A Review of MegaJournals

October 17, 2016

landscape-evolving

BACKGROUND

One issue that I’ve been following for a number of years is so called MegaJournals.

Mega journal as defined on Wikipedia.

Cue ‘Open Access and The Dramatic Growth of PLoS ONE‘ which I wrote for the figshare blog back in 2012. (As you will see, PLOS ONE started publishing papers in 2006).

The concept of OA “Megajournals” appears to have started around June 2011 as per this post by Mark Patterson (at that time with PLOS, now with eLife):

“Remarkably, PLoS ONE became the largest peer-reviewed journal in existence inside four years (and will publish as much as 1.5% of the articles indexed in PubMed in 2011), and over the past 12 months has been emulated by many other established publishers in various disciplines”.

plos-one-2012

doi:10.1371/journal.pbio.1001235.g001

A large part of the reason for the spike in the dramatic rise since Q1 & Q2 2011 is the fact that that was the time that PLoS ONE, received its first Impact Factor .That opened the floodgates in a big way (e.g. China) and it can clearly be seen from above that this fact has led to a significant effect.

Around the same time, Frank Norman posted a more broader and detailed post Megajournals which indeed was the conduit to my own post.

The trend towards Open Access has catalysed the creation of many new journals and new publishers. BioMedCentral, established in 2000, was a pioneer of open access publishing, launching a large number of journals. Public Library of Science (PLoS) initially established a small number of high-level journals, then in 2006 it launched PLoS ONE. This was the first of a new kind of journal, later dubbed mega-journal. PLoS ONE aimed to publish any article that met the test of scientific rigour, and eschewed any measure of importance or impact in its editorial and peer review process. In 2010, PLoS ONE published 6,749 articles, making it the largest journal in the world (by volume). Its success helped to persuade the mainstream publishing industry that fee-paid open access was a viable business model.

Recently I invited representatives from a number of open access publishers to discuss megajournals. Five of them gave presentations to an audience of scientists here, and one visited me subsequently to inform me about their operations.

I then revisited the output of PLOS ONE around a year later.

plosone

I was not alone in thinking that the exponential growth seemed unstoppable. With hindsight, such growth can equally be followed by exponential decay.

In May 2015, Mike Taylor posted Have we reached Peak Megajournal?

Bo-Christer Björk’s (2015) new paper in PeerJ asks the question “Have the “mega-journals” reached the limits to growth?”, and suggests that the answer may be yes. (Although, frustratingly, you can’t tell from the abstract that this is the conclusion.)

I was a bit disappointed that the paper didn’t include a graph showing its conclusion, and asked about this (thanks to PeerJ’s lightweight commenting system). Björk’s response acknowledged that a graph would have been helpful, and invited me to go ahead and make one, since the underlying data is freely available. So using OpenOffice’s cumbersome but adequate graphing facilities, I plotted the numbers from Björk’s table 3.

megajournal-volumes-2010-20151

As we can see, the result for total megajournal publications upholds the conclusion that megajournals have peaked and started to decline. But PLOS ONE (the dark blue line) enormously dominates all the other megajournals, with Nature’s Scientific Reports the only other publication to even be meaningfully visible on the graph. Since Scientific Reports seems to be still in the exponential phase of its growth and everything else is too low-volume to register, what we’re really seeing here is just a decline in PLOS ONE volume.

It’s interesting to think about what the fall-off in PLOS ONE volume means, but it’s certainly not the same thing as megajournals having topped out.

What do we see when we expand the lower part of the graph by taking out PLOS ONE and Scientific Reports?

megajournal-volumes-2010-2015-without-top2-recoloured2

So the establishment of new megajournals is very much a good thing, and their growth is to be encouraged. Many of the newer megajournals may well find (and I hate to admit this) that their submission rates increase when they’re handed their first impact factor, as happened with PLOS ONE.

Onward!

Touched upon in the posts by Norman and Taylor is Scientific Reports (SR). SR was launched in 2011 (with little fanfare) by Nature Publishing Group (now Springer Nature) and over the last couple of years has seen significant growth. Interestingly a few weeks after its launch, PLOS ran with the following post on their Official Blog:-

Welcome, Nature. Seriously.

welcome-nature1

We shall come back to SR shortly.

Whilst PLOS ONE has many supporters, it also has its critics, most notably, some of the individuals who blog for The Scholarly Kitchen:-

Is PLoS ONE Slowing Down?

The Rise and Fall of PLOS ONE’s Impact Factor (2012 = 3.730)

PLOS ONE Output Falls Following Impact Factor Decline

PLOS ONE Output Falls 25 Percent

PLOS ONE Shrinks by 11 Percent

As PLOS ONE Shrinks, 2015 Impact Factor Expected to Rise

What is clear however was that in terms of output, this seemed to have peaked around 2013/2014 and has subsequently been in decline ever since.

In August 2016, Scholarly Kitchen ran with a post:-

Scientific Reports On Track To Become Largest Journal In The World

scientific-reports-v-plos-one

An unpredictable publication flow and revenue stream through APCs will have very different effects on the two publishers. Springer Nature has an enormous, diversified stable of journals and revenue streams, which allows them to play a long-term strategy game with Scientific Reports. Annual revenue fluctuations with one journal are not going to put Springer Nature in financial trouble. In contrast, PLOS’ income is almost exclusively based on APC revenue, with 97% of their 2014 revenue coming from publication fees. More importantly, 91% of all 2015 papers published in PLOS journals were published in PLOS ONE, the remaining 9% split among six other journals. As revenue from PLOS ONE functions to subsidize the publication costs of these six other titles, downward pressure on PLOS ONE puts the entire organization at risk.

Over last weekend, I noted a very recent post on Times Higher Education:-

Mega-journals: the future, a stepping stone to it or a leap into the abyss?

Nature’s new kid on the block is now the biggest journal in the world. But while such giants are currently overturning the world of scholarly publishing, their long-term future is unclear, says Stephen Pinfield.

In September, Plos One was overtaken. Nature’s Scientific Reports published 1,940 research articles in that month, compared with Plos One’s 1,756. The figures for August were 1,691 and 1,735, respectively. Scientific Reports has grown rapidly since its launch in 2011, a rise that has coincided with (some have suggested, partly contributed to) a decline in Plos One. Like Plos One, Scientific Reports publishes across STEM, although in reality, the former has more papers in health and life sciences and the latter in physical sciences.

oamj

Pinfield’s projected figures for SR in 2016 are based on data from August and September 2016 alone. I them made the following graph based on data from here on SR.

scientific-reports-growth-1

After I tweeted details of Pinfield’s post and my own graph, things got rather interesting on Twitter. Here’s some of what I saw.

mj-post

mj-post1

mj-post2

Based upon available data, SR certainly appears to be on track to become the largest Journal in the world overtaking PLOS ONE but possibly not until early next year.

On the other hand however, whether megajournals are growing or shrinking might be seen as irrelevant. Put another way, a key question worth thinking about is whether there is a growing proportion of papers published (including as preprints, an increasingly popular way of dissemination information rapidly and freely) without being judged on ‘relevance’ or ‘expected citation potential’ or ‘perceived scientific quality’, but just on the basis of some basic objective criteria, e.g. the detail of the description of materials and methods, statistical robustness and logic of the conclusion in view of the data, etc.

Such objective criteria can, of course, also be applied by journals not known as Mega Journals. See Science (which needs communication) first, careers (which need selectivity) later, Velterop et al (2015).

I will conclude with the closing paragraph’s from Pinfield’s post:-

What remains to be seen is whether mega-journals, as currently constituted, will prove to be a major innovation that contribute to the reshaping of research publishing in an increasingly open access world, or whether their real importance will lie in being a stepping stone to even more radical forms of scholarly communication. This will partly depend on the extent to which the open access “wild animal” will be domesticated. Signs of that already abound, meaning that any change is more likely to be incremental rather than disruptive.

It is, of course, possible that mega-journals will sink without trace: that probably applies to some of the current smaller hopefuls. But there does now seem to be momentum behind some of larger titles, which means they, at least, are likely to continue to prosper. In the short term, though, what is clear is that the battle to publish the largest journal in the world seems to be swinging towards a new form of a very old journal, Nature.

Stephen Pinfield is professor of information services management at the University of Sheffield. He is currently principal investigator on an AHRC-funded project investigating mega-journals and the future of scholarly communication.

Steel, Graham (2016): A Review of MegaJournals. figshare.

https://dx.doi.org/10.6084/m9.figshare.4036410.v2

Retrieved: 12 55, Oct 17, 2016 (GMT)

Think Check Submit

September 26, 2016

thinkchecksubmit.org

Think. Check. Submit. from Think. Check. Submit. on Vimeo.

 

thinkchecksubmit

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Public Domain works by Charles Darwin are being legally sold online. Is this ethical ?

August 21, 2016

darwin manuscript

paywall

Early on Sunday morning (21st August 2016), I spotted the following (anonymized) #icanhazpdf request tweet:-

darwin tweet

After spotting this, I did indeed find that the publication of this Charles Darwin paper from 1858 is indeed sitting behind a paywall:-

darwin paywall

(Thankfully, the person who left the original #icanhazpdf request for the paper found a link to the free version).

darwin paywall1

Here’s some of the responses to my tweet:-

 

 

 

 

 

 

 

 

 

 

Thankfully, a quick online search threw up a number of open access copies of this work such as here on the Darwin Online website.

So, should works dating back to that era be out of copyright and sitting in the public domain ? YMMV it would seem.

Some tweets from Copyright Librarian Nancy Sims:-

 

 

 

 

 

 

So, after being initially surprised that this public domain work is being sold by a publisher (in this case Wiley), they are within their legal rights to do this.

Earlier this year, there was an interesting thread relating to such matters after I posted this tweet:-

This is also linked to this one:-

One person however is of the view that this is NOT legal:-

Others disagree with that view:-

Let’s see if Copyright expert Charles Oppenheim will comment:-

RESPONSE

 

 

Views of someone associated with a publisher:-

the_invisible_a @McDawg @HistGeekGirl it seems wrong in principle, even if it may technically be legal. Just shows how messed up laws are.

— Andrea Wiggins (@AndreaWiggins) August 21, 2016

(Jan Velterop implies that he is of the view that it’s legal to download this from Sci-Hub as the work itself is Public Domain)

 

Updated thoughts on live-streaming an event

July 19, 2016
This post is a re-assessment of a comment I left back in 2010 on the following blog post by Martin Fenner.
I shall leave the below intact from the original (other than some formatting). So as someone who regularly continues to follow Conferences/Events virtually, have my thoughts changed much since 2010 ? Essentially, not that much really.
Firstly, I’ve live-streamed many events since then having previously just briefly dabbled. One common misconception about live-streaming, is that if you do it, no-one will come to the event IRL. This came up in the discussion below with Mike & David. They have over two decades of first hand experience in the field. Essentially, they said “the opposite is true“.
In terms of the quality of live-streaming, this can vary massively. Some of the free applications that I used years ago either no longer exist or are now cluttered with adverts (unless you pay for a premium account). Now that there are many platforms that offer broadcasting/recording in HD, the quality of live-streaming had certainly improved, generally.
Over the last two years or so, a number of mobile APPs (e.g. Periscope, Meerkat & UStream etc.) have been released meaning that after a couple of taps, you can be live on the web. Again, the quality of these APPs can vary a lot. Archiving these recordings could be made easier (although I have limited experience in this particular area).
I still firmly believe that if you’re streaming from an event, getting a secure web connection remains important.
I also still firmly believe that post event, it’s really important to archive the recordings online ASAP before interest disappears.
Another entity to compliment live-streaming is live blogging.

 This is something I’ve dabbled with a couple of times. Firstly, briefly at Repository Fringe (Edinburgh) 2015 and also earlier for UKSG in 2014 e.g., here and here.  Being part of a team certainly helped given the size of this event.

One person I know who has much more experience than me (and most) in this is Nicola Osborne, Jisc MediaHub Manager / Digital Education Manager at EDINA. You can view her work here.

 All in all, live streaming/blogging is certainly here to stay and technology/software continues to revolutionize the possibilities for making events open to wide audiences online.
One caveat remains though. By not attending events IRL, you do miss out on face to face discussions/socializing/networking etc.

Interesting post Martin.

I’ll try to keep this as brief as possible. That wasn’t possible, so here goes.
From an general subjective Conference perspective namely focusing on the virtual attendee angle, I think one has to consider many variables such as:-

A) What subjects are you going to cover?
B) Who is your “target audience”?
C) How will you make them aware of the event?
D) Is it free or fee (#scio10 was $175 – #solo09 – £10 in person or £10 for Second Life)
E) How interactive do you wish to make it be for virtual attendees?
F) How does one tackle sessions that involve unpublished data?
etc.etc.

Now since we only appear to be able to use a max. of four url’s in the comments feed on NN at the moment, I’ll choose ’em sagaciously.
On Jan 10th, I posted this on my blog (sorry, link rot) before virtually attending last weekend’s events in North Carolina.

Based upon past experience(s), the thing that I was really looking forward to was the live-streaming/chat-room aspect of the Conference. Despite the much applauded wi-fi connection they had set up (extremely important these days and secured internet access to all present) c/o company SignalShare, it became clear fairly early on that there was -phlegm- a problem with the live-stream.

++ACTION POINT++ Must find out what went wrong so that we can learn from this for the future.

Each chunk (hourly sessions) of the event was split into five parallel sessions (Rooms A to E) and the aim was to live-stream content from all discussions in D & E. This meant that ahead of the event, virtual attendees could chose which sessions they wanted to attend. In the end alas, over the whole weekend, only about 1.5 hours worth was streamed and with very little notice.

I found this rather disappointing I have to say as discussed with Martin over the weekend (can a DM Twitter discussion be classed as a “personal communication”?) so time to follow events in other ways. I was pretty much glued to the #scio10 Twitter feed all weekend and I very much agree with AJCann’s comments above.
==
I like Martin’s Twitter suggestions !!

Richard Grant & I covered various aspects of Conference event coverage during a podcast we did with Mike Sefang & David Wallace (link rot, try here) in July 2008. (relevant section starts at 19’30”) As a result of that discussion and with the permission of NPGs Timo Hannay, Richard recorded audio of the Wrap-Up Panel: Embracing change: Taking online science into the future at Science Blogging 2008: London which was uploaded to web within a few hours. Cool….

As discussed with a few NN staffers, even though all sessions were video recorded, due to technical issues, none of the NN files ever appeared on the web. That said, Cameron Neylon recorded and from memory live-streamed (and also self archived) some of the sessions via his laptop. Also cool.

An observation from “Science Blogging 2008, North Carolina”:http://scienceblogs.com/clock/2008/01/science_blogging_conference_vi.php is as follows. Similar to what Cameron did in London, that year, a couple of individuals, Wayne Sutton and to a lessor extent, Deepak Singh, live-streamed events from their laptops. Within the space of a week (after that, little interest), their uploaded files had been viewed over 15,000 times which I think was pretty impressive. Observation from Science Online London: 2009. Video footage of 7 sessions were uploaded c/o NN’s Joanna Scott 2 weeks after the event. Total views ~ 500.

My take on this from this data is that if you are going to attract the attention of virtual attendees using video format, it needs to be instant ideally, or delayed by a day or two at the most, before interest fades. The same I guess applies to audio. As to Second Life, I personally have limited experience of this platform so am unable to comment. One for Lou & Jo to discuss as Lou has indicated earlier.

As Cameron Neylon has mentioned elsewhere on teh interwebs, as matters stand, livestreaming using a wi-fi connection is still very 50/50 in success terms. Whilst livestreaming from this years Science Online UK event shouldn’t be completely ruled out (we should at least try a secure [not wi-fi] web connection, IMO) all things considered, I have to say that I’m pretty much with Martin as per the last para of his post.

One final point. I really like the idea of Science Online 2010: London being a two day event, yay !! The meatspace socialising aspect of such events is a real draw and something that you miss by non physical presence. I can’t really add to Stephen’s comments above in this regard.

Oh waits, I still have a link final up my sleeve. Whilst I was unable to attend the pre Science Online 2009: London party in person, I did manage to fling together the following montage. Apols for re-posting here but I thought it was rather cool and in doing something like this, it gives virtual attendees a flavour of the social aspect of events, which I think is not “essential” but of general interest.

Oh bums, I appear to have have ran out of links so let’s see if I can post this without the “missing link”.

Oh sh*te, we can’t embed stuff from Vimeo here, so “el missing linky is here.”:http://vimeo.com/6306956

Essentials of Glycobiology

May 25, 2016
Originally posted on my now deceased blog on Friday, 17 October 2008

Essentials of Glycobiology – New Edition is freely available from the NLM/NCBI Bookshelf

As reported today on Open Access News (OAN):-

… Essentials of Glycobiology, the largest and most authoritative text in its field, will be freely available online beginning October 15, through collaboration between the Consortium of Glycobiology Editors, Cold Spring Harbor Laboratory Press, and the National Center for Biotechnology Information (NCBI), a division of the National Library of Medicine (NLM) at the National Institutes of Health (NIH). Fittingly, the release of the book follows soon after the October 14th celebration of International Open Access Day, which will highlight prior successes in providing such open access to research journals. …

Here is the book. The Foreword is a great place to start of course.

OAN Comments:

* Add this to the growing list of widely-used textbooks that are available OA.
* Who’s backing this is also noteworthy. It’s not an author who negotiated the right to self-archive a copy, or an OA startup publisher; it’s a scientific press and the National Library of Medicine.
* The first edition of the book has been OA since 2003. Apparently, the impact on sales of the print copy hasn’t been overwhelmingly negative, or it seems unlikely the publisher would support OA to the new edition.

My Comments:

Glycobiology is a most fascinating area that continues to gather interest over time.
I applaud all involved for contributing to and publishing this work to the widest audience on the planet.

Press Release: Novel publishing approach puts textbook in more hands

1 comment:

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Glycobiology – update

May 25, 2016

Originally posted on my now deceased blog on Saturday, 12 January 2008

Now that I’m blogging more often, I wish to expand further on one aspect of Glycobiology – 21st Century Style which I posted on this blog mid December.

Pentosan Polysulphate (or PPS for short)

PPS was something that I became interested in late 2002. As a result, this led me to become interested in the field of Glycobiology and making contact with at least two dozen leading Glycobiologists from around the world.

Since social networking is all the rage these days, I am currently co-admin of two Glycobiology related online groups, one on Facebook, the other, on Nature Network.

PPS may be a merely a drop in the Glycomics ocean, but it is the substance that I have the greatest knowledge and first hand experience of.

Since my email records only go back to Feb 2006 (I had to change computers and lost a lot of older emails), I cannot recall specifically when contact was made with a Linda Curreri based in Dunedin, New Zealand but it would have been during 2003. We still keep in touch.

Linda maintained a very well referenced and detailed website dedicated to Pentose Sugar. Linda like myself is a layperson but her general research knowledge was and remains sublime. A decision was taken last year by Linda to no longer maintain the site but I offered to come to the rescue if required.

A few months before then however, I had discovered the brilliant WayBackMachine c/o Archive.org

We then knew that despite the site being archived, it would be (and is) preserved perfectly as it was on the web.

I therefore for the first time am providing a link to archived website PENTOSE SUGAR

Further preservation was done in the form of book “Pentosan polysulphate : a medicine made from beech bark” by Linda Curreri early 2007. ISBN 9780473119720 (pbk.) : $12.00

—-

At the time of writing, there are 731 Papers about Pentosan archived in PubMed. Importantly however, only 98 are readable (open access) at full article level. That’s not a lot really.

When one considers the clinical usages and research areas of PPS, I find it quite staggering that so little research has been published thus far.

Let’s take arthritis for example. PubMed throws up over 175,000 Papers. When we add Pentosan to the search mix, the number falls to 32, and down further to only three at full article level.

For a condition that afflicts millions of patients, pretty much to date, only the non-human variety are allowed to receive PPS treatment.

But wait !!. Check out the ARTHOPHARM website in Australia and this page.

Go back, check and FULLY read through archived website PENTOSE SUGAR

Being a layperson and patient advocate with no loyalty to anyone other than patients, no patents pending (or ever likely) and no conflicts of interest to declare, I simply wrote this blog to place information in the public domain.

I will end with a Legal Precedent from 2002 and it’s wide ramifications. The following text is from the Pentose Sugar website.

“Law. Pentosan Polysulphate is not and cannot be patented. This places it in the public domain. However PPS is only available under patented trade names which appear on its packaging. This is a complete nonsense, because the brand name is not pentosan polusulphate and it is the trade name which is being marketed. The brand patenting merely protects the commercial property of the manufacturer. If a pharmaceutical company does not ‘develop’ PPS for specific indications and patent their brand name(s) this unique medicine does not become available as a treatment option. In effect legislation made up by law maker’s is blocking pentosan polysulphate’s availability for sick human’s. PPS is however readily available for scientific research.

In the London High Court in December 2002
, Dame Elizabeth Butler-Sloss ruled in favour of two teenagers with advanced vCJD to have pentosan polysulphate to treat this prion disease. The case had absolutely nothing to do with any patented brand name; it was about the right of two dying people to have a medicine that could save their lives .The medicine was the unpatented pentosan polysulphate. Dame Elizabeth’s decision set a precedent and it would seem that the legal constraints which surround this pentose medicine, though firmly in place are flimsy and could in fact be nul and void.

It could also be argued that due to the unique status of pentose sugar in human physiology that it is an absolute right of humans to source and assimilate pentose sugar whether it is a food sweetener or a medicine that has been compounded by a chemist, and neither medical specialists, government officials, man made laws or scientists and pharmaceutical companies ( both of which appear to claim the unpatented generic medicine PPS) have any right to prevent them. Whether by collusion or not, this is indeed happening….globally.

Scientists will always continue research even though principles have been proven, it is what they do, but this should not be used as an excuse to prevent pentosan polysulphate’s use in humans, because science has already proven the safety and worth of this medicine to the human organism.”

http://www.getgooglesearch.com/htmlcodes/search.html

5 comments:

Francis said…

Is the archived version of the pentosesugar website no longer available?
Also, I tried looking out for the book itself, but the only website reference for it doesn’t have any copies. Any working links would be appreciated. I dont mind paying directly to the author herself

Thank you,
Francis

McDawg said…

@ Francis. This link should work for the archived pentosesugar website:- http://web.archive.org/web/20041205094941/www.pentosesugar.com/toc.html

Shall email you the authors contact details.

Francis said…

Hey McDawg,

The webarchive is perfect. I haven’t received the author’s details though.
PS. I would like to know more about your expertise on Pentosan.

Thanks,
Francis

McDawg said…

@Francis.

If you would kindly drop me an email (steelgraham AT hotmail DOT com), I’ll see if I can assist you.

Kind regards,

Graham

McDawg said…

@ Francis. I tried to email you the information you were looking for but there is no email address in your profile. Overnight, I received the following message from Linda Curreri which she asked me to post on my blog.

HELLO FRANCIS,

TO PURCHASE A COPY OF THE BOOK PENTOSE SUGAR, A MEDICINE MADE FROM BEECH BARK, PLEASE EMAIL ME AT

lcurreri@xtra.co.nz

KIND REGARDS,

LINDA CURRERI [AUTHOR]

Glycobiology – 21st Century Style

May 25, 2016

Originally posted on my now deceased blog on Monday, 10 December 2007

Glycobiology – 21st Century Style


Glycobiology 21st Century Style

 

I’ve been thinking about an ‘appropriate’ image for this for quite some time, so here we go. All that I added was ’21st Century Style’.

SOURCE (C)

Follows some thoughts I had last year.

If accepted for publication, my co-authors and I will deliver something of substance in the New Year.

Complex sugar chains and glycosaminoglycan (GAG) side chains
make up an integral part of our mind and body.

It was an Albrecht Kossel who was awarded a Nobel back in 1910 as the first to recognize that nucleic acids contained a carbohydrate. Due to its 5 carbon molecular structure, he called it pentose “the stuff of genes”.

During the first half of the last Century, the chemical and biological structures of carbohydrates were very much a point of focus. Whilst this was to become an integral part of modern day molecular biology, at the time, they were not forerunners unlike other major classes of molecules. Largely, this was due to their (very) complex structures, difficulty in understanding their sequence(s), and the fact that their biosynthesis could not be directly predicted from the DNA template.

53 years ago Nature magazine published a scientific Paper by Maurice Wilkins and his two colleagues at King’s College, London, called “Molecular Structure of Deoxypentose Nucleic Acids” Wilkins M.H.F., A.R. Stokes A.R. & Wilson, H.R. Nature 171, 738-740 (1953)

Something called heparin was “discovered” by a second-year student at John Hopkins University in 1916. By the 1930’s, heparin came into use namely as an anti-coagulant. Essentially, this was made using animal ‘by products’ such as pig, dog and later, bovine gut material. By the early 1940’s, “purified” heparin was available for clinical and experimental use.

Post WW2, Germany was unable to import heparin and there was also a shortage of many basic resources such as sugar. A novel method of deriving synthesized heparin type substances led to the development of sulphanated pentose sugar made essentially from the bark of beechwood trees. The most commonly used term these days for this particular (Polyanion) substance is Pentosan Polysulphate or PPS. Its most common broad (oral) usage commenced in the 1960’s and continues in many countries (namely USA and mainland EU) in relation to the management of the common bladder complaint, internal cystitis (IC). SP54 (the purest form of PPS known continues to be manufactured by a small family run German company, Bene. Here is a page from the Bene website that lists it’s currently known broad usages.

Around the same time, Germany, Japan and the (former) Soviet Union also focused on Xylitol which is a five-carbon sugar alcohol, a natural carbohydrate which occurs freely in certain plant parts (for example, in fruits, and also in products made of them) and in the metabolism of humans. Xylitol has been known to organic chemistry at least from the 1890’s.

Where there is deficiency or excess of (Proteoglycans) PG’s this can play a lead role in the pathogenesis of a substantial range of common and rare conditions ranging from arthritis, diabetes, cancer, HIV/Aids through to protein folding neuro degenerative conditions such as Alzheimer’s disease (AD).

Semi synthesized HSPG’s (Heparan Sulphate Proteoglycans) over the last few years in particular are now referred to as Glycans. There are 14 Glycans in the family including Glypicans.

In 2005, Nature published a seminal Paper by Professor’s Fuster and Esko (5) entitled “The Sweet and Sour of Cancer: Glycans as Novel Therapeutic Targets” which reported on several significant developments.

In this Paper, Fuster and Esko et al demonstrated the potential use of Glycans in the treatment of many types of cancer/tumor and concluded the Paper with a “(this) might represent the ‘tip of an iceberg’ of therapeutic potential that awaits future discovery” type ending.

Have matters progressed since then?

Glycans have now been brought into real time Clinical usage, namely as surrogate markers in the treatment of a number of cancers.

How far are we from human trials of Glycan use for the likes of HIV, Cancers and Alzheimer’s disease?

Book, ‘Essentials of Glycobiology’ is available online and can be (Open Source)accessed via this book is currently being revised with an updated version was released this year via TA.

The Journal of Glycobiology published its first online Journal in September 1990.

Whilst there has been an increasing wider focus of attention in the Glycobiology field over the last few years in particular, some of the core principles from a cellular level stretch back over a Century.

In Australia and (limited extent) New Zealand in particular, Glycans continue to be used safely and successfully in the treatment of the arthritic joints (osteoarthritis) in both animal and man (1).

The latest reported commentary (2) from the most recent Global Conference on AD in Madrid is highly suggestive that diabetes, whilst certainly not the cause, has a degree of interlinkage with a number of neurodegenerative diseases.

With regards to Alzheimer’s (Amyloidosis generally) despite a substantial number of Peer reviewed published Papers showing Glycan promise in vitro and in vivo, there has been little/no interest from the Pharma Industry.

To sense the ‘sweet flavour’ of the future of Glycobiology in the 21st Century, the word Glycomics comes to mind (3,4).

Are such Generic based approaches deemed as potentially large threats to large Pharma?

(1) PMID:12014849PubMed http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=12014849&itool=iconabstr&query_hl=5&itool=pubmed_docsum
(2) http://www.wilmingtonstar.com/apps/pbcs.dll/article?AID=/20060722/NEWS/607220330/-1/State
(3) http://www.functionalglycomics.org/static/consortium/main.shtml
(4) http://glycomics.scripps.edu/pub/NatMethodsEditorial2005.pdf
(5) PMID: 16069816 [PubMed – indexed for MEDLINE]http://www.nature.com/nrc/journal/v5/n7/abs/nrc1649.html

1 comment:

Anonymous said…

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Open Science Enthusiast

April 22, 2016

@KLA2010 Just noted “Open science enthusiast” on your profile. Have used that term for myself a few times.

— ⓪ Grⓐhⓐm Steel (@McDawg) April 22, 2016

canScience

140 is too short, so …… I was going to use ‘TweetLonger’ but decided not to do so in the end.

As to who first came up with “Open Science Enthusiast”, we’ll never know and frankly, who cares…. To me, in short, it means “Citizen Scientist”.

I was present at Scotland’s 1st Open Knowledge (possibly 2nd) event (in Edinburgh back) in 2012. [2]

VLUU L200  / Samsung L200

At one point, those present were asked to describe themselves in just three words. Off the top of my head, I went for ‘Open Science Enthusiast’. I was the only one to do it in three words, so that was my starting point. – Since then, I’ve used it elsewhere even including peer reviewed papers such as:-

Buckland, A. et al., (2013). On the Mark? Responses to a Sting. Journal of Librarianship and Scholarly Communication. 2(1), p.eP1116. DOI: http://doi.org/10.7710/2162-3309.1116

The term has been used elsewhere, e.g. here by Dr Marcus Hanwell @mhanwell

best-of-science-2015

I predict that high on the list of many open science enthusiast’s new year’s resolutions will be the education of both established and future researchers on the importance of openness, licensing, sharing, and reproducibility.

Best of Opensource.com: Science  December 25th 2015

Marcus D. Hanwell | Marcus leads the Open Chemistry project, developing open source tools for chemistry, bioinformatics, and materials science research. He completed an experimental PhD in Physics at the University of Sheffield, a Google Summer of Code developing Avogadro and Kalzium, and a postdoctoral fellowship combining experimental and computational chemistry at the University of Pittsburgh before moving to Kitware

Also relevant if this lovely poignant quote from Dr Jennifer Molloy [1]

[1]Molloy quote

SOURCE

[2]

FULL REPORT of my experience in Edinburgh that day

Interview: “Open Views” featuring McDawg aka Steck

March 16, 2016

Sunday, 13 July 2008 (Originally posted on my now deceased blog)

sundar steck

BACKSTORY

12th October 2007, Prof Peter Suber and I & were interviewed on the same afternoon, back to back by Sundar Raman as part of the ongoing series called “Open Views”.

Peter’s can be found here.

Having previously released a snippet and patiently waiting for a landing space over at KRUU.fm, I decided to edit and self archive a copy of my own, now here.

Steel, Graham (2014): My first interview about open access from ~2007.. figshare.

https://dx.doi.org/10.6084/m9.figshare.1053210.v2

Retrieved: 23 01, Mar 16, 2016 (GMT)

Intended Intro music

White Lies by *Catch* by Steck
Genre: Pop (mainstream)

Intended Outro music

Wake Up Now – remastered by Tobin Mueller
Genre: Pop (mainstream)

Above image is mash up of this image from KRUU.fm.

CCBY1

The interview was a joint creation of McDawg and host from KRUU.fm.
Labels: graham steel, KRUU.fm, open access, open views, peter suber, sundar raman

“Wallets with a Serious Case of Stockholm Syndrome”: Sci-Hub and the Future of Scholarly Communication

February 29, 2016
Sci-Hub Logo

Originally posted here by Marcus Banks. Re-blogged in verbatim with permission to do so.

Following Aaron Swartz’s tragic suicide in 2013, there was a brief flurry of attempts to honor his legacy by increasing public access to research articles. Swartz had successfully accessed millions of articles from MIT’s licensed JSTOR database, in a way that drew the ire of JSTOR (which eventually dropped charges), MIT (which arrested Swartz), and the federal government (which alleged numerous violations of the Computer Fraud and Abuse Act).

People argued that the way to remember Swartz was to provide immediate, complete, non-embargoed access to research articles. Not reports to grant funders about progress along the way, not mere summaries of the results — but the actual papers from actual journals, complete with their DOIs and page numbers.

Indeed, in 2013 — well after the Internet had transitioned from a novel technology into an essential part of everyday life — we were still debating about how to maximize access to the fruits of a publication process that dates from the 1600’s. Activists claim that all of the scholarly literature should be free, publishers claim they add significant value to this literature that is worthy of compensation.

We are still having this debate in 2016, and if trends continue we will keep doing so for decades more. The great unleashing of the literature called for after Swartz’s death has not come to pass. There is too much money to be made in the current scholarly publication system — in which the only way to have immediate access to papers is to be affiliated with an institution rich enough to afford this, or to live in a poor enough nation that it is not an attractive market for publishers anyway.

Legally, the current system rests on a transfer of copyright from the authors of papers to publishers — with that transfer complete, the publishers then bundle articles into journals and license them back to libraries. These licensing terms carry costs that greatly exceed the rate of inflation, which is by now a very well-documented phenomenon. This is because journals are “inelastic” and “non-substitutable”; there is less ability to shop around on the basis of content, as each journal fills a unique niche. Meanwhile librarians feel duty bound to subscribe to all the leading titles in a field, leading inexorably to monopolistic pricing.

That pricing does not affect researchers, who are the consumers of scholarly work, because they do not pay it. The upshot is that the only balance sheet negatively impacted is that for the library. Hence we find that librarians, in the immortal words of John Dupuis, feel like “wallets with a serious case of Stockholm Syndrome.”

Open access journals, which are available without subscription or licensing barriers, most certainly improve access compared to subscription journals. But they are not necessarily any cheaper for libraries, especially those that foot the bill for the author processing charges (APCs) that sustain open access journals. As T. Scott Plutchak has often observed, access and affordability are two separate issues.

Everything I’ve written so far should be very familiar to observers of the scholarly communication scene, perhaps mind-numbingly so. The uneven balance of power between librarians and researchers, and ergo between librarians and publishers, are long-established sources of resentment in libraryland.

Enter Sci-Hub, a radical disruption with perhaps enough power to compel solutions to this intractable impasse.

What is Sci-Hub? A repository of academic papers that are supposed to be behind pay walls. To date Sci-Hub has collected more than 47 million academic research papers. It does so through bypassing the many access control mechanisms meant to restrict this content to authorized users. (Whether this comes via “donations” of institutional log-in credentials or phishing scams is unclear.) This effort necessarily involves infringing on copyright, but Sci-Hub founder Alexandra Elbakyan argues that she observes a higher law by making these papers available to all interested readers.

In a sense Sci-Hub’s approach is a refinement and improvement of the process Aaron Swartz utilized with JSTOR. As Graham Steel notes, Sci-Hub’s approach is much more effective at file sharing than the once upon a time cutting edge #ICanHazPDF.

Publishers are outraged. Elsevier successfully sued Sci-Hub in US court last year, seeking the site’s demise. After a brief pause last year (prior to the lawsuit’s conclusion), as of today Sci-Hub continues unabated. Elbakyan is from Kazakhstan, and the site’s servers are not in the United States. It also relies on sophisticated programming that bounces between servers around the globe. For all these reasons it would be very difficult to halt Sci-Hub on a permanent basis. Even if Sci-Hub itself did cease operations, another similar site could easily emerge in its place.

The genie is out of the bottle. The writing is on the wall. [Insert similar metaphor here]. If nothing else, Sci-Hub proves that the days of making money from regulating access to PDFs of journal articles is over.

Or does it? As observers of this controversy have noted, academic libraries are not going to cancel their journal licenses thanks to the newfound availability of articles on Sci-Hub. Those licensed packages are the lifeblood of Sci-Hub — which penetrates ostensibly secure university networks in order to fetch and cache articles — in any case. And of course an institutional actor such as a library would not make decisions based on a third party’s practices that infringe on copyright.

For these reasons Angela Cochran, Director of Journals at the American Society of Civil Engineers, is seeking common cause with librarians. In a much-discussed post on the Scholarly Kitchen, Cochran lays out the case against Sci-Hub and expresses her dismay that librarians and open access advocates have not spoken out against Sci-Hub’s “piracy.” Cochran is right that the methods used by Sci-Hub could put many other institutional computer systems at risk, which is why librarians and others should be concerned.

But Cochran is not familiar with that feeling of librarian Stockholm Syndrome that John DuPuis so aptly described. I’ve long raged against having to think about and deploy access control mechanisms within the libraries where I have worked. I became a librarian in order to maximize access to information, not to meter it out stingily. But dem’s the breaks baby cakes. Part of being an academic librarian today involves providing uncompensated copyright enforcement for publishing interests, in order to reinforce values you do not even believe in.

Hence Cochran’s disillusionment. I suspect many academic librarians and open access advocates support Sci-Hub’s ends if not its means. (Perhaps I am wrong on the library front, this ultimately depends on whether a librarian perceives themselves as a “soldier or revolutionary” in Rick Anderson’s formulation). If Cochran wishes to find common ground with the greatest number of librarians in the wake of Sci-Hub, I suggest seeking this in discussions of building a future for scholarly communication that serves the interests of publishers and librarians alike. Pointing a finger at Sci-Hub in outrage will not do the trick.

There is pathos in all this. Sci-Hub’s posting of PDFs would be a trivial event if PDFs were not where the action still is for scholarly communication. In a Web-centric world PDFs should be yesterday’s news as a means of sharing knowledge.

This is why it’s high past time for publishers and librarians to work together to move beyond the PDF, a topic I will explore more fully in a future post. Sci-Hub’s ultimate service, I hope, will be to speed this conversation along.

Marcus Banks is a health sciences library director.