, Inc. (the “Company”) received a letter from The NASDAQ Stock Market LLC (“NASDAQ”) notifying the Company that it is not in compliance with the requirement of NASDAQ Listing Rule 5450(a)(1) for continued listing on the NASDAQ Global Select Market as a result of the closing bid price of the Company’s common stock being below $1.00 for 30 consecutive business days. This notification has no effect on the listing of the Company’s common stock at this time.

In accordance with NASDAQ Listing Rule 5810(c)(3)(A), the Company has 180 calendar days, or until December 12, 2016, to regain compliance with NASDAQ Listing Rule 5450(a)(1). To regain compliance, the closing bid price of the Company’s common stock must be at least $1.00 for a minimum of 10 consecutive business. If the Company does not regain compliance during such period, it may be eligible for an additional compliance period of 180 calendar days, provided that the Company meets NASDAQ’s continued listing requirement for market value of publicly held shares and all other initial listing standards for the NASDAQ Capital Market, other than the minimum bid price requirement, and provides written notice to NASDAQ of its intention to cure the deficiency during the second compliance period. If the Company does not regain compliance during the initial compliance period and is not eligible for an additional compliance period, NASDAQ will provide notice that the Company’s common stock will be subject to delisting from the NASDAQ Capital Market. In that event, the Company may appeal such determination to a hearings panel.

The Company is currently evaluating its available options to resolve the deficiency and regain compliance with NASDAQ Listing Rule 5450(a)(1).

In other words, Amyris is now officially what’s called a “penny stock,” and stock valued at under a buck and restricted to trade on minor markets.

And while Amyris has promised and failed to deliver on its cheap fuel promises and shifted its development aims to tweaking its yeast to produce genetically engineered cosmetic chemicals, Bill Gates, an original investor from the company’s earliest days, gave Amyris $5 million in April to help cut costs on production of the drug for which he originally bankrolled Keasling and his students.

The drug is produced in Europe and Amyris realizes no profits from its sale.

But now comes more bad news and a possible reason for the continuing decline of the price of Amyris shares.

From the University of British Columbia:

The rapid decline in effectiveness of a widely used anti-malaria drug treatment on the Thailand-Myanmar border is linked to the increasing prevalence of specific mutations in the malaria parasite itself, according to a paper published in The Clinical infectious Disease Journal.

The mutations in specific regions of the parasite’s kelch gene – which are genetic markers of artemisinin resistance – were the decisive factor, the authors say, in the selection of parasites that are also resistant to mefloquine. This resulted in growing failure of the widely-used anti-malaria drug combination of mefloquine and artesunate, the first artemisinin combination therapy (ACT) on the Thai-Myanmar border.

Led by Dr. Aung Pyae Phyo of SMRU, the study used data from a 10-year study of 1,005 patients with uncomplicated P. falciparum malaria at Shoklo Malaria Research Unit (SMRU) clinics on the Thai-Myanmar border in northwest Thailand.

“This study demonstrates for the first time that artemisinin resistance leads to failure of the artemisinin partner drug, in this case, mefloquine. This means that the first line artemisinin combination therapy (ACT) introduced here in 1994 has finally fallen to resistance,” says François Nosten, Director of SMRU.

Resistance to artemisinin combination therapy drugs (ACTs) – the frontline treatments against malaria infection – poses a serious threat to the global control and eradication of malaria. If drug resistance spreads from Asia to the African sub-continent, or emerges in Africa independently, as has happened several times before, millions of lives, most of them children under the age of 5 in Africa, will be at risk.

The study shows that, contrary to the view sometimes expressed that resistance to artemisinin is not a direct threat, it is in fact responsible for the rapid demise of the partner drug and the failure of the drug combination, resulting in patients not being cured and further transmission of the malaria parasite.

“The evidence is clear: Artemisinin resistance leads to partner drug resistance and thereby the failure of artemisinin combination treatments,” said Oxford Professor Nicholas White, Chairman of the Mahidol Oxford Tropical Medicine Research Unit (MORU) and chair of the Worldwide Antimalarial Resistance Network (WWARN).

From the paper, a graph describes the rise of artemisinin-resistant genetic variants.

From the paper, a graph describes the rise of artemisinin-resistant genetic variants.

Given the very limited number of effective drugs, it is urgent to eliminate P. falciparum from the areas where it has developed resistance to the artemisinins, said Prof. White: “The spread of artemisinin resistant Plasmodium falciparum is perhaps the greatest threat to our current hopes of eliminating malaria from the world.”

A unit of the Bangkok-based MORU, SMRU is based in the refugee camps and migrant communities along the Thai-Myanmar border. Led by researchers based at SMRU (Thailand), the study was funded with the support of the Wellcome Trust (UK).

Reference:

Pyae Phyo A et al, Declining efficacy of artemisinin combination therapy against P. falciparum malaria on the Thai-Myanmar border (2003-2013): the role of parasite genetic factors [open access], Clinical Infectious Diseases, published online 16 June 2016.

How to create mini-NSAs to spy on social media


The NSA, the National Security Agency, is America’s super-agency for monitoring global communications. While it’s only nominally no to spy on US citizens, the policy is more honored in the breach than in the observance.

But, still, local law enforcement agencies can’t access the massive cache of our digitally expressed thoughts and feelings, and. my. how they’d like to.

So what to do?

Well, why not start with create a program to monitor social media for all the things cops want to know?

From the University of North Carolina, Charlotte:

Yong Ge, Ph.D., is an Assistant Professor in the College of Computing and Informatics’ Department of Computer Science.  Through funding from the National Institute of Health, Ge has developed a tool that leverages social media data to help analyze use patterns of illegal drugs by young adults across the country.

“Up until now the Substance Abuse and Mental Health Services Administration conducts a national survey once a year in which thousands of people are randomly selected to supply information,” says Ge.  “Essentially it tries to determine what types of illegal drugs people are using. Not only was it very costly but it generated hundreds of pages of information, some of which might not even be accurate based on the responses of those being surveyed.”

Ge says by doing the survey only once a year it makes it nearly impossible to capture the dynamics of illegal drug usage on an ongoing basis. He says through the use of social media analysis that has all changed.  Ge says they can now capture and analyze data on an ongoing basis, track trends, etc., which gives them a much more powerful tool to figure out what is actually going on out there.

Ge says another challenge is creating a database for all of the different names being used to describe drugs.

“People use many different street names to describe illegal drugs,” says Ge.  “Therefore we need to capture that data in order to get a good sampling of what people are using. It is very rare that folks will use the real names of the illegal drug.”

Ge says by tracking illegal drug use via social media analysis they are able to see where certain illegal drugs are being used, sort patterns of usage of drugs, detect new ways of using drugs, etc.  He says as they acquire this real time information they will be able to detect and report immediately what is trending and where.

Ge says eventually they hope to be able to supply this information to the Substance Abuse and Mental Health Services Administration and law enforcement authorities.

Julian Assange begins his fifth year of asylum


Today, 19 June 2016, marks the start of the fifth year of the political asylum of Wikileaks founder Julian Assange, who remains within the Ecuadorean Embassy in London, sheltered from extradition that would likely see his removal to the U.S. and trial on espionage charges for publishing diplomatic cables and other documents furnished by the now-imprisoned Chelsea Manning.

To commemorate the date and raise a renewed call for his freedom, notable figures in journalism, governance, human rights, law, environmentalism, academia, art, film, and even fashion raised their voices in events around the world.

For a full list of participants, see thje #freeassagenow website, but meanwhile, from The Press Project, here are a few videos recorded for the event:

We begin with a familiar face:

Noam Chomsky in support of Julian Assange


Next, a Slovenian philosopher:

Slavoj Žižek in support of Julian Assange


And a Chinese artist:

Ai Wei Wei in support of Julian Assange


Followed by a world renowned composer and musician:

Brian Eno in support of Julian Assange


And Italy’s most esteemed investigator reporter, a journalist who lives with round-the-clock police protection because of his brilliant exposes of organized crime:

Roberto Saviani in support of Julian Assange


Finally, the British fashion designer and human rights activist who brought the punk style into the mainstream:

Vivienne Westwood in support of Julian Assange