Monthly Archives: May 2017

Towards India’s own standard genome sequence – Telangana Today

Posted: May 6, 2017 at 3:14 am

Indian company to collect genomic code of 1 lakh Asians, including over 30,000 Indians from various parts of the country

Hyderabad: Imagine a repository of over 30,000 Indian genomes covering a wide variety of groups from various regions and ethnic backgrounds accessible to researchers and healthcare providers.

Such a large Indian genomic data will not only enable researchers in finding the patterns of how genes are expressed but also can help in spotting mutations, which could be the answer for personalized therapy protocols for cancer patients, cardio-vascular ailments, end-stage kidney ailments and many more.

An Indian company along with several others in Asia has taken up this amibtious project to collect the genomic code of a whopping 1 lakh Asians, which also includes over 30,000 Indians from various parts of the country.

In the past, there have been isolated attempts at finding genomic sequence of one or two Indian groups but this is for the first time that a concerted effort is being taken up to collect the genome sequence of such a large set of population.

Standard genome Indian researchers need to have access to standard Indian genomic data to isolate the genes responsible for causing ailments among Indians. Almost all the medical standards, for instance ideal BP levels, sugar levels or anything else is based on Caucasian population. In the coming years, we intend to sequence genome of Indians and hopefully reach towards a standardized Indian genome, says CEO (India), MedGenome, Girish Mehta.

Talking to Telangana Today, Mehta said that MedGenome, a Bengaluru-based company, has already committed US$ 10 million for the project. The overall cost of the 1 lakh Asian genome is close to Rs. 100 crore or over 120 million US dollars.

We are collaborating with Singapore and South East Asian biotech companies to take part in preparing this genomic sequence. This will be very important because we will not only get to know the standard Indian genome but also the Asian genomic sequence, which is vital to form new treatment protocols, Mehta said, during a visit to Hyderabad.

Back in 2014, the United Kingdom had launched its own 1 lakh genome project and similar projects are under way in Qatar, Europe and the US.

Unfortunately, we are second largest population but we still do not have our own standard genome code. Earlier, genome sequencing of a single human being was very expensive but technology is rapidly making it very affordable. This is a four-year project and hopefully it should be completed in time, Mehta added.

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The Tea Plant’s Genome Has Been Unlocked – And It’s 4 Times That of Coffee – ScienceAlert

Posted: at 3:14 am

From a single species of plant comes many teas. The tea tree, a shrub called Camellia sinensis, produces white, green, black and oolong teas. The tea's destiny is a matter of variables.

The final drink reflects the tea cultivar, the growing environment and how the leaves are processed - dried, crushed, steamed, blended. Farmers pluck 'baby' leaves, as one Snapple commercial put it in the mid-2000s, to begin making white tea.

And yet scientists in China, South Korea and the United States say there is another way to further tea's potential, beyond altering the dirt or the stages of harvest or processing.

DNA analysis could lead to "a more diversified set of tea flavours" by tracing the genes responsible for taste, according to Lizhi Gao, a botany professor at the Chinese Academy of Sciences' Kunming Institute of Botany.

He and colleagues have completed the "first high-quality" genome of the tea tree shrub, published this week in the journal Molecular Plant.

The plant took five years to analyse, thanks to the sheer number of DNA sequences involved.

"The tea tree genome is extremely large," Gao wrote in an email to The Washington Post - counting 3 billion base pairs, about four times the size of coffee's genome.

Of hot and invigorating drinks, coffee gets most of the buzz, at least in the United States: this country is home to 140 million daily coffee drinkers and the Starbucks Unicorn Frappuccino, and Americans consume more coffee than people anywhere else.

Researchers sequenced the genome of robusta coffee in 2014, hinting at a future of genetically modified coffees, as The Post reported at the time.

Scientists followed up with the arabica coffee genome in January.

Monday marked the tea tree's turn. It was a long time coming. Dried plants, recently found in a Chinese mausoleum, revealed that emperors in the Han Dynasty enjoyed tea 2,100 years ago, possibly as part of a soup.

The sovereigns were onto something. Today, 3 billion people drink tea, and by one estimate, for every mug of coffee consumed on the planet, humans drink three cups of tea.

Gao and his colleagues had to churn through the tea tree's huge levels of retrotransposons. These repeated DNA sequences, about 80 percent of the tea genome, duplicated themselves into the genome again and again over 50 million years of tea tree evolution.

"It is a mystery why retrotransposon sequences are abundant in this plant but not in another," Gao said.

But the researchers were most interested not in size but in the way tea produces tasty molecules.

"The tea-processing industries in tea-drinking countries, especially in China, have developed numerous tea products with diverse tea flavour," Gao said.

But processing techniques alone aren't enough, he said. Tea also depends on developing new plant varieties, containing unique combinations of flavourful molecules.

Three types of chemicals are most responsible for tea's taste. One is an amino acid only found in tea, called l-theanine, which in the last decade has been added to drinks that promote focus and concentration. (Such focus drinks are of dubious efficacy and lack supporting research.)

The second type of chemical is a class of flavonoid, or plant pigment molecule, called catechins. The third is caffeine, which evolved in tea independently of cacao and coffee, akin to the way both sea turtles and dolphins evolved flippers separately.

There are several theories as to why plants produce caffeine. Caffeine at high doses is a natural pesticide. But at low doses, as in some nectars, it may be giving insects a memorable jolt.

Caffeine was one tool in tea's repertoire of "disease defense and environmental stress tolerance" methods to help it adapt globally to diverse habitats, Gao said.

The tea genome answered a question the scientist had long pondered: Why can't we make tea from close Camelliasinensis cousins, such as the tea oil plant Camellia oleifera?

It turns out that C. oleifera and its 100 other Camellia relatives do not produce high amounts of the caffeine or catechin family of genes. (Caffeine and catechins are not proteins but secondary metabolites, which means many genes are required to construct them.)

Put another way, Gao said, the expression levels of caffeine- and catechin-related genes "determines the tea processing suitability".

The chief horticulturist at Britain's Royal Horticultural Society, Guy Barter, said plant breeders would welcome this work.

"Once you understand the basis for the flavours and the processing quality of the tea, you can then have genetic markers that breeders can look for when trying to produce new varieties," he told the BBC.

2017 Washington Post

This article was originally published by The Washington Post.

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Molecular study of skin proteins uncovers predisposition to eczema … – Medical News Today

Posted: at 3:13 am

New research shows for the first time that a lack of the key barrier protein filaggrin alone may be responsible for changes in skin proteins and pathways that make people susceptible to eczema. It builds on previous work that shows a lack of the protein is strongly tied to the development of eczema.

Researchers from Newcastle University in the United Kingdom and Stiefel - a GlaxoSmithKline company - report their findings in the Journal of Allergy and Clinical Immunology.

Lead investigator Nick Reynolds, a professor of dermatology at Newcastle University who also works as a skin and eczema specialist in Newcastle's Royal Victoria Infirmary, says that their discovery "reinforces the importance of filaggrin deficiency leading to problems with the barrier function in the skin and predisposing someone to eczema."

He and his colleagues also believe that the study could lead to the development of drugs that target the underlying causes of eczema rather than just alleviate the symptoms.

Eczema is a condition that is usually characterized by dry, itchy, cracked, and rough skin that mainly erupts on the hands, feet, and face, as well as behind the knees and inside the elbows.

It can also present with blisters that weep fluid when scratched. The condition can cause disturbed sleep and may profoundly affect quality of life.

The most common type of eczema is an inflammatory, non-contagious skin condition called atopic dermatitis that affects around 30 percent of people in the United States, most of them children and adolescents.

In this article, the word eczema refers specifically to atopic dermatitis.

The exact causes of eczema are unknown. However, research reveals that it is likely to arise from a combination of genetic and environmental factors and probably involves dysfunction of both the skin barrier and the immune system. People with eczema may also develop asthma and hay fever.

Fast facts about eczema

Learn more about eczema

In their study report, the researchers explain that filaggrin plays a key role in maintaining the barrier that protects the skin and that previous research has already established that a lack of the protein strongly predisposes people to eczema.

However, exactly what happens at the molecular level to link filaggrin deficiency to the development of eczema "remains incompletely understood," they note.

To further investigate the role of filaggrin, the researchers developed a 3-D model of human skin, in which, using molecular tools, they made the epidermis (the outside layer) deficient in filaggrin.

The model closely mimics what happens in the skin of people with eczema.

Using the model, the researchers were able to map the proteins and signaling pathways that lie "downstream" of filaggrin, and thus observe how the absence of the protein altered them.

They identified a number of signaling mechanisms that regulate inflammation, cell structure, stress response, and the function of the skin barrier.

The mapping of these pathways in the model appears to match that seen in people with eczema.

For example, the skin of people with active eczema has high levels of a protein coded by the gene KLK7. The team was able to show - from the model - that upregulation of KLK7 was one of the molecular consequences of filaggrin loss.

"This type of research allows scientists to develop treatments that target the actual root cause of the disease, rather than just managing its symptoms. Given the level of suffering eczema causes, this is a pivotal piece of research."

Nina Goad, British Association of Dermatologists

Learn how friendly skin bacteria keep harmful Staphylococcus aureus in check.

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Prevent an eczema flare-up by avoiding these 8 things – Fox News

Posted: at 3:13 am

Derived from the Greek language, the word eczema translates to something like to boil. And anyone who has atopic dermatitis the most common form of eczema can probably see why. The symptoms often shows up as red, itchy rashes on your arms and legs, and can sometimes cause open sores or resemble scaly skin.

Although its possible to develop atopic dermatitis for the first time as an adult, the majority of people experience it shortly after they were born, perhaps as young as two months old. Most people outgrow it in their early teens, but it can come back later in life, says Whitney High, MD, an associate professor of dermatology and pathology at the University of Colorado School of Medicine, in Denver. For some people, atopic dermatitis continues through into adulthood and never lets up.

The condition itself is likely hereditary, and usually runs in the same circles as allergic rhinitis and asthma. Families that have one child with eczema often have another child with asthma or even a third child with seasonal rhinitis or hay fever, he says.

To limit your odds of experiencing a flare-up, here are nine things to avoid.

1. Taking a luxurious bath A long soak in the tub might sound fantastic but if you have atopic dermatitis, spending too long in the bathtub can leave your skin feeling itchy and red. The next time you turn on the tap, remember the Goldilocks rule: the water should be not too hot, not too cold, but a lukewarm medium. Ideally, youll also limit your soak to no longer than 15 minutes a day, says Dr. High. We tell people to take good care of their skin by doing gentle bathing and not over-drying the skin, he says.

RELATED: The 7 best lotions for eczema, according to dermatologists

2. Wearing a wool sweater Any kind of abrasive texture, like wool or certain synthetic fibers, might irritate your skin, says Dr. High. A better wardrobe choice: soft, cotton clothing in a looser cut, which wont rub against your skin. You should also wash any new clothing you buy before wearing them some contain dyes that make the fabric appear nicer in the store, but may trigger a flare-up on your skin.

3. Using scented laundry detergents Scented laundry detergents and some dryer sheets can also bother your skin. Choose products that are free of fragrances and dyes; liquid ones tend to leave less irritating residues behind compared to powder versions. We like the all-FREE CLEAR laundry detergent thats specifically designed for people with sensitive skin; the product received a seal of acceptance from the National Eczema Association (NEA), which keeps a list of other helpful products on their website.

RELATED: The best laundry detergents for sensitive skin

4. Washing with anything besides fragrance-free soaps Similar to scented laundry detergents, scented hand soaps, bubble baths, body washes, and lotions can all cause your skin to feel dry and itchy. Use bland soaps, not highly perfumed or scented soaps, says Dr. High.

5. Scratching your skin Atopic dermatitis is sometimes called the itch that rashes. In other words, says Dr. High, some people think you have the itching sensation first, then do all the damage to the skin with the scratching and picking, which leads to the rash. And while its a good idea to reach for a moisturizer at the first sign of a tingle, you should also keep your fingernails trimmed and smooth that way, youll be less likely to puncture the skin if you do end up scratching at it.

6. Getting too hot or cold During the warmer months, the high temperatures (or, the sensation of heat, says Dr. High) can sometimes bother peoples skin. Not only that, but sweating can cause irritation, too. Likewise, the cold, dry weather in winter can also trigger itchiness.

7. Skipping moisturizer To avoid a flare-up, youll have to do more than just avoid certain products. You should also moisturize your skin at least twice a day to prevent it from becoming too dry or cracked, according to the American Academy of Dermatology. Look for mild, fragrance-free lotions Aveeno Eczema Therapy Moisturizing Cream and Cetaphils RestoraDerm Eczema Calming Body Moisturizer are two options or opt for petroleum jelly. Its also smart to try out a new product on a small area of your skin first, on the off chance that it causes your skin to feel itchy and irritated later on.

Although the majority of eczema flare-ups arent caused by a persons diet, there may be occasional cases where atopic dermatitis is exacerbated by food or drinks, says Dr. High. To pinpoint what might be triggering your flare, try keeping track of your daily routine (including meals) in a journal. By looking back at your past entries, you might be able to identify the culprits. For example, if you and your doctor think that milk is causing a flare, you might want to eliminate it from your diet while working with a nutritionist to help shore up your intake with other calcium-rich foods.

8. Letting stress take over Although stress can certainly trigger a flare, Dr. High says that its usually the last factor that doctors consider. But he also notes that all of his patients feel itchier at night, whether they have atopic dermatitis or any other itching skin condition. Its the time of the day when its quiet, says Dr. High. Youre not going to feel itchy when youre going a million miles an hour at your job. You dont have time to plug into all those body sensations.

This article originally appeared on Health.com.

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Potential New ALS Gene Leads to Extraordinary Aggregates – Alzforum

Posted: at 3:11 am

05 May 2017

A paper in the May 3 Science Translational Medicine identifies a potential new risk gene for amyotrophic lateral sclerosis (ALS). Mutations in ANXA11, which encodes the phospholipid binding protein annexin A11, turned up in people with both familial and sporadic forms of the disease, report scientists led by Christopher Shaw of Kings College London, Vincenzo Silani of the University of Milan, and John Landers of the University of Massachusetts Medical School, Worcester. Mutant proteins strayed from their normal binding partner, the calcyclin protein, and instead aggregated in the nucleus and cytoplasm. Annexin A11 appears to aid in vesicletransport.

This falls in line with themes we are seeing in all ALS mutations, which are impairments in proteostasis, autophagy, vesicular trafficking, and aggregation, said Matthew Harms, Columbia University, New York. It adds some genetic firepower to our interest in thosepathways.

Mutant annexin A11 inclusions take varied forms, including an ordered series of parallel tubules seen from the side (left) and top. [Courtesy of Science TranslationalMedicine/AAAS.]

This paper lists a handful of co-first authors: Bradley Smith, Simon Topp, and Han-Jou Chen of Kings College, with Claudia Fallini of UMass Worcester, and Hideki Shibata, Nagoya University, Japan. On their hunt for new ALS-associated genes, they analyzed whole exome sequences from 751 patients with familial disease and from 180 with sporadic ALS. They found six rare mutations in annexin A11 in 13 people, including a p.D40G amino acid substitution that segregated with disease in two families. These mutations were absent from 70,000 healthy controls. They clustered at the N-terminal tip of the protein. Previous studies suggest that annexin A11 aids in vesicular transport between the endoplasmic reticulum and Golgi apparatus (Shibata et al., 2015).

Carriers developed ALS at an average age of 67, with a classic ALS phenotype and primarily bulbar-onset disease, meaning they first had trouble speaking and swallowing. One patient who had the p.D40G mutation donated tissue for postmortem analysis. As is typical in ALS, neuron loss, astrogliosis, and phosphorylated TDP-43 inclusions pervaded their spinal cords; the latter also appeared in the medulla, temporal neocortex, andhippocampus.

The surprise came when the researchers stained for annexin A11. We saw the most extraordinary inclusions, Shaw told Alzforum. The skein-like patterns and tubular structures in motor neurons of the spinal cord were a far cry from the disordered blobs of TDP-43 that are typical of ALS neuropathology. They were unlike anything the scientists had ever seen, Shaw said (see image above). Add to that the torpedo-shaped structures in axons of the motor cortex, temporal neocortex, and hippocampus, and Shaw knew they were onto something. This mutant protein is actually aggregating in our patients, he said. That gave me 100 percent confidence that we had found a real gene causingpathology.

To find out how ANXA11 causes disease, the authors expressed several of the disease-associated variants or the wild-type protein in mouse primary motor neurons. Wild-type annexin A11 appeared in the nucleus, and in large, vesicle-like structures throughout the cytoplasm of the axons, soma, and dendrites. By contrast, the mutant proteins largely stayed out of vesicles; they aggregated instead. Their inclusions trapped functional, wild-type annexin A11 protein, implying they robbed the cell of the function of the normalprotein.

The variants also appeared to disrupt Annexin A11 binding to calcylin. Computer modeling predicted that the N-terminus of annexin A11 forms two helices, one in and the other next to the calcyclin binding site. Two of the six mutations appeared to disrupt formation of one of those helices. Immunoprecipitation assays revealed that while wild-type annexin A11 bound calcyclin, those mutants did not. The authors suggested that when annexin A11 cannot bind calcyclin, annexin A11 builds up in the cytoplasm and accumulates. As controls, the authors expressed non-pathogenic annexin A11 variants that appear in the general population; these variants left calcyclin bindingintact.

That last step was important, and provides a model for how these assays should be done in the future, said Harms, adding, It demonstrated that the ALS-specific functional defect was coming from mutations that they found in the patients. In general, researchers should always compare suspected pathogenic mutations to non-pathogenic ones to avoid assays picking up on nonspecific effects. Harms agreed this paper offers clear evidence that the p.D40G mutationwhich segregates with disease and leads to those unusual inclusionsis causative of ALS. More work needs to be done to see if the other five mutations are pathogenic, hesaid.

Shaw said his collaborators are now making transgenic zebrafish and mouse models with the mutations so they can study them in whole organisms.Gwyneth DickeyZakaib

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Understanding genetic variations in black women could improve cancer outcomes – UChicago News

Posted: at 3:11 am

Although the odds of developing breast cancer are nearly identical for black and white women, black women are 42 percent more likely to die from the disease. This mortality gapdriven by social and environmental, as well as biological factorscontinues to persist.

A large, multi-institutional study, published May 4 in JAMA Oncology, was designed to understand this gap by beginning to unravel the germline genetic variations and tumor biological differences between black and white women with breast cancer. This is the first ancestry-based comprehensive analysis of multiple platforms of genomic and proteomic data of its kind, the authors note.

Findings from this study could lead to more personalized risk assessment for women of African heritage and hasten the development of novel approaches designed to diagnose specific subtypes of aggressive breast cancers early and treat them effectively.

One new finding is that black women with hormone receptor positive, HER2-negative breast cancer had a higher risk-of-recurrence score than white women. The study also confirmed that black patients were typically diagnosed at a younger age and were more likely to develop aggressive breast-cancer subtypes, including basal-like or triple-negative cancerstumors lacking estrogen receptors, progesterone receptors and HER2as well as other aggressive tumor subtypes.

People have long associated breast cancer mortality in black women with poverty, or stress, or lack of access to care, but our results show that much of the increased risk for black women can be attributed to tumor biological differences, which are probably genetically determined, said study author Olufunmilayo Olopade,the Walter L. Palmer Distinguished Service Professor in Medicine and Human Genetics at the University of Chicago.

The good news, she said, is that as we learn more about these genetic variations, we can combine that information with clinical data to stratify risk and better predict recurrencesespecially for highly treatable cancersand develop interventions to improve treatment outcomes.

This is a great example of how team science and investments in science can accelerate progress in identifying the best therapies for the most aggressive breast cancers, said co-author Charles Perou, a member of the University of North Carolina Lineberger Comprehensive Cancer Center and professor of genetics, and pathology & laboratory medicine at the UNC School of Medicine.

In the largest dataset to date that has good representation of tumors from black women, we did not find much difference between the somatic mutations driving tumors in black and white women, he added. Yet black women were more likely to develop aggressive molecular subtypes of breast cancer. Now we provide data showing that differences in germline genetics may be responsible for up to 40 percent of the likelihood of developing one tumor subtype versus another.

The study used DNA data collected from 930 women154 of predominantly African ancestry and 776 of European ancestryavailable through The Cancer Genome Atlas, established by the National Cancer Institute and the National Human Genome Research Institute. The researchers combed through the data methodically, looking for racial differences in germline variations, somatic mutations, subtypes of breast cancers, survival time, as well as gene expression, protein expression and DNA methylation patterns.

Most significantly, explained first author Dezheng Huo, associate professor of public health sciences at the University of Chicago, we observed a higher genetic contribution to estrogen-receptor negative breast cancer in blacks.

Black women were more likely to get these highly aggressive cancers. This is one of the first studies to connect genetics to this racial difference in tumor subtype frequencies.

The study also revealed 142 genes that showed differences in expression levels according to race. One gene, CRYBB2, was consistently higher in tumors from black patients within each breast cancer subtype, as well as in normal tissues, suggesting it may be a race-specific gene.

The researchers also found somatic mutations in 13 genes or DNA segments that differed in frequency in tumors from black and white women. One of them, a mutated gene called TP53, was more common in black women than white women and was a strong predictor of disease recurrence.

Despite the relatively short follow-up time in the TCGA dataset, we were able to detect a significant racial disparity in patient survival using breast cancer-free interval as the endpoint between patients of African and European ancestries, said co-first author Hai Hu, vice president for research at the Chan Soon-Shiong Institute of Molecular Medicine at Windber. Most of the worst outcomes came from basal-like subtype breast cancer patients of African Ancestry.

Black women in all categories, including the most common breast cancers, were likely to have a worse prognosis, Olopade said.

Understanding the basic, underlying genetic differences between black and white women, the higher risk scores and the increased risk of recurrence should lead us to alternative treatment strategies, said Perou.

The crucial long-term benefit of this study, according to Olopade, is that it is a step toward the development of polygenic biomarkers, tools that can help us better understand each patients prognosis and, as we learn more, play a role in choosing the best treatment.

Genes matter, she added. This is a foot in the door for precision medicine, for scientifically targeted treatment.

This study now outlines a path for us to personalize breast cancer risk assessment and develop better strategies to empower all women, especially black women, to know their genetics and be more proactive in managing their risk, Perou said.

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Censorship of addiction research is an abuse of science – Nature.com

Posted: at 3:09 am

Christopher Furlong/Getty

Addiction research can produce results that governments and funders are not keen to share.

Kypros Kypri was pleased to receive funding from a government agency in the Australian state of New South Wales to study problem drinking. But when the contract arrived in 2012, he was surprised to find a demand that the agency could review and sign off on any reports before they were published. Other language allowed the agency to terminate funding without notice or explanation.

Kypri, who now studies the epidemiology of alcohol-related injuries at Australias University of Newcastle, saw this as a threat to academic freedom and so fought for months to have the fine print removed. Eventually, it was. But he has since realized that his experience is not unusual. In March, Kypri and his colleagues published the results of a survey indicating that many researchers who study addiction think that funders have interfered with their work most commonly by censoring it (P. Miller et al. Addict. Behav. 72, 100105; 2017).

The survey was completed by 322 authors who had published in the journal Addiction, and a little more than one-third of them reported interference at least once in their careers. That proportion must be taken with a pinch of salt it is possible that researchers who had experienced interference were more motivated to respond to the survey than those who had not, for example. And some of the reports go back almost a decade. But the survey nevertheless captures more than 100 experiences of research interference, spread across Europe, Australasia and North America.

There is a long and well chronicled history of private companies striving to keep tight reins on the results of research that they fund, particularly when it comes to studies of tobacco or pharmaceuticals. The survey showed that this remains a problem despite public attention, which is disappointing. Indeed, respondents reported their perception that such interference is on the rise.

But there has been less attention paid to censorship by government agencies, which is perhaps motivated by fears that politically sensitive results will highlight flaws in public programmes and so generate bad publicity. Some researchers and academic institutions accept clauses such as those that Kypri encountered as standard contract language. More should object, as he did.

Survey respondents highlighted a fear that standing up to funders could jeopardize their future funding opportunities particularly given that emerging for-profit research organizations might be more willing to accept limitations on their publications and study designs. Other researchers may believe the clauses to be harmless and unlikely to be brought to bear on their work.

To accept such limits, however, runs counter to the public interest. And the addiction-research survey shows that such clauses are not harmless. One European respondent said a epidemiology publication had been blocked because it was not in the interest of the sponsoring government department; another, from North America, said the government had enforced a request from an industry representative to remove recommendations in an epidemiology report. Researchers from Australasia looking at fatal drug overdoses said that after they published data that were embarrassing to the government department, they were denied access to that departments data. Interference can also come in other forms. Researchers must be wary of limits that public or private funders may attempt to place on study design or data sharing. For example, one senior researcher in North America said that his team was allowed to access a particular data set only if it agreed not to ask a politically sensitive question about the effectiveness of a government policy. Journals and journalists should make it a habit to inquire about the conditions, if any, imposed on researchers by their funders, so that those conditions can be disclosed when results are disseminated to the wider public.

Trends in some countries are encouraging. Kypri has encountered many researchers in the United States who say their institutions would not let them accept research contracts with clauses that allowed funder interference. In 2016, the UK government was forced to exempt scientific research contracts from new rules that would have banned government-funded organizations from lobbying for change.

Since his experience in 2012, Kypri has begun to systematically collect examples of clauses in government contracts that could enable interference in research. He worries that in some areas, particularly his own Australia, the clauses have become so common that they are viewed as normal. But his experience shows that it is possible to push back and perhaps even find compromises that satisfy both funder and researcher without compromising research integrity.

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This Tech Company’s Anti-Censorship Stance Is Helping Hate Speech – Mother Jones

Posted: at 3:09 am

Matthew Prince, chief executive officer of Cloudflare, speaks at a 2011 conference in China. Li Yuze/ Xinhua via Zuma

This story originally appeared on ProPublica.

Since its launch in 2013, the neo-Nazi website The Daily Stormer has quickly become the go-to spot for racists on the internet. Women are whores, blacks are inferior and a shadowy Jewish cabal is organizing a genocide against white people. The site can count among its readers Dylann Roof, the white teenager who slaughtered nine African Americans in Charleston in 2015, and James Jackson, who fatally stabbed an elderly black man with a sword in the streets of New York earlier this year.

Traffic is up lately, too, at white supremacist sites like The Right Stuff, Iron March, American Renaissance and Stormfront, one of the oldest white nationalist sites on the internet.

The operations of such extreme sites are made possible, in part, by an otherwise very mainstream internet companyCloudflare. Based in San Francisco, Cloudflare operates more than 100 data centers spread across the world, serving as a sort of middleman for websitesspeeding up delivery of a site's content and protecting it from several kinds of attacks. Cloudflare says that some 10 percent of web requests flow through its network, and the company's mainstream clients range from the FBI to the dating site OKCupid.

The widespread use of Cloudflare's services by racist groups is not an accident. Cloudflare has said it is not in the business of censoring websites and will not deny its services to even the most offensive purveyors of hate.

"A website is speech. It is not a bomb," Cloudflare's CEO Matthew Prince wrote in a 2013 blog post defending his company's stance. "There is no imminent danger it creates and no provider has an affirmative obligation to monitor and make determinations about the theoretically harmful nature of speech a site may contain."

Cloudflare also has an added appeal to sites such as The Daily Stormer. It turns over to the hate sites the personal information of people who criticize their content. For instance, when a reader figures out that Cloudflare is the internet company serving sites like The Daily Stormer, they sometimes write to the company to protest. Cloudflare, per its policy, then relays the name and email address of the person complaining to the hate site, often to the surprise and regret of those complaining.

The widespread use of Cloudflare's services by racist groups is not an accident.

This has led to campaigns of harassment against those writing in to protest the offensive material. People have been threatened and harassed.

ProPublica reached out to a handful of people targeted by The Daily Stormer after they or someone close to them complained to Cloudflare about the site's content. All but three declined to talk on the record, citing fear of further harassment or a desire to not relive it. Most said they had no idea their report would be passed on, though Cloudflare does state on the reporting form that they "will notify the site owner."

"I wasn't aware that my information would be sent on. I suppose I, naively, had an expectation of privacy," said Jennifer Dalton, who had complained that The Daily Stormer was asking its readers to harass Twitter users after the election.

Andrew Anglin, the owner of The Daily Stormer, has been candid about how he feels about people reporting his site for its content.

"We need to make it clear to all of these people that there are consequences for messing with us," Anglin wrote in one online post. "We are not a bunch of babies to be kicked around. We will take revenge. And we will do it now."

ProPublica asked Cloudflare's top lawyer about its policy of sharing information on those who complain about racist sites. The lawyer, Doug Kramer, Cloudflare's general counsel, defended the company's policies by saying it is "base constitutional law that people can face their accusers." Kramer suggested that some of the people attacking Cloudflare's customers had their own questionable motives.

Hate sites such as The Daily Stormer have become a focus of intense interest since the racially divisive 2016 electionhow popular they are, who supports them, how they are financed. Most of their operators supported Donald Trump and helped spread a variety of conspiracy theories aimed at damaging Hillary Clinton. But they clearly have also become a renewed source of concern for law enforcement.

In testimony Tuesday before the Senate Judiciary Committee, Chief Will D. Johnson, chair of the International Association of Chiefs of Police Human and Civil Rights Committee, highlighted the reach and threat of hate on the Internet.

"The internet provides extremists with an unprecedented ability to spread hate and recruit followers," he said. "Individual racists and organized hate groups now have the power to reach a global audience of millions and to communicate among like-minded individuals easily, inexpensively, and anonymously.

"Although hate speech is offensive and hurtful, the First Amendment usually protects such expression," Johnson said. "However, there is a growing trend to use the Internet to intimidate and harass individuals on the basis of their race, religion, sexual orientation, gender, gender identity, disability, or national origin."

A look at Cloudflare's policies and operations sheds some light on how sites promoting incendiary speech and even violent behavior can exist and even thrive.

Jacob Sommer, a lawyer with extensive experience in internet privacy and security issues, said there is no legal requirement for a company like Cloudflare to regulate the sites on their service, though many internet service providers choose to. It comes down to a company's sense of corporate responsibility, he said.

"There is a growing trend to use the Internet to intimidate and harass individuals on the basis of their race, religion, sexual orientation, gender, gender identity, disability, or national origin."

For the most part, Sommers said, a lot of companies don't want "this stuff" on their networks. He said those companies resist having their networks become "a hive of hate speech."

Jonathan Vick, associate director for investigative technology and cyberhate response at the Anti-Defamation League, agrees. He said that many of the hosts they talk to want to get hate sites off their networks.

"Even the most intransigent of them, when they're given evidence of something really problematic, they do respond," he said.

Cloudflare has raised at least $180 million in venture capital since its inception in 2009, much of it from some of the most prominent venture capital firms and tech companies in the country. The service is what's known as a content delivery network, and offers protection from several cyber threats including "denial of service" attacks, where hundreds of computers make requests to a website at once, overwhelming it and bringing it down.

Company officials have said Cloudflare's core belief is in the free and open nature of the internet. But given its outsize role in protecting a range of websites, Cloudflare has found itself the target of critics.

In 2015, the company came under fire from the hacker collective Anonymous for reportedly allowing ISIS propaganda sites on its network. At the time, Prince, the company's CEO, dismissed the claim as "armchair analysis by kids," and told Fox Business that the company would not knowingly accept money from a terrorist organization.

Kramer, in an interview with ProPublica, reiterated that the company would not accept money from ISIS. But he said that was not for moral or ethical reasons. Rather, he said, Cloudflare did not have dealings with terrorists groups such as ISIS because there are significant and specific laws restricting them from doing so.

In the end, Kramer said, seedy and objectionable sites made up a tiny fraction of the company's clients.

"We've got 6 million customers," he told ProPublica. "It's easy to find these edge cases."

One of the people ProPublica spoke with whose information had been shared with The Daily Stormer's operators said his complaint had been posted on the site, but that he was "not interested in talking about my experience as it's not something I want to revisit." Someone else whose information was posted on the site said that while she did get a few odd emails, she wasn't aware her information had been made public. She followed up to say she was going to abandon her email account now that she knew.

"The entire situation makes me feel uneasy," she said.

Scott Ernest had complained about The Daily Stormer's conduct after Anglin, its owner, had used the site to allegedly harass a woman in the town of Whitefish, Montana. After his complaint, Ernest wound up on the receiving end of about two dozen harassing emails or phone calls.

"Fuck off and die," read one email. "Go away and die," read another. Those commenting on the site speculated on everything from Ernest's hygiene to asking, suggestively, why it appeared in a Facebook post that Ernest had a child at his house.

Ernest said the emails and phone calls he received were not traumatizing, but they were worrying.

"His threats of harassment can turn into violence," he said of Anglin.

Anglin appears quite comfortable with his arrangement with Cloudflare. It doesn't cost him much eitherjust $200 a month, according to public posts on the site.

"[A]ny complaints filed against the site go to Cloudflare, and Cloudflare then sends me an email telling me someone said I was doing something bad and that it is my responsibility to figure out if I am doing that," he wrote in a 2015 post on his site. "Cloudflare does not regulate content, so it is meaningless."

Representatives from Rackspace and GoDaddy, two popular web hosts, said they try to regulate the kinds of sites on their services. For Rackspace, that means drawing the line at hosting white supremacist content or hate speech. For GoDaddy, that means not hosting the sort of abusive publication of personal information that Anglin frequently engages in.

"There is certainly content that, while we respect freedom of speech, we don't want to be associated with it," said Arleen Hess, senior manager of GoDaddy's digital crimes unit.

Both companies also said they would not pass along contact information for people who complain about offensive content to the groups generating it.

Getting booted around from service to service can make it hard to run a hate site, but Cloudflare gives the sites a solid footing.

Amazon Web Services, one of the most popular web hosts and content delivery networks, would not say how they handle abuse complaints beyond pointing to an "acceptable use" policy that restricts objectionable, abusive and harmful content. They also pointed to their abuse form, which says the company will keep your contact information private.

According to Vick at the ADL, the fact that Cloudflare takes money from Anglin is different from if he'd just used their free service.

"That's a direct relationship," he said. "That raises questions in my mind."

Some companies offering other services vital to success on the web have chosen not to do business with Anglin's The Daily Stormer. Google, PayPal and Coinbase, for instance, have chosen to cut off his accounts rather than support his activities. Getting booted around from service to service can make it hard to run a hate site, but Cloudflare gives the sites a solid footing.

And, by The Daily Stormer's account, advice and assurances. In a post, the site's architect, Andrew Auernheimer, said he had personal relationships with people at Cloudflare, and they had assured him the company would work to protect the site in a variety of waysincluding by not turning over data to European courts. Cloudflare has data centers in European countries such as Germany, which have strict hate speech and privacy laws.

Company officials offered differing responses when asked about Auernheimer's post. Kramer, Cloudflare's general counsel, said he had no knowledge of employee conversations with Auernheimer. Later, in an email, the company said Auernheimer was a well-known hacker, and that as a result at least one senior company official "has chatted with him on occasion and has spoken to him about Cloudflare's position on not censoring the internet."

A former Cloudflare employee, Ryan Lackey, said in an interview that while he doesn't condone a lot of what Auernheimer does, he did on occasion give technical advice as a friend and helped some of the Stormer's issues get resolved.

"I am hardcore libertarian/classical liberal about free speechsomething like Daily Stormer has every right to publish, and it is better for everyone if all ideas are out on the internet to do battle in that sphere," he said.

Vick at the ADL agrees that Anglin has a right to publish, but said people have the right to hold to task the Internet companies that enable him.

"Andrew Anglin has the right to be out there and say what he wants to say. But the people who object to what he has to say have a right to object as well," he said. "You should be able to respond to everybody in the chain."

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This Tech Company's Anti-Censorship Stance Is Helping Hate Speech - Mother Jones

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Wikipedia Is Turkey’s First Major Censorship Target, Post-Referendum. What Will Be Next? – Global Voices Online

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Global Voices Online
Wikipedia Is Turkey's First Major Censorship Target, Post-Referendum. What Will Be Next?
Global Voices Online
As a result, Turkey joined China as one of the few countries in the world to order a complete block on Wikipedia, rather than simply censoring individual pages. The sledgehammer attack on the resource echoes the zeal with which the government seemingly ...

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Wikipedia Is Turkey's First Major Censorship Target, Post-Referendum. What Will Be Next? - Global Voices Online

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Increased censorship when Palestine is mentioned, says British hunger striker – Middle East Monitor

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Students from the University of Edinburgh have gone on hunger strike to join activists across Europe, in solidarity with the nearly 1,600 Palestinian prisoners who are currently on hunger strike.

Earlier this week students and non-student groups from England, Scotland, Ireland, Spain, Belgium, Switzerland and Italy announced that they were joining 1,560 Palestinian prisoners who have been on hunger strike for over two weeks.

University of Edinburgh student Daniel Yahia said he was on hunger strike to protest against the treatment of Palestinian prisoners by Israeli authorities and over the universitys unethical investment in corporations that support the Israeli occupation.

Yahia told MEMO that the University of Edinburgh has invested in a number of corporations including Caterpillar that are highly influential in maintaining the apartheid regime.

He raised several complaints against the university, which he accused of supressing pro-Palestinian activism while favouring pro-Israeli groups.

Last April the student union voted for [Boycott, Divestment and Sanctions] BDS, which was democratically pushed through, despite intimidation from the right and Zionists. A few days later external pressure led the university to reverse this democratic process.

The motion to support BDS was passed on 31 March by 249 votes for and 153 against, with 22 abstentions, giving a majority of 74. The board of trustees of the University of Edinburgh Students Association, however, refused to enforce the BDS policy.

This is only one of the many ways in which the University of Edinburgh discriminates against pro-Palestine activism.

As soon as Palestine is involved, censorship intensifies, he explained, pointing to the cancellation of an event he was organising during Israel Apartheid Week. He told MEMO that on the day of the first Apartheid Week event on 20 March, the Communist Society, of which he is a member, was told that it could not hold the events on campus because the communist society was not affiliated with the Students Association.

Yahia accused the university of making up falsehoods as the society had held numerous events within the university even though it is not a member of the Students Association. He also mentioned that pro-Israeli groups boasted how pressure from above led to the event being cancelled.

Accusations of double standards and discrimination did not end there. Yahia also mentioned a row with the university over membership of the Students Association. He said that the application by the Communist Society to join the student body was declined twice while the Israel Engagement Society was accepted into the union within 48 hours of its application.

A University of Edinburgh spokesperson told MEMO: The University would always be very concerned by any proposed hunger strike, and would urge anyone considering this to consider their own health very carefully and take professional advice about the implications of such a course of action. We believe that the most constructive way for students to raise concerns is through our established representative channels such as the Students Association.

We place great value on free-speech, tolerance and mutual respect of people, no matter what their ethnic, religious or racial status. We welcome and promote discussion of current affairs, which sometimes involves highly contentious matters, and, as part of that, we recognise the right of students to freedom of expression and protest, providing any protests are safe, law-abiding and peaceful and debate is conducted within a framework of dignity and respect.

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Increased censorship when Palestine is mentioned, says British hunger striker - Middle East Monitor

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