technology:genomics

  • The U.S. Is Purging Chinese Americans From Top Cancer Research - Bloomberg
    https://www.bloomberg.com/news/features/2019-06-13/the-u-s-is-purging-chinese-americans-from-top-cancer-research

    In January, Wu, an award-winning epidemiologist and naturalized American citizen , quietly stepped down as director of the Center for Public Health and Translational Genomics at the University of Texas MD Anderson Cancer Center after a three-month investigation into her professional ties in China. Her resignation, and the departures in recent months of three other top Chinese American scientists from Houston-based MD Anderson, stem from a Trump administration drive to counter Chinese influence at U.S. research institutions.

    #Chine #Etats-unis #air_du_temps #régression

  • New report exposes global reach of powerful governments who equip, finance and train other countries to spy on their populations

    Privacy International has today released a report that looks at how powerful governments are financing, training and equipping countries — including authoritarian regimes — with surveillance capabilities. The report warns that rather than increasing security, this is entrenching authoritarianism.

    Countries with powerful security agencies are spending literally billions to equip, finance, and train security and surveillance agencies around the world — including authoritarian regimes. This is resulting in entrenched authoritarianism, further facilitation of abuse against people, and diversion of resources from long-term development programmes.

    The report, titled ‘Teach ’em to Phish: State Sponsors of Surveillance’ is available to download here.

    Examples from the report include:

    In 2001, the US spent $5.7 billion in security aid. In 2017 it spent over $20 billion [1]. In 2015, military and non-military security assistance in the US amounted to an estimated 35% of its entire foreign aid expenditure [2]. The report provides examples of how US Departments of State, Defense, and Justice all facilitate foreign countries’ surveillance capabilities, as well as an overview of how large arms companies have embedded themselves into such programmes, including at surveillance training bases in the US. Examples provided include how these agencies have provided communications intercept and other surveillance technology, how they fund wiretapping programmes, and how they train foreign spy agencies in surveillance techniques around the world.

    The EU and individual European countries are sponsoring surveillance globally. The EU is already spending billions developing border control and surveillance capabilities in foreign countries to deter migration to Europe. For example, the EU is supporting Sudan’s leader with tens of millions of Euros aimed at capacity building for border management. The EU is now looking to massively increase its expenditure aimed at building border control and surveillance capabilities globally under the forthcoming Multiannual Financial Framework, which will determine its budget for 2021–2027. Other EU projects include developing the surveillance capabilities of security agencies in Tunisia, Burkina Faso, Somalia, Iraq and elsewhere. European countries such as France, Germany, and the UK are sponsoring surveillance worldwide, for example, providing training and equipment to “Cyber Police Officers” in Ukraine, as well as to agencies in Saudi Arabia, and across Africa.

    Surveillance capabilities are also being supported by China’s government under the ‘Belt and Road Initiative’ and other efforts to expand into international markets. Chinese companies have reportedly supplied surveillance capabilities to Bolivia, Venezuela, and Ecuador [3]. In Ecuador, China Electronics Corporation supplied a network of cameras — including some fitted with facial recognition capabilities — to the country’s 24 provinces, as well as a system to locate and identify mobile phones.

    Edin Omanovic, Privacy International’s Surveillance Programme Lead, said

    “The global rush to make sure that surveillance is as universal and pervasive as possible is as astonishing as it is disturbing. The breadth of institutions, countries, agencies, and arms companies that are involved shows how there is no real long-term policy or strategic thinking driving any of this. It’s a free-for-all, where capabilities developed by some of the world’s most powerful spy agencies are being thrown at anyone willing to serve their interests, including dictators and killers whose only goal is to cling to power.

    “If these ‘benefactor’ countries truly want to assist other countries to be secure and stable, they should build schools, hospitals, and other infrastructure, and promote democracy and human rights. This is what communities need for safety, security, and prosperity. What we don’t need is powerful and wealthy countries giving money to arms companies to build border control and surveillance infrastructure. This only serves the interests of those powerful, wealthy countries. As our report shows, instead of putting resources into long-term development solutions, such programmes further entrench authoritarianism and spur abuses around the world — the very things which cause insecurity in the first place.”

    https://privacyinternational.org/press-release/2161/press-release-new-report-exposes-global-reach-powerful-governm

    #surveillance #surveillance_de_masse #rapport

    Pour télécharger le rapport “Teach ’em to Phish: State Sponsors of Surveillance”:
    https://privacyinternational.org/sites/default/files/2018-07/Teach-em-to-Phish-report.pdf

    ping @fil

    • China Uses DNA to Track Its People, With the Help of American Expertise

      The Chinese authorities turned to a Massachusetts company and a prominent Yale researcher as they built an enormous system of surveillance and control.

      The authorities called it a free health check. Tahir Imin had his doubts.

      They drew blood from the 38-year-old Muslim, scanned his face, recorded his voice and took his fingerprints. They didn’t bother to check his heart or kidneys, and they rebuffed his request to see the results.

      “They said, ‘You don’t have the right to ask about this,’” Mr. Imin said. “‘If you want to ask more,’ they said, ‘you can go to the police.’”

      Mr. Imin was one of millions of people caught up in a vast Chinese campaign of surveillance and oppression. To give it teeth, the Chinese authorities are collecting DNA — and they got unlikely corporate and academic help from the United States to do it.

      China wants to make the country’s Uighurs, a predominantly Muslim ethnic group, more subservient to the Communist Party. It has detained up to a million people in what China calls “re-education” camps, drawing condemnation from human rights groups and a threat of sanctions from the Trump administration.

      Collecting genetic material is a key part of China’s campaign, according to human rights groups and Uighur activists. They say a comprehensive DNA database could be used to chase down any Uighurs who resist conforming to the campaign.

      Police forces in the United States and elsewhere use genetic material from family members to find suspects and solve crimes. Chinese officials, who are building a broad nationwide database of DNA samples, have cited the crime-fighting benefits of China’s own genetic studies.

      To bolster their DNA capabilities, scientists affiliated with China’s police used equipment made by Thermo Fisher, a Massachusetts company. For comparison with Uighur DNA, they also relied on genetic material from people around the world that was provided by #Kenneth_Kidd, a prominent #Yale_University geneticist.

      On Wednesday, #Thermo_Fisher said it would no longer sell its equipment in Xinjiang, the part of China where the campaign to track Uighurs is mostly taking place. The company said separately in an earlier statement to The New York Times that it was working with American officials to figure out how its technology was being used.

      Dr. Kidd said he had been unaware of how his material and know-how were being used. He said he believed Chinese scientists were acting within scientific norms that require informed consent by DNA donors.

      China’s campaign poses a direct challenge to the scientific community and the way it makes cutting-edge knowledge publicly available. The campaign relies in part on public DNA databases and commercial technology, much of it made or managed in the United States. In turn, Chinese scientists have contributed Uighur DNA samples to a global database, potentially violating scientific norms of consent.

      Cooperation from the global scientific community “legitimizes this type of genetic surveillance,” said Mark Munsterhjelm, an assistant professor at the University of Windsor in Ontario who has closely tracked the use of American technology in Xinjiang.

      Swabbing Millions

      In Xinjiang, in northwestern China, the program was known as “#Physicals_for_All.”

      From 2016 to 2017, nearly 36 million people took part in it, according to Xinhua, China’s official news agency. The authorities collected DNA samples, images of irises and other personal data, according to Uighurs and human rights groups. It is unclear whether some residents participated more than once — Xinjiang has a population of about 24.5 million.

      In a statement, the Xinjiang government denied that it collects DNA samples as part of the free medical checkups. It said the DNA machines that were bought by the Xinjiang authorities were for “internal use.”

      China has for decades maintained an iron grip in Xinjiang. In recent years, it has blamed Uighurs for a series of terrorist attacks in Xinjiang and elsewhere in China, including a 2013 incident in which a driver struck two people in Tiananmen Square in Beijing.

      In late 2016, the Communist Party embarked on a campaign to turn the Uighurs and other largely Muslim minority groups into loyal supporters. The government locked up hundreds of thousands of them in what it called job training camps, touted as a way to escape poverty, backwardness and radical Islam. It also began to take DNA samples.

      In at least some of the cases, people didn’t give up their genetic material voluntarily. To mobilize Uighurs for the free medical checkups, police and local cadres called or sent them text messages, telling them the checkups were required, according to Uighurs interviewed by The Times.

      “There was a pretty strong coercive element to it,” said Darren Byler, an anthropologist at the University of Washington who studies the plight of the Uighurs. “They had no choice.”

      Calling Dr. Kidd

      Kenneth Kidd first visited China in 1981 and remained curious about the country. So when he received an invitation in 2010 for an expenses-paid trip to visit Beijing, he said yes.

      Dr. Kidd is a major figure in the genetics field. The 77-year-old Yale professor has helped to make DNA evidence more acceptable in American courts.

      His Chinese hosts had their own background in law enforcement. They were scientists from the Ministry of Public Security — essentially, China’s police.

      During that trip, Dr. Kidd met Li Caixia, the chief forensic physician of the ministry’s Institute of Forensic Science. The relationship deepened. In December 2014, Dr. Li arrived at Dr. Kidd’s lab for an 11-month stint. She took some DNA samples back to China.

      “I had thought we were sharing samples for collaborative research,” said Dr. Kidd.

      Dr. Kidd is not the only prominent foreign geneticist to have worked with the Chinese authorities. Bruce Budowle, a professor at the University of North Texas, says in his online biography that he “has served or is serving” as a member of an academic committee at the ministry’s Institute of Forensic Science.

      Jeff Carlton, a university spokesman, said in a statement that Professor Budowle’s role with the ministry was “only symbolic in nature” and that he had “done no work on its behalf.”

      “Dr. Budowle and his team abhor the use of DNA technology to persecute ethnic or religious groups,” Mr. Carlton said in the statement. “Their work focuses on criminal investigations and combating human trafficking to serve humanity.”

      Dr. Kidd’s data became part of China’s DNA drive.

      In 2014, ministry researchers published a paper describing a way for scientists to tell one ethnic group from another. It cited, as an example, the ability to distinguish Uighurs from Indians. The authors said they used 40 DNA samples taken from Uighurs in China and samples from other ethnic groups from Dr. Kidd’s Yale lab.

      In patent applications filed in China in 2013 and 2017, ministry researchers described ways to sort people by ethnicity by screening their genetic makeup. They took genetic material from Uighurs and compared it with DNA from other ethnic groups. In the 2017 filing, researchers explained that their system would help in “inferring the geographical origin from the DNA of suspects at crime scenes.”

      For outside comparisons, they used DNA samples provided by Dr. Kidd’s lab, the 2017 filing said. They also used samples from the 1000 Genomes Project, a public catalog of genes from around the world.

      Paul Flicek, member of the steering committee of the 1000 Genomes Project, said that its data was unrestricted and that “there is no obvious problem” if it was being used as a way to determine where a DNA sample came from.

      The data flow also went the other way.

      Chinese government researchers contributed the data of 2,143 Uighurs to the Allele Frequency Database, an online search platform run by Dr. Kidd that was partly funded by the United States Department of Justice until last year. The database, known as Alfred, contains DNA data from more than 700 populations around the world.

      This sharing of data could violate scientific norms of informed consent because it is not clear whether the Uighurs volunteered their DNA samples to the Chinese authorities, said Arthur Caplan, the founding head of the division of medical ethics at New York University’s School of Medicine. He said that “no one should be in a database without express consent.”

      “Honestly, there’s been a kind of naïveté on the part of American scientists presuming that other people will follow the same rules and standards wherever they come from,” Dr. Caplan said.

      Dr. Kidd said he was “not particularly happy” that the ministry had cited him in its patents, saying his data shouldn’t be used in ways that could allow people or institutions to potentially profit from it. If the Chinese authorities used data they got from their earlier collaborations with him, he added, there is little he can do to stop them.

      He said he was unaware of the filings until he was contacted by The Times.

      Dr. Kidd also said he considered his collaboration with the ministry to be no different from his work with police and forensics labs elsewhere. He said governments should have access to data about minorities, not just the dominant ethnic group, in order to have an accurate picture of the whole population.

      As for the consent issue, he said the burden of meeting that standard lay with the Chinese researchers, though he said reports about what Uighurs are subjected to in China raised some difficult questions.

      “I would assume they had appropriate informed consent on the samples,” he said, “though I must say what I’ve been hearing in the news recently about the treatment of the Uighurs raises concerns.”
      Machine Learning

      In 2015, Dr. Kidd and Dr. Budowle spoke at a genomics conference in the Chinese city of Xi’an. It was underwritten in part by Thermo Fisher, a company that has come under intense criticism for its equipment sales in China, and Illumina, a San Diego company that makes gene sequencing instruments. Illumina did not respond to requests for comment.

      China is ramping up spending on health care and research. The Chinese market for gene-sequencing equipment and other technologies was worth $1 billion in 2017 and could more than double in five years, according to CCID Consulting, a research firm. But the Chinese market is loosely regulated, and it isn’t always clear where the equipment goes or to what uses it is put.

      Thermo Fisher sells everything from lab instruments to forensic DNA testing kits to DNA mapping machines, which help scientists decipher a person’s ethnicity and identify diseases to which he or she is particularly vulnerable. China accounted for 10 percent of Thermo Fisher’s $20.9 billion in revenue, according to the company’s 2017 annual report, and it employs nearly 5,000 people there.

      “Our greatest success story in emerging markets continues to be China,” it said in the report.

      China used Thermo Fisher’s equipment to map the genes of its people, according to five Ministry of Public Security patent filings.

      The company has also sold equipment directly to the authorities in Xinjiang, where the campaign to control the Uighurs has been most intense. At least some of the equipment was intended for use by the police, according to procurement documents. The authorities there said in the documents that the machines were important for DNA inspections in criminal cases and had “no substitutes in China.”

      In February 2013, six ministry researchers credited Thermo Fisher’s Applied Biosystems brand, as well as other companies, with helping to analyze the DNA samples of Han, Uighur and Tibetan people in China, according to a patent filing. The researchers said understanding how to differentiate between such DNA samples was necessary for fighting terrorism “because these cases were becoming more difficult to crack.”

      The researchers said they had obtained 95 Uighur DNA samples, some of which were given to them by the police. Other samples were provided by Uighurs voluntarily, they said.

      Thermo Fisher was criticized by Senator Marco Rubio, Republican of Florida, and others who asked the Commerce Department to prohibit American companies from selling technology to China that could be used for purposes of surveillance and tracking.

      On Wednesday, Thermo Fisher said it would stop selling its equipment in Xinjiang, a decision it said was “consistent with Thermo Fisher’s values, ethics code and policies.”

      “As the world leader in serving science, we recognize the importance of considering how our products and services are used — or may be used — by our customers,” it said.

      Human rights groups praised Thermo Fisher’s move. Still, they said, equipment and information flows into China should be better monitored, to make sure the authorities elsewhere don’t send them to Xinjiang.

      “It’s an important step, and one hopes that they apply the language in their own statement to commercial activity across China, and that other companies are assessing their sales and operations, especially in Xinjiang,” said Sophie Richardson, the China director of Human Rights Watch.

      American lawmakers and officials are taking a hard look at the situation in Xinjiang. The Trump administration is considering sanctions against Chinese officials and companies over China’s treatment of the Uighurs.

      China’s tracking campaign unnerved people like Tahir Hamut. In May 2017, the police in the city of Urumqi in Xinjiang drew the 49-year-old Uighur’s blood, took his fingerprints, recorded his voice and took a scan of his face. He was called back a month later for what he was told was a free health check at a local clinic.

      Mr. Hamut, a filmmaker who is now living in Virginia, said he saw between 20 to 40 Uighurs in line. He said it was absurd to think that such frightened people had consented to submit their DNA.

      “No one in this situation, not under this much pressure and facing such personal danger, would agree to give their blood samples for research,” Mr. Hamut said. “It’s just inconceivable.”

      https://www.nytimes.com/2019/02/21/business/china-xinjiang-uighur-dna-thermo-fisher.html?action=click&module=MoreInSect
      #USA #Etats-Unis #ADN #DNA #Ouïghours #université #science #génétique #base_de_données

  • #blockchain, Crypto, and Genomics — How They Can Work Together To Protect Your Data
    https://hackernoon.com/blockchain-crypto-and-genomics-how-they-can-work-together-to-protect-you

    Blockchain, Crypto, and Genomics — How They Can Work Together To Protect Your DataThroughout the last couple of years, data protection has emerged as a leading issue among companies and governing bodies. This is especially true in the United States where several incidents have been identified as a major cause for concern. A few examples include the following:In September 2017, Equifax suffered a massive breach that exposed sensitive data about millions of Americans. Some of the exposed data included passport numbers, driver’s license numbers, and social security numbers.In September 2018, an attack on Facebook’s computer network exposed personal information of nearly 50 million users.In November 2018, Marriott announced that its Starwood guest reservation database had been breached. Private (...)

    #cryptocurrency #genetics #data-protection #dna

  • Will The Real Robot Please Stand Up
    https://hackernoon.com/will-the-real-robot-please-stand-up-6199e0e1665e?source=rss----3a8144eab

    AI, #blockchain, and the value of being human with Singularity University’s Reese Jones and Project Shivom’s Henry Ines at Blockchain Economic ForumMartine Paris / Via Martine ParisWhat does the world’s first decentralized AI humanoid, Sophia the Robot, have to do with owning the data that makes us human?“A lot!” said Henry Ines, Chief Innovation Officer of Shivom, in his interview with me at the recent Blockchain Economic Forum in San Francisco. Ines, a former DFJ DragonFund partner, just completed a $35 million ICO to fund the building of Shivom’s #genomics hub and is now partnering with the makers of Sophia’s brain, SingularityNET, to use AI-driven analytics and machine learning tools to power the dawn of precision medicine.“A Tylenol that’s right for you might be different than a Tylenol (...)

    #robotics #cryptocurrency #artificial-intelligence

  • Linguistic red flags from Facebook posts can predict future depression diagnoses — ScienceDaily
    https://www.sciencedaily.com/releases/2018/10/181015150643.htm

    Research finds that the language people use in their Facebook posts can predict a future diagnosis of depression as accurately as the tools clinicians use in medical settings to screen for the disease.

    In any given year, depression affects more than 6 percent of the adult population in the United States — some 16 million people — but fewer than half receive the treatment they need. What if an algorithm could scan social media and point to linguistic red flags of the disease before a formal medical diagnosis had been made?

    Ah oui, ce serait fantastique pour les Big Pharma : la dépression est une maladie complexe, dont les symptômes graves sont souvent confondus avec la déprime qui est un état sychologique que nous connaissons tous. Notre Facebook, couplé avec notre assistant vocal Amazon nous gorgerait de Valium, et tout irait pour le mieux dans le Meilleur des mondes.

    Considering conditions such as depression, anxiety, and PTSD , for example, you find more signals in the way people express themselves digitally."

    For six years, the WWBP, based in Penn’s Positive Psychology Center and Stony Brook’s Human Language Analysis Lab, has been studying how the words people use reflect inner feelings and contentedness. In 2014, Johannes Eichstaedt, WWBP founding research scientist, started to wonder whether it was possible for social media to predict mental health outcomes, particularly for depression.

    “Social media data contain markers akin to the genome,” Eichstaedt explains. “With surprisingly similar methods to those used in genomics, we can comb social media data to find these markers. Depression appears to be something quite detectable in this way; it really changes people’s use of social media in a way that something like skin disease or diabetes doesn’t.”

    Il y a au moins une bonne nouvelle sur la déontologie scientifique :

    Rather than do what previous studies had done — recruit participants who self-reported depression — the researchers identified data from people consenting to share Facebook statuses and electronic medical-record information, and then analyzed the statuses using machine-learning techniques to distinguish those with a formal depression diagnosis.

    Les marqueurs considérés sont aussi des marqueurs sociaux et économiques, qu’il faudrait traiter autrement qu’avec des médicaments.

    They learned that these markers comprised emotional, cognitive, and interpersonal processes such as hostility and loneliness, sadness and rumination, and that they could predict future depression as early as three months before first documentation of the illness in a medical record.

    La conclusion est fantastique : il faut rendre le balayage obligatoire !!!

    Eichstaedt sees long-term potential in using these data as a form of unobtrusive screening. “The hope is that one day, these screening systems can be integrated into systems of care,” he says. “This tool raises yellow flags; eventually the hope is that you could directly funnel people it identifies into scalable treatment modalities.”

    Despite some limitations to the study, including its strictly urban sample, and limitations in the field itself — not every depression diagnosis in a medical record meets the gold standard that structured clinical interviews provide, for example — the findings offer a potential new way to uncover and get help for those suffering from depression.

    #Dépression #Facebook #Foutaises #Hubris_scientifique #Big_pharma #Psychologie

  • It’s better to be born rich than gifted (https://www.washingtonpost...
    https://diasp.eu/p/7851925

    It’s better to be born rich than gifted

    The least-gifted children of high-income parents graduate from college at higher rates than the most-gifted children of low-income parents, and other dispatches from the point where genetics… Article word count: 1221

    HN Discussion: https://news.ycombinator.com/item?id=18209249 Posted by joeyespo (karma: 19076) Post stats: Points: 73 - Comments: 37 - 2018-10-13T18:16:19Z

    #HackerNews #better #born #gifted #its #rich #than

    Article content:

    A revolution in genomics is creeping into economics. It allows us to say something we might have suspected, but could never confirm: money trumps genes.

    Using one new, genome-based measure, economists found genetic endowments are distributed almost equally among children in low-income and high-income (...)

  • New studies show how easy it is to identify people using genetic databases - STAT
    https://www.statnews.com/2018/10/11/genetic-databases-privacy

    n recent months, consumer genealogy websites have unleashed a revolution in forensics, allowing law enforcement to use family trees to track down the notorious Golden State Killer in California and solve other cold cases across the country. But while the technique has put alleged killers behind bars, it has also raised questions about the implications for genetic privacy.

    According to a pair of studies published Thursday, your genetic privacy may have already eroded even further than previously realized.

    In an analysis published in the journal Science, researchers used a database run by the genealogy company MyHeritage to look at the genetic information of nearly 1.3 million anonymized people who’ve had their DNA analyzed by a direct-to-consumer genomics company. For nearly 60 percent of those people, it was possible to track down someone whose DNA was similar enough to indicate they were third cousins or closer in relation; for another 15 percent of the samples, second cousins or closer could be found.

    Yaniv Erlich, the lead author on the Science paper, said his team’s findings should prompt regulators and others to reconsider the assumption that genetic information is de-identified. “It’s really not the case. At least technically, it seems feasible to identify some significant part of the population” with such investigations, said Erlich, who’s a computer scientist at Columbia University and chief science officer at MyHeritage.

    The Science paper counted 12 cold cases that were solved between April and August of this year when law enforcement turned to building family trees based on genetic data; a 13th case was an active investigation.

    The most famous criminal identified this way: the Golden State Killer, who terrorized California with a series of rapes and murders in the 1970s and 1980s. With the help of a genetic genealogist, investigators uploaded a DNA sample collected from an old crime scene to a public genealogy database, built family trees, and tracked down relatives. They winnowed down their list of potential suspects to one man with blue eyes, and in April, they made the landmark arrest.

    To crack that case, the California investigators used GEDmatch, an online database that allows people who got their DNA analyzed by companies like 23andMe and Ancestry to upload their raw genetic data so that they can track down distant relatives. MyHeritage’s database — which contains data from 1.75 million people, mostly Americans who’ve gotten their DNA analyzed by MyHeritage’s genetic testing business — works similarly, although it explicitly prohibits forensic searches. (23andMe warns users about the privacy risks of uploading their genetic data to such third party sites.)

    “For me, these articles are fascinating and important and we shouldn’t shy away from the privacy concerns that these articles raise. But at the same time, we should keep in mind the personal and societal value that we believe that we are accruing as we make these large collections,” said Green, who was not involved in the new studies and is an adviser for genomics companies including Helix and Veritas Genetics.

    He pointed to the potential of genomics not only to reunite family members and put criminals behind bars, but also to predict and prevent heritable diseases and develop new drugs.

    As with using social media and paying with credit cards online, reaping the benefits of genetic testing requires accepting a certain level of privacy risk, Green said. “We make these tradeoffs knowing that we’re trading some vulnerability for the advantages,” he said.

    #Génomique #ADN #Vie_privée

  • Using FPGA superpowers to speed up cloud workloads with #inaccel
    https://hackernoon.com/using-fpga-superpowers-to-speed-up-cloud-workloads-with-inaccel-182058c9

    There is nothing new under the Sun, the saying goes, and that also holds true for Field Programmable Gate Arrays. FPGAs though are back with a rage, with major cloud vendors offering FPGA-as-a-service and chip manufacturers renewing their interest in the space. Among other facts, Intel acquired Altera for $16B and is now shipping the new Intel Xeon CPUs with an integrated FPGA.At the same time, applications like data analytics, machine learning, and genomics are extremely computationally intensive and require a large amount of processing power -let alone manpower- to manage the clusters. To face this challenge, warehouse data centers and cloud providers have recently started to adopt the use of hardware accelerators.Hardware accelerators (e.g. FPGAs) can speed up the application (...)

    #field-programmable-arrays #fpga-superpowers #cloud-computing #programmable-gate-array

  • Genomic Inquiries
    https://hackernoon.com/genomic-inquiries-5c675aff55ec?source=rss----3a8144eabfe3---4

    Photo by NeONBRAND on UnsplashI’ve been reading a book personalized #medicine called Genomic Messages by George Annas and Sherman Elias. It is an excellent book that gives the lay of the land when it comes to #genomics as it relates to the everyday person.In some regards, this book may be considered not that recent as it was published in 2015. It seems as though everyday there is a new headline of a breakthrough at a university for genetics or translational medicine in relation to curing disease. And, though these things may be true, there are significant ramifications of moving forward with these discoveries and technologies.Personalized MedicineAlong with the word blockchain and AI — personalized medicine or precision medicine has joined the ranks of hype. In fact, it has been the dream of (...)

    #healthcare #health #genomic-inquiries

  • Quantum Computers Disrupting #healthcare
    https://hackernoon.com/quantum-computers-disrupting-healthcare-e3dac9a891ef?source=rss----3a814

    Quantum Computing…sounds mind blowing already.It seems like another huge buzzword I get it, but whats all the hype? Why are super smart people spending their time developing and researching quantum computers?Companies like Google, Microsoft, IBM and super successful startups such as D-Wave and Rigetti Computing are investing millions and millions of dollars into quantum computers.Why? Because they are building the world’s most powerful computer to ever exist.Before I tell you how Quantum Computing will disrupt the healthcare industry, lets get you caught up with what the heck it is.In short Quantum Computers use phenomenons called superposition and entanglement to create qubits with special computational power determined by the laws of quantum mechanics.Qubits are unlike binary bits, (...)

    #quantum-computing #quantum-physics #science #genomics

  • Framework for African Genomics and Biobanking
    https://h3africa.org/9-news/361-framework-for-african-genomics-and-biobanking

    The number of genomics research and biobanking projects taking place on the African content is growing steadily. A critical feature of such research is the broad sharing of data and samples for secondary use by investigators who were not originally involved in their collection. Such ‘open science’ holds considerable potential for facilitating scientific discovery but it also evokes important ethical challenges that need to be addressed for its successful implementation, not least where research takes place in the African research context, which evokes questions about equity and fairness. Whilst the ethical and regulatory constructs to allow sharing and re-use of scientific resources are being developed, it is not surprising that the ethical review and regulatory infrastructure in Africa does not yet accommodate sharing and secondary use. Yet African people’s broad genetic diversity could be a key to addressing the high burden of disease in the continent and Africa offers many unique opportunities to advance an ethic of sharing. This Framework aims to set out the principles and actions that should be considered as pertinent ethical concerns for genomic research and biobanking in Africa.
    The Framework takes account of pertinent concerns raised regarding scientific and medical research in Africa. One such concern is the perception that research collaborations have been largely unfair for African researchers and participants. This Framework seeks to foster a progressive regulatory ethos that will empower African research participants, communities and researchers to engage with, and benefit from, genomic research and biobanking in a fair and mutually beneficial manner.
    This Framework is inspired by communal or solidarity-based worldviews that are important in many African countries. Such worldviews recognize that individuals are shaped by their relations to people around them, and emphasize respectful and harmonious relationships between individuals. It places central importance on reciprocity, consultation and accountability as key ethical values. This worldview would suggest that sharing to contribute to the ultimate wellbeing and humanness of others would be broadly supported in Africa. But such sharing must always be matched with reciprocity – i.e. as much as the individual contributes to the community, the community also contributes to the individual’s sustainable wellbeing. Similarly, sharing should happen responsibly, with input from all those affected and with mechanisms by which to hold research teams accountable. By supporting genomics research in this way, African populations could contribute to cutting edge research, which, though expensive at the moment, has strong potential for better returns in reduced health care costs from diseases amenable to improved control as a result of a better understanding of their genomic determinants.

    #Médecine #Biotechnologies #Banques_de_gènes #Ethique #Afrique

  • #Nebula_Genomics will leverage #blockchain technology to eliminate middlemen and empower people to own their personal #genomic_data. This will effectively lower sequencing costs and enhance data privacy, resulting in growth of genomic data. Our open protocol will leverage the genomic data growth by enabling data buyers to efficiently aggregate standardized data from many individual people and genomic databanks.”

    Nice and interesting project but (see later).

    Official corporate Web site: https://www.nebulagenomics.io

    The detailed white paper: https://www.nebulagenomics.io/assets/documents/NEBULA_whitepaper_v4.52.pdf

    A summary, with an interview of the founders: http://www.sciencemag.org/news/2018/02/q-george-church-and-company-genomic-sequencing-blockchain-and-better-dru

    #DNS #DNS_sequencing #genomics

    After reading the white paper, some comments:

    Sentences such as “Nebula network addresses are cryptographic identifiers that are not associated with any personal information.” are worrying because they seem to indicate that the authors do not really understand the concept of “personal information”. “Personal information” is not only when you name is on it. There have been a lot of research on tracing blockchain addresses.

    The white paper sometimes make bold claims, then seriously reduces them. For instancen it talks about “#homomorphic_encryption”, something which is very cool for the mathematically inclined, but offers very poor performances. Later, the paper speaks only of “partially homomorphic encryption”.

    Most of the security seems to rely, not on homomorphic encryption, but on Intel’s #Software_Guard_ Extensions (#SGX). SGX is an interesting technology, but quite recent. (Also, it comes from the company that puts a backdoor on every processor, through the Management Engine.) Relying on Intel security one month after Meltdown and Spectre seems audacious.

    It is not clear if the “Nebula blockchain” is a private one or a public one, like Blockstack. Private blockchains remove most of the security of a blockchain.

    “we want to support research conducted by non-profit institutions, such as universities.” In countries where researchers in public institutions are allowed to create for-profit companies with the results of research funded by “non-profit” research, the concept of “non-profit” is quite blurred.

  • Why Did a Billionaire Give $75 Million to a Philosophy Department? - Facts So Romantic
    http://nautil.us/blog/why-did-a-billionaire-give-75-million-to-a-philosophy-department

    Philosophy matters. The new challenges of the genomics revolution, the rise of AI, the growth in inequality, societal fragmentation, and our capacity for devastating war all invite philosophical perspective.Painting by Otto Scholderer / WikicommonsLast week, for the first time in recent memory, a news story in this troubling period had me, a bachelor of arts in philosophy, sitting up straight in stunned delight. Johns Hopkins University was gifted $75 million to expand its philosophy department to near-twice its size—more professors (13 to 22 over a decade) and postdoctoral fellows and graduate students, as well more undergraduate courses. It’s apparently the largest donation any philosophy department has ever received, and for Johns Hopkins, it’s the largest gift the university has ever (...)

  • How to Build an Artificial Womb
    https://io9.gizmodo.com/how-to-build-an-artificial-womb-476464703

    Artificial wombs are a staple of science fiction, but could we really build one? As time passes, we’re inching closer and closer to the day when it will finally become possible to grow a baby entirely outside the human body. Here’s what we’ll need to do to pull it off.

    Top image by Mondolithic Studios.
    More than just an incubator

    A fully functional artificial uterus will be substantially more complex than a modern incubator, a clunky (and somewhat obtrusive) device that provides a preemie with oxygen, protection from cold, hydration and nutrition (via intravenous catheter or NG tube), and adequate levels of humidity.
    Recent Video from Gizmodo
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    The World’s First Ping-Pong Robot
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    Even in the best of cases, the current state-of-the-art doesn’t allow for viability outside of the womb until mid to late second trimester. Prior to that, a mother’s womb is the only option. Quite obviously, future incubators, or a full-blown artificial uterus, will push the limits of viability further and further until the entire gestational cycle can happen external to the body.

    We’re still several decades away, but the two primary areas that need to be developed include biotechnology (for things like personalized genomics and tissue engineering) and nanotechnology (to facilitate micro-scale interactions and growth through artificial means). Smart computer systems and monitoring devices should also be developed to track the progress of the fetus’s growth, while automatically adjusting for changing conditions.

    #utérus_artificiel

  • Google Has Released an AI Tool That Makes Sense of Your Genome - MIT Technology Review
    https://www.technologyreview.com/s/609647/google-has-released-an-ai-tool-that-makes-sense-of-your-genome

    DeepVariant was developed by researchers from the Google Brain team, a group that focuses on developing and applying AI techniques, and Verily, another Alphabet subsidiary that is focused on the life sciences.

    The team collected millions of high-throughput reads and fully sequenced genomes from the Genome in a Bottle (GIAB) project, a public-private effort to promote genomic sequencing tools and techniques. They fed the data to a deep-learning system and painstakingly tweaked the parameters of the model until it learned to interpret sequenced data with a high level of accuracy.

    “The success of DeepVariant is important because it demonstrates that in genomics, deep learning can be used to automatically train systems that perform better than complicated hand-engineered systems,” says Brendan Frey, CEO of Deep Genomics.

    The release of DeepVariant is the latest sign that machine learning may be poised to boost progress in genomics.

    DeepVariant will also be available on the Google Cloud Platform. Google and its competitors are furiously adding machine-learning features to their cloud platforms in an effort to lure anyone who might want to tap into the latest AI techniques (see “Ambient AI Is About to Devour the Software Industry”).

    #Génomique #Google #Deep_learning

  • How to Spend $1,900 on Gene Tests Without Learning a Thing - MIT Technology Review
    https://www.technologyreview.com/s/609103/how-to-spend-1900-on-gene-tests-without-learning-a-thing

    But instead of air purifiers, bacon toasters, and other electronic gadgets that no one really needs, people with money to burn can spend $149 on a scarf whose pattern is personalized using their genes, DNA diet apps, or even genetically influenced wine recommendations.

    Eric Topol, an influential heart doctor and geneticist at the Scripps Research Institute in La Jolla, California, says he’s had enough. To Topol, too many of these apps amount to genetic astrology. “The data has no basis. It’s pseudoscience—complete, utter nothing,” he says. He calculated that a consumer could spend $1,900 on 17 apps and learn almost nothing of value.

    Earlier this year, the U.S. Food and Drug Administration signaled that it would unwind what had been a de facto ban on a range of direct-to-consumer gene reports. What’s followed has been a quick expansion of gene tests that range from reasonable to downright silly.

    Aside from Helix, many others are selling DNA tests, too. One, being advertised on TV, is “Soccer Genomics,” which promises a “personalized report that will help guide player development.” And for $99, a company called Orig3n will sell you a test that claims to predict your kid’s ability to learn languages. Last month, that company had to cancel a planned giveaway of DNA tests at a Baltimore Ravens game, after objections from state regulators.

    Mais ils ne sont responsables de rien... un peu comme les plateformes et les fake-news... ce sont ceux qui y croient qui ont tort. Ben voyons.

    In response to critics, Helix cofounder Justin Kao cautions against a “paternalistic” attitude toward what kind of information consumers should be able to spend their money on. “People should be able to choose how they want to interact and experience DNA-powered insights and decide for themselves what is of value to them,” he says.

    #Génomique #Tests_génétiques #DTCtests #Arnaques

  • Ancient genomic changes associated with domestication of the horse | Science
    http://science.sciencemag.org/content/356/6336/442.full

    Ancient genomics of horse domestication
    The domestication of the horse was a seminal event in human cultural evolution. Librado et al. obtained genome sequences from 14 horses from the Bronze and Iron Ages, about 2000 to 4000 years ago, soon after domestication. They identified variants determining coat color and genes selected during the domestication process. They could also see evidence of admixture with archaic horses and the demography of the domestication process, which included the accumulation of deleterious variants. The horse appears to have undergone a different type of domestication process than animals that were domesticated simply for food.

    Abstract
    The genomic changes underlying both early and late stages of horse domestication remain largely unknown. We examined the genomes of 14 early domestic horses from the Bronze and Iron Ages, dating to between ~4.1 and 2.3 thousand years before present. We find early domestication selection patterns supporting the neural crest hypothesis, which provides a unified developmental origin for common domestic traits. Within the past 2.3 thousand years, horses lost genetic diversity and archaic DNA tracts introgressed from a now-extinct lineage. They accumulated deleterious mutations later than expected under the cost-of-domestication hypothesis, probably because of breeding from limited numbers of stallions. We also reveal that Iron Age Scythian steppe nomads implemented breeding strategies involving no detectable inbreeding and selection for coat-color variation and robust forelimbs.

    (article accessible en entier)

  • L’#ADN révèle les secrets du #tardigrade, résistant suprême
    http://www.lemonde.fr/sciences/article/2017/07/31/l-adn-revele-les-secrets-du-tardigrade-resistant-supreme_5167103_1650684.htm

    « Shinjirarenai ! », « Amazing ! », « Incroyable ! ». Dans toutes les langues, l’adjectif résonne souvent à l’unisson à l’évocation du nom d’une petite bête : le tardigrade. D’origine obscure et doté de facultés de survie inouïes, l’animal microscopique, surnommé « ourson d’eau » à cause de ses griffes, intrigue les scientifiques. Un groupe de biologistes britanniques et japonais a donc entrepris d’explorer son génome. Cette plongée dans les arcanes de son ADN leur a permis d’en percer certains mystères. Publiée le 27 juillet dans la revue PLOS Biology, leur étude apporte des révélations sur deux fronts distincts : la position exacte de l’animal au sein du vivant et les mécanismes génétiques à l’origine de ses capacités de #résistance.

    #nématodes #immortalité

  • New images of complex microbiome environments visualized by Berkeley Metagenomics Lab and Stamen…
    https://hi.stamen.com/uc-berkeley-metagenomics-lab-releases-new-images-of-complex-microbiome-en

    What is metagenomics?

    A metagenome is a collection of DNA sequences from the organisms present in an environment at the time a sample is taken. Metagenomics is the study of these genomic sequences. Metagenomics has been around in various forms since the early 2000s. Initially, the approach was referred to as “community genomics” because the sequencing approaches were used to study natural microbial communities. It wasn’t until the mid 2000s that it acquired its “meta” label. In the first studies, both genome reconstruction-based approaches and analyses of collections of genes without organism affiliation were used. Both of these methods are distinct from investigations of specific marker genes that had been used previously to phylogenetically “fingerprint” environments.

    The primary difference is that genome sequences provide some insight into what all the organisms might be doing. Fingerprinting methods mostly tell us how closely organisms are related to each other.

    #recherche #microbiome #image #écosystème #adn

  • Rosalind’s Ghost: Biology, Collaboration, and the Female, by Caroline Wagner (PLOS Biology)
    http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001003

    Zeng et al. find the gap to be so great, with such a low participation of women, that it appears to constitute “gender segregation.” The number of women coauthoring in genomics is so far below expectation that chance or shorter careers cannot be the reason for the disparity.

    Perhaps the most enigmatic finding from Zeng et al. is that women do not repeat coauthorships as frequently as male counterparts. On one hand, this might indicate practices related to active search for new ideas, as the authors note: “….[w]e find evidence for the hypothesis that female scientists are more open to novel collaborations…” Furthermore, this resonates with our work on Nobel Laureates, in which the communication networks suggested that prize winners were more likely than elite peers to reach outside of their immediate networks to seek new ideas. However, it is clear from their data that this characteristic of women’s teams is not translating into citations, publications, and certainly not into scientific prizes.

    #recherche #biologie #femmes #discrimination

  • 1 in 5 scientific papers on genes contain errors because of Excel

    The spreadsheet software Microsoft Excel, when used with default settings, is known to convert gene names to dates and floating-point numbers. A programmatic scan of leading genomics journals reveals that approximately one-fifth of papers with supplementary Excel gene lists contain erroneous gene name conversions.

    The problem is that there are some gene names/acronyms like SEPT2 and MARCH1, which Excel then converts to dates “2-Sep” and “1-Mar”

    Copy-pasting large data sets hid the errors for years. Researches would probably have noticed if they entered the data one Excel cell at a time.

    Gene name errors are widespread in the scientific literature

    http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1044-7

    The problem of Excel software inadvertently converting gene symbols to dates and floating-point numbers was originally described in 2004 [1]. For example, gene symbols such as SEPT2 (Septin 2) and MARCH1 [Membrane-Associated Ring Finger (C3HC4) 1, E3 Ubiquitin Protein Ligase] are converted by default to ‘2-Sep’ and ‘1-Mar’, respectively. Furthermore, RIKEN identifiers were described to be automatically converted to floating point numbers (i.e. from accession ‘2310009E13’ to ‘2.31E+13’). Since that report, we have uncovered further instances where gene symbols were converted to dates in supplementary data of recently published papers (e.g. ‘SEPT2’ converted to ‘2006/09/02’). This suggests that gene name errors continue to be a problem in supplementary files accompanying articles. Inadvertent gene symbol conversion is problematic because these supplementary files are an important resource in the genomics community that are frequently reused. Our aim here is to raise awareness of the problem.

    [...]

    To date, there is no way to permanently deactivate automatic conversion to dates in MS Excel and other spreadsheet software such as LibreOffice Calc or Apache OpenOffice Calc. We note, however, that the spreadsheet program Google Sheets did not convert any gene names to dates or numbers when typed or pasted; notably, when these sheets were later reopened with Excel, LibreOffice Calc or OpenOffice Calc, gene symbols such as SEPT1 and MARCH1 were protected from date conversion.

    [...]

    In conclusion, we show that inadvertent gene name conversion errors persist in the scientific literature, but these should be easy to avoid if researchers, reviewers, editorial staff and database curators remain vigilant.

  • Winning the Cancer War: Start With the Deepest Intelligence - Facts So Romantic
    http://nautil.us/blog/winning-the-cancer-war-start-with-the-deepest-intelligence

    This is the first in a three-part series, “Winning the Cancer War,” by Patrick Soon-Shiong, MD, FRCS(C), FACS In 2003, government agencies proclaimed we solved cancer because we solved the human genome. We thought we could halt cancer in its tracks by targeting mutations in our DNA and stopping those “cancer drivers.” This spurred the great genomics buildout over the last ten years. Hundreds of academic medical centers and companies began developing their own gene panels—everything from 40 DNA gene panel to 500 gene panels, from breast cancer panels to lung cancer panels, and everything in between—all in a tremendous race to treat cancer with targeted drugs. Large pharma and biotechs joined the bandwagon. They invested billions of dollars and utilized insights from limited gene panels as (...)

  • Gene-edited ’micropigs’ to be sold as pets at Chinese institute : Nature News & Comment
    http://www.nature.com/news/gene-edited-micropigs-to-be-sold-as-pets-at-chinese-institute-1.18448

    Cutting-edge gene-editing techniques have produced an unexpected byproduct — tiny pigs that a leading Chinese genomics institute will soon sell as pets.
    [...] The animals weigh about 15 kilograms when mature, or about the same as a medium-sized dog.

    At the summit, the institute quoted a price tag of 10,000 yuan (US$1,600) for the micropigs, but that was just to "help us better evaluate the market”, says Yong Li, technical director of BGI’s animal-science platform. In future, customers will be offered pigs with different coat colours and patterns, which BGI says it can also set through gene editing.

    #zootechnie #cochon #élevage

  • Geneticists Begin Tests of an #Internet for DNA
    http://www.technologyreview.com/news/533416/geneticists-begin-tests-of-an-internet-for-dna

    A coalition of geneticists and computer programmers calling itself the Global Alliance for Genomics and Health is developing protocols for exchanging DNA information across the Internet. The researchers hope their work could be as important to medical science as HTTP, the protocol created by Tim Berners-Lee in 1989, was to the Web.

    One of the group’s first demonstration projects is a simple search engine that combs through the DNA letters of thousands of human genomes stored at nine locations, including Google’s server farms and the University of Leicester, in the U.K. According to the group, which includes key players in the Human Genome Project, the search engine is the start of a kind of Internet of DNA that may eventually link millions of genomes together.

    The technologies being developed are application program interfaces, or APIs, that let different gene databases communicate. Pooling information could speed discoveries about what genes do and help doctors diagnose rare birth defects by matching children with suspected gene mutations to others who are known to have them.

    The alliance was conceived two years ago at a meeting in New York of 50 scientists who were concerned that genome data was trapped in private databases, tied down by legal consent agreements with patients, limited by privacy rules, or jealously controlled by scientists to further their own scientific work. It styles itself after the World Wide Web Consortium, or W3C, a body that oversees standards for the Web.

    #génétique

  • Les entrailles de Léviathan - une vue de l’intérieur de la bête

    The Genealogy of a Gene : Patents, HIV/AIDS, and Race | American Academy in Berlin
    http://www.americanacademy.de/home/program/upcoming/genealogy-gene-patents-hivaids-and-race

    Tuesday, November 04, 2014, 07:30 pm

    Social Sciences
    The Genealogy of a Gene: Patents, HIV/AIDS, and Race, Bosch Public Policy Lecture

    In this lecture, Myles Jackson will explain how he has used the CCR5 gene as a heuristic tool to probe three critical developments in biotechnology from 1990 to 2010: gene patenting, HIV/AIDS diagnostics and therapeutics, and race and genomics. Taking an interdisciplinary approach, Jackson ties together intellectual property, the sociology of race, and molecular biology by showing how certain patent regimes have rewarded different forms of intellectual property. The decision to patent genes was not inevitable, Jackson argues, nor “natural.” Likewise, there is nothing inevitable about using race as a major category of human classification. Jackson explains the economic and political interests that rationalized those choices — and explains the alternatives. He attempts to resurrect the past in order to illustrate the alternative paths not taken and explain why they were never chosen.

    Sign up for The Genealogy of a Gene: Patents, HIV/AIDS, and Race

    On peut encore s’inscrire à la conférence.

    #racisme #genealogie #aids #brevets #usa