Showing posts with label articles. Show all posts
Showing posts with label articles. Show all posts

Wednesday, August 5, 2020

Some links to useful articles about the coronavirus

For those of you who might want more in-depth information and reporting about the coronavirus pandemic, these links to articles in The Atlantic will prove useful. 


I've included the list of articles to give you an idea of what they are about. I've read a few of them already and they are well-written and informative. 

The Atlantic’s guide to understanding COVID-19

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Friday, January 18, 2013

The future of scientific publishing

Open Access (OA) is in the wind these days, especially if you work in academia and publish articles as part of your research work. If you work at a university or are a student there, you will come across the term Open Access. What is Open Access? Wikipedia provides a very good definition; I urge you to read their page about Open Access—it will give you a good background: http://en.wikipedia.org/wiki/Open_access. Open Access is ‘the practice of providing unrestricted access via the Internet to peer-reviewed scholarly journal articles’. Simply put, it means that if you as a potential reader (whether you work at a university or not) find a scientific or medical article of interest online that you’d like to read, that you can click on the link to that article and read it online or download it for future reading from the website of the journal that published it. You may think this is common practice and not problematic; neither are true. You may not have considered what underlies your being allowed to access an article online if you are a student or researcher at a university. Your access to those articles is not necessarily ‘open’, or traditionally has not been open. That is because most published articles are closed access publications in non-OA subscription-based journals; they have been published in a specific journal, and that journal restricts access to a published article by making individual readers pay for the privilege of accessing it, if you are not working at a university. Or they make university libraries pay exorbitant subscription fees in order to provide online access to those articles and/or print copies containing those articles to students and academics at all levels.

Many people know little to nothing about OA, or if they’ve heard about it, it’s not something to which they’ve paid much attention. That’s understandable, since unless you have a career in academic research science where your research work can be published in a journal of some sort, you’re not likely to care too much about the scientific publishing process or about how much it costs to publish an article these days or about how much it can cost to access that published article afterwards. There are even academics who know very little about it, taking for granted that their published articles are accessible to all who are interested, or that they will have access to published articles that they are interested in. What some of them haven’t understood is that the university libraries have ensured that they have had access to innumerable journals in their fields of interest—chemistry, biology, physics, medicine, geology, etc. up to this point. This is because the libraries have paid costly subscription fees to gain online access and/or to receive print copies of the journals. These subscriptions are part of their annual budgets. This system has been in place for many years.

As a scientist, I am interested in promoting Open Access publishing, for a number of reasons.  First and foremost, I believe it is the future of scientific publishing, and I’d like the future to be here now. (I also believe that self-publishing is the future if you want to publish your own books; it allows you to bypass traditional publishing houses that mostly reject first-time authors. I wrote a post about that in 2010: http://paulamdeangelis.blogspot.no/2010/08/publish-your-book-using-createspace.html). We academics already do most of the prep work before we submit our scientific articles, prep work that was previously done by the journals; we format the text and prepare figures and tables according to guidelines provided by the journal, we upload those formatted files to the journal website, and we edit the compiled version of the article that the journal provides to us after receiving the uploaded files. In other words, we now do much of the work that the journals used to do for us before; they are not doing us any favors. If you’ve ever submitted an article online for publication, you will know what I’m talking about; the process is not for sissies. In addition, we often pay just to submit our articles to a journal, even to a journal that the university library already subscribes to (e.g. Cancer Research) although not all journals have this requirement. We also must pay page charges if we want color figures, or if our article goes over the page limit. We must pay to get reprints of an article or pay to receive a pdf version of our article created by the journal that represents the final published version. If you choose to receive a pdf file of the published article, you are not allowed by the journal to distribute free copies of your published article to those who might want to read it. For that privilege, you are expected to pay for journal reprints. It’s a costly business for many scientists, whose budgets continue to dwindle with each year that passes.  

I chose to publish one of my scientific articles in the OA journal Molecular Cancer already back in 2004; that’s how strongly I believed in the future of OA publishing then, and still do now. Gold OA journals provide immediate access to your published article on their websites; Molecular Cancer is one of the journals offered by BioMed Central, which is the first OA science publisher (started up in 2000) and one of the largest in the world. You as a potential reader do not have to pay them to access my article; I do not have to pay them for permission to distribute my article freely to whomever I choose. In fact, I am including the link to my 2004 article here, if you’d like to read it: http://www.biomedcentral.com/content/pdf/1476-4598-3-11.pdf.
I chose to publish in Molecular Cancer again in 2006 because I had had such a good experience with them in 2004; here is the link to that article: http://www.molecular-cancer.com/content/pdf/1476-4598-5-20.pdf. This article, by the way, is a highly-accessed article (yes, you get to know the statistics for your article—how many times it’s been accessed/downloaded, and when—quite useful). That makes me feel pretty good, because I know that the work is solid and that the data are quite interesting.

I use the word ‘chose’; the fact is that my articles went through rigorous peer review before they were accepted for publication. There is NO guarantee that your article will automatically be accepted for publication in an OA journal; there is still editorial and peer review to go through. I have had a total of three articles to date published in OA journals (the third one a collaborative effort with Italian colleagues in 2009: http://www.molecular-cancer.com/content/pdf/1476-4598-8-55.pdf). But I have also had two articles that were not accepted for publication in this journal. That has not discouraged me. It merely reinforces my opinion that the OA system works just as well as traditional non-OA publishing; it is not ‘easier’ to get published in OA journals than in non-OA journals. There are good OA journals and poor quality OA journals, just as there are good and bad non-OA journals. The impact factor for Molecular Cancer is 3.99, pretty good—around the middle of the scale. But I don’t worry too much about impact factor, even though most of my peers do and even though we are encouraged to do so by our workplaces; I am more concerned with reaching potential readers and making my work accessible to a larger public. Because of course the potential reach is global. I probably should care more about impact factor, because it gets your research ‘noticed’ and funded by granting agencies—the more publications you have in high impact-factor non-OA subscription-based journals (like Nature and Science), the better your chances of getting your research projects funded. These are the ‘eye of the needle’ journals—only an elite few ever get to publish here. And the reasons for that could fill another blog post. To give an example of how non-OA journals make it difficult to get access to articles, check out this article in Science magazine; if you want to access and/or to download it, you have to pay for that privilege: 
http://www.sciencemag.org/content/339/6117/303, unless you work or study at a university that subscribes to this journal. As far as I'm concerned, this is an incredibly old-fashioned and elitist way of doing things. 

Is OA publishing free for authors? Not necessarily, but it can be if the university or institution you work for is a member institution. I refer you to the ‘article-processing charges FAQ’ page on the BioMed Central website; it explains this aspect better than I can: http://www.molecular-cancer.com/about/apcfaq. The major and most important point for pushing for open access journals is that once research articles are published in them, they are immediately and freely-accessible to anyone in the world who wants to access them. That is not the case for non-OA subscription-based journals.  

If you would like to read more about Open Access, I recommend the following websites:
·         Open Access http://en.wikipedia.org/wiki/Open_access
·         Directory of Open Access journals http://www.doaj.org/
·         Open Access Directory http://oad.simmons.edu/oadwiki/Main_Page
·         The Development of Open Access Journal Publishing from 1993 to 2009
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0020961
·         Video describing Open Access http://www.phdcomics.com/tv/#015

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Tuesday, August 28, 2012

Doing my part to save some trees

I don’t remember the exact date I stopped printing out paper copies of most of the scientific articles, manuscripts, grant applications and other documents that are sent to me for review and editing. I do know that I have been doing my part to save trees on this planet for many years now by not printing out paper copies of every document or article that is sent to me or that I come across during my online travels. I am always surprised when a student tells me, as happened yesterday, that she has misplaced the only copy of a manuscript draft that was edited as a paper copy and given back to her by her supervisor. When I asked if she couldn’t just check her email to access the edited document again, my assumption being that her supervisor does as I do—edits and comments an article draft via ‘track changes’ in Word and then saves it as a computer file--the answer was that her supervisor doesn’t edit/review documents on the computer. She edits and comments in the margins of a paper version of the article and gives it back to the student this way. So if that paper version gets misplaced, I understand how it could be a problem for the student. One could hope that her supervisor made a paper copy of her edits before she gave the edited article back to her student.

I know there are mixed opinions among academics about reading and editing manuscripts on your computer prior to their submission for publication. Personally, I like doing both on my computer. I have no problems following an article’s logic and buildup on my computer screen, and I love having ‘track changes’ available to me so that I can edit manuscript drafts onscreen if that is the task at hand. In the old days, an edited manuscript that you had gotten back as several copies from your co-authors could be a daunting proposition to tackle; some of them were a mess in terms of the pencil scribbles in the margins, the curlicue arrows directing you to move this paragraph to another page or to a paragraph below on the same page, comments at the top of the page telling you what to consider to include in the next draft, and so on. It is no easier to go painstakingly through such an edited manuscript than it is to correct a manuscript edited through ‘track changes’. In fact, I think the latter is much easier; you can choose to accept or delete inserted or deleted text, you can accept or reject format changes, and you can move text around as you like and still see where you removed text from in the final version.   

I also no longer print out the pdf versions of published articles; I read them online as well. It is a rare occurrence these days for me to print out an article; if I do, it is usually an extensive review article. I simply don’t see the point anymore of wasting all this paper. Additionally, the articles of interest are freely available for the most part, so that there is no danger of getting access to an article and then suddenly losing that access. One can get around this problem anyway by saving a version of the pdf file on your own computer to peruse at a later date. I am one of those people who welcome a paperless workplace and household. Offices stay neater as do homes, a win-win situation all around. 
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Will Smith - Men In Black (Video Version)

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