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Colby Vorland
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Wondering on thoughts about the ethics of full text databases like LibGen? It has a whole bunch of free full texts- see this recent study http://onlinelibrary.wiley.com/doi/10.1002/asi.23445/abstract

"36% of all DOI articles are available for free at LibGen. This figure is even higher (68%) for three major publishers: Elsevier, Springer, and Wiley"

I am considering having Lazy Scholar do an auto check of this, but hesitant to link to illegally obtained full texts. As a librarian, +Aaron Tay, would you be less likely to recommend a software that did this? It also appears that it may not survive much longer anyway, at least in current form https://torrentfreak.com/libgen-goes-down-as-legal-pressure-mounts-150622/

I suppose I could make it a "hidden" feature, so it would have to be activated by activating a setting that isn't visible unless you know where it is.
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I'll keep it off then- thanks!
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This post moved over from the Google Group from March 31

The inaugural beta version starts at 100, so that you are not confused.

This version adds the ability to annotate papers and PDFs using hypothes.is. Because of this I had to add/improve the ability for the extension to detect PDFs from non-journal websites. Clicking the annotation graphic simply loads the PDF through hypothes.is's site. This has the advantage of being able to quickly share the URL with annotations to people who don't have the extension installed. Here are some screenshots (click to view the entire shot):











Another thing that is partially built into this version but still needs work is a way to unload tabs that contain papers/PDFs from memory, since I always open too many papers and this slows down my computer. There are great extensions that do this (like https://chrome.google.com/webstore/detail/the-great-suspender/klbibkeccnjlkjkiokjodocebajanakg), but I wanted to include a way to do it with just tabs with scientific papers. Thoughts on this idea and what could be helpful would be great.
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This post moved over from the Google Group from April 11

Just pushed out a new version (101) that fixes the problem of the iframe only loading on pages that are PDFs.
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Hello G+, anyone still here?
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Technically yes.
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another book review
Dr. Mike Gibney, an accomplished researcher (mainly now in the really fascinating area of nutritional genomics) and professor who has served on high-level committees/advisory boards and is involved in...
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AJHG · Biophysical Journal · Cancer Cell · Cell · Cell Host & Microbe · Cell Metabolism · Cell Reports · Cell Stem Cell · Chemistry & Biology · Current Biology · Developmental Cell · Immunity ...
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Colby Vorland
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This post moved over from the Google Group from June 5

Browser/mobile (non-extension) version of Lazy Scholar

I am developing a version of Lazy Scholar that does not require an extension. This is difficult because I have to route the query through the browser as Google Scholar blocks queries from a server (why I developed as an extension in the first place). I have succeeded in testing by doing the following:

- User appends LS domain in front of URL of paper, ie "somenewlazyscholardomain.com/http://jn.nutrition.org/content/133/2/374.full"
- Server posts the paper info to a database and listens for an answer
- Firefox extension is connected to this database and listens for new posts. When it sees a post, it queries Google Scholar for the paper and posts the results back to the database.
- Server sees the results and shows the infobar to the user.

The advantage of this:
1) A simple javascript bookmarklet can be clicked to append the "somenewlazyscholardomain.com" in front of papers if the user doesn't want to (or can't) install an extension or is on an unsupported browser like Safari
2) This works in mobile browsers as well

The problem is that this requires enough browsers to be connected to the database throughout the day. I also feel like I need to make this opt in because it in effect is using resources of the user. I have a lot more testing and tweaking to do but would like to push it out to the Chrome beta version soon to see if it works well and also create a Firefox beta version. Please let me know if you are interesting in helping to test this out.
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This post moved over from the Google Group from July 14


Ok I am ready to test this out on a larger scale. May need to roll it out as an optional setting to everyone though unless we can get some more people in this beta.

Basically the new method builds an anonymous peer-to-peer network through the extension. A user loading the page in the browser by adding the new domain in front of a scholarly url joins the network and sends a request to only one of the browsers, which sends back the results and loads them in the familiar iframe (the same that the extension shows). This dramatically reduces the resources needed because it bypasses routing through a central server as I was trying to do with the old way.

I am pretty excited to get this infrastructure working because it could open up a lot of possibilities for storing scholarly data in a distributed manner and doing distributed searching/computations, so I can keep the cost of this project reduced.
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Random thoughts on the Subway azodicarbonamide nonsense from last week.

ICYMI: "Food babe" Vani Hari posted this fearmongering article about Subway using azodicarbonamide in their bread last week: http://foodbabe.com/2014/02/04/launching-petition-subway-will-finally-hear-us-loud-clear/ and petitioned Subway to remove it.

It received an astonishing 174,000 facebook likes as I write this and just about every major news outlet picked it up: https://www.google.com/search?q=subway+azodicarbonamide&rlz=1C1CHFX_enUS524US524&oq=subway+azo&aqs=chrome.1.69i57j0l3.3239j0j9&sourceid=chrome&espv=210&es_sm=93&ie=UTF-8#q=subway+azodicarbonamide&tbm=nws

EVEN BEFORE CONSIDERING THE MISREPRESENTATION OF TOXICOLOGY RESEARCH, let's look at why a simple 10 minute assessment of Hari's credibility should give pause to any reporter giving her the time of day.

-She has a degree in computer science, not nutrition or anything with a background in learning how to read research: http://clclt.com/charlotte/lust-list-2012/Content?oid=2616360

More importantly, she shows that she lacks the ability to identify credible resources:
-Thinks the flu vaccines is not efficacious and thinks it is toxic http://foodbabe.com/2011/10/04/should-i-get-the-flu-shot/

-Thinks microwaves are a risk because of radiation, destroying nutrients, and changing the structure of water (seriously) http://foodbabe.com/2012/07/30/why-its-time-to-throw-out-your-microwave/?sb

-Says artificial sweeteners cause cancer, obesity; links to Mercola who is the internet's worst health source http://foodbabe.com/2013/01/25/coca-colas-low-calorie-beverages-will-kill-you-before-they-solve-obesity/?sb

-Thinks GMOs cause obesity (same link above)

-Includes links throughout to naturalnews.com, the 2nd worst health source on the internet e.g. http://foodbabe.com/2012/04/16/panera-bread-the-healthiest-fast-food/?sb

-She has stated in the media that "When you look at the ingredients, if you can't spell it or pronounce it, you probably shouldn't eat it," http://abcnews.go.com/Health/protesters-target-subway-chemical-sandwich-bread/story?id=22373414 this is of course an absurd rule (can the average person pronounce pyridoxine hydrochloride - vitamin B6?)

There is a common theme in these and all other posts: she picks out an ingredient she thinks is scary, links to poor sources to play up a health risk by misinterpreting toxicology studies (using large doses of anything causes cancer or other health problems at high doses- even natural plant chemicals http://toxnet.nlm.nih.gov/cpdb/MOEtext.html#cram), and doesn't look to science-based organizations. She often appeals to moms, pitting big companies against their child's health. Of course, nothing I highlighted is evidence-based: the flu vaccine works and is not toxic, microwaves are safe (and actually increase some nutrients), GMOs are considered safe by all credible science organizations, and artificial sweeteners do not cause cancer. These are some of the most studied topics in health that we have strong answers to, yet she gets them completely wrong. Reporters should recognize this and not lend her the attention they give her!

Hari links to a WHO report of azodicarbonamide, saying they "linked it to asthma and other allergic reactions."  http://foodbabe.com/tag/sara-lee-bread/

From the summary of the report: (http://www.inchem.org/documents/cicads/cicads/cicad16.htm)
_ Azodicarbonamide is of low acute toxicity and does not cause
    skin, eye, or respiratory tract irritation in experimental animals.
    Results from a poorly conducted skin sensitization study were
    negative, and there was no evidence of an asthmatic-type response in guinea-pigs in one study._

Even back in 1966 is was well studied and shown not to be a risk (http://www.inchem.org/documents/jecfa/jecmono/40abcj28.htm):

 _Azodicarbonamide has been extensively studied and the theoretical point with regard to the possible effect of unconverted azodicarbonamide was covered by experiments using overtreated flour or bread made from it. The evidence strongly supports the view that azodicarbonamide is rapidly and completely converted to biurea on wetting and that this substance is stable in bread. Biurea itself is metabolically inert, has low toxicity and does not present any carcinogenic hazard. _

Back to the latest WHO report:

There is concern of occupational exposure "at workplaces where azodicarbonamide is manufactured or used.", because exposure is much higher. This does not mean the tiny amounts from food will present any risk! In fact, the report states about beer and bread that "_It is not clear if unreacted azodicarbonamide is present in these products_"

It is notable that a breakdown product of azodicarbonamide - semicarbazide - that Hari says is cancer causing, is found naturally, for example one study found it in fish, shrimp, chicken, deer meat, eggs, and cheese (http://www.ncbi.nlm.nih.gov/pubmed/15204530, hat tip https://twitter.com/Editor4FPD/status/431939956236222464). The EFSA concludes that the risk of foods with semicarbazide is "very small" (http://www.efsa.europa.eu/en/press/news/afc031015.htm) and it is only "weakly carcinogenic" - even at the high doses used. 

Here is a more coherent take from food scientist John Coupland http://johncoupland.tumblr.com/post/75935663638/the-food-babe-and-sudden-change-in-our-food-system

More later, perhaps...
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Dr. Oz's is also top grade BS supportive of pseudosciences such as faith healing, homeopathy and psychic communication with the dead. So the Food Babe is just up his alley
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I wrote this chrome extension to save time looking for full texts of abstracts. 
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collected & played with some ways to display & quantify tweets in R, this is the result
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aurora watch
 
Yesterday's X1.4 class solar flare and the associated Coronal Mass Ejection (CME). These coronal mass ejections (CMEs) are balloon-shaped bursts of solar wind rising above the solar corona, expanding as they climb. 

Solar plasma is heated to tens of millions of degrees, and electrons, protons, and heavy nuclei are accelerated to near the speed of light. The super-heated electrons from CMEs move along the magnetic field lines faster than the solar wind can flow. Rearrangement of the magnetic field, and solar flares may result in the formation of a shock that accelerates particles ahead of the CME loop.

Each CME releases up to 100 billion kg (220 billion lb) of this material, and the speed of the ejection can reach 1400 km/second like in yesterday's flare. Solar flares and CMEs are currently the biggest "explosions" in our solar system, roughly approaching the power in ONE BILLION hydrogen bombs!

With the arrival of this CME on Saturday July 14, 2012 at 10:20 UT (plus/minus 7 hours), we will most likely experience geomagnetic activities. The estimated Kp is between 6 and 8, which translates into moderate to severe geomagnetic storms. 

One very positive about this event is that aurorae could be visible between the yellow and the red line. Of course the weather has to cooperate and light pollution of a city can wash out the aurorae. This time around the Moon is not playing a big role. 

Perhaps you can't see the aurorae with your eyes, but your camera on long-exposure might. Give it a try and let us know! 

Credit: NOAA / NASA

#SpaceWeather   #NASA   #NOAA   #Aurora  
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a book review
There is no shortage of junk diet and fitness books on the market that try to persuade you to follow their vision of perfect health. Tim Caulfield's “The Cure for Everything: Untangling Twisted Me...
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I got it through bookdepository.com instead. Took about a week
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Thirst for nutritional science, hunger for truth. Also, make bad puns.
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