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This is me, Horst Ibelgaufts, the author of COPE.


picture of the author


I am pleased that you have consulted my encyclopaedia. Curiosity - what else? - must have brought you to this entry. If a (strange) link from within COPE brought you here consider it as one of my private jokes (i.e., some terms have been programmed to act as synonyms for Zzzz ... zzzz ... zzzz.

But since you are on this page now, let me be frightfully educational. I'll share with you my (unsorted) list of some strange examples of scientific writings I have come across during the preparation of COPE. As time goes by I shall provide suitable references. When I started this entry quite some time ago, I thought it best to be more general and show consideration by giving no references. Well, I have changed my mind.


Quite a few scientists do not seem to be capable of expressing themselves unambiguously. Some of the examples below make you wonder what editors and reviewers are good for. Sometimes I feel that the former nowadays only shuffle computer disks or files holding publications from one desk or computer to another and care for the market value of publications, while the latter are just concerned with pressing scientific issues (have our own papers been cited appropriately?) and cannot be bothered with linguistic intricacies and matters of style - if they have noticed them in the first place. (BTW, I wonder whether you jumped back in the sentence above to find out who "the former" and "the latter" are. Just a matter of (bad) style, of course :-), but what an impediment to understand quickly what one reads (and you'll find more of this in the examples below).


Let me repeat and slightly rephrase a statement I cite in my foreword to COPE: "Demonstration that under certain circumstances certain differences are observable between different reactions taking place in various systems." Very informative statement, this. But the original - I have forgotten where I got it from - was meant as a joke. The examples below show that some of them easily match the quality of the statement above in their succinct evasion of facts.

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Be brief
¥ 1123 out of 1772 characters in the abstract taken up by an explanations of acronyms used (Calixto et al, 2004). Good Gracious. If there was an editor, he or she must be practicing for a new career as a politician. On second thought, however - a safe way to be detected by these automatic text mining and string search algorithms. Right? Right!

¥ I probably miss a point when I see the long list of abbreviations taking up 22 % of the abstract. But then, it is a review and one can again always hope that it pleases a text miner (Dai and Rabie, 2007)
¥ an abstract of 1894 characters, which includes 800 characters for abbreviations (Palmqvist et al, 2008)
¥ almost 50 % of the abstract text taken up by references (Daniel et al, 2009)
¥ 1236 characters out of 3522 in abstract used for citations (Tang et al, 2009)


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acrynomaniac acronymania
I refrain from creating subcategories ("funny peculiar - not funny ha ha", "idiotic", "Tom-Dick-and-Harry") but admit that it itches in the fingertips.
¥ try to query a databank to find follow-up articles dealing with MICE. The same goes for AMID, BLAME, DARK, ICE, LICE, LIGHT, MINOR, SECRET, TACTILE, and others that I cannot be bothered to look up now. No joke, really, but then some of them are good for making limericks, which, I suppose, was not the original intention of the authors. :-) (Or are these acronyms all meant to be frightfully educational, forcing users to use MeSH terms rather than freetext searches in Pubmed or encouraging/precipitating/raising awareness of unrelated subjects?)
¥ my all-time favourite, the mother of all battles with useless abbreviations, so to speak, is UGF.
Why not check databanks before creating a new acronym that already has multiple other meanings. Drop me a line if you come across other noteworthy specimens.


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'broader views' are a just a bloody nuisance
believe me, it is more than a truly British phenomenon (bloody, I mean).
¥ Reading that certain factors are expressed in hematopoietic cells and other factors are not always makes me cringe. Of all the umpteenth cell types I know I can exclude neurons, chondrocytes, fibroblasts, epithelial cells, endothelial cells and others when I come across this term, but that still leaves me with a wide choice, does it not: myeloid cells (erythrocytes, thrombocytes, neutrophils, monocytes and macrophages, eosinophils, basophils, mast cells) and lymphoid cells (B-cells, various types of T-cells, NK-cells). So, which ones, please
¥ what I said above goes, of course, for all the umpteen publications using collective terms such as brain cells, liver cells, gut cells, glial cells, blood cells, leukocytes, lymphocytes, granulocytes, vascular cells, et blah cetera.
¥ the ultimate folly (at least for me) is a statement like the following: 'CTFP stimulated proliferation and migration ... ... of cells in culture.' (Smith et al, 2006). After what I said above, I don't think I have to explain that further. After all, as the Cell lines and Cell types subdictionaries of COPE show, there are only a few options to choose from.

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hey-you nomenclature
¥ articles reporting 'activities' without biochemical characterization and without giving them a proper name. This applies equally to articles describing the "initial biochemical characterization" of a factor reporting on, for example, a tentative molecular mass or pI. This reminds me of a cartoon I saw many years ago where one old man sees a group of youngsters approaching the park bench on which he was sitting. "you can always tell if they come from a large family", he mutters to himself. All children wore T-shirts with their name on it, bar one, which had "Hey you".

¥ some people really do have nerves with names, and no mistake. I do wonder why one would want to call a factor nIL-1F [novel IL-1 family] (Wang T et al, 2009). As "noteworthy" as UGF, isn't it?


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nebulous or not so nebulous irrelevancies
¥ 'the relevance or significance of the reported findings will be discussed' Surely, something of significance should be stated in the abstract. Or would an explicit statement of the significance have blown up the abstract, I wonder?
¥ 'cautionary points and broad recommendations are made with regard to use of this antibody' (Sewell et al, 1987) Good Gracious, this is one sentence out of 3 in the abstract, the first sentence telling you little more than the name of the antibody and that it was used on epithelial cell types and the second informing you that "other" epithelial markers were also studied
'please note that the abbreviation for the gene is given in italics and the abbreviation for the protein expressed by the gene is given in capital letters' (Buxton et al, 2001). Well, thanks for the information, but does that belong into an abstract?

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called to the bar
¥ there is one thing that positively makes me cringe: reports of serum levels of cytokines, growth factors, or interleukins, or whatever other factor with data presented in a bar diagram with error bars (and sometimes other fancy lines that are not explained) and no mention of the real figures in the entire publication. Of course, one can always print out the graph, magnify it by photocopying, and use a ruler (Liao et al, 2004; Zhu et al, 2011; Zhao et al, 2010; Mihret et al, 2012; mind you there are many more examples. These are just the ones I encountered recently and remembered to include here). I simply refuse to cite such articles in the Cytokine Concentrations in Biological Fluids section of COPE. What am I? A graphic artist with a ruler and a lot of patience to sort out data points that make a diagram look like an artists impression of a snow storm (Mihret et al, 2012)?

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dŽjˆ vue 1
¥ I have seen abstracts reporting a "surprising observation". Indeed, sometimes I realize that the same surprising observation was made in the same lab (and published) some years earlier. Am I to assume a total brain drain from the lab with newcomers filling the void not knowing about previously published results? Surely not, as some of the authors are the same. Apart from that, a pubmed search reveals 234 articles with "surprising observations" in the abstract. I am surprised.
¥ identical abstracts in two different journals with a bit of exon shuffling among the authors. What was that about 'publish or perish'?
¥ '...results are consistent with previous observations...' The abstract cites earlier publications essentially reporting the same data - or should I say: 'same data reporting mainly the same authors'? But let us be positive: is it not always uplifting to hear that some experiments, when repeated, seem to yield the same results even though they are reported by the same conglomerate of authors? Again, I have observed that more or less the same stuff appears in two different journals either in the same year or a couple of years after the first publication. Ah, I forget: as everyone knows who has ever applied for a professorial position, applicants are frequently reduced to spreadsheet format of the type "so and so many publications in so and so many high impact factor journals, with so and so many as first author etc etc. Every published article counts. (books, dictionaries, encyclopedias, including COPE, by the way, don't count and can actually have adverse effects on your career, but that is another (long) story and, thank goodness, personal history best forgotten).


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dŽjˆ vue 2
¥ identical abstracts in two different journals with a bit of exon shuffling among the authors, sometimes not even years apart. What was that about 'publish or perish'? I have decided now to list such examples as I come across them (again). For a first example see: Hashimoto et al (2002), Hashimoto et al (2002)

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inverse linguistic insults
¥ statements that factor-2 expression is inversely correlated with whatever (lethality, mortality, malignancy), or negatives (repression, inhibition, downregulation) sounds frightfully learned. Why not simply say, for example that low expression of factor-2 correlates with a high degree of lethality - if it is really necessary to talk about correlation, even though a sentence such as 'the lower the expression factor-2 the higher the lethality' or something similar would express the same fact.
¥ I admit that my command of English is so poor that I have to read the following statement several times to understand its implications: 'receptor expression correlated reciprocally with an ongoing unresponsiveness to receptor agonists' (Salentin et al, 2003)
¥ 'Inverse regulation of plasticity-related immediate early genes by calcineurin in hippocampal neurons' (Lam BY et al, 2009) in an article title is also nice. Just wonder what it means.


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guess who - guess what
¥ stating in the title or abstract that whatever biological process or activity is affected by cytokines is as informative as the witness of a hit-and-run accident informing the police that the car was driven by a human being
¥ what do authors mean by 'factor-2 modulates/affects/influences (expression or something else, activity, cell functions, etc)'? Three of the most uninformative words in a scientific abstract that I can think of (especially when the "effect" is in the title of the article and there is no abstract at all (as one of many examples: Biffoni et al "Effects of beta-casomorphins and met-enkephalin on human natural killer activity". Sounds like politicians who simply don't want to show colour. Whatever effect there is, it is either positive or negative (increases, decreases, shortens, prolonged, etc etc). This should be made clear by using appropriate terms. And journals (cited in PubMed, of course, that allow articles without abstracts .... (choose your pet expletive!)
¥ when one is not in the know, statements like the following about changes that are not observed are quite confusing. Do cells express these antigens, or don't they? 'CD14, CD15s, CD64, and CDw65 molecules were downregulated to background levels. No major changes were observed for CD11a, CD32, CD33, CD48, CD50, CD86, CD92, CD93, or CD97' (Pickl et al, 1996).
¥ 'Effects of M-CSF on the activities of murine monocytes and peritoneal macrophages in vivo' (Katsura et al, 1992). Why not be more specific and informative by using verbs such as 'upregulate, downregulate, prevent, block, inhibit, repress, etc'. Would you imagine a newspaper headline such as "Effects of an armed man on shopping crouds"? Sounds like one of these non-headlines on the front page of Yahoo, where this is used to make you click further on so that you can be exposed to yet another lot of unwanted and boring advertisements.
¥ 'Induction of cytokines and chemokines in human endothelial cells by ...' There are several ways of making a title similar to this even less informative. What about 'Induction of cytokines and chemokines in specific primate cell types', 'Induction of protein mediators in specific primate cell types', 'Modulation of protein mediator expression in primate cells'. Titles of this type are as good as a newspaper headline reporting that 'the president said something' - but then presidents and other politicians, like lawyers, are not known exactly for being able and willing to make clear statements. But do scientists have to take them as role models?
¥ 'Opposite regulation of tissue factor expression by calcineurin in monocytes and endothelial cells' (Hšlschermann et al, 2001). I can assume only that in one cell type tissue factor expression is upregulated whereas it is downregulated in the other cell type or vice versa. To me this sounds like a newspaper headline: 'President and Leader of opposition shot. One dead.'
¥ 'IL10 and IL4 have contrasting effects on release of soluble TNF-alpha receptor by cultured monocytes' (Joyce et al, 1994) well, who does what then?
¥ 'inflammatory cytokines' when the article only deals with two specific factors that might as well have been named
¥ 'effects of factor-2 on ABC cells' when the article only describes one or two specific effects that could have been named
¥ 'epidermal cells' when the article deals specifically with keratinocytes or Langerhans cells
¥ 'the remainder of the activity was largely retained by an affinity column coated with an antiserum that recognizes IL6 and a number of other known and unknown cytokines' (Hoeben et al, 1996) Why not name at least the known cytokines?
¥ 'Activities of (name any cytokine) on (name any cell type)'. Surely, if the publication is not a review or if there had been many different activities, the authors would have maximized their scientific findings into a couple of different publications. So why not name the activities explicitely in the title? The same goes for articles that have something like 'differential effects' or 'differential expression' in their title. After all, one could have gotten a lot of mileage out of "differential effects and expression". Just imagine: paper 1 describes the expression of a factor in one cell type. Paper 2 reports expression in another cell type. And if there were alternatively spliced isoforms involved - the possibilities are countless :-)
¥ 'we have studied the expression of a wide range of pro- and anti-inflammatory cytokines and their receptors...' (Morris and Esiri, 1998) I am sure that two lines would have sufficed to name the cytokines studied.
¥ 'confirmed that rat aortic vascular endothelial cells expressed semaphorin 3A as well as other class 3 semaphorins (sema 3s). well, since there aren't that many class 3 semaphorins it would have been more informative just to name the others instead of using the rather awkward plural form sema3s (Damon, 2006)
¥ To learn that factor-2 elicits a biological response in a given cell type is nice. It would have been nicer even if the authors had provided species information, especially when the small print reveals that factor-2 from one species was actually active in another species (see also: Cytokine Inter-species Reactivities). Incidentally, many abstracts/articles leave you in the dark about the species identity of cytokines or growth factors employed in in vitro or in vivo bioassays
¥ "pro-angiogenic, anti-angiogenic, pro-apoptotic, anti-apoptotic, pro-inflammatory, anti-inflammatory - factors" Titles of scientific articles make heavy use of these adjectives when in reality, only two or three factors were studied in most instances. So why not name them.
¥ 'Pro-inflammatory cytokines induce expression of matrix-metabolizing enzymes in human cervical smooth muscle cells' (Watari et al, 1999). With only a few factors around and so few genes available for expression the title is quite clear, isn't it?
¥ 'Pro-inflammatory cytokines induce expression of matrix-metabolizing enzymes in human cervical smooth muscle cells' (Parker et al, 1990). The same. The article is about TGF-beta and bFGF. I just remember, I only sell pots and pans. But advertising myself as the kitchenware specialist sounds much better.
¥ "Various TLR1-9 ligands and NOD2 agonist muramyldipeptide (MDP) were investigated. Our results showed that certain combination of ligands had additive effects on upregulating microglial P2X4R at both mRNA and protein levels, and induced nitric oxide increase and TNF-alpha production" (Guo et al, 2006). How very informative (apart from the fact, of course, that a freetext search for TLR-1, TLR-2, TLR-3, TLR-4, TLR-5, TLR-6, TLR-7, TLR-8, TLR-9 is not possible.
¥ "we find that CT-1 induces and suppresses the expression of the same set of neuropeptide and neurotransmitter synthetic enzyme mRNAs as do LIF and CNTF" (Cheng et al, 1997). A one-liner about which neuropeptides and neurotransmitters would have been very helpful
¥ "Nine different chemokine mRNA and proteins were expressed because of noncognate interactions between T-cells and endothelial cells. Cognate interactions induced de novo expression of four chemokines and upregulation of seven chemokines. Levels of CCL3, CCL8, and CXCL10 secreted into supernatants were in the nanomolar range and were chemotactic for T-cells and monocytes. Blocking antibodies to HLA-DR and LFA-3 abrogated production of CCL3, CCL8, and CXCL10. Blocking antibodies to IFN-gamma and TNF-alpha inhibited CCL8 and CXCL10 but not CCL3 production. CCL3 and CXCL10 were produced by both T-cells and endothelial cells (Tay et al, 2004). Which cell types produce what then? One of many examples of reports describing results of coculture assays and keep me guessing.

¥ "... we show that BILF1 heterodimerizes with various chemokine receptors ..." well, it looks as if naming the few chemokine receptors (and thus to have been more informative) would have blown up beyond tolerable proportion the short abstract of only 130 words (Vischer et al, 2008). BAH!
¥ "... a number of members of the matrix metalloproteinase (MMP) and a disintegrin and metalloproteinase with a thrombospondin (ADAMTS) families were significantly downregulated. ....". How much is "a number"? Too many to name the few Matrix metalloproteinases and ADAM protein family members in the abstract? Usually, when one finds sentences like this "a number" means "a few", and these could have mentioned.

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Yes, we have no bananas?
¥ "... None of them remained stable in the presence of gastrointestinal enzymes: they were partially, or even totally hydrolyzed to smaller peptides - yet the observed ACE inhibitory effects were not severely affected for two of those peptides." (Tavares et al, 2011). 'them' is peptides derived from alpha-lactalbumin and beta-lactoglobulin that inhibit angiotensin-1 converting enzyme (CD143). Hm hm, Now, why did I put this here and under a heading like this?

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positional effects
¥ ' ... its depletion in glioma and glioma-derived stem-like cells led to decreased cell proliferation and apoptosis.' (Augustin et al, 2012). What the authors want to say is "decreases cell proliferation and induces apoptosis". Anyone not really quite versed in proliferation and cell death matters will fall into the 'led to decreased' positional trap.

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a knife without a blade from which the handle is missing
¥ 'her plasma histidine-rich glycoprotein level was only 21 % of the normal level of 109.5 ± 51.5 % (mean ± 2 SD)' (Shigekiyo et al, 1993). what? micrograms, milligrams, grams? Per what?
¥ 'mean Histidine-rich glycoprotein level of blood-type AB subjects, 125 ± 28 %, was found to be significantly greater than the means for subjects with A and O blood-types, 103 ± 35 % and 105 ± 30 % respectively' (Drasin and Sahud, 1996). Oh well, as long as it is not parts of drams per fluid drachm or something like this (much more fun :-) than metric). But still, I would have like to know what units.
¥ (0.45 ± 0.09 vs. 0.38 ± 0.08 vs. 0.40 ± 0.07; P<0.0005); (2.91 ± 1.25 vs. 1.74 ± 0.77; P <0.001); (3.21 ± 1.24 vs. 2.60 ± 1.24; P <0.0001); (1.31 ± 0.54 vs. 1.16 ± 0.34 vs. 2.78 ± 1.10; P <0.0001) I am confident (P <0.0001) and annoyed and won't even bother with telling you what these figures without units are all about (Choi et al, 2012)

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whodunnits:
¥ 'expression of hepatocyte growth factor is induced by the interaction between human mesangial cells and monocytes' (Koyama et al, 2003). 'Interaction between human monocytes and vascular smooth muscle cells induces vascular endothelial growth factor expression' (Hojo et al, 2000). At least the authors already state in the abstract that both cell types produce the factor. Often, authors just don't.
¥ 'Neutrophils, monocytes, and lymphocytes bind to endothelial cells through .... name any CD antigen you can think of'. It would not require much linguistic finesse to make quite clear which cell type expresses the CD antigen or its counter-receptor. After all, we are not talking about two people holding hands and most of us don't go to bed with a CD antigen facts book to memorize numbers and recall them like the products of the multiplication table.

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pomposity:
¥ to use something like 'cytokine profile' in the title of an article describing the comparison of different monocyte populations is pompous when you find out that expression of just two cytokines was assayed.
¥ Likewise, to speak of 'cytokine-stimulated human MŸller cells' obviously adds more weight to a title even though the only cytokine studied was IL1-beta (in addition to LPS, which surely is not a cytokine (Yoshida et al, 2001).


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Vanity Fair:
¥ what I meant as a joke, namely the generation of some extra unnecessary new names such as nokines or dangerokine (and a few others that you may or may not discover) also happens in reality. I have no respect for people who, without necessity, invent a new name (cartonectin) for something that has already a given name (cartducin) and is known also under other names, mainly for those who are interested more in domain structures than functional activities (C1QTNF3 [C1q and tumor necrosis factor related protein 3]. (SchŠffler et al, 2007). But there is always the chance, of course, that I have missed a point again and that this new name was necessary and not just given out of personal vanity. Or should I just lean back and say 'who cares?' After all, another dictionary entry for the factor-collecting lexicologist.


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O Tempora O mores:
¥ "Disclosure of potential conflicts of interest is found at the end of this article." O Tempora O Mores. Why do I find a sentence like this at the end of a scientific abstract? (Lawrence et al, 2007). Just wait a bit and the ominous "No animals were harmed or hurt during the performance of the experiments and only some scientists involved in this work suffered a bit" et blah cetera will also turn up. Should the abstract also contain a sentence like "the authors declare that no competing interests exist"? (would wearing an Armani lab coat (to get better results) received as a gift maybe from a company representative be seen as "conflicting"?)


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When in Rome do as the Romans do?

I am old-fashioned, and I am not in Rome. Numbers for me are numbers and letters are letters. I positively loathe Roman numerals. Designations containing them should be banned from biomedical literature.


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Get a free drink if you read my paper
¥ "Since these tissues consist of a variety of cells, we sought to identify the primary cell(s) responsible for LGR7 expression and relaxin responsiveness" (Horton et al, 2009). Well, if the abstract containing this sentence does not qualify for an entry here, nothing does. Now, since I don't have access to this publication I shall never know what could easily have been added to the abstract.
¥ '... several members of these molecule families (e. g., CD40L, CD30, CD27, OX40) have been studied. Most of these molecules are expressed also by tonsillar B-cells.' (DŸrkop et al, 1997). And which is/are not?
¥ 'showed significant increases in 16 out of 34 factors tested' (Nagorsen et al, 2004). If the abstract can list 10/16 factors, it can also list all 16 factors.
¥ 'a number of cytokine mRNAs are expressed de novo' (Borkowski et al, 1997). Oh well, we all know that there are only a few cytokines anyway. So an educated guess cannot be far from the truth, right? The only excuse in this particular case seems to be that the full article is available in Pubmed Central - and even then ...
¥ 'These gene fragments were sequenced and found to correspond to known genes, although only one has previously been isolated from chondrocytes.' (Jefferies et al, 1998) Learning from the abstract that the authors just talk about 3 genes I wonder what prevented them from naming them.
¥ 'expresses a number of lineage-specific markers as well as a broad array of intercellular adhesion molecules' Unless a publication deals with microarray gene expression studies nothing can be so "broad" that it cannot be stated explicitly in an abstract, not to mention the markers (Dialynas et al, 1997)
¥ 'Among all CC-Chemokines and CXC-Chemokines genes studied, only MCP-1 and IL8 mRNA were expressed by nonstimulated normal fibroblasts'. So, which chemokines were studied? (Galindo et al, 2001)
¥ 'Effects of galanin on hormone secretion from in situ perfused rat pancreas and on glucose production in rat hepatocytes in vitro' in this case 'effect on glucose production' means no effect. (Silvestre et al, 1987)
¥ 'expression of 17 MMP genes was defined by Q-RT-PCR. Several MMP genes were profoundly upregulated and every tumor showed overexpression of at least four MMP genes.' To this I can say only "Hier steh ich nun, ich armer Tor. Und bin so schlau als wie zuvor' (drop me a line if you want a translation :-) (Martinez et al, 2005)
¥ 'Levels of type-1 hereditary hemochromatosis gene (HFE), transferrin, hepcidin, transferrin receptors 1 and 2, Ferroportin-1, divalent metal transporter 1 (DMT1), natural resistance-associated macrophage protein 1 (Nramp1), ceruloplasmin, hephaestin, and glyceraldehyde 3-phosphate dehydrogenase (GAPDH), were measured by quantitative reverse-transriptase polyerase chain reaction. We show that hepatocytes express almost all the iron-related genes tested ...' (Zhang et al, 2004). Keep me guessing, please, as I have nothing else to do.
¥ 'DDR1 and DDR2 mRNAs were detected in each major human cell type of the cornea. .... DDR1 and DDR2 proteins were detected in all three major cell types in culture and in human corneal tissue. ...' (Mohan et al, 2001) - oh well, everyone knows all (three) major cell types so why bother to name them
¥ 'Double immunofluorescence with cell-type specific markers showed that multiple cell types in the injured brain produce MCP-1' (Denker et al, 2007). Naming the cell types would have been much more informative.

¥ The tissue distribution of ADAMTS14, the regulation of the gene expression by various cytokines and the activity of the recombinant enzyme are evaluated. The potential function of ADAMTS14 as a physiological aminoprocollagen peptidase in vivo is discussed (Colige et al, 2002).
¥ Good gracious! Even though these people are talking about the results of a microarray study they refer to just a few genes of interest, which they could have named: 'In the CTCM group, four genes were upregulated, three genes were downregulated, a single protein was downregulated and a single protein was upregulated when compared to the control group. When the CTCM-treated group was compared to the SLT-IIv group, expression of one gene was found to be increased, and all other genes were decreased, with five proteins downregulated (Yi P et al, 2010).
¥ 'Obvious differences were observed in proteinases' expression pattern between the investigated cell types (Baginski et al, 2011). Well, three different cell types and quite a few peptidases were studied. These are all listed in the Methods section of the abstract. It would have been much more informative had they been listed with the cell types.
¥ '... these peptidases hydrolyse a series of neuropeptides with similar rates and at sites reminiscent of those elicited by classically purified human brain EP24.16c. All neuropeptides, except neurotensin, were similarly cleaved by recombinant endopeptidase 3.4.24.15 (EP24.15, thimet oligopeptidase)' (Rioli et al, 1998). Nice to know that neurotensin was an exception. Even nicer: to have been told in the abstract what this series of neuropeptides was.
¥ Retinol-binding protein 4 (RBP4): a biomarker for subclinical atherosclerosis? (Stuck and Kahn, 2009). I shall never know. Pubmed says 'No abstract available' and I have no access to the publication. oh well ...
¥ '... with most of the genes preferentially expressed by professional antigen-presenting cells (dendritic cells, macrophages and B cells) and neutrophils.' (Flornes et al, 2004). You want/need to know more than "most"? Your library does not have the journal? Just pay EUR 34.95 to the publishers. I am beginning to wonder whether scientists are approached by publishers to write things like this. Times are getting harder. Scientists should ask for royalties.

¥ and this attitude of uttering what I consider the scientific counterpart of politician's plattitudes seems to be universal. All the more so when the only thing I can get from a Chinese language article is something like this ' ... 21 genes were significantly upregulated, including 10 growth factors and associated molecules, 10 extracellular matrix and its associated protein and 1 cell adhesion molecules. Two genes were significantly downregulated, including 1 growth factors and associated molecules and 1 cell adhesion molecules.' (Li YM et al, 2007)


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to be or not to be
¥ 'Is the effect of IL1 on glutathione oxidation in cultured human fibroblasts involved in transcription factor NF-kappa-B activation?' (Renard et al, 2001). Well, is it? Why use a question mark in the title when the abstract states that the authors were unable to show a direct relationship between IL1-induced glutathione oxidation and NF-kappa-B activation.
¥ Is the transient secretory response of chromaffin cells due to inactivation of calcium channels?' (Burgoyne Cheek, 1985). Cheeky. The abstract tells you that it isn't
¥ 'Is the presence of IL2 receptor-alpha in the serum of colorectal liver metastases patients derived from hepatic natural killer cells?' (Vermijlen et al, 2002). Well, if it is, why not say so? If it is not, why not state it? If the issue remains unresolved why bother to publish? (oh, silly me. How could I forget! Every paper counts. I knew that even before I saw that applicants for a professorship were sorted by the numbers of published papers in the spreadsheet, with a special column stating the number of publications with the applicant being first author.
¥ 'Is blah-blah antigen expressed on so-and-so cells?' well, with titles like this it is hardly astonishing that you find out the answer only after having read the abstract - and sometimes not even then.
I always wonder if Isaac Newton ever considered publishing his findings under the title 'Do all apples fall if dropped?' - which is not to say, of course, that the impact of any of these question mark articles comes anywhere near to the significance of Newtons's findings
¥ 'Before conducting detailed neurochemical and behavioral examinations of a recently generated relaxin 3 knock-out mouse strain, the present study determined whether this mouse was a viable model of relaxin 3 deficiency' (Smith et al, 2009). Is it or is it not? That is the question that the abstract could have answered easily.
¥ 'Is T-cadherin (CDH13, H-cadherin) expression related to lung metastasis of osteosarcoma?' (Takeuchi et al, 2000). Oh well, is it not nice when there are still open questions? And I, the poor blighter sitting in an office in the third world, shall never know for want of access to the publication
¥ 'Is 100KF an isoform of hemopexin? Immunochemical characterization of the vasoactive plasma factor 100KF' (Cheung PK et al, 1999). Is it? Well, the authors conclude that hemopexin may be closely related or identical to the active moiety of 100KF.
¥ 'Are antimicrobial peptides new players in skin cancer development?' (Emelianov, 2012). Well, probably not. Otherwise, we would have had a positive statement, right? Yet another addition to the list of published "papers".
¥ 'Is prolonged stem cell mobilization detrimental for hematopoiesis?' (Chigaev et al, 2011). Well, it is, as the abstract states clearly.


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Saying one thing but meaning another
¥ 'Expressions of CD1a and CD83 of Langerhans cells in the local lesions of epidermodysplasia verruciformis patients' sounds all ok before you discover that the abstract states that no CD83+) Langerhans cells are detected (Liang et al, 2009)
¥ 'functional analysis and expression of CXCR1 and CXCR2 on human eosinophils' (Petering et al, 1999) Nice title. Only, the abstract clearly states that the two receptors are NOT expressed by these cells either before or after cytokine stimulation.
¥ 'A study of the effects of angiotensins 1, 2, 3 and bradykinin on the replication of bovine retinal capillary endothelial cells and pericytes' (Porta et al, 1992). And what would have been wrong with stating in the title that none of the compounds is mitogenic for the cell types mentioned? A "Study in Scarlet" I can tolerate (more than that); a study of effects that are not there is a bit odd.
¥ 'Adhesion dependent release of hepatocyte growth factor and interleukin-1 receptor antagonist from human blood granulocytes and monocytes' (Takeda et al, 2004). Only granulocytes release HGF
¥ 'Expression of stem cell factor and c-kit mRNA in cultured endothelial cells, monocytes and cloned human bone marrow stromal cells' (Aye et al, 1992). Increasingly, I find, article titles following such a pattern have a meaning that deviates from normal English usage, which would suggest that all cells mentioned express all factors. Reading the abstract one frequently finds out that some cells do, other don't express one or the other of the factors mentioned. Hence the meaning of such phrases is "We studied the expression of blah blah blah but you have to read the abstract (or worse: the article) to find out who expresses what"
¥ just keep in mind that when people talk about cell lines and overexpression of a given cytokine or growth factor this often means "forced overexpression". Sometimes you learn this from the abstract. Sometimes this information can be gleaned from the Materials and Methods section of a publication
¥ "Expression of CD44s and CD44 splice variants in human melanoma" (Ranuncolo et al, 2002). To title an article like this is one thing. Until you read the abstract and find out that the splice variants studied are not expressed.
¥ 'Detection of this and that in so and so cells' says the title. The abstract tells you explicitly that this and that is NOT detected.
¥ 'Human kallikrein 3 (prostate specific antigen) and human kallikrein 5 expression in salivary gland tumors' sounds the title, but the abstract states that kallikrein-3 is NOT expressed (Darling et al, 2006)
¥ 'Effects of blah blah on blah blah cell types' well, don't be so sure that there is an effect. Not infrequently this titles like mean "we looked if there was an effect but there was none.
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respectively yours
¥ 'Mean ± SEM values in patients with grade 0 (n=23), grade 1 (n=12), grade 2 (n=14), grade 3 (n=16), and grade 4 (n=9) were 4.50 ± 0.46, 9.10 ± 1.0, 12.98 ± 1.22, 21.51 ± 2.63, and 58.26 ± 19.7 pg/mL, respectively' (Odeh et al, 2004). Surely, something like this can be, and should be, reorganized to make it more palatable.
¥ 'DHEA, DHEAS, and Allo protected rat chromaffin cells and the rat pheochromocytoma PC12 cell line, an established model for the study of adrenomedullary cell apoptosis and survival, against serum deprivation-induced apoptosis. Their effects were time- and dose-dependent, with EC50 1.8, 1.1, and 1.5 nM, respectively' (Charalampopoulos et al, 2006). Oh Goodness, why not make this a) longer, b) more scientific, c) more unpalatable by using compound names rather than acronyms, insert some more explanatory relative clauses, and - well, I forgot what I wanted to read, oh, say, respectively...
¥ 'As soon as 3 h after the antibody treatment, a marked increase in the number of chromaffin cells expressing mRNA encoding, respectively, enkephalin, calcitonin gene-related peptide, galanin, neurotensin and substance P was seen' (Dagerlind et al, 1994). Maybe I miss the point, respectively, inserted this sentence only to have some more internal hyperlinks. Who knows.
¥ '100 % and 80 % of the five tumors tested exhibited V1a and V1b transcripts, respectively' (Grazzini et al, 1999). Sounds, of course much more scientific than "all 5 tumors expressed V1a, and 4 of them expressed V1b.
¥ 'The diadenosine polyphosphates, Ap3A, Ap4A, Ap5A and Ap6A, displaced [3H]-Ap4A from the two binding sites, the Ki values being 1.0 nM, 0.013 nM, 0.013 nM and 0.013 nM for the very high affinity binding site and 0.5 microM, 0.13 microM, 0.062 microM and 0.75 microM for the second binding site. 3.' (Pintor et al, 1991). Oh well, one glance at the sentence and you have the full picture, eh? This is even more true in the following example:
¥ 'Using these kits, the minimum detectable concentrations of IFN-gamma, IL1-beta, IL2, IL4, IL5, IL6, IL9, IL10, IL12p70, IL13, IL17A, IL22, and TNF-alpha were 1.6 pg/ml, 4.2 pg/ml, 16.4 pg/ml, 20.8 pg/ml, 1.6 pg/ml, 1.2 pg/ml, 1.5 pg/ml, 1.9 pg/ml, 1.5 pg/ml, 4.5 pg/ml, 2.5 pg/ml, and 43.3 pg/ml, respectively.' (Chen H et al, 2012). I just love such matching type sentences that allow me to practice my counting skills; the more so when I see that 13 factors are matched to 12 values (note: I changed the spelling to that used in COPE so that the terms can be hypertexted)


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differentially yours
¥ I have seen so many publications reporting differential expression of one factor or the other. So well, so good. What I am complaining about is that even only a couple of proteins are identified they are often not named, which is bad and just shows that authors have not yet come to grips with the art of makingan abstract as informative as possible. But what I really grumble about is that even if these factors are mentioned one is still left in the dark. Is it asking too much to state explicitly, for example, in a comparison of two or three cell types which cell expresses what rather than referring to these proteins as being 'differentially expressed?


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make a dictionary maker happy
¥ abstracts and articles, where factor-2 comes into play: the abstract reports the identification of a new factor under one name and this factor is then renamed in the small print to 'reflect the unique bioactivities of the factor'. I have come across publications also reporting the identification of a novel factor in the title of the article and the authors then rename the factor in the small print of the article because the new name reflects the observed bioactivities better than the name used in the title. I remember that this happened at least once in a publication in Nature, but for the life of me I cannot remember which factor it was (but the article started in the right-hand column on the left page :-(.


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so much space and so little to say
¥ abstracts containing three or four lines of cited references instead of data. Worse: wasting a lot of lines with all the umpteen author names. To give some examples: Nearly 55 % of the abstract in the publication by Wagener et al (2009) is made up by cited references.


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don't include me
¥ '... 'including MMP-1, MMP-3, MMP-5, MMP-11, and MMP-13' Phrases containing the seemingly inoccuous word "including" always make me wonder whether the authors wanted to say "the factors we mention are the only ones we found" or, if not, why they did not name the other factors that, presumably, were expressed also. After all, if one is not dealing with DNA chip or antibody array data that would not be too much to ask, wouldn't it?
BTW: I admit that COPE also contains such "including" statements and work is under way to remedy the situation. This is a bit difficult as I live and work in a 3rd world country with limited access to primary literature and I cannot afford paying the exorbitant prices publishers ask for access to their online publications. I call it exorbitant if first publishers ask scientists to pay for publication heavily in the form of page charges and later ask up to 40 USD for access to a single online article. BAH! Scientists should all decide to publish through open access resources.


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find me if you can
¥ 'Embryonic stem cells can be induced in vitro, by coculture with the stromal line RP.0.10 and a mixture of interleukins 3, 6, and 7, to differentiate into T (Joro75(+)) and B (B-220(+)) lymphocyte progenitors and other (Thy1(+), PGP1(+), c-kit(+), Joro75(-), B220(-), F4/80(-), Mac-1(-)) hemopoietic precursors' (Gutierrez-Ramos and Palacios, 1992)
Surely, sentences such as the one above, can be rephrased conveniently to facilitate freetext searches in databanks. IL3, IL6, IL7 are lost in a freetext search. The same goes for searches for T-cells and B-cells. The point is that one cannot rely on all these terms having been incorporated into the MeSH indexing of the article.
¥ 'Serum levels of matrix metalloproteinases (MMP-1, -2, -3, -7, -8, and -9) ....' (Pelisek et al, 2011) or '... including MMP-1, 2, 3, 7, 10, 11, 13 and 26 transcripts.' (Carroll et al, 2007) or 'Left ventricular (LV) mRNA [MMP-1,-2,-3,-7,-9,-11,-13,-14; TIMP-1,-2,-3,-4]' (Li H et al, 2007). One does not easily find these articles when doing freetext searches for MMP-2, MMP-3, MMP-7, MMP-8, MMP-9, MMP-10, MMP-11, MMP-13, MMP-14, MMP-26, TIMP-2, TIMP-3, TIMP-4.
¥ '... ... expression of BMP1, 2, 3, 4, 5, 6, 7, 8a, 8b, 9, 10, FGF1, 2, 3, 4, 5, 6, 7, 8, 10, and MMP1a, 2, 3, 7, 8, 9, 12, and 14.' (Sautter et al, 2011). Oh well, more of the same. Needless to say, that none of these factors appears in the list of MeSH terms. If COPE were written like that there wouldn't be any backlinks to provide value-added information: BMP1, BMP2, BMP3, BMP4, BMP5, BMP6, BMP7, BMP8a, BMP8b, BMP9, BMP10, FGF-1, FGF-2, FGF-3, FGF-4, FGF-5, FGF-6, FGF-7, FGF-8, FGF-10, and MMP-1a, MMP-2, MMP-3, MMP-7, MMP-8, MMP-9, MMP-12, and MMP-14.
¥ 'Among BMP2, 4, 6, and 7, BMP6 is the most consistent and potent regulator of osteoblast differentiation and, of these BMPs, only BMP6 gene expression is detected prior to hMSC osteoblast differentiation' (Friedman et al, 2006). Again, such an article will fall through the net when searching for BMP4 and BMP7. The MeSH index only contains BMP6
¥ '... another 13 ABC-transporters, including ABCA4, A5, A9, A13, B2, B9, C1, C5, D3, D4, F2, G1, and G4 were primarily expressed in Kupffer cells' (Ye et al, 2008) along the same line, really. They don't do freetext searches anymore, don't they?
¥ the addition of prefixes to indicate human, bovine, murine, rat etc factors makes it equally easy to find the factors in question in a freetext search (mEGF, hIAP, rIan-5, for murine EGF, human IAP, rat Ian-5, respectively). Apart from that, some prefixed letters have double meanings.

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(Talking {in} [brackets]) and leaving some space(s)
¥ I can understand that the use of brackets in chemical nomenclature, for example, 2«-(4-Ethoxyphenyl)-5-(4-methyl-1-piperazinyl)-2,5«-bi-1H-benzimidazole, is more than a simple spelling convention. I am always at a loss to understand, however, why I do come across so many scientific abstracts using bracketed atrocities like (IL)-1 (for IL1), bone morphogenetic protein (BMP) 4 (for BMP4), bone morphogenetic protein (BMP)2 (for BMP2), C-C chemokine ligand (CCL) 2 (for CCL2) etc.

¥ ' ... significantly increased serum concentrations (p < 0.05) of CCL 2, CCL 3, CCL 4, CCL 7, CCL 20, CXCL 1, CXCL 8, CXCL 9, CXCL 10 and CXCL 11, and (b) significantly decreased serum concentrations, (p < 0.05) of CCL 5, CCL 11, CCL 17, CCL 22, CCL 24 and CCL 26 .... ' ' ... an involvement of activated Th(1), cells and NK cells (CCL-2, -3, -4, -20, CXCL-9,-10,-11), neutrophils (CCL-20, CXCL-1,-8) and monocytes (CCL-2,-3,-4, -7, CXCL-10), upon co-operation of other cell types ....' (Pelikan et al, 2012). I am also guilty, of course, of not following strict guidelines for writing gene symbols (all capitalized or not capitalized), but leaving out the spaces after CCL or use a hypen would have been better to facilitate a fretext search for CCL2, CCL3, CCL4, CCL5, CCL7, CCL11, CCL17, CCL20, CCL22, CCL24, CCL26, CXCL1, CXCL8, CXCL9, CXCL10, and CXCL11. The second part of the list is a typical example of what I have described under "find me if you can" (above). I wonder whether Pubmed will really have all chemokines listed in the MeSH index as at the time of writing the article has not yet been indext.
¥ having found articles where title and abstract use two different spelling variants of a term occur (such as PAR-1 and (PAR)-1) occur I am sure if I delved into Pubmed I could also come up with articles using the other spelling variants (PAR1, (PAR) 1, PAR(1), PAR-(1)). I positively loathe brackets when they are absolutely superfluous. Oh, wait. Silly me! And many apologies indeed. This is a service to those doing freetext searches. This way one does find the article, no matter what ...


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Brazen it out
¥ The use of any one of the many different names for a given protein rather than the approved gene symbol in some articles dealing with microarray gene expression analysis is bad enough. I get truly mad when authors are too lazy to provide the one and only reliable bit of information (no double meaning intended here!): the databank accession number! Editors/referees who let this pass and authors who do this deserve a medal and then be shot right through it. (I am a peace-loving person. This was a figure of speech! I hasten to state explicitly that this is NOT to be interpreted as a public call to violence!!).
¥ the same goes for authors who present jpg images for their expression profile data and only list the gene symbol (which, of course, cannot be copy/pasted from a jpg and cannot be sorted - and keep me going back and forth between databanks to find out what they are talking about and if it is of potential interest). Never heard of spreadsheets as supplementary tables that also include at least one of the accepted long names of the proteins? (for one example see: Roesch et al, 2008).
¥ and again: just maddening to have a supplementary table with all the expression information as a pdf file with tables on umpteenth pages in portrait mode. Oh, I forgot: one cannot sort the information, of course, and one can also not easily copy/paste it into a spreadsheet. Reminds me of a Scottish friend who used to say in this very nice accent of his: They deserve a medal and then you shoot right through it (Nelson et al, 2007)
¥ and the same goes again for those authors who just provide the gene symbol and the accession number but leave out at least one of the accepted long names. Am I the only one who does not know by heart all the umpteen thousand gene symbols (approved or not) in a microarray study. Some studies I consult for filling in expression profile information in COPE entries cost me hours to look up gene symbols and names just to make sure that what I think they talk about is what they do talk about (Rozsa et al, 2006; Barbier et al, 2011, but there are, of course, lots and lots of others who steal our time this way).


_____________________________________________________________________________


While I am at it let me grind also at one or two things about electronic information resources:


I don't know my ABC
After so many decades of computing experience databanks still exert their little bit of linguistic imperialism and refuse to handle an extended alphabet containing umlauts (Finnish, German) and other diacritical marks. Thus, Mšller, KrŸger, MŸller, GŠrtner, MŸllerian inhibiting substance, etc. are robbed of their little bit of foreign identity by being reduced to Moller, Kruger, Muller, Gartner, Mullerian inhibiting substance. They do not even bother to use the replacement forms for Umlauts (Moeller, Krueger, Mueller, Gaertner, Muellerian inhibiting substance, etc).
I seem to remember having read somewhere in a British journal (probably Nature) that some German-speaking Drosophila melanogaster biologists 'hit back'. Hitting what? Their genes called 'zerknŸllt' and 'KrŸppel' are converted also to 'zerknullt' and 'Kruppel' (or worse: zerknU*llt Kr<*ppel, when you download files).


Note added in January 2008: Lo, and behold. Things begin to happen. I have noticed that Pubmed now has correct spellings of German umlauts (the abominable Š, š, Ÿ) and also some other diacritical characters. I am pleased. The problem stil persists, of course, if you copy/paste from pdf files into a word processor. I still get author names like Zº±iga-Pfl¼cker, J¤¤skel¤inen, M¤enp¤¤, and others and have problems with Greek letters, and sometimes, when I try to copy/paste something from a pdf file I get very weird results indeed (not to mention my attempts to use a search function with words containing these characters). Besides, some word processors are more accomodating than others when to comes to key in special characters, some are downright #$%^$#*$%, actually.

Well, be this as it may, I don't have the time to go through all the umpteenth thousands of COPE references to correct my spellings now (which were taken from older Pubmed versions). Am I to expect future correspondence accusing me of "language imperialism" now? I hope not.
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thanks for wasting my time
Before, journal articles not citing full references made me go to the library. Now, their electronic counterparts make me click through to Medline when I need the full reference, title and all - IF they provide a link in the first place. It is most annoying that many publishers still stick to incomplete references without article titles. I never believed in the age-old but lame publisher's excuse of space restrictions, and with electronic articles there is even less excuse for wasting our time. Most annoying also is that even on their own journal pages, some publishers will give you, of course, the volume number but leave out the issue (which other publishers may require for full citation and which is the format that PubMed uses).
In the same vein, I wonder why scientists have not crowded together yet to enforce one single style of citations rather than the umpteenth variants one can find in citation managers. But maybe there is no such thing as the "scientific community", and what we really need is some sort of Academic Labor Union? But that probably would not be considered "politically correct" in some circles - and who cares about the academic proletariat anyway, whose time is wasted.

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publish and damn the publishers
I observe that publishers are quick in establishing inline links from their online publications to providers of biological reagents apart from having "buy this article " buttons selling us our own articles at breath-taking rates. Probably they call this functionality and "service", but I hazard the opinion that we, as scientists, would like to see quite different functionalities provided by online publications. Full citations, for one thing. I always wonder why scientists have not rebelled at all against the stupidity of having umpteenth different reference formats to comply with (I know makers of citation managers will hate this).
Surely, it would not hurt publishers much to make available, through PubMed, at least articles dealing with nomenclature issues. After all, the academic proletariat (a.k.a. the scientific community) mostly pays to have their results published.


We should all switch to open access articles!


... and yet another observation - although I am a bit doubtful about it still. To me it seems that the number of publisher's journal pages that make it rather difficult or impossible to find author contact information is increasing. I grant it that often people do not stay in one lab and hence change their email contacts. Still. Suspicious as I am: I just see this as a deliberate move to increase the chances of selling the online article - I mean, what would happen if all friendly colleagues provided all others with a user-friendly pdf reprint? Or, as an afterthought, have scientists discovered that in our age of vanishing privacy (think of all the bloggers, facebookers, tweeters who mostly have nothing to report but do it profusely with words and images) it is not good to trade one's email contacts around?


Oh well, read Some personal remarks if you want to know more about the joys, trials, and tribulations of a dictionary maker and drop me a line if you want to suggest other MAFIA examples. (I simply had to create this EUA).


And, by the way, remember: there is life beyond the lab with quite a number of ways to excite your cytokines and the cytokine network. These are probably more pleasant than spending your time in front of the computer screen.


Copyright © 2012 by H IBELGAUFTS. All rights reserved.
ENTRY LAST MODIFIED: March 2013
Always in moderation. Further suggestions always most welcome. Just drop me a line



 

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