Screenshot of the day: Proteomics apologizes to PubMed’s readership.

Last time I said: Although the paper was retracted from the online version of Proteomics, you can still make historical screenshots on the PubMed version.

Now the chance is over. But what is really funny: finally, PubMed ‘Related Links’ algorithm gives us the proper context of the Warda-Han-Mighty paper, just take a look at the first 2 related articles on the right:

Ferenczi and Winnicott: searching for a “missing link” (of the soul). Am J Psychoanal. 2007 Sep;67(3):221-34.

A Thomistic understanding of human death. Bioethics.2005 Feb;19(1):29-48.

I would have never thought that PubMed could be a source of such fun.

Nature’s Great Beyond on the Warda-Han-Proteomics-Creator paper

Peer review, ‘a mighty creator’ and an almighty row

However the paper was only retracted for “a substantial overlap of the content of this article with previously published articles in other journals.”, not for the strange “mighty creator” line. Peer review isn’t perfect but you’d hope it would catch something like this.

Warda speaks: “We say the truth, I not burrow any sentences from others.”

The Warda-Han-Proteomics saga continues and finds its way to the show/entertainment business. We’ve already listened to Han, now it’s time for Warda to speak, which he did in an email to James Randerson over at the Guardian Science blog, which makes think (indeed ‘rethink’ as W suggests) that the Warda-Han pair is probably the Laurel and Hardy of the science showbiz.

Screenshot of the day: Warda-Han-Still-Missing-Link paper retracted!

First of all: thanks to the commenters/scientists (the online flash mobbers) for being the most efficient part of the science blogosphere! Although the paper was retracted from the online version of Proteomics, you can still make historical screenshots on the PubMed version.

Blogosphere links in chronological order:

The Warda-Han-Proteomics scandal: fingerprints of plagiarism, too

We have now a well-developed and sad case example of irresponsible scientific editing and publishing: the Warda-Han advanced online paper by the academic journal Proteomics: Mitochondria, the missing link between body and soul: Proteomic prospective evidence. What started as an abstract-based hunch and question about the quality of a recent review, addressed to and amplified by the the scientific blogosphere may probably end as a piece of investigative journalism in the mainstream media with serious consequences and conclusions on scientific publishing. Right now, the real investigation takes place at the comment section of the PZ Myers post A baffling failure of peer review over at Pharyngula. The story there is quickly unfolding thanks to the smart and open-eyed (Google-savvy) contributors who figured out amongst others that Warda and Han significantly reduced their review writing efforts by borrowing many sentences from other colleagues’ papers. Here I’d like to mention and cite only 3 comments:

The fingerprints of a mighty creator in Proteomics, impact factor >5

Creationism/intelligent design is not really an issue for me as I am a biologist working with mitochondria and stem cells, also a life extension supporter, whose angle on things and projections are based on the recent advancements in science and technology. As far as I know, creationism/ID neither suggests any new experiments or heuristic solutions in my research field, nor does it help to plan&build new technologies to extend healthy lifespan. From my point of view, thinking about creationism is a waste of valuable scientific/technological processor time.

But I am not used to encounter with explicit creationism and the fingerprints of a mighty creator as an explanatory force behind a natural phenomenon in scientific peer-review journals. That’s exactly what happened to me in a recent review published online by the Wiley journal, Proteomics (ISI Impact Factor 2006: 5.735) by Mohamad Warda and Jin Han, entitled Mitochondria, the missing link between body and soul: Proteomic prospective evidence.

Last week when I wrote the post Can you tell a good article from a bad based on the abstract and the title alone? on the review I had only 10 minutes for figuring out the post between 2 experiments in the lab during lunchtime. The only thing that came into my mind reading the abstract – popped out of PubMed feeds – was that something stinks here. Now it’s Mardi Gras day and I have a couple of minutes more to address this issue and hopefully no more.

Myrmecologist and blogger Alex Wild picked one sentence from the paper in a comment, and here is the complete paragraph:

Alternatively, instead of sinking in a swamp of endless debates about the evolution of mitochondria, it is better to come up with a unified assumption that all living cells undergo a certain degree of convergence or divergence to or from each other to meet their survival in specific habitats. Proteomics data greatly assist this realistic assumption that connects all kinds of life. More logically, the points that show proteomics overlapping between different forms of life are more likely to be interpreted as a reflection of a single common fingerprint initiated by a mighty creator than relying on a single cell that is, in a doubtful way, surprisingly originating all other kinds of life.

This is the closing paragraph of the section Mitochondrial integrated function disproves endosymbiotic hypothesis of mitochondrial evolution. The mitochondrial part of the well established evolutionary endosymbiotic theory claims that ATP-producing mitochondria were ancient prokariotic invaders of host prokariotic cells eventually turned out to be the common ancestors of eukaryotic cells. I always found this hypothesis one of the most fruitful scientific concepts as it constantly suggest new ideas and warns that current eukaryotic cells are the products of an evolutionary, accidental and instable alliance between the mitos and their hosts. As the endosymbiotic theory is the mainstream academic theory of mitochondrial evolution it is a challenge for scientists to attack it with counterarguments and that’s what Warda and Han are aiming for in that section. What they are doing seems like a legitimate discussion of a scientific theory but ends with the logically unacceptable jump to the fingerprints of a mighty creator as an alternative explanation.

Before I cite the section in question in full length and recommend to my readers to analyze it, I also like to suggest the detailed comment of D. Spencer saying amongst others:

If Wiley and the journal Proteomics allow this into print (it is currently only “published” online) they can kiss goodbye to any hope that Proteomics will ever again be regarded as a serious scientific publication.

Here is the complete section by Warda and Han without references that could be found in the full text:

Can you tell a good article from a bad based on the abstract and the title alone?

Many times people only have access to the abstract of peer-review articles, and nothing more. There are different abstract styles (sometimes they’re going too far or on the contrary) in the literature and I’d be curious to hear about your opinion on the following review abstract and title. I became interested and suspicious reading these lines especially the one highlighted in bold.

Mitochondria, the missing link between body and soul: Proteomic prospective evidence.

Stat freaks, are you ready to play with the SCImago Journal & Country Rank?

Finally the Google PageRank algorithm, the core analysis tool of the current web is back to where its idea is originated from, scientific citation analysis. The recently launched SCImago Journal & Country Rank database uses an algorithm very similar to PageRank. It has a new metric: the SCImago Journal Rank (SJR). According to Nature:

A new Internet database lets users generate on-the-fly citation statistics of published research papers for free. The tool also calculates papers’ impact factors using a new algorithm similar to PageRank, the algorithm Google uses to rank web pages. The open-access database is collaborating with Elsevier, the giant Amsterdam-based science publisher, and its underlying data come from Scopus, a subscription abstracts database created by Elsevier.

The SJR also analyses the citation links between journals in a series of iterative cycles, in the same way as the Google PageRank algorithm. This means not all citations are considered equal; those coming from journals with higher SJRs are given more weight. The main difference between SJR and Google’s PageRank is that SJR uses a citation window of three years.

From now on every stat geek can compare journals to journals, countries to countries based on different metrics like citable documents, cites, self-cites or the new h-index and get a ticket to recursive heaven. Of course I started with the comparison of Nature and Science to find something very different. I couldn’t. I predict that self-cites will show a lot on how things are going on at different scientific journals and the stats will be used as serious arguments in many blog posts. But here let me share some graphs on the quick comparison of USA, UK and China in the category of Aging.

First graph: citable documents

23andMe on the biparental inheritance of mitochondrial DNA and more

In my former blog post inF.A.Q. for 23andMe: what if I have mitochondrial DNA from Pa? I meditated on 23andMe‘s capability of detecting paternal mitochondrial DNA in their customers’ saliva with their Illumina microarray chips scanning around 2000 mitochondrial single nucleotide variants. Published here the initial answer of the 23andMe Editorial Team to this fairly technical, but nevertheless crucial question with permission granted. Besides, I am happy to report that I am working on a blogterview with one of the key member of 23andMe’s Research Team. Hopefully I’ll be able to get back to you with some first-hand information on the science and technology behind the personal genome service of 23andMe and on how 23andMe can facilitate academic research.

Dear Attila Csordas,

Thank you for your interest in 23andMe’s research mission. The question of paternal inheritance of mtDNA is a fascinating one, and the debate in the literature has continued over the past couple of decades. Currently, there is little evidence for paternal inheritance of mtDNA, outside of isolated individuals. However, the array platform lets us resolve multiple SNP states independently. 23andMe’s technology and throughput may indeed provide a novel way to address the question. We will include the question in our consideration of research projects. In the meantime, here are a couple of articles discussing the subject:

Bandelt et al., “More evidence for non-maternal inheritance of mitochondrial DNA?”
Chinnery, “The Transmission and Segregation of Mitochondrial DNA in Homo Sapiens” in Human Mitochondrial DNA and the Evolution of Homo Sapiens.

Sincerely,

The Editorial Team at 23andMe

The question is crucial for a personalized genetics company like 23andMe providing Maternal Ancestry Tree service for the customers based on the exclusively maternal inheritance of mitochondrial DNA. As one of my correspondent partner wrote:

Unofficial and hypercritical peer review of a paper on p53′s role in hESC regulation

Once I wrote shortly about the following peer review paper which was popped out of my PubMed feeds to draw some attention to it: Han Qin, Tianxin Yu, Tingting Qing, Yanxia Liu, Yang Zhao, Jun Cai, Jian Li, Zhihua Song, Xiuxia Qu, Peng Zhou, Jiong Wu, Mingxiao Ding, Hongkui Deng
Regulation of apoptosis and differentiation by p53 in human embryonic stem cells.
J Biol Chem. 2007 Feb 23;282(8):5842-52 doi:10.1074/jbc.M610464200

Now I got a very thorough comment on this paper by an author nicknamed “wolf” which systematically goes through the paper and gives a highly critical peer review of it. So I just publish the comments and next ask the authors (the first or the last) of the criticized paper and give them the possibility to defend their experiments and statements. My role here is the role of the blog”publisher”.

Comments re Qin paper p53 and hESC apoptosis by “wolf”:

This paper starts with making a fundamental mistake in not determining the kinetics of UV induced apoptosis and therefore missing the modulation of p53 target genes.
Subsequently they attempt to explain the absence of this by using transient transfections and analysing the cells at timepoints when half of the cells (mainly the undiff cells) are already dead and then interpret the data of the differentiated transfected (more resistant) hESC as if they were undiff hESC. The paper then desperately tries to come up with explanations for their own contradictory results). The data set further lacks controls (lentiviral mock transduced cells, no isotype controls etc), uses the wrong assays (such as PI staining to assess apoptosis, morphological assessment of differentiation by surface area) and lacks insight into the mechanisms controlling apoptosis (no cyt c release, no idea how p53 by itself might trigger mitochondrial apoptosis, etc).

Specifically;

Materials and Methods

Page 2: The authors use mainly one line of late passage hESC (p42-p68) grown in KSOR, which are highly CD30 positive leading to alterations in apoptosis regulation. We use three hESC lines at passages before p12 only.

Page 3: endoderm differentiation occurs in 4 days after Activin addition ? This is very quick with >80 % of hESC expressing sox17 after 100 ng/ml activin ?

Page 3: In immunostaining no antibody controls were used instead of isotype control with identical concentrations. We use isotype controls for all our immunos.

BioMed Search relaunched

BioMed Search, the Google-like BioMedical Image Search Engine is alive after a long off period as it was relaunched about 1 month ago.

Current informal science communication in the lab (say in lab meetings or in journal clubs) is centered around interpreting figures. BioMed Search catches somehow the essence of this communication with indexing the images, figures, diagrams, tables of about 1 million images from peer review articles. The primary source is Highwire press and Biomed Central – informed me Alex Ksikes, sole creator of BioMed Search.

I wouldn’t be surprised if one day Google (whose Scholar does not have a special figure search engine) bought this pretty useful service.

Looking forward to further updates.

Meet the nodes, “clustered hubs” and links of clathrin-mediated endocytosis

Network biology is a way to integrate fragmented benchwork data in order to understand complex biological phenomena. In a recent Nature paper, entitled Integrating molecular and network biology to decode endocytosis Cambridge (UK) researchers authors Eva Schmid and Harvey McMahon of MRC, Cambridge give a good example of a predictive and experimentally useful systems biology approach. As in many cases in the current literature, the formal, printed article is just the tip of the iceberg, and the “supplementary information” section is as crucial.

Clathrin-mediated endocytosis (CME) is an important vesicle biogenesis pathway. Cargo is packaged into vesicles that are surrounded by a coat predominantly made of the protein clathrin and adaptor protein complexes. For instance at the synapse, clathrin-coated vesicles (CCVs) participate in retrieval of synaptic vesicles following exocytosis.

Authors identify 2 hubs in this pathway: AP2 and clathrin triskelion and instead of putting them into the existing hub subtypes (‘date’ and ‘party’ hubs) they argue that neither are hubs at the beginning of CME, but mature into hubs by clustering either on the membrane or through polymerization. It is likely that many pathway/party hub proteins will oligomerize or cluster to function as pathway hubs. ‘Clustered hubs’ are a new subtype of hubs not previously described

I found Figure 3 particulary refreshing which depicts functional and connectivity views of vesicle formation in nerve terminals. (2 pieces included)

Experimentally testable consequences of the study:

The role of Journal Club in lab life and how to move the genre to the web

Regular (daily, weekly) Journal Clubs are crucially important events in the life of labs. Reviewing other labs’ results is a way to get synchronized with all the data accumulated by a particular subdiscipline. Moreover it is the most obvious everyday form (conferences are not that frequent) of secondary peer review of the given paper, when experts in one lab heavily criticize the story, methods, data and assumptions of experts in the other competitor lab. There is an education component: as the Wikipedia article says Journal Clubs help make the student become more familiar with the advanced literature and help improve the students’ skills of understanding and debating current topics of active interest in their field.
On the philosophical-psychological level a Regular Journal Club continuously confirm the identity and unity of the lab and the functional team behind it.

Now the question is how to move the Journal Club format to the web without losing its merits and retaining its role in a lab’s life?

Short answer:

Journal Club slideshow: MSC lung repair via lung-derived microvesicles

Embedded is my classical style (no design, based on the figure section, Powerpoint instead of Keynote) Journal Club presentation on the following paper with the help of SlideShare: Alteration of Marrow Cell Gene Expression, Protein Production and Engraftment into Lung by Lung-derived Microvesicles: A Novel Mechanism for Phenotype Modulation by Aliotta JM, Sanchez-Guijo FM, Dooner GJ, Johnson KW, Dooner MS, Greer KA, Greer D, Pimentel J, Kolankiewicz LM, Puente N, Faradyan S, Ferland P, Bearer EL, Passero MA, Adedi M, Colvin GA, Quesenberry PJ. Stem Cells. 2007 Jul 2 Thanks for the permission, Jason Aliotta. After the abstract you can find some critical points we digged out during our journal club answered by the first author, Jason Aliotta himself.

[slideshare id=94338&doc=microvesiclesslide4419&w=425]

Abstract: Numerous animal studies have demonstrated that adult marrow-derived cells can contribute to the cellular component of the lung. Lung injury is a major variable in this process; however, the mechanism remains unknown. We hypothesize that injured lung is capable of inducing epigenetic modifications of marrow cells, influencing them to assume phenotypic characteristics of lung cells. We report that, under certain conditions, radiation injured lung induced expression of pulmonary epithelial cell-specific genes and prosurfactant B protein in cocultured whole bone marrow cells separated by a cell-impermeable membrane.

The Niche: The Stem Cell Blog hosted by Nature Stem Cell Reports

How many fine niche stem cell blogs do you know? 4-3-2-1? How many with an attractive, easy to remember name? 0? Good, short, actual and proper blog names are rare. Let me introduce you The Niche which intends to become THE Stem Cell Blog in the niche of the niches. It is the newest Nature blog hosted by the also newly launched Nature Reports Stem Cells “to provide an informal forum for debate and commentary on stem cell research and its wider implications for ethics, policy, business, and medicine.”

Here is the RSS feed for the posts: http://blogs.nature.com/reports/theniche/atom.xml

also don’t forget to subscribe to the comments: http://blogs.nature.com/reports/theniche/index.rdf

Nature Reports Stem Cells is live from now on…for stem cell enthusiasts

No more waiting: Nature Reports Stem Cells (NRSC) launched today, and so finally there is a fully web native, scientifically high-end (naturally), freely accessible, all-in-one stem cell research hub site for everyone (especially for the researchers) to read, share, contribute and turn the acquired insights back into new experiments, policies, ethics, businesses and clinical trials.

Edited by the devoted small team Natalie DeWitt (Editor at Large), Monya Baker (News Editor) and Jessica Kolman (Editorial Assistant), based in Nature’s San Francisco office, California (where else?) NRSC has a bunch of usual and unusual ways: news, featured editor, journal club with user recommended articles and voting system, interviews, events and the really exciting and experimental Insider the paper section. From the first editorial of NRSC: “Inside the Paper posts edited discussions between authors and reviewers during peer review. Such transparency should not only deepen readers’ understandings of individual research publications, it will expose the workings of peer review itself. In the coming months, we plan to launch a Toolbox section will aggregate information on stem-cell protocols, reagents, and cell lines that would otherwise require trawling through literature or having serendipitous conversations at conferences.”

Forget about submitting your scientific papers written in Word 2007

Wow, I feel fresh air, although I am not sure whether the following news is a beginning of any deeper changes or not: From Science Authors Guideline: “Because of changes Microsoft has made in its recent Word release that are incompatible with our internal workflow, which was built around previous versions of the software, Science cannot at present accept any files in the new .docx format produced through Microsoft Word 2007, either for initial submission or for revision. Users of this release of Word should convert these files to a format compatible with Word 2003 or Word for Macintosh 2004 (or, for initial submission, to a PDF file) before submitting to Science.”

Tips: Undernews: SCIENCE PUBS REJECT ARTICLES WRITTEN IN WORD 2007
O’Reilly Radar: Science and Nature rejecting Word 2007 Manuscripts

One commenter in Undernews said: “This isn’t just Science and Nature. All Wiley journals now include the instructions: “[Journal] does not accept Microsoft Word 2007 documents at this time. Please use Word’s “Save As” option to save your document as an older (.doc) file type.” So don’t think it’s a singular problem — I’m sure if you visited all the science journal publications, you’d find similar instructions as well.”

What can I say: Prepare for the age of Google Office manuscripts and figures! All you need is a gmail account.

P.S. I made an attempt to coedit my ongoing first author article (desperately waiting for submission) by publishing the draft on Google Docs and adding the coauthors as collaborators, but only one coauthor (a med student) was kind enough to make one little correction this way. The rest is….well the majority of science people are living within the narrow world of Microsoft Office.

Editing my doctoral thesis on stem cells in a blog: Why not?

OK folks, after reading the official rules about how to get and manage a doctoral thesis, and after speaking with my supervisor asking for his permission, I’ve decided to edit my ongoing doctoral thesis in Pimm. Or at least the introduction of it, which is intended to be no other than a review-like summary of some current results in the stem cell biology of different tissues, organs. What will remain hidden in the first round (but can follow later): the data-heavy yet unpublished results and the discussion, conclusion session. Objectives, Materials & Methods: we shall see it. Sounds like there are complete parts of the thesis, but that’s dead wrong, at this time my doctoral thesis is in an embryonic form. Also no idea on how challenging, meaningful this project, a sub-series in Pimm, will be. What I know is that continuous experimentation with genres and frames is the essence of free blogging!
After all, what do I risk here? If someday I’d like to write a review out of the published introduction, can this cause a publishing problem? According to Maxine Clarke, Publishing Executive Editor of Nature (i.e. peer review and publishing policy expert) the status of a thesis is: “No, a doctoral thesis does not count as “previously published” and yes, you can submit work that was part of your thesis, with an appropriate citation.”

I also asked Maxine by mail and she was kind enough to enlighten me: There is no problem with you publishing your thesis in this way, so far as consideration for publication of any part of it for a Nature journal is concerned (or any NPG journal). We encourage communication between scientists via discussion of work and unpublished drafts in the form of theses, meetings, preprint servers, online scientific forums (between scientists) etc.

Informational emergency in the operating room: does it count as a right?

I found this exciting case in the book (yes, I am still reading those) of Lancet editor-in-chief Richard Horton called: Second Opinion: Doctors, Diseases and Decisions in Modern Medicine

“Surgery is all about action, not reflection. But information is sometimes critical, even in the operating room. In 2002, surgeons in Australia were working frantically to save the life of a critically injured man. One of the surgeons recalled that he had read an article in a medical journal that he was sure would help his team right there and then. The problem was that he could not remember which article. What could he do? A call was put out to the British Library archives. Although it was received at 3 AM British time, library staff were able to track down the 1996 paper in the European Journal of Emergency Medicine within twenty minutes and send it to the desperate Australian surgeons.”

What could be the answer today, in 2007 for that question: What could he do?

PubMed, Google Scholar, Connotea, CiteUlike?

Even if the surgeon found the title or abstract of the paper within seconds with one of these or other apps, would he/she be able to download the whole (copyrighted) content somehow within minutes too without an institutional subscription referring to informational and life emergency?

Could this exceptional information and life emergency be interpreted as a basic right with complementary duties? If yes, as a positive or negative right?

Cell’s Superhero Cover: the role of comics in science popularization

I’ve just realized how cool is Cell magazine May 4 issue’s cover (the one with the Scientist Enter the Blogosphere report by Laura Bonetta) with the S-nitrosothiol superhero T-shirt. This substance may have some therapeutic utility in diseases such as heart failure and asthma.

Illustration: Cell and me this morning.

Cartoons are terrific education tools, let’s consider howtoons for instance. Howtoons are cartoons showing kids of all ages “How To” build things. What about cartoons for scientists?

Bone marrow stem cells, the great cancer pretenders?

In the lack of subscription to Stem Cells, I could not download the whole article or the subscription restricted supplemental data (at Stem Cells it seems people haven’t heard of free supplemental information) but this story is really interesting: Bone Marrow Contributes to Epithelial Cancers in Mice and Humans as Developmental Mimicry

In brief: in women underwent male (Y chromosome tracked) bone marrow transplantation, different types of cancer were developed and the malignant tissue often contained small areas of male marrow cells. The same happened with BM transplanted mice with the same cancers. “When they viewed the cancerous tissues under the microscope, they found marrow cells shared outward features of the cancer cells.

“Our results indicate these cells act as developmental mimics; they come in and look like the surrounding neoplastic tissue but they aren’t actually the seed of cancer,” explains Dr. Christopher Cogle, first author the Stem Cells article. “At the worst, these cells could help support cancerous tissue by providing it with growth factors or proteins that help the cancer grow and survive. At the very least, these marrow cells are just being tricked into coming into the cancerous environment and then made to walk and talk like they don’t usually do.”

These results highlight the role of the local destination niche to the phenotype of the migrant and highly mobile bone marrow cells.

Source: Bone Marrow Stem Cells Mimic Cancer but Do Not Initiate It

Illustration: lung cancer stem cells from Christopher Cogle’s homepage.

2 models of embryonic and adult blood formation: Figure by Ueno and Weissman

If you have previously thought (in your spare time) that the conventional wisdom concerning blood formation is that the yolk sac’s embryonic blood-forming cells serve only the embryo, while the source of adult blood-forming stem cells is the region called aorta-gonad-mesonephros (AGM), it’s time to think it again due the elegant experiments of Samokhalov et al.: Cell tracing shows the contribution of the yolk sac to adult haematopoiesis Nature 446, 1056-1061 (26 April 2007)

Legend: a, The ‘separate’ model.

Looking for user friendly, attractive peer review article titles….

These two titles are freshly out of my feed readers: B-type natriuretic peptide inhibited angiotensin II-stimulated cholesterol biosynthesis, cholesterol transfer and steroidogenesis in primary human adrenocortical cells. and

In vivo expression of human ATP:cob(I)alamin adenosyltransferase (ATR) using recombinant adeno-associated virus (rAAV) serotypes 2 and 8.

How user friendly these titles are? Let’s examine me: Theoretically I have some (limited) background knowledge on these topics as they are covered by my Google Reader with some properly chosen search terms. For the first trial I see only familiar characters in a weird arrangement without any intelligence flash in my mind, for the second some mental forms are beginning to take shape, for the third a little more context enter, but instead of a fourth title trial I skip to the abstract in case I’m interested in what follows based on the previous title impressions. But I’d truly appreciate if I could capture at least half of the title at first. And the titles above are not the worst at all. After reading the steroidogenesis-one many times, it became my friend. But people would like to put less energy into conceiving a simple title and more to understand and apply the new results. A good title is about the proper filtering of the proper reader and vice versa.

Yes, there must be some good policies on titles of peer review articles. In case of the steroid paper, the Instructions to Authors for Endocrinology says on title requirements: Full title (a concise statement of the article’s major contents)

PNAS has a longer title guide for instance, this paragraph is from an older version of PNAS Information for Authors: Title: Titles should be simple, informative, and comprehensible for a broad scientific audience. Authors should avoid nonstandard abbreviations and colonic phrases. Titles may not be phrased as questions. Titles are limited to three lines or 135 characters including spaces.

Free Nature Reviews Neuroscience Issue in May

From the Nautilus blog by Maxine Clarke: “Nature Reviews Neuroscience is the no. 1 monthly review journal in neuroscience, with an impact factor of 20.951. In May, online access to the entire issue is free.”

I would like to offer these articles which could be of interest for stem cell biologists:

Research Highlights

Neurogenesis: Single stress shortens survival

Cell fate: Unlocking the right combination

Stem cells: Together we are stronger

Reviews

Transcriptional regulation of vertebrate axon guidance and synapse formation

Cell cycle regulation in the postmitotic neuron: oxymoron or new biology?

Stories from my PubMed feeds: hESCs, p53, apoptosis and differentiation

Short peer-review storytelling : One big technical problem of human embryonic stem cells (hESCs) (in contrast to mouse embryonic stem cells) that hESCs normally undergo high rates of spontaneous apoptosis and differentiation, making them difficult to maintain in culture. Now we are getting to know a bit more on the molecular background of these processes. In an article in the prestigious Journal of Biological Chemistry Qin et al.’s studies reveal the important roles of p53 as a critical mediator of human embryonic stem cells survival and differentiation.

Regulation of apoptosis and differentiation by p53 in human embryonic stem cells.

J Biol Chem. 2007 Feb 23;282(8):5842-52

“Here we demonstrate that p53 protein accumulates in apoptotic hESCs induced by agents that damage DNA. However, despite the accumulation of p53, it nevertheless fails to activate the transcription of its target genes. This inability of p53 to activate its target genes has not been observed in other cell types, including mESCs. We further demonstrate that p53 induces apoptosis of hESCs through a mitochondrial pathway. Reducing p53 expression in hESCs in turn reduces both DNA damage-induced apoptosis as well as spontaneous apoptosis. Reducing p53 expression also reduces spontaneous differentiation and slows the differentiation rate of hESCs.”

Figure 2 for the pros:

Blogxperiment: What are the good ways to summarize peer-review articles?

In future posts I’d like to do a blogxperiment based on comments feedback. My general question is: What is the best way to summarize peer-review articles for a more general readership and transmit scholarly knowledge and literature? What are the opportunities used in blog posts? Figures, abstracts, dense citations, other summarize options, journalist lingo, superficial metasentences, more original contributions from the blogger? My sample article will be a review first, not an original publication on mitochondrial division: The Machines that Divide and Fuse Mitochondria

And simply start the experiment with the abstract:

I also might have asked: What are the good ways to popularize peer-review articles?

Nature Publishing Editor on the idea of a public scientific multimedia site

Maxine Clarke, Publishing Executive Editor of Nature and blogger of Peer-to-Peer got interested in the problem of “supporting information” and in the idea of an open access, peer-review supporting information aggregator website. She shared with me her valuable thoughts and informations by mail, from which I now publish parts with the permission of Maxine Clarke (emphasis by me).

On the possibility of a community-approved public multimedia site (videos, audios, pictures) with open access supporting information from peer-review journals.

It would indeed be nice for authors and readers to have such a facility. If there were to be a multimedia database, accepted by the community, we’d be happy to consider making deposition mandatory. Our principle is that data described in our papers are freely available, so if there were a community-approved public multimedia site, which included annotatation and curation, we’d be happy to consider making it a condition of publication for movies etc to be deposited in it. It would need to be publisher-independent to work, so that authors could upload multimedia data wherever they’d published their paper.

The main point for us at Nature is that as a publisher we have to be confident that material published off our website is properly curated, archived and preserved. For example, when we introduced the microarray deposition policy we ensured that there was full community support for the two databases (in one of which, authors’ choice, we require deposition) before implementing the policy. So for this video idea to work, the “database” concerned would need to be publicly accessible (not commercial), curated, annotated etc.

On the status of online supporting information at Nature:

Supplementary Information on the Nature website is free, though you have to register. (Confirmed, see screenshot of a 3D supplementary animation showing that the gut-associated lymphoid tissue comprised of different subsets of haematopoietic cells, Veiga-Fernandes et al.)

On the problem and handling of online supporting information:

Let’s make ‘supplementary’ peer-review scientific videos free and youtubish!

In the last post on “supporting information” section I claimed that the problematic status of supporting information comes from the heterogeneity of its data, on the one hand genuine online multimedial files, on the other hand “paperlike” data. Big differences also occur concerning the importance of the data. The source of the heterogeneity is the traditional, offline, peer-review article format, which is not able to embrace multimedia files, videos, audios, big resolution pictures.

If you are working in a field, like cell and molecular biology, you are probably a heavyweight user of various imaging methods like laser scanning confocal microscopy, deconvolution microscopy or just lean on normal fluorescence microscopy. Increasingly you are involved in the making of gigabyte sized time lapse videos on living cells or 3D imaging visualizations made by special software, illustrating the biological phenomenon, pattern or effect you are publishing an article on. So scientific videos are more and more important part of scientific arguments in the life sciences.

But these videos can only be published online, under the humiliating title “supplementary information” since offline it is not possible to include videos in every Nature volume (although theorethically some thin film paper ultraexpensive technology can do that in the future). Examples of 3D visualizations are Wang et al.: Endothelial cells derived from human embryonic stem cells form durable blood vessels in vivo in Nature Biotechnology (see left), and Zhu et al.:Spatiotemporal control of spindle midzone formation by PRC1 in human cells, PNAS (see right).

So here ‘d like to suggest for researchers who are making videos and upload it, the powerful editors of peer-review journals, coders, geeks in the uprising web video market to meditate on the possibility of liberating the so called supplementary science videos of peer-review articles and give some light to them by making them freely available and distributable on the web! What about a strict, searchable scientific video sharing site?

Points of persuasion:

1. the web is the natural home of multimedia files of scientific studies, not the published journal articles, so why not make available them in an open access style?

2. there must be some working creative commons like license construction referring to just multimedia parts of the supporting information section, not the whole article, which is good for the Publishing Groups, does not hurt their interests, but does enormous good for individual researchers, searching information outside their academic institutions for the public (if you heard of any type of license like this, please inform me, I am ignorant in this respect)

3. videos, 3D animations are convincing, sometimes crucial forces of scientific arguments in life sciences, so what about a free abstract+supporting information construction?

4. from a presentation point of view, videos are really spectacular and the liberation of science videos can do much for popularizing science worldwebwide

5. imagine a youtube-like video site collecting these videos and make them available for every web user

6. timing: the current web is dominantly about videos and video sharing

What I have in mind here, is a JoVE like website, serving as an ideal host of peer-review scientific videos, animations, audios….

The closest relative is BioMed Search, a Google-like Biomedical Image Search Engine which is currently unavailable due to some problems.

Update: Maxine Clarke, Publishing Executive Editor of Nature and blogger of Peer-to-Peer on the problem of “supporting information” and in the idea of an open access, peer-review supporting information aggregator website:
Nature Publishing Editor on the idea of a public scientific multimedia site

The problem of online “supporting information” in peer-review articles

Most articles published in peer-review journals are organized into the following sections: Title, Authors, Affiliations, Abstract, Introduction, Results, Discussion, Materials and Methods (it could stand before Results), Acknowledgments, References, and Figure Legends. But every current researcher in the field of life sciences has already had some time with the stepsibling of those full blooded formal sections, the so called “supporting” or “supplementary” information section of online peer-review articles. Example: Supporting Information of advance online PNAS article Role of the chromobox protein CBX7 in lymphomagenesis.

The concept of “Supporting information” is a natural internet born online product (assume but not sure), unfortunately suffering from some conceptual problems. Before the internet most data belonging to a complete study, but not published in formal offline articles out of different reasons, were communicated personally (conferences, meetings, phone calls), or by mail, or were published later in books, sometimes as distinct articles otherwise never came into publicity and remained hidden in lab notebooks.

With the rising of the internet additional data, not suited to the formal offline article, moreover multimedial files (videos, audios, big resolution pictures) could find their way to online publication as supplementaries.

Because of this birth “Supplementary information” is a mixed concept (or a Restbegriff). The authors uplopad every information as supplementary info which are important for their story but do not fit with the main offline article form. For instance they publish cell culture data, additional nuclear genotyping, explaining cartoons, things, measuerments that can be excluded from the strict line of argument published in the paper, but othervise necessary to gain a larger picture, a more complete understanding and get enough experimental details in order to repeat the experiments properly which is a crucial point in accepting scientific results. Long story short: there are 2 heterogeneous types of information in the online “supplementary” sections of scientific articles: i., web genuine digital multimedial files that cannot be published offline, but otherwise crucial and ii., additional “paperlike” data, which theorethically could be published in the main article, but there is not enough space for that due to formal editorial restrictions or simply they are not fit into the main argument, the storyline of the published study.

The problematic status of supporting information comes from the above heterogeneity of its data: namely there is not a unifying principle by which these data could be presented as one besides the fact that they are the accessories of a published formal article. Sometimes you can read the supplementaries as a draft of an independent article, as the alternative “story” of the published one with (slightly) different results and conclusions in focus. And the artificial heterogeneity of supporting information is originating from the fact, that scientific results must be published (or perish!) in a traditional peer-review way in an offline, linear, strictly copyrighted journal so the scientifically more and more important multimedia files simply cannot fit into the world of traditionally formalized, published, copyrighted journals. From that problematic status I would like to derive an open-source like argument concerning supporting information in one of my next posts.

Update:
Let’s make ’supplementary’ peer-review scientific videos free and youtubish!
Nature Publishing Editor on the idea of a public scientific multimedia site

Nature: About supplementary information

JoVE 2.0 makes science social and pop: video sharing, comments, interviews

You must definitely check the completely redesigned, upgraded JoVE website to see the enhanced present of online science! Journal of Visualized Experiments (JoVE) is an online journal publishing visualized (video-based) biological research studies. It was launched in November, 2006 and now due to the hard work and entrepreneurial spirit of editor Moshe Pritsker, web developer Nikita Bernstein and others it became a mature adventure, that is sporadic with its advanced features within the current online scientific community. What are the main novelties? Well, they are mostly technical and partly content related. First, on the right the videos have a cool textual chapter menu, so you can jump instantly to the part you are interested most. (See the picture below) Second, related to the protocol video Studying aggression in Drosophila (fruit flies) there is an interview with Edward Kravitz. I find the interview option a huge step forward, if it will be regular here besides the protocol videos, that has the chance to make JoVE and life sciences really popular on the web. Interviews can serve almost as videoblogs.

Third, if you are logged in, you can comment the videos and start a discussion and this is a big opportunity for life scientists to share video protocols and insider tricks and to learn techniques and repeat experiments properly.

Cord blood stem cell therapy without immune suppression?

The first scientific review of the rationale for the practical use of umbilical cord stem cells without the use of immune suppression was published in the Journal of Translational Medicine and it is freely available: “the authors propose that expanding the use of cord blood to non-preconditioned adult recipients for regenerative purposes would be a great step for the practical advancement of stem cell therapeutics. By overcoming allogeneic barriers in regenerative medicine, the fundamental limitations of autologous cell therapy may result in effective standardized “off-the-shelf” cellular products for regenerative therapeutics.” Source

Early progenitor cell number as organ size determinant: pancreas

Developmental biology is the gold mine of stem cell biology. A pioneer, but elegant quantitative cell biology paper was published in Nature advance online publication on 28, January 2007 by U.S. researchers Stanger, Tanaka, Melton along developmental lines.
Based on the strict regulation of vertebrate development it was thought that extrinsic or systemic signals, growth factors and apoptotic factors have a decisive role in determining and restoring the final size and shape of an organ even after big cellular loss during embryogenesis and regeneration. Extrinsic signals regulate size in many vertebrate tissues, including blood, liver, muscle and the central nervous system by controlling cell proliferation or by modulating cell death. Not in mice’s pancreas! Two different methods—cell ablation and tissue complementation—were used to perturb precursor cell number during the earliest stages of pancreatic and liver development. Liver was chosen because of its close developmental relationship to the pancreas. Transgenic mice strains were used, in which pancreatic and hepatic progenitor cell number can be regulated, ablated, restored. To assess the capacity for compensatory growth, embryos were generated in which many, but not all, progenitor cells were ablated.

Setting aside the complicated (really) technological details it was showed, that “compensatory growth during pancreas development is either quite limited or does not occur at all. Thus, embryonic progenitor cells represent a critical and limiting determinant of pancreas size.

How to filter and read PubMed articles through RSS feeds?

How many people out of you, life scientists, are regularly updating their PubMed searches through RSS feeds? According to the Read/Write Read Blog 2006 Web Technology Trends “While 2006 can’t be seen as the breakthrough year for RSS in the mainstream, we will probably see RSS bloom in 2007″. It’s January, 2007, so let’s upgrade a little bit.

PubMed is despite all its problems and oldschoolness is the major information source of peer review articles in the field of life sciences. You can make it a little more fresher if you create and save your PubMed searches as RSS feeds. With that users can retrieve new items of their saved PubMed searches since the last time they were connected to their RSS reader. There are numerous RSS readers to choose from, many available for free: Google Reader, NetNewsWire Lite, even web browsers, like Safari, Firefox have built-in readers. Here is the text&screenshot tale of how to activate this useful option:

1. Run a search in PubMed. Say you’re hungry for the novel articles and reviews to the search term “skeletal muscle stem cells” (as I am now), because you are writing an article draft.

2. Choose RSS Feed from the Send to pull-down menu in order to create a feed for that concrete search.

Nature Medicine 2.0 alarms by its editor in chief

Oops, the folks at Nature Publishing Group are more and more watching us, the people of the second-generation Internet, you know the two point oh. Recently, the editor chief of Nature Medicine (impact factor 28.878 in 2005), Juan Carlos Lopez wrote and editorial and even a blog post concerning “what is the Web 2.0–driven scientific publishing world going to look like?” The editorial is a static monologue by form, but at the end of it, there is an outgoing link to the dynamic blog post. And a post is successful, when it becomes a dialogue and that success is fulfilled only through comments.

In the traditional academic environment an editor in chief of a peer-review journal like Nat. Med. is in a position of enormous power from a point of view of an experimental scientist interested in submitting a paper. But this time it is not the case, the emphasis is on the survival of the traditional brand based and peer review model: “One idea is that the community will increasingly do without high-profile journals to decide what an important paper is and what it is not. If many scientists get together to discuss papers in social-networking sites, they may provide visibility to papers published in obscure journals and deprecate articles from more visible titles. If this becomes the case, and if high-profile journals make enough editorial mistakes while selecting the papers we publish, then the value of those publications will indeed go down.” In a fractionated tribal niche world, like the current web “is there room for journals like Nature Medicine?”

Big volume brain repair through escaped neural stem cells in mice

In the 15th, December Cell issue Kuo et al. published a study according to which “mice whose brains were severely damaged by loss of the genes “Numb” and “Numblike” in one region just after birth showed substantial mending within weeks. The researchers attributed that repair to neural stem cell “escapees” that had somehow retained or restored the genes’ activity and, with it, their regenerative potential.” Effectively a big brain hole was largely repaired. The finding casts a light on the amplification of the neural plascticity in the subventricular zone stem cell niche. Here you can read the abstract.

Google Scholar: story, goal, founding engineer and team

Probably you people in life sciences and biomedical fields with open eyes to current academic and advanced web developments (like BioMed Search and JovE) have happened to meet and try sometimes Google Scholar, Google’s own scholarly search engine, leaving PubMed for a moment behind. Now here is an interview with Scholar’s founding engineer, Anurag Acharya on the story, aim and progress of Scholar:

“Can you tell us something about how Google Scholar came about?

Alex Verstak and I used to work on building Google’s web index. This was very hectic work and after several years of it, the two of us took a break — a sabbatical of sorts — for a few months. Google Scholar came out of that sabbatical. I had already been working on including scholarly literature in Google’s index. For the sabbatical, we worked on improving indexing, automatically extracting metadata and ranking for scholarly literature. Our hope was to weave this information into Google web search. But “there’s many a slip betwixt the cup and the lip.” A working demo we sent out internally became popular and Google Scholar was born.

The image of science: Google-like Biomedical Image Search Engine for pros

Check out the brand new BioMed Search, it is fantastic, currently over 1 million images have been indexed from peer-review journals in biomedical fields and more is on its way. BioMed Search has been created by Alex Ksikes, currently a Ph.D. candidate in Computer Science with focus in Computational Learning Theory at the University of Cambridge (good town, good to be here). The About says: “The goal of BioMed search is to organize figures, images or schema found in biomedical articles. BioMed Search indexes image captions along with the citations to these images. “ Pictures can be seen with full and thumbnail view. Recent Searches, my favourite, show terms recently searched for, with which you can catch research trends. If the number of users grew exponentially, a digg-like real-time spy could spectacularly dinamise the site.

With BioMed Search you can search for general terms like mitochondria, phrases like “proteomics”, search in the title of the articles only for “Mfn1″, get images from an article with a concrete PMID (PubMed Identifier), find images authored by “Nicholls”, limit results to content from a specific year date:1996 (actually just from 1996 presently), and limit search to a specific journal. And this is just by default.

Young science people with an entrepreneurial spirit full of diy hacker skills backed by current web technologies, like Alex Ksikes, who is a real coder, and Moshe Pritsker, biologist, founder of Journal of Visualized Experiments make filtered academic information instantly and easily accessible. And so academic scholar science becomes not just updated, but simply …cool.

via Google Blogoscoped, thanks Anna for the terrific tip.

Thanks Alex Ksikes to make this happen.

JoVE stats: blogosphere and Nature News traffic before official launch

The first official issue of the new biological video protocol site JoVE or Journal of Visualized Experiments will be available today 11 pm EST, November 30, 2006. The graph shows November traffic in term of unique visitors, first 2.5 weeks mainly uploaders, authors, editors and editors’ friends used the page, from 17th there was a mild scientific blogosphere coverage, like Pimm, Blog around the clock and Easternblot, and from 24th, November, it was the Nature News article (no longer available, only to subscribers) aided by blogs, that generated the heaviest traffic, that led even to a server change.

Moshe Pritsker, founder and editor of JoVE says: “The first launch means more organized format (articles by categories), certain dates of issue. Later we plan to increase the qualities of the video-articles. The idea is to create a scientific publication with all the characteristics of publication, to avoid the Youtubish comparison, while remaining flexible. The site will have a different design and more video-articles, including ones from famous ES cell labs.”

Thanks Moshe for the data.

More on science video protocols: Science: video protocols can help to share the tacit dimension, Early science protocol video: OpenWetWare Drosophila CHiP

Human heart mitochondria and nitric oxide production: hard work

I’ve almost missed the publication of an article by our group back home, in Budapest which is my first real first author peer-review article published in Life Sciences, impact factor, 2.512 as of 2005. The peer-review process was hard (illustration: me under the hood) and bloody, because it is a negative result, so you have to be more careful and logically step-by-step. We’ve eventually showed that Human heart mitochondria do not produce physiologically relevant quantities of nitric oxide. Take care, it is hardcore science without any popular tone. Abstract here:

hESCs derived from single blastomere by Lanza et al.: second trial in Nature with success

In science you can always correct yourself. In stem cell research it is of utmost importance to correct what you’re claiming, if you’ve claimed it not accurately enough before. Now in November 23 Nature magazine the Lanza group has a corrected manuscript on Human embryonic stem cell lines derived from single blastomeres on the possibility to generate human embryonic stem cells from a single cell that is isolated from an in vitro eight-celled embryo during routine preimplantatation genetic diagnosis (PGD). So it is an ethically non-controversial way to collect human embryonic stem cells, although it is working only in the case of in vitro fertilized embryos. Safety concerns of the protocol are perturbations of genomic imprinting due to the longer time the embryo remains in vitro during the process. As Joe Leigh Simpson says in the News and Views commentary: “This work with human blastomeres follows a demonstration by the same group that ES cells can be derived from single mouse blastomere. In these earlier mouse experiments, an intact viable embryo developed that consisted of the seven remaining blastomeres; by contrast, in the work with human cells, multiple blastomeres were taken from the 8-cell stage and no embryos were allowed to remain in culture. This was a source of confusion in the earlier online publication.”

See also: Editor’s Summary, Bodyhack, New York Times