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November 07 2013

TERRA 823: The Venom Trail

The Venom Trail explores the path venom takes through a body and how the same chemicals are used to make medicine to combat the symptoms. Produced by Steve Spence.

October 28 2013

Four short links: 28 October 2013

  1. A Cyber Attack Against Israel Shut Down a RoadThe hackers targeted the Tunnels’ camera system which put the roadway into an immediate lockdown mode, shutting it down for twenty minutes. The next day the attackers managed to break in for even longer during the heavy morning rush hour, shutting the entire system for eight hours. Because all that is digital melts into code, and code is an unsolved problem.
  2. Random Decision Forests (PDF) — “Due to the nature of the algorithm, most Random Decision Forest implementations provide an extraordinary amount of information about the final state of the classifier and how it derived from the training data.” (via Greg Borenstein)
  3. BITalino — 149 Euro microcontroller board full of physiological sensors: muscles, skin conductivity, light, acceleration, and heartbeat. A platform for healthcare hardware hacking?
  4. How to Be a Programmer — a braindump from a guru.

August 23 2013

Four short links: 23 August 2013

  1. Bradley Manning and the Two Americas (Quinn Norton) — The first America built the Internet, but the second America moved onto it. And they both think they own the place now. The best explanation you’ll find for wtf is going on.
  2. Staggering Cost of Inventing New Drugs (Forbes) — $5BB to develop a new drug; and subject to an inverse-Moore’s law: A 2012 article in Nature Reviews Drug Discovery says the number of drugs invented per billion dollars of R&D invested has been cut in half every nine years for half a century.
  3. Who’s Watching You — (Tim Bray) threat modelling. Everyone should know this.
  4. Data Mining with Weka — learn data mining with the popular open source Weka platform.

Recherche en France : La réalité rattrappe la fiction Halb Kuh, halb Maschine | Technology Review

Recherche en France : La réalité rattrappe la fiction

Halb Kuh, halb Maschine | Technology Review
http://www.heise.de/tr/artikel/Halb-Kuh-halb-Maschine-1874532.html
http://upload.wikimedia.org/wikipedia/en/9/93/Crank_two_ver2.jpg

Ein französisches Unternehmen hat ein Kunstherz entwickelt, das im Vergleich zu bisherigen Apparaten bioverträglicher ist und ohne eine pneumatische Steuereinheit außerhalb des Körpers auskommt.
...
Außerhalb des Körpers befindet sich nur noch die tragbare Stromversorgung, die über ein Kabel mit dem Herz verbunden ist. Das Kunstherz von Carmat entstand in Zusammenarbeit mit dem europäischen Luftfahrt- und Rüstungskonzern EADS und dem Chirurgen Alain Carpentier. Er hatte vor Jahren maßgeblich die Herzklappen-Chirurgie entwickelt.

William Cohn, Herzchirurg an der Texas Heart Institution in Houston, ist von dem Kunstherz beeindruckt: „Es ist ein brillantes Gerät.“ Er mache sich aber noch über dessen Größe und mechanische Haltbarkeit Gedanken. Bei 100.000 Herzschlägen pro Tag hielten heutige Kunstherzen nur ein paar Jahre, sagt Cohn. Je mehr bewegliche Teile sie enthalten, desto größer ist die Gefahr, dass sie irgendwann versagen.

http://en.wikipedia.org/wiki/Crank:_High_Voltage

On November 7, 2005, Chev Chelios (Jason Statham) lands in the middle of an intersection after falling out of a helicopter. He is scooped off the street via snow shovel by a group of Chinese medics and removed from the scene. Chelios wakes up in a makeshift hospital and sees doctors removing his heart while Johnny Vang (Art Hsu) watches. The doctors place Chelios’s heart in a white cooler with a padlock, and place a clear plastic artificial heart in his chest. He wakes up three months later and escapes. He notices a yellow battery pack is attached to him and sets out to find his heart. After a gunfight and interrogation of a thug, he learns the location of Johnny Vang: the Cypress Social Club.
...

#cinema #medicine #science_fiction #sciences

August 14 2013

5 pourcent des enfants allemands entre 8 et 17 ans souffrent de douleurs chroniques. Chronische…

5 pourcent des enfants allemands entre 8 et 17 ans souffrent de douleurs chroniques.

Chronische Schmerzen : Wenn der Hausarzt mit seinem Latein am Ende ist - Nachrichten Gesundheit - DIE WELT
http://www.welt.de/gesundheit/article118966681/Wenn-der-Hausarzt-mit-seinem-Latein-am-Ende-ist.html

Fünf Prozent aller Kinder im Alter von acht bis 17 leiden unter chronischen Schmerzen

L’article raconte que le nombre de cas est assez grand pour en faire un business model . Une clinique spécialisée transforme la douleurs en revenus.

Der „Leuchtturm“ ist eine Therapie-Einrichtung im Deutschen Kinderschmerz-Zentrum (DKSZ) der Vestischen Kinder- und Jugendklinik in Datteln (Nordrhein-Westfalen).

Le traitement décrit dans l’article est concu contre les douleurs psychosomatiques.

#maladie #douleurs #medicine

July 19 2013

Four short links: 19 July 2013

  1. Operative Design — A catalogue of spatial verbs. (via Adafruit)
  2. Open Source Malaria — open science drug discovery.
  3. Surviving Being (Senior) Tech Management (Kellan Elliott-McCrea) — Perspective is the thin line between a challenging but manageable problem, and chittering balled up in the corner.
  4. Disposable UAVs Inspired by Paper Planes (DIY Drones) — The first design, modeled after a paper plane, is created from a cellulose sheet that has electronic circuits ink-jet printed directly onto its body. Once the circuits have been laid on the plane’s frame, the craft is exposed to a UV curing process, turning the planes body into a flexible circuit board. These circuits are then connected to the planes “avionics system”, two elevons attached to the rear of the craft, which give the UAV the ability to steer itself to its destination.

June 27 2013

Science Podcast - Tracking Voyager, soil microbes, fighting cancer, and more (28 June 2013)

Edward Stone describes signals sent from Voyager as it reaches the edge of the solar system; Ferran Garcia-Pichel discusses climate change's effect on microorganisms; Jennifer Couzin-Frankel outlines a personalized technique to fight cancer.

March 26 2013

Four short links: 26 March 2013

  1. Patent on Medical Trial Design to Reduce Placebo Effectdrug companies say these failures are happening not because their drugs are ineffective, but because placebos have recently become more effective in clinical trials. [...] The whole idea that placebo effect is getting in the way of producing meaningful results is repugnant, I think, to anyone with scientific training. What’s even more repugnant, however, is that Fava’s group didn’t stop with a mere paper in Psychotherapy and Psychosomatics. They went on to apply for, and obtain, U.S. patents on SPCD. (via Ben Goldacre)
  2. OpenMalaria (Google Code) — an open source C++ program for simulating malaria epidemiology and the impacts on that epidemiology of interventions against malaria. It is based on microsimulations of Plasmodium falciparum malaria in humans, originally developed for simulating malaria vaccines. (via Victoria Stodden)
  3. Pricing Experiments You Might Not Know But Can Learn From — compendium of ideas and experiments for pricing.
  4. Retrominer — mining Bitcoins on a NES. I’m delighted by the conceit, and noticing that Bitcoin is now sufficiently part of the zeitgeist as to feature in playful hacks.

February 27 2013

Four short links: 27 February 2013

  1. Open Source Cancer Informatics Software (NCIP) — we have tackled the main recommendation that came out of our June meeting with open-source thought leaders: Keep it simple. Make barriers to entry as low as possible, and reuse available resources. Specifically, we have adopted a software license that is approved by the Open Source Initiative (OSI) and have begun to migrate the code developed under the cancer Biomedical Informatics Grid® (caBIG®) Program to a public repository. Our goal in taking these steps is to remove as many barriers as possible to community participation in the continuing development of these assets. Awesome! (via John Scott)
  2. NPR’s Framework for Easy Apps — their three architectural maxims: Servers are for chumps; If it doesn’t work on mobile, it doesn’t work; and Build for use. Refactor for reuse..
  3. Random Junk in People’s Labs (Reddit) — reminded me of the contents of my “tmp” and “Downloads” and “Documents” directories: unstructured historical crap with no expiration and no current use. (Caution: swearing in the title of the Reddit post) (via Mihalyi Csikszentmihalyi)
  4. Sync — BitTorrent’s alpha-level tech to “automatically sync files between computers via secure, distributed technology.” Not only is it “slick for alpha” (as one friend described), it’s bloody useful: I know at least one multimillion-dollar project built on their own homegrown implementation of this same idea. (via Jason Ryan)

October 18 2012

Four short links: 18 October 2012

  1. Let’s Pool Our Medical Data (TED) — John Wilbanks (of Science Commons fame) gives a strong talk for creating an open, massive, mine-able database of data about health and genomics from many sources. Money quote: Facebook would never make a change to something as important as an advertising with a sample size as small as a Phase 3 clinical trial.
  2. Verizon Sells App Use, Browsing Habits, Location (CNet) — Verizon Wireless has begun selling information about its customers’ geographical locations, app usage, and Web browsing activities, a move that raises privacy questions and could brush up against federal wiretapping law. To Verizon, even when you do pay for it, you’re still the product. Carriers: they’re like graverobbing organ harvesters but without the strict ethical standards.
  3. IBM Watson About to Launch in Medicine (Fast Company) — This fall, after six months of teaching their treatment guidelines to Watson, the doctors at Sloan-Kettering will begin testing the IBM machine on real patients. [...] On the screen, a colorful globe spins. In a few seconds, Watson offers three possible courses of chemotherapy, charted as bars with varying levels of confidence–one choice above 90% and two above 80%. “Watson doesn’t give you the answer,” Kris says. “It gives you a range of answers.” Then it’s up to [the doctor] to make the call. (via Reddit)
  4. Robot Kills Weeds With 98% AccuracyDuring tests, this automated system gathered over a million images as it moved through the fields. Its Computer Vision System was able to detect and segment individual plants – even those that were touching each other – with 98% accuracy.

October 04 2012

Four short links: 4 October 2012

  1. As We May Think (Vannevar Bush) — incredibly prescient piece he wrote for The Atlantic in 1945.
  2. Transparency and Topic Models (YouTube) — a talk from DataGotham 2012, by Hanna Wallach. She uses latent Dirichlet allocation topic models to mine text data in declassified documents where the metadata are useless. She’s working on predicting classification durations (AWESOME!). (via Matt Biddulph)
  3. Slippy Map of the Ancient World — this. is. so. cool!
  4. Technology in the NFLX2IMPACT’s Concussion Management System (CMS) is a great example of this trend. CMS, when combined with a digital mouth guard, also made by X2, enables coaches to see head impact data in real-time and asses concussions through monitoring the accelerometers in a players mouth guard. That data helps teams to decide whether to keep a player on the field or take them off for their own safety. Insert referee joke here.

September 18 2012

When data disrupts health care

Health care appears immune to disruption. It’s a space where the stakes are high, the incumbents are entrenched, and lessons from other industries don’t always apply.

Yet, in a recent conversation between Tim O’Reilly and Roger Magoulas it became evident that we’re approaching an unparalleled opportunity for health care change. O’Reilly and Magoulas explained how the convergence of data access, changing perspectives on privacy, and the enormous expense of care are pushing the health space toward disruption.

As always, the primary catalyst is money. The United States is facing what Magoulas called an “existential crisis in health care costs” [discussed at the 3:43 mark]. Everyone can see that the current model is unsustainable. It simply doesn’t scale. And that means we’ve arrived at a place where party lines are irrelevant and tough solutions are the only options.

“Who is it that said change happens when the pain of not changing is greater than the pain of changing?” O’Reilly asked. “We’re now reaching that point.” [3:55]

(Note: The source of that quote is hard to pin down, but the sentiment certainly applies.)

This willingness to change is shifting perspectives on health data. Some patients are making their personal data available so they and others can benefit. Magoulas noted that even health companies, which have long guarded their data, are warming to collaboration.

At the same time there’s a growing understanding that health data must be contextualized. Simply having genomic information and patient histories isn’t good enough. True insight — the kind that can improve quality of life — is only possible when datasets are combined.

“Genes aren’t destiny,” Magoulas said. “It’s how they interact with other things. I think people are starting to see that. It’s the same with the EHR [Electronic Health Record]. The EHR doesn’t solve anything. It’s part of a puzzle.” [4:13]

And here’s where the opportunity lies. Extracting meaning from datasets is a process data scientists and Silicon Valley entrepreneurs have already refined. That means the same skills that improve mindless ad-click rates can now be applied to something profound.

“There’s this huge opportunity for those people with those talents, with that experience, to come and start working on stuff that really matters,” O’Reilly said. “They can save lives and they can save money in one of the biggest and most critical industries of the future.” [5:20]

The language O’Reilly and Magoulas used throughout their conversation was telling. “Save lives,” “work on stuff that matters,” “huge opportunity” — these aren’t frivolous phrases. The health care disruption they discussed will touch everyone, which is why it’s imperative the best minds come together to shape these changes.

The full conversation between O’Reilly and Magoulas is available in the following video.

Here are key points with direct links to those segments:

  • Internet companies used data to solve John Wanamaker’s advertising dilemma (“Half the money I spend on advertising is wasted; the trouble is I don’t know which half”). Similar methods can apply to health care. [17 seconds in]
  • The “quasi-market system” of health care makes it harder to disrupt than other industries. [3:15]
  • The U.S. is facing an existential crisis around health care costs. “This is bigger than one company.” [3:43]
  • We can benefit from the multiple data types coming “on stream” at the same time. These include electronic medical records, inexpensive gene sequencing, and personal sensor data. [4:28]
  • The availability of different datasets presents an opportunity for Silicon Valley because data scientists and technologists already have the skills to manage the data. Important results can be found when this data is correlated: “The great thing is we know it can work.” [5:20]
  • Personal data donation is a trend to watch. [6:40]
  • Disruption is often associated with trivial additions to the consumer Internet. With an undisrupted market like health care, technical skills can create real change. [7:04]
  • “There’s no question this is going to be a huge field.” [8:15]

If the disruption of health care and associated opportunities interests you, O’Reilly has more to offer. Check out our interviews, ongoing coverage, our recent report, “Solving the Wanamaker problem for health care,” and the upcoming Strata Rx conference in San Francisco.

This post was originally published on strata.oreilly.com.

August 10 2012

Four short links: 10 August 2012

  1. The Coffee-Ring Effect (YouTube) — beautiful video of what happens in liquids as they evaporate, explaining why coffee stains are rings, and how to create liquids with even evaporative coating.
  2. The Importance of Quantitative Thinking Medicine (PDF) — scaling laws underly aging, metabolism, drug delivery, BMI, and more. Full of wow moments, like Fractals are a common feature of many complex systems ranging from river networks, earthquakes, and the internet to stock markets and cities. [...] Geometrically, the nested levels of continuous branching and crenulations inherent in fractal­like structures optimise the transport of information, energy, and resources by maximising the surface areas across which these essential features of life flow within any volume. Because of their fractal nature, these effective surface areas are much larger than their apparent physical size. For example, even though the volume of our lungs is about 5–6 L, the total surface area of all the alveoli is almost the size of a tennis court and the total length of airways is about 2500 km. Even more striking is that if all the arteries, veins, and capillaries of an individual’s circulatory system were laid end to end, its total length would be about 100000 km, or nearly two and a half times around the earth.
  3. Autonomous Robotic Plane at MIT (YouTube) — hypnotic to watch it discover the room. A product of the Robust Robotics Group at MIT.
  4. Electric Sheep — hypnotic screensaver, where the sleeping computers collaborate on animations. You can vote up or down the animation on your screen, changing the global gene pool. Popular animations survive and propagate.

July 06 2012

TERRA 712: Vitamin ConspiraC

Do you take vitamin C when you get sick? Well, now you don't have to! Filmmaker Christina Choate urges you to skip the pill and eat plants instead. In her quest to find the truth about vitamin C, she introduces the man responsible for popularizing vitamin C supplements, retraces the history of scurvy, explains the vitamin's evolution, biochemistry and richest sources. With wit and humor, she de-bunks popular myths and takes a stand against the quick-fix health industry.

June 26 2012

Health records support genetics research at Children's Hospital of Philadelphia

Michael Italia leads a team of programmers and scientists at Children's Hospital of Philadelphia (CHOP), Center for Biomedical Informatics, where they develop applications, data repositories, and web interfaces to support CHOP's leading roles in both treatment and research. Recently we recorded an interview discussing the collection of data at CHOP and its use to improve both care and long-term research.

Italia, who will speak on this topic at OSCON, describes how the informatics staff derived structured data from electronic health record (EHR) forms developed by audiologists to support both research and clinical care. He describes the custom web interface that makes data available to researchers and discusses the exciting potential of genomic sequencing to improve care. He also lists tools used to collect and display data, many of which are open source.

Particular topics in this video include:

  • The relationship between clinical care and research at Children's. [Discussed at the 00:22 mark]
  • The value of research using clinical data. [Discussed at the 02:30 mark]
  • The challenge of getting good data from health records. [Discussed at the 03:30 mark]
  • Tools for capturing, exporting, and displaying data. [Discussed at the 05:41 mark]
  • Making data useful to clinicians through a simple, modular web interface; tools used. [Discussed at the 12:07 mark]
  • Size of the database and user cohort. [Discussed at the 17:19 mark]
  • The ethical and technical issues of genome sequencing in medical treatment; benefits of sequencing. [Discussed at the 18:23 mark]
  • "Pick out the signal from the noise": integrating genetic information into the electronic health record and "actionable information". [Discussed at the 24:27 mark]

You can view the entire conversation in the following video:

OSCON 2012 Health Care Track — The conjunction of open source and open data with health technology promises to improve creaking infrastructure and give greater control and engagement to patients. Learn more at OSCON 2012, being held July 16-20 in Portland, Oregon.

Save 20% on registration with the code RADAR

Related:

June 25 2012

Four short links: 25 June 2012

  1. Stop Treating People Like Idiots (Tom Steinberg) -- governments miss the easy opportunities to link the tradeoffs they make to the point where the impacts are felt. My argument is this: key compromises or decisions should be linked to from the points where people obtain a service, or at the points where they learn about one. If my bins are only collected once a fortnight, the reason why should be one click away from the page that describes the collection times.
  2. UK Study Finds Mixed Telemedicine Benefits -- The results, in a paper to the British Medical Journal published today, found telehealth can help patients with long-term conditions avoid emergency hospital care, and also reduce deaths. However, the estimated scale of hospital cost savings is modest and may not be sufficient to offset the cost of the technology, the report finds. Overall the evidence does not warrant full scale roll-out but more careful exploration, it says. (via Mike Pearson)
  3. Pay Attention to What Nick Denton is Doing With Comments (Nieman Lab) -- Most news sites have come to treat comments as little more than a necessary evil, a kind of padded room where the third estate can vent, largely at will, and tolerated mainly as a way of generating pageviews. This exhausted consensus makes what Gawker is doing so important. Nick Denton, Gawker’s founder and publisher, Thomas Plunkett, head of technology, and the technical staff have re-designed Gawker to serve the people reading the comments, rather than the people writing them.
  4. Informed Consent Source of Confusion (Nature) -- fascinating look at the downstream uses of collected bio data and the difficulty in gaining informed consent: what you might learn about yourself (do I want to know I have an 8.3% greater chance of developing Alzheimers? What would I do with that knowledge besides worry?), what others might learn about you (will my records be subpoenable?), and what others might make from the knowledge (will my data be used for someone else's financial benefit?). (via Ed Yong)

June 21 2012

Four short links: 21 June 2012

  1. Test, Learn, Adapt (PDF) -- UK Cabinet Office paper on randomised trials for public policy. Ben Goldacre cowrote.
  2. UK EscapeTheCity Raises GBP600k in Crowd Equity -- took just eight days, using the Crowdcube platform for equity-based crowd investment.
  3. DIY Bio SOPs -- CC-licensed set of standard operating procedures for a bio lab. These are the SOPs that I provided to the Irish EPA as part of my "Consent Conditions" for "Contained Use of Class 1 Genetically Modified Microorganisms". (via Alison Marigold)
  4. Shuffling Cards -- shuffle a deck of cards until it's randomised. That order of cards probably hasn't ever been seen before in the history of mankind.

May 11 2012

Four short links: 11 May 2012

  1. Stanford Med School Contemplates Flipped Classroom -- the real challenge isn't sending kids home with videos to watch, it's using tools like OceanBrowser to keep on top of what they're doing. Few profs at universities have cared whether students learned or not.
  2. Inclusive Tech Companies Win The Talent War (Gina Trapani) -- she speaks the truth, and gently. The original CNN story flushed out an incredible number of vitriolic commenters apparently lacking the gene for irony.
  3. Buyers and Sellers Guide to Web Design and Development Firms (Lance Wiggs) -- great idea, particularly "how to be a good client". There are plenty of dodgy web shops, but more projects fail because of the clients than many would like to admit.
  4. What Does It Mean to Say That Something Causes 16% of Cancers? (Discover Magazine) -- hey, all you infographic jockeys with your aspirations to add Data Scientist to your business card: read this and realize how hard it is to make sense of a lot of numbers and then communicate that sense. Data Science isn't about Hadoop any more than Accounting is about columns. Both try to tell a story (the original meaning of your company's "accounts") and what counts is the informed, disciplined, honest effort of knowing that your story is honest.

May 07 2012

Four short links: 7 May 2012

  1. Liquid Feedback -- MIT-licensed voting software from the Pirate Party. See this Spiegel Online piece about how it is used for more details. (via Tim O'Reilly)
  2. Putting Gestures Into Objects (Ars Technica) -- Disney and CMU have a system called Touché, where objects can tell whether they're being clasped, swiped, pinched, etc. and by how many fingers. (via BoingBoing)
  3. Real-time Facebook 'likes' Displayed On Brazilian Fashion Retailer's Clothes Racks (The Verge) -- each hanger has a digital counter reflecting the number of likes.
  4. Foldit Games Next Play: Crowdsourcing Better Drug Design (Nature Blogs) -- “We’ve moved beyond just determining structures in nature,” Cooper, who is based at the University of Washington’s Center for Game Science in Seattle, told Nature Medicine. “We’re able to use the game to design brand new therapeutic enzymes.” He says players are now working on the ground-up design of a protein that would act as an inhibitor of the influenza A virus, and he expects to expand the drug development uses of the game to small molecule design within the next year.

April 24 2012

Four short links: 24 April 2012

  1. 3D-Printing Pharmaceuticals (BoingBoing) -- Prof Cronin added: "3D printers are becoming increasingly common and affordable. It's entirely possible that, in the future, we could see chemical engineering technology which is prohibitively expensive today filter down to laboratories and small commercial enterprises. "Even more importantly, we could use 3D printers to revolutionise access to health care in the developing world, allowing diagnosis and treatment to happen in a much more efficient and economical way than is possible now.
  2. Bolt Action Tactical Pen (Uncrate) -- silliness.
  3. Ken Robinson's Sunday Sermon (Vimeo) -- In our culture, not to know is to be at fault socially… People pretend to know lots of things they don’t know. Because the worst thing to do is appear to be uninformed about something, to not have an opinion… We should know the limits of our knowledge and understand what we don’t know, and be willing to explore things we don’t know without feeling embarrassed of not knowing about them. If you work with someone who hides ignorance or failure, you're working with a timebomb and one of your highest priorities should be to change that mindset or replace the person. (via Maria Popova)
  4. Using Android Camera in HTML Apps (David Calhoun) -- From your browser you can now upload pictures and videos from the camera as well as sounds from the microphone. The returned data should be available to manipulate via the File API (via Josh Clark)

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