Wikipedia:Peer review/Aryl hydrocarbon receptor/archive1

Aryl hydrocarbon receptor
I've listed this article for peer review because I have extensively worked on the scientific aspect of the article but would appreciate a grammar review.

Thanks,

Demantos 19:31, 3 December 2007 (UTC)

Review by Jeff
A good start: the facts are here and the refs are very thorough. Rewriting (not just punctuation and spelling) will improve the article significantly.
 * The article should put information into context better, so that the average reader can understand what is going on. For example:
 * "Non-ligand bound Ahr is retained in the cytoplasm as an inactive protein complex consisting of a dimer of Hsp90 " the phrase 'Non-ligand bound' is incomprehensible to the average reader, but if I write:
 * "When no ligands of the receptor are present, Ahr is retained in the cytoplasm as an inactive protein complex...When a ligand enters the cell and binds to the receptor, this inactive protein complex dissociates, allowing importation of the receptor into the nucleus so that it can interact with the cell's DNA."
 * This sentence can be the lead of the paragraph or section, after which you can discuss the details. The idea is to tell the big story first so we can understand it in context, and only then can you explain the details.


 * This receptor is responsible for activating the body's response to xenobiotics, right? So this should be explained clearly in the lead. 
 * The opening sentence is: "The Aryl hydrocarbon receptor (AhR) is a member of the family of basic-helix-loop-helix transcription factors." Is this really the most important thing about this protein, and does it help explain the essence of the receptor to a casual reader? Consider replacing with the suggestion above.
 * The lead should summarize all important aspects of the receptor, such as who discovered it and when, what the receptor's purpose is, and why scientists are still researching it.
 * There is a problem with licensing of Image:AhR.jpg. This has a half-written fair use rationale, but a free version can be made! We can't have fair-use material if free versions can be made. In fact, I will volunteer to make a free version of this, but I'm going to tag the existing version as a copyvio. ("reprinted with permission" where is the documentation? What is the permission given, and who gave it? if permission really has been given, should have an OTRS ticket). As for Image:AhRSignaling colour.png, I'm not entirely happy since it is almost an exact re-drawing of the original and a free version could easily be made. I'm not quite sure what to do with that one, so I'll leave it alone for now.
 * Are there any crystal structures available? How about any structures or models of any of the binding domains? I can access Sybyl and Chem3D for rendering structures if coordinates or other structure information is available.
 * Abbreviations: I recommend not using abbreviations unless you really need them, so if you only use a term once or twice, why bother abbreviating? Abbreviations are very hard to read, and make the article look like an alphabet soup. On the other hand, there are things than should not be spelled out, such as CYP1A1, Hsp90, XAP2. Just say: "...the metabolic enzyme CYP1A1..." (no need to say "cytochrome P450, family 1, subfamily A, polypeptide 1" or spell them all out). The choice of what words to spell out should be made carefully.
 * Abbreviations: Even more annoying than an unnecessary abbreviation is re-defining the abbreviation over and over: "...aryl hydrocarbon receptor nuclear translocator(ARNT)..." and later "...AhR Nuclear Transporter (ARNT)..." (note inconsistency) Why say it more than once? Clunky abbreviations are a pet peeve of mine in journal articles, so I'm sorry if this sounds terse. For ARNT I would suggest saying: "...AhR's dimerization partner, a nuclear transporter called ARNT." Also use consistent CAPS on AhR or Ahr.
 * "...the end result is a variety of differential changes in gene expression." add perhaps 2 sentences summarizing what these changes are.
 * Avoid sentences like "reviewed by[8][9]." and "as shown in[52][53][54][46]." (don't use a footnote as the object of a sentence!) and the period should come before the refs.
 * I hope I don't sound too harsh; I don't mean it to be. The article needs some rewriting so that non-experts can read it, but the content and refs are good. I would suggest one more image, if possible, would be a structure or model of the receptor, or at least one of the subdomains. And perhaps a structure of a typical aryl hydrocarbon with a caption like "Polychlorinated dibenzodioxins such as TCDD activate the aryl hydrocarbon receptor, activating the xenobiotic response element" I'm happy to answer more questions, take another look, and help out if I have time. Jeff Dahl (Talk • contribs) 22:00, 4 December 2007 (UTC)


 * A script has been used to generate a semi-automated review of the article for issues relating to grammar and house style. If you would find such a review helpful, please click here. Thanks, APR t 19:44, 5 December 2007 (UTC)


 * Nice work. 1) The lead needs to be made accessible to non specialists. It's a detailed topic, so the whole article doesn't need to be accessible, but the lead section should be maximally so. The first sentence "Aryl hydrocarbon receptor (AhR) is a member of the family of basic-helix-loop-helix transcription factors." tells me absolutely nothing about the topic, and I have a fair amount of science background. The next sentence and the rest of the lead don't provide much more; it's not until the very last two words that I can tell what the topic is related to. Luckily the article is short, so there is a fair amount of room to add context here and there. Particularly in the lead you should minimize the use of overly complicated terms where possible, and define them in context when not. For example I can read the Transcription factor article to find out in general what AhR is, but in general the reader shouldn't have to. Also the lead section should be 2 or 3 paragraphs, see WP:LEAD. 2) In all that research, which is impressive by the way, would you say there are no other important bits of material you have left out? Without references and markup it's pretty short for a featured article candidate. - Taxman Talk 19:29, 6 December 2007 (UTC)