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Dean Pomerleau

Getting Full PDFs of Papers

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Between Greg and I, it seems like a day of helpful meta-tips - i.e. practical tips not related to diet or health. Here is a meta-tip I recently discovered. 

 

For anyone serious about researching diet, health, or any other scientific topic, it can be frustrating trying to get the full text of a published paper that is behind a paywall, unless you are affiliated with a university or other research institution. 

 

I've been relying on Al Pater to serve as a conduit to full-text of articles I want to read but which aren't freely available. But I feel bad imposing on Al, and he's not always available. I recently discovered two amazingly effective alternatives. The first uses Twitter to find a kindly soul with access to Journals (i.e. the equivalent of Al Pater). The steps are as follows, taken from the wikipedia page on the method:

 

  1. Request an article by tweeting an article's title, DOI, PMID, or link. In the tweet you include your email address, and the hashtag "#ICanHazPDF". Here is what my tweet looked like to get the Adventist prostate cancer paper:

    6b90XLo.png
     
  2. Someone who has access to the article will then email it to you.
  3. You then delete the original tweet.

Obvious downsides to this method include tweeting your email address, and, although you delete the tweet, the (semi-public) record of requesting a paywall-protected paper.

 

An even better solution if it works for you, is the website solution http://sci-hub.io/

 

Simply:

  1. Go to the website http://sci-hub.io/ . Don't be disturbed by the Russian language text on the page...
  2. Paste the URL of the journal page for the paper you want the PDF for (not it's Pubmed page) into the box that it gives you. For the Adventist prostate cancer study, it was: http://ajcn.nutrition.org/content/early/2015/11/11/ajcn.114.106450.long
  3. After a few seconds, up pops the full text of the paper. It seems to work for a large fraction (95%?) of papers that out there but paywall protected.

This second method has been a bit hit or miss for me, but if it works, it is a lot easier than the #ICanHazPDF Twitter method. But I imagine it may not be available indefinitely...

 

Yes, I know it is piracy, but information (esp. health information) yearns to be free...

 

--Dean

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Dean,

 

Is it just me, or is the CRS website slow today?

 

Speaking of PDFs, how do you produce a PDF of your COM page?

 

James Cain attached his COM page in PDF format here.

 

With Chrome on Linux, I can only save the webpage as HTML.

 

Within COM, I can only export as CSV.

 

Any experience with this?

 

 

EDIT: added link

Edited by Greg Scott

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Greg,

 

I'm not finding the CRS website slower than usual today.

 

This is again focused on Chrome for Windows, but here is how I make a PDF of any webpage, including a snapshot of my CRON-O-Meter.com daily diary.

 

  1. Click on the three bar "menu" icon in the upper right of the Chrome browser window, highlighted below:
    NApe6kH.png
     
  2. Select the "Print..." option from the dropdown menu that appears.
  3. Then, for me a window pops up with printing options. I click the "Change..." button, highlighted below to change the printer:
    KWpyjxa.png
     
  4. Then I select the "Save as PDF" option as highlighted below:

    qCKLvmY.png
  5. Then I click 'Print'.
  6. It will then prompt me for a location to save the PDF file, and create it.

The option of printing to a PDF from Chrome and the specific procedure, may be different for you as a Chrome for Linux user...

 

--Dean

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Although I am not without ethical or security qualms about Sci-Hub, I do use it intermittently and would like to support it financially. However, the only way to donate to support the project is with BitCoin, which I don't use. Would anyone out there with an account be willing to make a donation by proxy if I sent hir a cheque or suitably-denominated Amazon gift card?

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Michael,

 

Bitcoin is not an "account" so to speak - that is the beauty of the decentralized, libertarian nature of the virtual currency, which I thought you of all people would be aware of and appreciate.

 

Bitcoin is a cool experiment in alternative ways of storing and transferring value designed for the digital age, which I wholeheartedly support. Getting started is very easy. I recommend creating an account at Coinbase.com to converting dollars to bitcoin for those who are interested. 

 

But if you'd rather not bother and have someone else donate to Sci-hub.io on your behalf, I'd be happy to do it. I'll do the same since I too appreciate and benefit a lot from the service sci-hub.io provides. I see Al Pater is using it as well to provide links the full texts of studies he posts.

 

Just let me know how much you'd like to donate.

 

--Dean

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Bitcoin is not an "account" so to speak - that is the beauty of the decentralized, libertarian nature of the virtual currency, which I thought you of all people would be aware of and appreciate.

Certainly it wouldn't be accurate to say that BC "is" an account, but you have to have an account specialized in BC in order to to use it. Is that the only distinction you're drawing?

 

I don't like BC's rather perverse, oxymoronic properties of being at once inflexibly determined in supply (unlike fiat currencies, which allow central bankers to manage them to guide their issuers' economies — something I and most economists regard as a strength, but hated by gold bugs and proponents of established wealth per se like Steve Forbes, who love gold and promote BC precisely because of its supposed stability as a "store of value") and yet wildly fluctuating in actual traded value (although less so in recent months). Plus there have been all the problems with collapsing exchanges, apparent fraud, etc. And, frankly, I don't like the inconvenience, or the fact that using it is likely to be counted as a suspicious activity.

 

But if you'd rather not bother and have someone else donate to Sci-hub.io on your behalf, I'd be happy to do it. I'll do the same since I too appreciate and benefit a lot from the service sci-hub.io provides.

Super — thanks for stepping up, both on my behalf and your own! I'll work things out further with you via email.

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Michael,

 

Certainly it wouldn't be accurate to say that BC [bitcoin] "is" an account, but you have to have an account specialized in BC in order to to use it. Is that the only distinction you're drawing?

 

You have to have an account with a bitcoin service like Coinbase.com [1] if you want to purchase bitcoin using your bank account or credit card. But if you've got a friend like me, who is happy to send you bitcoin directly, there is no need for such an account.

 

...unlike fiat currencies, which allow central bankers to manage them to guide their issuers' economies — something I and most economists regard as a strength, 

 

Interesting - I happen to agree with you on this, but I pegged you for a more libertarian type, who might appreciate the inability of government to inflate bitcoin like they've done with other currency, to the detriment of people on fixed income and generally people who save money.

 

Plus there have been all the problems with collapsing exchanges, apparent fraud, etc. And, frankly, I don't like the inconvenience, or the fact that using it is likely to be counted as a suspicious activity.

 

All of that is grossly exaggerated, as far as I'm concerned, especially the part about inconvenience.

 

In fact, to demonstrate this to you, I'd really like to show you how easy and secure it is to anonymously receive and then send bitcoin, for the transaction to sci-hob.io we'd like to do. What I'm proposing, and will send you more details about via email, is to use a wallet you generate via Rushwallet.com (perhaps in a private browsing session in your browser, for extra security). It is a really cool service, that allows you to instantly create a unique bitcoin wallet (really just an address, or long string of alpha-numeric characters for storing bitcoin) simply by moving your mouse around to generate a random address and 'private key' that is stored only locally on your computer. You can then send me the unique bitcoin address so generated, so I can send bitcoin to your wallet (address), from which you can send to the sci-hub.io wallet (address) yourself. It will take you about 2 minutes total for both sides of the transaction (receive from me and send to sci-hob.io).

 

I hope you'll see via this transaction that bitcoin can service as digital cash. It will be like I've handed you the money directly. Once I've sent you the bitcoin, you can spend it anywhere bitcoin is accepted, including overstock.com, whose very progress CEO I like to support whenever possible. You can even use bitcoin to buy Amazon gift cards (and get 5% back) via gyft.com.  See [2] below for some more information about the Rushwallet.com service.

 

Michael, all I request is that you to check out rushwallet.com. I won't force you to try it. If you'd prefer, I'll send bitcoin directly to sci-hob.io on your behalf.

 

More via email.

 

Addendum - for anyone else in the CRS (besides Michael) who is interested in giving bitcoin a try via Rushwallet.com or any other wallet service, I'm happy to help you out, by sending bitcoin to your wallet address in return for an Amazon gift card in the same amount. Just contact me privately to work out the details. My email is dean at pomerleaus dot com.

 

--Dean

 

[1] If anyone is interested in giving bitcoin a try by purchasing bitcoin through Coinbase.com, follow this referral link and once you've purchased $100 worth of bitcoin we'll both get an additional $10.

 

[2] Here is part of FAQ from Rushwallet.com to illustrate how simple it is:

 

RushWallet is an instant cross-platform bitcoin wallet. By not requiring annoying logins and passwords, RushWallet makes bitcoin simple to setup and easy to use.
 
Only you have control of your wallet and bitcoins
 
RushWallet neither holds nor has access to your bitcoins or private keys. All information is stored on the client-side, so only you have control of your wallet and your bitcoins.
 
Your URL is Your Key
 
Bookmark your wallet’s secret URL to access your RushWallet in the future. Please note, this is your private URL so do not share it with anyone. If you lose this URL your bitcoins will be lost forever.
 
Add a password for extra security
 
When creating your RushWallet we offer the option to add a password to your account. You will need to enter this password every time you access your wallet. For your own security we do not store any customer data, so don’t forget your password!
 
Please note, all transactions sent from your wallet include a 0.0002 mining fee. This fee helps support the bitcoin network and ensures your transaction goes through quickly.

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All,

 

Here is a really interesting article on the (IMO) noble struggle of the young woman in Russian who runs sci-hub.io. She is valently trying, singlehandedly, to loosen the stranglehold peer-reviewed journals have on scientific knowledge and research results via their exorbitant fees to access full text PDFs of papers.

 

I'd never thought about the comparison, but 'pirating' a PDF via sci-hub.io is very different from pirating a song, movie or video game. When you pirate one of the latter, you're ripping off the artist or developer who created it.

 

But for scientific papers, the author never sees a dime of the money that scientific journals collect for the right to access the information they didn't create. Heck, they didn't even pay the authors to do the research or write the papers. In fact, they sometimes even charge authors for the privilege of publishing their work (e.g. in page overage charges).

 

Now that I think about it, it seems like quite a racket. I don't feel nearly so bad (or bad at all) for using sci-hub.io so extensively in researching my posts to these forums.  I hope the scientific journals don't succeed in their efforts to shut her down, thereby breaking all the sci-hub.io links I've posted...

 

In fact, Michael - would you still like to donate to sci-hub.io?

 

I haven't yet, since I've been waiting for you so we can do a joint bitcoin transaction. How about it? If anyone else wants to join in with a donation, I'm happy to coordinate it, and supply the bitcoin in return for Amazon gift cards.

 

--Dean

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I guess what really ticks me off about journals' fees, is that guess who pays for the research?  For almost all of it, we do.

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Good point Al. Yes, taxpayer's fund most health-related research via government grants, and then we get charged again to see the details of the research we paid for. Not cool.

 

How about putting your money where your mouth is and donating to sci-hub.io? A set of us (who will remain nameless for privacy reasons - except obviously for me) just did.

 

Here is the record of our transaction on the Bitcoin blockchain:

 

 AAZhTJk.png

That amounts to 0.1901 bitcoin, at the current price of $USD 389.00 / Bitcoin.

 

From the blockchain link above, it appears that sci-hub.io has received nearly 100 donations in the last few months totally just under $4K. Alexandra is woefully underfunded relative to the juggernaut of publishers she's fighting, and could definitely use the help!

 

--Dean

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How about putting your money where your mouth is and donating to sci-hub.io? A set of us (who will remain nameless for privacy reasons - except obviously for me) just did.

Still having student loan debt and other financial obligations, and a relatively modest salary, I tend to withhold donations for practical reasons. Still, Sci-hub.io has recently made my shortlist of organizations I try to financially support, even if only in a small way. The way I see it, even with a decent inter-library loan system for getting full-text papers, they've saved me more money that I've donated in saved time and frustration, and they actually provide access to some papers I otherwise can't get. Wikipedia is on the short list too for similar reasons--the intellectual value and digital content I receive from them for free is almost criminal.

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As president of the CR Society I have to be careful about advocating in any way for something that is or even might be illegal, so mum's the word on Sci-Hub.

 

About Wikipedia: I was a fan until I started participating as an editor, and then I slowly realized not only that most of what Jaron Lanier has written about Wikipedia is true, but that there even more disturbing aspects to Wikipedia, above all the Lord of the Flies–like social phenomena that seem to arise. This is largely restricted to topics outside the natural sciences, however.

 

I supported Citizendium for a while, but they just aren't taking off, in part, in my view, because of the decision not to begin as a fork of Wikipedia (which would have created a space with tons of content people could go to to get most questions answered, which would have led to greater publicity, and greater participation). But they may succeed in the end.

 

We desperately need an alternative to Wikipedia.

 

- Brian

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Brian,

 

Thanks for the pointer to the Jaron Lanier article. Lanier reminds me a lot of Nietzsche, so I'm not surprised that we both agree with him, at least on some things. I thought his Publisher's Weekly review of Lanier's book You are Not a Gadget summarizes his perspective pretty well (my emphasis):

 

 Laniers argues that “Web 2.0 sites such as Wikipedia undervalue humans in favor of anonymity and crowd identity… have created a hive mind mentality emphasizing quantity over quality.” Further, the argument of his book is that “the Open Culture/Hive ideology prioritizes getting stuff for free over creators being able to survive by making stuff.” ... He believes that the minority of people, who actually have something to offer, should be protected against the “numb mob“.

 

Very Nietzschean. On the other side, in defense of the "Wisdom of Crowds" approach to knowledge creation, is this rebuttal article by a person from the Wikipedia Research Initiative, which I found interesting, but not entirely convincing.

 

I think things have (if anything) gotten worse in the 10 years since Lanier wrote that article about Wikipedia . The news cycle seems more and more like a competition between the online representatives of traditional media outlets (e.g. newspapers, cable news networks) as well as news aggregators (like Reddit, popurls.com) competing with each other for clicks and eyeballs by having the most outrageous, 'click-baity' titles. The recent hype over the 'miracle' anti-aging cure of removing senescent cells in mice is just one example that comes to mind in the area of health/longevity, which we have discussed and (hopefully somewhat deflated) here. Few medical news reporters seem to even read the papers associated with the studies they are reporting on. Instead, medical 'breakthroughs' are being disseminated via press releases, and coverage of press releases, rather than people reading the peer-reviewed publications to understand what they really found, and the caveats associated with the research.

 

Part of the problem (which comes back to the topic of this thread), is that it's very hard to actually access the peer-reviewed publications, and that is why services like sci-hub.io that open up access are providing such a valuable service.

 

--Dean

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Grrr....

 

According to this article (posted to the sci-hub twitter feed) the publisher Elsevier has been issuing takedown notices of PDF papers published in their journals which have subsequently been posted by the authors (like me - many years ago!) to the service Academia.edu, a website where scientists share PDFs of their publications. There is an interesting discussion between an advocate of open access and the Elsevier public relations person "Director of Access & Policy" in the comment section below the article. The Elsevier person has the audacity to claim they are issuing said takedown notices to protect the authors! What a joke...

 

That really get's my goat (which is an English idiom with a surprisingly complex history).

 

--Dean

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All,

 

Here is somewhat good news for those paranoid people (you know who you are...) who are nervous about accessing papers on publisher's websites via sci-hub.io for fear of Big Brother surveilling your access via a questionable/illegal website to "steal" copyrighted material. It's also good news for people (like me) who are a bit concerned about all the sci-hub.io links people post to the forums breaking when/if sci-hub.io gets taken down by The Man.

 

Apparently, whenever sci-hub.io retrieves a paper, it squirrels away a copy to Library Genesis (LibGen), which according to its page on Wikipedia (sorry Brian...), is:

 

"a search engine for scientific articles and books, which allows free access to otherwise paywalled content. Among other sources it carries PDFs of content from Elsevier's ScienceDirect web-portal."

 

Here is the (current) LibGen search interface (and an overseas mirror) to content archived via sci-hub.io. FYI, I've found that searching via the DOI number, rather than PMID, seems to work better to find papers previously accessed via sci-hub.io. Take for example, the recent Nature paper on the mice study about killing senescent cells discussed here and known to have been previously accessed via sci-hub.io. Searching LibGen for it via it's PMID (26840489) doesn't seem to work, but searching by its DOI number (10.1038/nature16932) does. 

 

Not surprisingly, LibGen is being targeted (along with sci-hub.io) in court by the publishers, as (ironically) discussed in this (rather slanted) article from, of all places, Nature. So who knows how long this supplemental means of accessing academic publications will be available...

 

--Dean

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OK - here is a related moral quandary I'd like feedback on. Here is the situation.

 

I'm in the midst of reading a rather obscure book (The Specter of the Absurd: Sources and Criticisms of Modern Nihilism - but the book's identity isn't important)  in physical, dead-tree form that I borrowed from my local public library. 

 

Reading the above stories about sci-hub.io and LibGen, I came across another website, BookFi, that has copies of millions of ebooks, including the obscure book I'm reading the hard-copy of right now, which unfortunately is due back at the library next week. It's a tough read, and I'm unlikely to be able to finish it before it's due back. Plus I much prefer reading books in ebook form, since I can annotate them etc. So I'm considering downloading the electronic copy...

 

But at the same time, unlike sci-hub.io/LibGen, which are taking money from scientific journal publishers, not the study authors (who don't see a penny of the exorbitant fees the publishers charge to access their journal articles), book authors do receive royalties, and so sites like BookFi are in general ripping off content creators, which I don't at all condone or want to support.

 

But in this case, my tax dollars have already gone to my local library to purchase a copy of the book, so I am legitimately entitled to access it - heck I even have it in my hot little hands at this very moment. So in a way, getting an electronic copy of the same book from BookFi could be considered getting access to a book I've already 'paid for' and am entitled to read, just in a different format.

 

So what do people think about this little moral conundrum? Am I doing something wrong if I download from BookFi an electronic copy of the library book I'm in the midst of reading, or is it ok?

 

--Dean

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About Wikipedia: I was a fan until I started participating as an editor, and then I slowly realized not only that most of what Jaron Lanier has written about Wikipedia is true, but that there even more disturbing aspects to Wikipedia, above all the Lord of the Flies–like social phenomena that seem to arise. This is largely restricted to topics outside the natural sciences, however.

 

I agree with you here, and will say that I almost exclusively use it for natural science information. I also know enough about the natural sciences in general, and especially my own content areas, to almost never see any bias or misinformation.

 

I dabbled with being a Wikipedia contributor early in its history, and then a bit later on too, but never really got into it. Those experiences did help me better appreciate the Jaron Lanier's viewpoint, but I also think Wikipedia has come a long way in the 10 years since. Wikipedia is the logical expression of our culture, technology, and information science. Sure, it's got pros and cons but I'm not sure there's another realistic possibility given these things, at least for where we are as a civilization. For better or worse, it's kind of the best we've got for what it is. If an individual understands exactly what Wikipedia is and what it is not then they can appropriately assess and utilize the wealth of information there. The issue, then, is trying to improve the general public's skepticism of Wikipedia and information in general.

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But in this case, my tax dollars have already gone to my local library to purchase a copy of the book, so I am legitimately entitled to access it - heck I even have it in my hot little hands at this very moment. So in a way, getting an electronic copy of the same book from BookFi could be considered getting access to a book I've already 'paid for' and am entitled to read, just in a different format.

 

So what do people think about this little moral conundrum? Am I doing something wrong if I download from BookFi an electronic copy of the library book I'm in the midst of reading, or is it ok?

 

I think this is akin to steaming music from Spotify, iTunes, etc. where you pay to get unlimited access to their media library and a portion of your money goes to the streaming service and a (smaller) portion goes to the artists. If you really wanted to support the artists you'd probably do better to buy their music rather than stream it (though I'll admit I don't know the breakdown of either option's eventual artist payout). I guess you could also illegally download the artist's music and then make a donation to the artist for what you feel is a fair amount. With these options the moral question then becomes how much money is "fair" compensation for the artists.

 

The take-home is that there's no absolute right or wrong in your situation--much as there's never a true "right" or "wrong" in any situation besides what value we individually or culturally place on these. Ultimately, pay what you feel is morally acceptable to you.

 

Or you could just use your library's ebook subscription services, assuming it has one, or something like OpenLibrary's interlibrary ebook loan program to check out a "legal" ebook copy. You can get a "legal" copy through a number of means. At the end of the day do you want to feel morally assuaged because your process is legal based on cultural standards, or would you rather feel morally assuaged because you supported the author though financial or other acceptable means that meet your own moral standards?

 

 

Edit--

It seems sometimes books aren't available in ebook format, and Specter of the Absurd is sort of one of those. The only places I found it were for sale through Google Play Books or for free (illegally) through BookFi. Google digitizes a lot of books and doesn't share these with other vendors or ebook services, so a lot of content is exclusively available through Google Books. BookFi probably got a copy from someone who bought the Google Books version, bypassed the DRM, and saved the info as an epub file. This latter option is actually pretty easy to do with multiple readily available programs--search Google for "download google play books" or similar.

 

But in this case, my tax dollars have already gone to my local library to purchase a copy of the book, so I am legitimately entitled to access it...

If it helps, this would be my line of thinking and I'd have no moral qualms about illegally obtaining the ebook provided I had legal access to a physical copy.

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Thanks James for your cogent thoughts on my dilemma.

 

You are right about the particular book I'm reading only being available from my library in hardcover form (no ebook). Even Amazon only sells it in hardcover or paperback, no Kindle edition. I could buy it in ebook form from Google Play as you point out, but it's $18.33, for a book I already have in hardcopy form from my library, simply so I could finish reading it as an ebook. Not a very appealing alternative.

 

BookFi is looking like a more attraction option...

 

--Dean

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If an individual understands exactly what Wikipedia is and what it is not then they can appropriately assess and utilize the wealth of information there. The issue, then, is trying to improve the general public's skepticism of Wikipedia and information in general.

 

 

James, I think that sums up the problem very nicely. But I would stress that Wikipedia, not just the general public, should contribute to the solution. One idea I thought of is to have the landing page for a topic be the Discussion page, not the main page. Seems weird, but it would highlight the in-flux nature of most knowledge. The main page is just a (temporary) snapshot of the crystallization of debates on the Discussion page for the subject, the result of a battle temporarily won by one side. Its importance should be de-emphasized.

 

(Again, all of this is more clearly relevant for subjects outside the natural sciences.)

 

But I think the world would benefit tremendously if there were several large, collective knowledge projects like Wikipedia.

 

- Brian

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HI!

 

There's a service that I have available as a faculty member at the University of Rochester -- they'll get me the .pdf of any research paper that i want.  (Applies to books, too -- but sometimes they simply get me the book, rather than the .pdf).

 

So, I can get .pdf's of papers that you might be interested in -- although I probably am not supposed to do this?  I'll check at UR.

 

  -- Saul

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I tried to get the full pdf of this paper sent out by Al today through sci-hub, but failed. Could someone help me? Thanks!

---

Message: 2

Date: Fri, 26 Feb 2016 19:58:18 -0600

From: "Al Pater" <alpater@shaw.ca>

To: <CR@lists.calorierestriction.org>

Subject: [CR] The impact of nutrients on the aging rate: a complex

interaction of demographic, environmental and genetic factors.

Message-ID: <89BF19408B864906858F94F976881739@V500930>

Content-Type: text/plain; format=flowed; charset="Windows-1252";

reply-type=original

 

The 46 page review is extensive and fairly devoid of much new information

for me.

 

 

The impact of nutrients on the aging rate: a complex interaction of

demographic, environmental and genetic factors.

Dato S, Bellizzia D, Rose G, Passarino G.

Mech Ageing Dev. 2016 Feb 10. pii: S0047-6374(16)30008-2. doi:

10.1016/j.mad.2016.02.005. [Epub ahead of print] Review.

PMID: 26876763

http://sci-hub.io/10.1016/j.mad.2016.02.005

 

Abstract

 

Nutrition has a strong influence on the health status of the elderly, with

many dietary components associated to either an increased risk of disease or

to an improvement of the quality of life and to a delay of age-related

pathologies. A direct effect of a reduced caloric intake on the delay of

aging phenotypes is documented in several organisms. The role of nutrients

in the regulation of human lifespan is not easy to disentangle, influenced

by a complex interaction of nutrition with environmental and genetic

factors. The individual genetic background is fundamental for mediating the

effects of nutritional components on aging. Classical genetic factors able

to influence nutrient metabolism are considered those belonging to

insulin/insulin growth factor (INS/IGF-1) signaling, TOR signaling and

Sirtuins, but also genes involved in inflammatory/immune response and

antioxidant activity can have a major role. Considering the worldwide

increasing interest in nutrition to prevent age related diseases and achieve

a healthy aging, in this review we will discuss this complex interaction, in

the light of metabolic changes occurring with aging, with the aim of

shedding a light on the enormous complexity of the metabolic scenario

underlying longevity phenotype.

Copyright ? 2016. Published by Elsevier Ireland Ltd.

 

KEYWORDS:

 

dietary interventions; epigenetics; health span; human longevity; nutrition

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