Magnifying Power to the People with the Foldscope

The microscope holds a place on the short list of inventions that have changed the world and revolutionized our understanding of science. Microscopes are crucially important public health tools, allowing workers to identify pathogens and correctly diagnose the cause of illnesses. As educational tools, they can excite and engage students, revealing a world invisible to the naked eye. And, as many people who’d love a microscope but don’t have one can tell you, they are also expensive. Millions of doctors, health workers, and patients worldwide lack the resources to benefit from this vital tool, and millions of students have never seen a microscope before. In a dramatic step to address this problem, researchers from Stanford University have designed ultra-low-cost microscopes built from an inexpensive yet durable material: paper. They recently published their designs and data in PLOS ONE.

Foldscope template

Meet the Foldscope. Borrowing from the time-honored tradition of origami, the Foldscope is a multi-functional microscope that can be assembled much like a paper doll. Users cut the pieces from a pattern of cardstock, fold it according to the printed lines, and add the battery, LED, and lens, and?voilà?a microscope. Foldscope schematicClick here to watch a video of how one is assembled. Some of their coolest features are as follows:

  • Foldscopes are highly adaptable and can be configured for bright-field and dark-field microscopy, to hold multiple lenses, or to illuminate fluorescent stains (with a special LED).

Foldscope Configurations

  • They can be designed for low or high powers and are capable of magnifying an image more than 2,000-fold.
  • They accept standard microscope slides, and the viewer can move the lens back and forth across the slide by pushing or pulling on paper tabs.
  • Users can focus the microscope by pushing or pulling paper tabs that change the lens’ position.
  • Foldscopes are compact and light, especially when compared with conventional field microscopes. They also weigh less than 10 grams each, or about the weight of two nickels.
  • They are difficult to break. You can stomp on them without doing much damage, and they can survive harsh field environments and encounters with children.

Stepping on FoldscopeWhat’s the total cost, you ask? According to authors, it’s less than a dollar.  At that price, it’s easy to imagine widespread use of Foldscopes by many who previously could not afford traditional microscopes. In this TED Talk, Manu Prakash demonstrates the Foldscopes and explains his hopes for them. The authors envision mass producing them and distributing different designs optimized for detecting the pathogens that cause specific diseases, such as Leishmaniasis and E. coli.  They could even include simple instructions for how to treat and prepare slides for specific diagnostic tests or provide pathogen identification guides to help health workers in the field make diagnoses.  This is just one way in which the ability to see tiny things could make a huge difference in the world.

Related links:

Low-Cost Mobile Phone Microscopy with a Reversed Mobile Phone Camera Lens

Community Health Workers and Mobile Technology: A Systematic Review of the Literature

Citation: Cybulski JS, Clements J, Prakash M (2014) Foldscope: Origami-Based Paper Microscope. PLoS ONE 9(6): e98781. doi:10.1371/journal.pone.0098781

Images: Images are from Figures 1 and 2 of the published paper

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Open Access in China: Time is of the Essence

The two Chinese OA Mandates (NSFC and CAS) came fast (2014), but the possibility of complying with them is coming slowly (no repository till 2016).

In addition, articles need not be deposited until 12 months after publication.

In most fields, especially the fast-moving sciences, the benefits of Open Access (maximised uptake, usage, impact and progress) are biggest and most important within the first year of publication. That is the growth tip of research. Access losses in the first year are never fully caught up in later years. The iron needs to be struck when it is hot.

There are two very simple steps that China can take to minimise the needless loss of research uptake, usage and impact because of lost time:

(1) China should set up the repositories immediately, using the available free softwares such as EPrints and DSpace. It requires only a server and a few hours worth of set-up time and the repository is ready for deposits. There is no reason whatsoever to wait two years. It would also be sensible to have distributed local repositories ? at universities and research institutions ? rather than just one central one. Each institution can easily set up its own repository. All repositories are interoperable and if and when desired, their contents can be automatically exported to or harvested by central repositories.

(2) Although an OA embargo of 12 months is allowed, China should mandate that deposit itself must be immediate (immediately upon acceptance for publication). Access to the deposit can be set as closed access instead of OA during the embargo if desired, but EPrints and DSpace repositories have the ?Request-Copy? Button for closed-access deposits so that individual users can request and authors can provide an individual copy for research purposes with one click each. The repository automatically emails the copy if the author clicks Yes.

Long-awaited OA policy from WHO

“From the +World Health Organization:  “From 1 July 2014, articles authored or co-authored by WHO staff will have to be published in an open-access journal or a hybrid open-access journal under the terms of a Creative Commons 3.0 intergovernmental organization (IGO) ported licence, or in a subscription journal that allows for the depositing of the accepted author manuscript in Europe PubMed Central (Europe PMC) within 12 months of the official publication date. Similarly, articles produced by recipients of WHO funding will have to be published in an open-access journal or a hybrid open-access journal under the terms of a standard Creative Commons licence or in a subscription journal that allows for the depositing of the article in Europe PMC within 12 months of the official publication date….”

Also see my preview of this policy from January 2014…
https://plus.google.com/+PeterSuber/posts/1YjoHUvYvXe
…and almost 100 of my blog posts on WHO steps toward OA over the past 10 years.

http://goo.gl/Lz03rA “

Long-awaited OA policy from WHO

“From the +World Health Organization:  “From 1 July 2014, articles authored or co-authored by WHO staff will have to be published in an open-access journal or a hybrid open-access journal under the terms of a Creative Commons 3.0 intergovernmental organization (IGO) ported licence, or in a subscription journal that allows for the depositing of the accepted author manuscript in Europe PubMed Central (Europe PMC) within 12 months of the official publication date. Similarly, articles produced by recipients of WHO funding will have to be published in an open-access journal or a hybrid open-access journal under the terms of a standard Creative Commons licence or in a subscription journal that allows for the depositing of the article in Europe PMC within 12 months of the official publication date….”

Also see my preview of this policy from January 2014…
https://plus.google.com/+PeterSuber/posts/1YjoHUvYvXe
…and almost 100 of my blog posts on WHO steps toward OA over the past 10 years.

http://goo.gl/Lz03rA “

Music, Language, and the Brain: Are You Experienced?

Have you ever thought about everything that goes into playing music or speaking two languages? Musicians for example need to listen to themselves and others as they play, use this sensory information to call up learned actions, decide what is important and what isn’t for this specific moment, continuously integrate these decisions into their playing, and sync up with the players around them. Likewise, someone who is bilingual must decide based on context which language to use, and since both languages will be fairly automatic, suppress one while recalling and speaking the other, all while continuously modifying their behavior based on their interactions with another listener/speaker. All of this must happen quickly enough for the conversation or song to flow and sound natural and coherent. It sounds exhausting, yet it all happens in milliseconds!

Playing music or speaking two languages are challenging experiences and complex tasks for our brains. Past research has shown that learning to play music or speak a second language can improve brain function, but it is not known exactly how this happens. Psychology researchers in a recent PLOS ONE article examined how being either a musician or a bilingual changed the way the brain functions. Although we sometimes think of music as a universal language, their results indicate that the two experiences enhance brain function in different ways.

heat map

One way to test changes in brain function is by using Event Related Potentials (ERPs). ERPs are electrical signals (brain waves) our brains give off immediately after receiving a stimulus from the outside world. They occur in fairly predictable patterns with slight variations depending on the individual brain. These variations, visualized in the figure above with the darkest red and blue areas showing the most intense electrical signals, can clue researchers into how brain function differs between individuals and groups, in this case musicians and bilinguals.

The ERP experiment performed here consisted of a go/nogo task that is frequently used to study brain activity when it is actively suppressing a specific behavior, also called inhibition. In this study, the authors asked research participants to sit in front of a computer while simple shapes appeared on screen, and they were to press a key when the shape was white—the most common-colored shape in the task—but not when purple, the least frequent color in the task. In other words, they responded to some stimuli (go) and inhibited their response to others (nogo). This is a similar task to playing music or speaking a second language because the brain has to identify relevant external sensory information, call on a set of learned rules about that information, and make a choice about what action to take.

 waves

The authors combined and compared correct responses to each stimulus type in control (non-musician, non-bilingual) groups, musician groups, and bilingual groups. The figure above compares the brainwaves of different groups over time using stimulus related brainwave components called N2, P2, and LP. As can be seen above, these peaks and valleys were significantly different between the groups in the nogo instances. The N2 wave is associated with the brain’s initial recognition of the meaning or significance of the stimulus and was strongest in the bilingual group. The P2 on the other hand, is associated with the early stages of putting a stimulus into a meaningful context as it relates to an associated behavior, and was strongest in the musician group. Finally, the authors note a wave called LP wave, which showed a prolonged monitoring response in the bilingual group. The authors believe this may mean bilinguals take more time to make sure their initial reaction is correct.

In other words, given a task that involved identifying a specific target and subsequently responding or not responding based on learned rules, these results suggest that musicians’ brains may be better at quickly assigning context and an appropriate response to information because they have a lot of practice turning visual and auditory stimuli into motor responses. Bilinguals, on the other hand, show a strong activation response to stimuli along with prolonged regulation of competing behaviors, likely because of their experience with suppressing the less relevant language in any given situation. Therefore, despite both musicianship and bilingual experiences improving brain function relative to controls, the aspects of brain function they improve are different. As games and activities for the purpose of “brain training” become popular, the researchers hope this work will help with testing the effectiveness of brain training.

Citation: Moreno S, Wodniecka Z, Tays W, Alain C, Bialystok E (2014) Inhibitory Control in Bilinguals and Musicians: Event Related Potential (ERP) Evidence for Experience-Specific Effects. PLoS ONE 9(4): e94169. doi:10.1371/journal.pone.0094169 

Images are Figures 1 and 2 from the article.

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Hackday 2014-06-19 in Edinburgh – a radically new approach to Scholarly Communication in the Digital Enlightenment

Summary: Help us change the way we communicate Science and the Humanities in the Digital Enlightenment. Free [1] EVERYONE can help.Edinburgh is the capital of the Scottish Enlightenment where free thinkers changed the way we think about and run the world. Next week (June 19th) we’ll be running a hackday to change the way that we communicate Science and the  Humanities.

For 400 years we have relied on the “printed journal” and “articles” (e.g. “PDFs”) and now we’re doing something completely different. Authors should be able to do what *they* want and readers should be able to read in the way *they* want. And readers aren’t just lecturers, they are 4-year olds, patients and machines. 4-year olds LOVE DINOSAURS.

We’ve built most of the basics. We are going to:

  • SCRAPE material from PLOS (and other Open) articles. And some of these are FUN! They’re about DINOSAURS!!
  • EXTRACT the information. Which papers talk about DINOSAURS? Do they have pictures?
  • REPUBLISH as a book. Make your OWN E-BOOK with Pictures of DINOSAURS with their FULL LATIN NAMES!!

[I’m serious about the 4-year olds. I have two high quality data points where 4-year olds LOVE Binomial names. This hackday is NOT designed for kids… but future ones maybe]

For the Techies:

  • Ross Mounce has zillions of Open DOIs about dinosaurs (i.e. a list of papers).
  • Richard Smith-Unna has built the world’s latest and greatest scraper (quickscrape) for journal articles. Anyone who can edit a file can learn to use it in 5 minutes
  • Peter Murray-Rust and friends have written AMI which can extract many types of information from articles. The simplest method is regexes, but we can do phylogenetic trees from diagrams, chemistry and much else. All in a giant Java Jar. This can filter out either the articles you want or just the bits you want!
  • Peter Sefton has built scholarly authoring systems that academics actually want to use!! We’ll probably use eBook technology which can reassemble the bits that AMI has found and you want to read. All the adverts are gone! We can make ebooks for a given subject, or today’s publications, or methods for cloning mosquitoes or all the graphs about climate change…
In hackdays YOU decide what you want to do, find friends and explore. You might create something wonderful or you might just have fun.
YES! Edinburgh has DINSOSAUR skeletons.
Mark writes:
“Room 1.15, Informatics Forum, University of Edinburgh, George Square, Edinburgh”
This room has tables and seats for 12 people comfortably, and another 8 folding seats for people to dot around – I was not sure how big we were aiming, but the Forum also has a fair bit of open space if we need to de-camp some people. There is a computer and a projector too, and a whiteboard.
I should keep track of how many people plan to attend, to make sure we have space. So, could we add the following to the summary:
“If you would like to join us, please email mark@cottagelabs.com to confirm attendance”
[we think Cameron said food provided by PLoS! – we’re checking ]

We launch The Content Mine In Vienna, Interviews, Talks and our first public Workshop

Last week was one of the most exciting in my life – but also among the hardest I have worked. I travelled from Budapest to Vienna to be the guest of the Austrian Science Fund (FWF) and to give a lecture: http://www.fwf.ac.at/en/aktuelles_detail.asp?N_ID=597 .. I changed the title to “Open Notebook Science” in honour of the late Jean-Claude Bradley and to promote his ideas. My talk’s on Slideshare: [http://www.slideshare.net/petermurrayrust/open-notebook-science].

Before that I had given two interviews – one to ORF ( http://en.wikipedia.org/wiki/ORF_%28broadcaster%29 ) , the Austrian public Broadcasting network Österreichischer Rundfunk Here’s the interview – I haven’t seen a translation but web translaters give a reasonable version http://science.orf.at/stories/1740033/ I explained why science was important beyond the walls of academia and why we needed to liberate scientific knowledge.

Then the “launch” of The Content Mine ( http://contentmine.org ), my Shuttleworth Fellowship project, which aims to extract 100,000,000 facts from the scientific literature. The philosophy is not that *I* do this but that *WE* do this. To do that we have to:

  • have reliable, compelling, distributable software. That’s hard. But we’ve got one of the best small teams in the world – it would be harder to think of a better one. That’s because we are developer-scholars – we are not only very experience in the coding and design of information , but we are also expert in our own right in our fields (Chemistry, Phylogenetics, Plant Genetics, and Informatics/ScholarlyPublishing). That means we know where we are going, know what works (or rather what *doesn’t* work!) and know who else in the world is doing similar stuff. And because I’m funded by the Shuttleworth Foundation there’s a guarantee  that we won’t get bought by Elsevier or Macmillan or Thomson-Reuters. I wouldn’t swap any of the team for ten million dollars – that’s how important they are to my life.
  • show YOU how to become part of US. The goal is to create a community. We’re in very good touch with Wikimedia, Mozilla, Software Carpentry, OpenStretMap, Open Knowledge, Blue Obelisk, Apache, so our community will be recognisable in that environment. And also think of WellcomeTrust, Austrian Science Fund, RCUK, NIH, to get a feel for how we relate to science funders. We’ve only been going 3 months so we want to see a community evolve rather than design it prematurely. When it’s strong and energetic it will start to suggest where we should be going organisationally. We also work closely with domain repositories such as PubChem, EuropePubMedCentral, Treebank, Dryad, Crystallography Open Database, etc.
  • At present we are reaching out through workshops. We’re doing several this summer – Edinburgh, Berlin/OKFest, Wikimania, OK Brazil, and one or two more yet to be finalised. We’re informed by the Software carpentry philosophy, where we ru a workshop for a sponsor, and during the workshop train apprentices. Then these apprentices wll be able to help run new workshops and then perhaps their own workshops. So although Michelle and I ran this workshop, there will be later ones with different leaders.

So we ran our first public workshop on 2014-06-04 at  Institute of Science and Technology Austria (IST Austria) We advertised it as:

Workshop with Peter Murray-Rust and Michelle Brook: “Can we build an intelligent scientific reader?”

Venue: IST Austria, Am Campus 1, 3400 Klosterneuburg
Time: 4th of June 2014, 10:00 a.m. – 4 p.m. (ballroom)
Participants: 10 places are still available (first come, first serve)
Registration: send an email (incl. first name, surname, institution, email) asap but until 30/5/2014 to falk.reckling@fwf.ac.at

Workshop Description
The workshop will be suitable for anyone interested in biological science and not frightened of installing and running pre-prepared programs and data (following written guidance and with support from those present in the room). The aim is to introduce computational methods for processing scientific papers, enabling analysis of multiple papers in a rapid fashion. These techniques include how to download multiple files, extract concepts and facts from the literature and figures, using Natural Language Processing and Computer Vision.

Technical expertise required
Very little expertise is required beyond general use of a computer. Much more important is a willingness to learn and experiment. However we will ensure options are made available for those who are confident/technically able, including providing opportunities to develop their own tools for analysis.

We got 18 brave people, mainly compsci but also bioscientists and it went well. Michelle is getting formal feedback. We’re hard at work taking our own criticism on board (Michelle collected a very thorough set of observations). It was hard work, but we now know we can do it and it works. The main emphasis was on understanding the concept (with highlighter pens and paper!), scraping, extraction, and how to work as a community. We’ve got attendees who want to folow up on how they can use it! That’s the philosophy.

Then the next day an all-day hack run by OKFN Austria (Stefan Kasberger and Peter Kraker (Panton Fellow) – http://okfn.at/2014/05/19/content-mining-meetup-with-peter-murray-rust/. A wonderful hackspace (metalab), couches, soft drinks + honour payment, bits of kit lying around – grafitti – you know the sort of thing.

And then at the end 4 invited speakers (including PMR). We are very impressed by OKFN Austria – the day drew perhaps 25 people. And a lovely city.

But Exhausting! At the  end I crashed for a long night. (In writing my Shuttleworth Quarterly report I was aksed “What was your greatest loss during this quarter?” Answer: SLEEP!

Much more to come – a hackday in Edinburgh next week to be announced later today.

 

My MPs say “You can ignore Elsevier’s TDM click-through API and we urge your library to do so too”

 

A little while ago I wrote to Minister David Willetts through my MP Julian Huppert on two issues;

  1. Elsevier’s misselling of Open Access Articles (later described by Elsevier as their “bumpy road to Open Access”)
  2. Elsevier’s unnecessary click-through API which would constrain researchers and get them and librraies to sign away their rights.

Today I have got a reply on both points which I reproduce below.

1) TL;DR They’ve talked with Elsevier about the bumpy road (i.e. charging people for Open Access). You’ll have to read between the lines as to what was actually said, but it might be “David, we’re terribly sorry, grovel grovel [1]”

2) They held firm and said “yes, the point of the law was that researchers could mine facts (etc.) without having to sign publisher APIs”. “Yes, PMR has a right to do it and you can’t stop it”. After all, if they didn’t say that, what’s the point of the law? Elsevier and the other publishers have lost that battle and should move on.

Just in case any other publishers think the message wasn’t clear, here it is. So thank you very much David and Julian. You have worked hard and consistently for that. And I and other researchers in the UK will show that your effort has unleased a massive potential for increasing wealth, human well-being and enhancing the status of the UK. I’ll be blogging on that RSN.

 

 

 

I have redacted my address so that GCHQ can’t say where I live and tell the NSA. (Ha!)

willetts1

 

 

TL;DR Elsevier are very slowly responding to my criticisms. It seems the more money a company takes in the harder it is for them to get their Systems right.  Good that they encourage Gold OA; Bad that they exercise no price control; Ugly that they think “Access to Research” is more than a cosmetic gesture. (That’s the one where citizens can cyle through the snow to their nearest library, have an hour to read a dumb screen, cannot cut and paste, cannot copy and cannot print; what we want is legal access over the Internet, not some Charles Dickens stupidity).

NOW the more exciting part…

willetts2

TL;DR. A UK academic has the legal right to carry out TDM for non-commercial purposes unless THEIR LIBRARY stops them, by agreeing that they will act as publisher police. And , LIBRARIES, the goverment is making sure you know this. Ignorance is unacceptable. So why might you sign? The publisher might sweet-talk you into doing this, just like washing machine salesforce sell you “insurance” that is worse than your current legal rights. Remember PPI? Click through licences are as honest as misselled PPI.  They’ll offer you a “better price” if you agree to constrain your researcher

The carrot for not signingis that your researchers will thank you and praise the library for freeing them from Elsevier’s wish to agree to their research project. You will have a warm fuzzy feeling that you have stood up for freedom. Libraries are more important to reseachers than publishers!

The stick… you can’t hide. The FOI-flying squad can find out whether you’ve signed the click through or other TDM restrictions. Resistance is futile. No “it’s too difficult to tell you, ” “we can’t find our contracts”, etc. There’ll be a giant UK spreadsheet (promise!) with your institution on it.

It’s easy. When a publisher salesperson comes to you mumble the mantra: “Yes to TDM; no to click-through”. They’ll try anything, but use the Force and be strong.

[1] a well-known parliamentary expression

OpenCon 2014 Announces First Travel Scholarship Sponsors

Inaugural Sponsors Encourage Others to Consider Support

The Right to Research Coalition and SPARC are pleased to announce the support of three leading research libraries for OpenCon 2014: The Student and Early Career Researcher Conference on Open Access, Open Education, and Open Data. The libraries at Emory University, Grand Valley State University, and the University of Kansas have each committed to sponsor a travel scholarship to OpenCon 2014 for a student or early career researcher on their campus.

OpenCon 2014 will convene participants from around the world, and serve as a powerful catalyst for projects led by the next generation of scholars and researchers to advance the conference’s three focus areas.

The scholarships provided by these sponsoring libraries will reserve a fully funded place at the meeting, including travel, for a participant from each university.  Each sponsorship accomplishes two goals: providing the selected attendee from each institution with experience and training on OpenCon’s three issue areas to bring back to campus; and helping to support the attendance of other leading young researchers from around the world who would not otherwise be able to participate.

The Right to Research Coalition and SPARC encourage other libraries and institutions to consider making a similar commitment.  You can find more information about sponsoring a travel scholarship as well as other sponsorship opportunities here: www.righttoresearch.org/act/opencon/sponsor.

Below, you can read why each of our first travel scholarship sponsors see it as a sound investment for their library and an important commitment to support student and early career researcher involvement in opening up scholarly communication.  A contact email address for each is provided if you would like to contact our inaugural scholarship sponsors directly to discuss their motivations for sponsorship. 

Lorraine Haricombe: Dean of Libraries, University of Kansas
Contact: aemmett [at] ku [dot] edu

“The University of Kansas Libraries enthusiastically supports the travel sponsorships program for graduate students and early career researchers from around the globe to attend OpenCon 2014. We strongly believe that the current generation of graduate students and early career researchers stand poised to not only inherit, but also shape the scholarly communication landscape. OpenCon promises to bring together the best young minds and budding advocates for openness in the scholarly communication ecosystem and offer them the chance to learn and consult on the system that is theirs to shape.  We recognize the importance and readiness of the next generation of scholars becoming knowledgeable and experienced advocates for an equitable and innovative system of scholarly communication. We are proud to be a sponsor of the inaugural OpenCon conference in North America!”
 

Lisa Macklin: Director, Scholarly Communications Office, Emory University Libraries and Information Technology
Contact: lmackli [at] emory [dot] edu 

“Emory University Library and Information Technology Services is pleased to support a Travel Scholarship to OpenCon 2014. The goal of Emory’s open access policy, repositories, and publishing fund is to distribute research by Emory authors as widely as possible through open access, increasing the impact of that research, and also to raise awareness of open access for scholarship, educational materials and data. Having an Emory student or early career researcher attend OpenCon 2014 will provide them with valuable experience and an international perspective that they can share to benefit others on our campus. We’re planning to host local events afterward for the Emory delegate to share their experiences with the Emory community and advance the conversation around opening up access to research results. We think OpenCon 2014 directly supports this goal and is also in keeping with Emory’s vision to create “positive transformation in the world through courageous leadership in teaching, research, scholarship, health care, and social action.”
  

Lee Van Orsdel: Dean of University Libraries, Grand Valley State University
Contact: vanorsdl[at] gvsu [dot] edu 

“There is good reason to believe that today’s graduate and undergraduate students will see the advent of a truly open system of global information sharing for text and data of all kinds.  ‘Open,’ to them, is the natural state of things, a value they were literally raised on.  Today’s junior faculty—early career researchers—will have opportunity to shape the transition to that better world.  It’s a brilliant plan to bring the two groups together for OpenCon 2014, where they can deepen their understanding of the issues, share ideas and experiences, receive advocacy training and hammer out strategies to achieve the changes both want to see.  Grand Valley State University Libraries are proud to sponsor a scholarship to support this fresh and promising approach to building stronger coalitions for change.“
 

You can find more information about OpenCon 2014, sign up for updates on the meeting, and learn about sponsorship opportunities at www.righttoresearch.org/act/opencon.
 

Nederland wordt proeftuin voor gratis wetenschap

©ANP. 07-06-2014. Staatssecretaris Sander Dekker wil dat vanaf 2016 minimaal de helft van de wetenschappelijke publicaties gratis leesbaar zijn.

Nederland wordt een proeftuin voor het gratis verspreiden van wetenschappelijke artikelen. Dit najaar wordt dat de centrale inzet bij de onderhandelingen tussen universiteiten en de grote wetenschappelijke uitgeverijen over nieuwe langjarige bibliotheekcontracten.