Wednesday, 22 October 2008

Joke of the Month Award #1.3 - "Irish Coffee"

An Irish woman of advanced age visited her physician to ask his
advice in reviving her husband's libido.

'What about trying Viagra?' asked the doctor.

'Not a chance', she said. 'He won't even take an aspirin.'

'Not a problem,' replied the doctor. 'Give him an 'Irish Viagra'.

It's when you drop the Viagra tablet into his coffee. He won't even taste
it. Give it a try and call me in a week to let me know how things went..'

It wasn't a week later when she called the doctor, who directly
inquired as to her progress. The poor dear exclaimed, 'Oh, faith ,
bejaysus and begorrah!

T'was horrid! Just terrible, doctor!'

'Really? What happened?' asked the doctor.

'Well, I did as you advised and slipped it in his coffee and the
effect was almost immediate. He jumped straight up, with a twinkle in
his eye and with his pants a-bulging fiercely! With one swoop of his
arm, he sent me cups and tablecloth flying, ripped me clothes to
tatters and took me then and there passionately on the tabletop! It
was a nightmare, I tell you, an absolute nightmare!'

'Why so terrible?' asked the doctor, 'Do you mean the sex your
husband provided wasn't good?'

'Feckin jaysus, 'twas the best sex I've had in 25 years! But sure as
I'm sittin here, I'll never be able to show my face in Starbucks

b'dum tish

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

Holy Sh*t: Man Walks On F*cking Moon

H/T here.


In at number 3 on the charts this week Pop Pickers, it's...... The Police:-

Wednesday, 15 October 2008

New articles this week in PLoS ONE Published October 9-15, 2008

Genetic Disruption of Both Tryptophan Hydroxylase Genes Dramatically Reduces Serotonin and Affects Behavior in Models Sensitive to Antidepressants
Katerina V. Savelieva et al.

ANGLOR: A Composite Machine-Learning Algorithm for Protein Backbone Torsion Angle Prediction
Sitao Wu et al.

The Genetic Liability to Disability Retirement: A 30-Year Follow-Up Study of 24,000 Finnish Twins
Karoliina Harkonmäki et al.

A Nationwide Survey of the Quality of Antimalarials in Retail Outlets in Tanzania
Harparkash Kaur et al.

Evolutionarily Conserved Transcriptional Co-Expression Guiding Embryonic Stem Cell Differentiation
Yu Sun et al.

Whole Blood Interferon-Gamma Responses to Mycobacterium tuberculosis Antigens in Young Household Contacts of Persons with Tuberculosis in Uganda

Deborah A. Lewinsohn et al.

Tumor-Infiltrating T Cells Correlate with NY-ESO-1-Specific Autoantibodies in Ovarian Cancer

Katy Milne et al.

Oseltamivir Is Adequately Absorbed Following Nasogastric Administration to Adult Patients with Severe H5N1 Influenza
Walter R. J. Taylor et al.

Optimal-Foraging Predator Favors Commensalistic Batesian Mimicry
Atsushi Honma et al.

Rare Codons Cluster
Thomas F. Clarke et al.

Composition and Function of Haemolymphatic Tissues in the European Common Shrew
Daniel P. Bray et al.

Discovery of a Distinct Superfamily of Kunitz-Type Toxin (KTT) from Tarantulas
Chun-Hua Yuan et al.

Gene Expression Profiling of Two Distinct Neuronal Populations in the Rodent Spinal Cord
Jesper Ryge et al.

Accuracy of Immunodiagnostic Tests for Active Tuberculosis Using Single and Combined Results: A Multicenter TBNET-Study
Delia Goletti et al.

An Analysis of Human MicroRNA and Disease Associations
Ming Lu et al.

Detection and Molecular Characterization of 9000-Year-Old Mycobacterium tuberculosis from a Neolithic Settlement in the Eastern Mediterranean
Israel Hershkovitz et al.

Comparison of Population-Based Association Study Methods Correcting for Population Stratification
Feng Zhang et al.

Distribution and Effects of Nonsense Polymorphisms in Human Genes
Yumi Yamaguchi-Kabata et al.

Inhibition of α-Synuclein Fibrillization by Dopamine Is Mediated by Interactions with Five C-Terminal Residues and with E83 in the NAC Region
Fernando E. Herrera et al.

Accuracy of Predicting the Genetic Risk of Disease Using a Genome-Wide Approach

Hans D. Daetwyler et al.

Sensory Response System of Social Behavior Tied to Female Reproductive Traits
Jennifer M. Tsuruda et al.

ROCK1 and LIMK2 Interact in Spread but Not Blebbing Cancer Cells
Kerry F. Shea et al.

Differential Effects of Aging on Fore– and Hindpaw Maps of Rat Somatosensory Cortex
Marianne David-Jürgens et al.

Genetic Traces of Recent Long-Distance Dispersal in a Predominantly Self-Recruiting Coral
Madeleine J. H. van Oppen et al.

Repression of FLOWERING LOCUS C and FLOWERING LOCUS T by the Arabidopsis Polycomb Repressive Complex 2 Components
Danhua Jiang et al.

M-CSF Signals through the MAPK/ERK Pathway via Sp1 to Induce VEGF Production and Induces Angiogenesis In Vivo
Jennifer M. Curry et al.

Y-SNPs Do Not Indicate Hybridisation between European Aurochs and Domestic Cattle
Ruth Bollongino et al.

Human Keratinocytes Are Vanilloid Resistant

László Pecze et al.

Worm Grunting, Fiddling, and Charming—Humans Unknowingly Mimic a Predator to Harvest Bait
Kenneth C. Catania

Epithelial to Mesenchymal Transition of a Primary Prostate Cell Line with Switches of Cell Adhesion Modules but without Malignant Transformation
Xi-Song Ke et al.

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers
Nathan A. Baird et al.

Dendritic Cells Release HLA-B-Associated Transcript-3 Positive Exosomes to Regulate Natural Killer Function
Venkateswara Rao Simhadri et al.

A New Antigen Retrieval Technique for Human Brain Tissue

Raúl Alelú-Paz et al.

Underutilization of Social Insurance among the Poor: Evidence from the Philippines

Stella Quimbo et al.

Interleukin-10 Promotes Pathological Angiogenesis by Regulating Macrophage Response to Hypoxia during Development
Dru S. Dace et al.

Beneficial Effects of HIV Peptidase Inhibitors on Fonsecaea pedrosoi: Promising Compounds to Arrest Key Fungal Biological Processes and Virulence
Vanila F. Palmeira et al.

Knockdown of MBP-1 in Human Foreskin Fibroblasts Induces p53-p21 Dependent Senescence

Asish K. Ghosh et al.

Different Transcriptional Control of Metabolism and Extracellular Matrix in Visceral and Subcutaneous Fat of Obese and Rimonabant Treated Mice
Carine Poussin et al.

A-Type GABA Receptor as a Central Target of TRPM8 Agonist Menthol
Xiao-Bing Zhang et al.

Functional Deficits in nNOSμ-Deficient Skeletal Muscle: Myopathy in nNOS Knockout Mice
Justin M. Percival et al.

A Functional Role for 4qA/B in the Structural Rearrangement of the 4q35 Region and in the Regulation of FRG1 and ANT1 in Facioscapulohumeral Dystrophy

Iryna Pirozhkova et al.

Requirement of RIZ1 for Cancer Prevention by Methyl-Balanced Diet

Wenyun Zhou et al.

Impaired Autophagy of an Intracellular Pathogen Induced by a Crohn's Disease Associated ATG16L1 Variant
Petric Kuballa et al.

Symphysiotomy in Zimbabwe; Postoperative Outcome, Width of the Symphysis Joint, and Knowledge, Attitudes and Practice among Doctors and Midwives

Hege Langli Ersdal et al.

Positive Regulation of DNA Double Strand Break Repair Activity during Differentiation of Long Life Span Cells: The Example of Adipogenesis

Aline Meulle et al.

Factors Contributing to the Biofilm-Deficient Phenotype of Staphylococcus aureus sarA Mutants

Laura H. Tsang et al.

Evolutionary Signatures of Common Human Cis-Regulatory Haplotypes
Ching Ouyang et al.

A Non-Canonical Function of Zebrafish Telomerase Reverse Transcriptase Is Required for Developmental Hematopoiesis
Shintaro Imamura et al.

ama1 Genes of Sympatric Plasmodium vivax and P. falciparum from Venezuela Differ Significantly in Genetic Diversity and Recombination Frequency
Rosalynn L. Ord et al.

Dysfunction of Nrf-2 in CF Epithelia Leads to Excess Intracellular H2O2 and Inflammatory Cytokine Production

Junnan Chen et al.

Probing Metagenomics by Rapid Cluster Analysis of Very Large Datasets

Weizhong Li et al.

Genome Wide Identification of Recessive Cancer Genes by Combinatorial Mutation Analysis
Stefano Volinia et al.

Mutants of GABA Transaminase (POP2) Suppress the Severe Phenotype of succinic semialdehyde dehydrogenase (ssadh) Mutants in Arabidopsis
Frank Ludewig et al.

Cortical Activations in Humans Grasp-Related Areas Depend on Hand Used and Handedness
Chiara Begliomini et al.

Hemispheric Specialization in Dogs for Processing Different Acoustic Stimuli

Marcello Siniscalchi et al.

Rapid Chromosome Evolution in Recently Formed Polyploids in Tragopogon (Asteraceae)
K. Yoong Lim et al.

Tree of Life Based on Genome Context Networks
Guohui Ding et al.

Discovery and Expansion of Gene Modules by Seeking Isolated Groups in a Random Graph Process
Jochen Brumm et al.

CD44s and CD44v6 Expression in Head and Neck Epithelia

Brigitte Mack et al.

Effect of Adjunct Metformin Treatment in Patients with Type-1 Diabetes and Persistent Inadequate Glycaemic Control. A Randomized Study
Søren Søgaard Lund et al.

Mutual Mate Choice: When it Pays Both Sexes to Avoid Inbreeding
Mathieu Lihoreau et al.

Virulent Synergistic Effect between Enterococcus faecalis and Escherichia coli Assayed by Using the Caenorhabditis elegans Model
Jean-Philippe Lavigne et al.

EXiS (Excellence in Science) Open Choice

Since I've been following Prion disease (PrPd) research for seven years now, I've studied a lot of literature in this and other fields.

Upon my latest search of the NeuroPrion database, (of which I have access to but can't widely share) I noted a stack of new Manuscripts about Kuru. When I checked PubMed, I found many of them archived there, at full article level.

It didn't take long to track down this page:-

Volume 363, Number 1510 / November 27, 2008
Theme Issue ‘The end of kuru: 50 years of research into an extraordinary disease’ compiled by John Collinge and Michael P. Alpers

That's 52 new Open Access Manuscripts relating to Kuru research. Kudos to all involved for making all of this broadly accessible for free. I've never seen such a glut of material on Kuru before so have a lot of reading to do. I do wonder however, if these articles will remain OA ??


EXiS Open Choice

EXiS (Excellence in Science) Open Choice is an 'author-pays' model that operates alongside our established subscription model. Under this scheme submission of an article is free, but if it is accepted for publication, the authors are asked to pay a fee to have their article made freely available to all immediately on publication.

By selecting this option, authors benefit in a number of ways:

* the same standards of high-quality, rapid peer-review and production
* the potential for greatly increased dissemination and citation
* publisher deposit of the article in PubMedCentral
* liberal licensing policy through Creative Commons 2.5
* satisfies the requirements of research funders requiring open access publication, such as the NIH,MRC and Wellcome Trust (see

* publication is both online and in print

For more information about this journal service please see the FAQs and press release

For a list of our EXiS Open Choice charges see here.


Tuesday, 14 October 2008

OHS - Open Housekeeping Stuff

I do my best to maintain my apartment to pretty reasonable standards.

Yesterday, with under an hours notice, some visitors popped by.

As such, some general last minute general cleaning, I thought would suffice.


Just before they left, one guest had a few comments to make so I prepared a Steel House Complaint Form:-

The individual who completed the form apologised from the onset for their grammatical errors. Fair enough - she be aged 10.


1) SQUKEK FRIGE - OK, I have some WD-40 somewhere
2) BROKE TILES - yes, there are three tiles I need to replace in the bathroom
3) WOBELY CHAIRS - two of my four kitchen table chairs need minor screwdriver TLC
4) NON CLEAN FISH TANK - can't argue with that and will clean the tank this week


Subject: Launch of OASPA
Date: Tue, 14 Oct 2008 09:25:23 -0700

Apology for cross posting:


14 October 2008, London. The Open Access Scholarly Publishers Association, OASPA, announces its official launch today in conjunction with an OA Day celebration hosted by the Wellcome Trust in London. The mission of OASPA is to support and represent the interests of Open Access (OA) journals publishers globally in all scientific, technical, and scholarly disciplines through an exchange of information, setting of industry standards, advancing business and publishing models, advocating for gold OA journals publishing, education and the promotion of innovation.

From having first emerged as a new publishing model over a decade ago, OA publishing has become an embedded feature of the scholarly publishing landscape: The Directory of Open Access Journals (DOAJ) lists over 3500 peer-reviewed journals; a growing number of professional organizations offer OA publications; university libraries increasingly support OA publishing services; funding organizations support and encourage OA publishing; and a long tail of independent editorial teams and societies now publish their titles OA. Professional OA publishers such as BioMed Central and the Public Library of Science (PLoS) have been in business for over five years, while some scientist/scholar publishers (editorial teams operating independently of a professional publisher) have published their OA journals for a decade or more. Moreover, a number of traditional publishing houses are now engaging in Open Access activities, the recent acquisition of BioMed Central by Springer and the SAGE-Hindawi partnership being two cases in point. By bringing together those who share an interest in developing appropriate business models, tools and standards to support OA journals publishing, it is hoped that success in these areas can be achieved more quickly to the benefit of not only OASPA members, but more importantly, for the scholarly community that OA publishers serve.

Membership in OASPA is open to both scholar publishers and professional publishing organizations, including university presses and for profit and non-profit organizations. Members are expected to demonstrate a genuine interest in OA journals publishing by having signed either the Berlin or Budapest Declarations and must publish at least one full OA journal. Other individuals and organizations who support OA journals publishing or who are interested in exploring opportunities are also welcome. Membership criteria and an application form can be found on the OASPA website,

The founding members of OASPA represent a broad spectrum of OA publishers and include: BioMed Central, Co-Action Publishing, Copernicus, Hindawi Publishing Corporation, Journal of Medical Internet Research (Gunther Eysenbach), Medical Education Online (David Solomon), the Public Library of Science (PLoS), SAGE, SPARC Europe and Utrecht University Library (Igitur). Representatives from each of these publishers will form an interim board until a first General Meeting is held during 2009.

Open Access Scholarly Publishers’ Association, OASPA, is launched today 14 October 2008 in response to long-time informal discussions among Open Access publishers, and aims to represent the interests of OA journals publishers globally. For more information about the organization, visit the OASPA website at:

The Wellcome Trust is the largest charity in the UK. It funds innovative biomedical research, in the UK and internationally, spending over £600 million each year to support the brightest scientists with the best ideas. The Wellcome Trust supports public debate about biomedical research and its impact on health and wellbeing.

Open Access (OA) scholarly publication refers to the dissemination of peer-reviewed manuscripts containing original research or scholarship immediately upon publication, at no charge to user groups, without requiring registration or other restrictions to access. OA publications also allow users to "copy, use, distribute, transmit and display the work publicly and to make and distribute derivative works, in any digital medium for any responsible purpose, subject to proper attribution of authorship...."

Press Contact:
Caroline Sutton
Tel/skype: +46 (0)18 495 1126
Cell: +47 90 69 05 06


For background information, check out the related posts on OAN.

Monday, 13 October 2008

Test the Monkey


Here it goes a demo..
Let me know

b cool,

Why I am an OA Advocate

Why does Open Access matter to me?

I became involved in patient advocacy in September 2001 just under two years after I lost my brother to a fatal, rare neurodegenerative disease. During the early years of this work, I commenced the process of studying peer reviewed scientific, technical and medical (STM) research.

This namely involved paper copies of Toll Access (TA) articles passed to the support group I was involved with by highly regarded UK researchers in the field. Whilst 'we' were able to share such STM research (with family members of the organisation) by post using "fair use", I knew that Copyright restricted me from sharing any such material with a wider audience - the organisations website.

Despite this restriction, simply by placing as much information online in an open manner wherever possible, in the space of year, traffic had increased by over 4000%. As such, even before I knew what Open Access was, it was abundantly clear that being open was the main key to outreaching.

When did I become aware of Open Access?

That would have been mid 2006. Up until the day in question, I had a pretty simple system in place to obtain PDF's of TA manuscripts from authors.

On the day in question, I noted from the Abstract of the Manuscript that I was looking for, there was a link to the full article. Yay.

PLoS Pathogens
was the first OA Journal that I came across.

Not only could I access the Manuscript I was looking for, but the real eye opener was that I was able to access the entire Journal online for free!

As I said in this recent interview:-

One of my main eternal frustrations remains not being able to share my extensive library of papers due to Draconian copyright restrictions. Creative Commons is a dream come true..... Indeed, I'm wearing one of my PLoS t-shirts right now =) Prof Lawrence Lessig, you remain a STAR !!

Why should scientific and medical research be an open-access resource for the world?

To me, it makes so little sense in this day and age to carry out and share STM research in a closed environment as was done for centuries before the advent of OA.

May I quote in part, Associate Professor Bevin P. Engelward, the winner of the 1993 Nobel Prize for Physiology or Medicine from this 2007 PLoS Biology article:-

...In an age rife with the potential for infectious pandemics, bioterrorism, and toxic environmental calamity, and at a time when we need new ways to cure terrible illnesses, public access is our society's compelling answer to accelerating the best science possible. This advance is much needed, both by researchers working in academic settings and in the private sector. Indeed, we should demand no less. We invite our fellow scientists to join in the demand for open access to biomedical literature.

Science, progress, societal benefits from that is a pretty concise focus.

Indeed, here's a shot of Peter Murray-Rust and McDawg discussing their forthcoming OA related Manuscript in London, August 2008.

(Image c/o Joe Dunckley's sciblog Flickr stream)

What do you do to support Open Access, and what can others do?

Simple. Spread the word.

My most blogged about post to date is precisely about this.

The blogosphere is an astonishingly great place to share and discover information. I've blogged fairly extensively about OA since I started blogging late 2007.


The musician in me cannot omit something poignant on this post. As such, here's McDawg's favourite mix of Peter Gabriel's Shock The Monkey arising as a result of this competition.

Peter Gabriel fully supports initiatives such as Creative Commons, The Open Society Institute, Students For Free Culture etc.

Wednesday, 8 October 2008

Brisbane Declaration

[Forwarding from Tom Cochrane, Deputy Vice-Chancellor, Queensland University of Technology. --Peter Suber.]

08 October 2008 20:16:40

Following the conference on Open Access and Research held in September in Australia, and hosted by Queensland University of Technology, the following statement was developed and has the endorsement of over sixty participants.

Brisbane Declaration


The participants recognise Open Access as a strategic enabling activity, on which research and inquiry will rely at international, national, university, group and individual levels.


Therefore the participants resolve the following as a summary of the basic strategies that Australia must adopt:

1. Every citizen should have free open access to publicly funded research, data and knowledge.

2. Every Australian university should have access to a digital repository to store its research outputs for this purpose.

3. As a minimum, this repository should contain all materials reported in the Higher Education Research Data Collection (HERDC).

4. The deposit of materials should take place as soon as possible, and in the case of published research articles should be of the author’s final draft at the time of acceptance so as to maximize open access to the material.

Brisbane, September, 2008

Saturday, 4 October 2008

Open Access Day on FriendFeed

Readers of this blog and/or people who know me are aware of my ongoing involvement in the Open Access Community although some of what I do is behind the scenes.

Back in April, thanks to suggestions in this thread at Nature Network, we came up with the idea of Open Access Week. You can find a summary of that on McBlawg here. As a result of that, McDawg has already been consulted over plans for next year's Open Access Week. Further details to follow nearer the time.

In the meantime, after some behind the scenes work, on August 28th, seconds after the official announcement was made about Open Access Day, I spread the word here on FriendFeed.

In the lead up to the day itself, there's been loads of coverage in the blogosphere already (simply Google open access day) so I don't intend to expand upon that.

It just so happens that McDawg is off work during the week that the event is being held. I'm particularly glad to see that the suggestion of live worldwide broadcasts of events has become a reality. Kudos to the organisers.


Cut to the chase. There's going to be a frenzy of OA related items taking place on or around 14th October such as video, audio, synchroblogging etc.

As has been done recently to great effect, a brilliant way (this is simply one) to capture all of this and archive it, is to set up a dedicated room over at FriendFeed (FF).

Recent examples (FF Rooms) are BioBarCamp and Science Blogging 2008: London (now Called Science Online at FF).

As such, as of today, I've set up a Room at FF called "Open Access Day". Not just because they were the first two to join, but Martin Fenner and Michael Nielsen have been handed Administrator status like McDawg.





I, or should I say we have no idea how successful or not this concept will be. That said, like the other Rooms mentioned above, providing we can attract a reasonable amount of room members, the idea is:-

Open Access Day is on October 14th. This day is organised by SPARC, Students for FreeCulture and PLoS. This room has been set up to capture events before during and after the day on FF.

Feel free to join the Room, participate and join the discussion that will gather in pace over the next ten days.

Wednesday, 1 October 2008

"Science v's Sport" - The New Online Debate

Please do go and check out this rather excellent post on Dr Jenny Rohn's tip-top blog, Mind The Gap.

I tend to agree with Dr Rohn on all fronts thus far, and as she said in her closing para:-

"...At that moment, I wondered how we could get more coverage of science into the world; not rehashed, regurgitated and mangled press-released data, but the sweaty, messy, human endeavor as it unfolds before us, outcome uncertain and all to play for. Such attention might not be comfortable for scientists, but if mere athletes can stand the heat, why couldn’t we?"

Midway through the comments thus far is the following in terms of the coverage of sport.

From Stephen Curry:-

"Sport also has the advantage over science that it is utterly, utterly pointless and therefore lends itself to hyping/trivialisation by the media as so wonderfully demonstrated here:"

Cue this rather majestic piece.....