User talk:Boghog/Archive 9

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Changed citation style in Aequorin

I note you have changed the citation style to Vancouver in this article. Generally under the MOS citation style is not to be changed. What is the special reason here? Chiswick Chap (talk) 08:46, 2 January 2015 (UTC)

This article already followed the author Vancouver style (multiple authors stored in a single |author= parameter). The only difference in changing from {{cite journal}} to {{vcite2 journal}} (and |author= to |vauthors=) is generation of clean meta data. Otherwise the displayed citations look identical. Boghog (talk) 08:52, 2 January 2015 (UTC)
Oh good. Very glad it's not about to break out in an AWB-inspired rash all over! Chiswick Chap (talk) 08:57, 2 January 2015 (UTC)

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Wondering why you are switching to vcite2

In this edit [1]? Doc James (talk · contribs · email) 19:44, 3 January 2015 (UTC)

As explained in the section directly above, if the article already uses Vancouver formatted authors as Testosterone does, then the displayed citations using {{cite journal}} or {{vcite2 journal}} will look identical. The only difference is that the citations will now produce clean author metadata and in addition keep the malfunctioning Citation bot away (see this this discussion). For more background, also see this discussion.
What I would ultimately like to do is convince the maintainers of {{cite journal}} to add an optional |vauthors= parameter to {{cite journal}}. That way compact author lists will be fully supported. If we do nothing, storing multiple authors in a single |author= parameter may be deprecated in the future. Boghog (talk) 20:01, 3 January 2015 (UTC)
Okay thanks. The difficulty I face; however, is that the cite template is supported across the 100 languages I am working in while the vcite2 is not. This is a pain for translation. We really need to get the WMF to provide a few standard ref formatting options across all languages. Doc James (talk · contribs · email) 20:12, 3 January 2015 (UTC)
Sorry, I forgot about the translation project. I have restored the standard {{cite journal}} templates to the Testosterone article for now. The conversion back and forth is rather trivial (search and replace "{{vcite2 journal | vauthors" with "{{cite journal | author"). This is one additional reason to add |vauthors= parameter to the standard {{cite journal}} template. Boghog (talk) 20:19, 3 January 2015 (UTC)
Am not planning on translating this article anytime soon. Was just commenting just in case this was going to be a more wide spread thing. Doc James (talk · contribs · email) 20:29, 3 January 2015 (UTC)
Can w make sure this template is installed in all other languages before we change all refs to vcite2? When it is I will than support changing all articles to it.
Also if we are going to go with vcite too can we get the ref tool in the top of the edit box to use it? Doc James (talk · contribs · email) 19:34, 13 January 2015 (UTC)
In the short term, if one want to translate into another language, all one needs to do is to do a search and replace of "vcite2 | vauthors" with "cite | author". The {{cite journal}} and {{vcite2 journal}} templates are identical except that the later supports an optional |vauthors= parameter. The only consequence of replacing |vauthors= with |author= is that the former generates clean author metadata whereas the later does not. In all other respects, the displayed citations look identical. As requested here, what I really would like to see is the |vauthors= parameter be supported directly by the {{cite journal}} template. If that is done, then I think we can convince the maintainers of WP:REFTOOLS to add |vauthors= as an option. I have been expanding the use of {{vcite2 journal}} template, especially within Gene Wiki project to make sure that there are no issues with the new template. I have not notice any issues, so the next step would be to make a request here. I foresee some resistance to the proposal, so I would really need some support from WP:MED to make this fly. So my question to you is (a) do you think this is a good idea and (b), if so, would you support it? Boghog (talk) 20:00, 13 January 2015 (UTC)
I am of the opinion that we need greater consistency around citation style not less. This includes greater consistency between languages. There are dozens of steps to translate an article into another language. I am not inclined to add more. Doc James (talk · contribs · email) 21:13, 13 January 2015 (UTC)
Even if |vauthors= were to be added to other languages citation templates? Then there would be zero extra steps. Boghog (talk) 21:17, 13 January 2015 (UTC)
This is really quite silly. Even if |vauthors= were not added to other languages cite templates, there would be still no extra steps. For example, to translate into Spanish, one must replace "cite journal | author" with "cita publicación | autor". If the article used vcite2, then would instead replace "vcite2 journal | vauthor2" with the same "cita publicación | autor". No extra steps. Boghog (talk) 21:27, 13 January 2015 (UTC)
If |vauthors= were added to the other language citation templates I would support as there would be zero extra steps. It has taken a massive amount of work to install the citation templates in 100+ languages already. User:CFCF did most of it.
First of all we should get consensus here on En that this should be done widely. I have no strong feels about it and would support as long as it does not make the work I do more difficult. Doc James (talk · contribs · email) 21:29, 13 January 2015 (UTC)
Exactly. That is what I was suggesting above. Boghog (talk) 21:33, 13 January 2015 (UTC)
Great, glad we are on the same page :-) Doc James (talk · contribs · email) 22:35, 13 January 2015 (UTC)

Reference Errors on 24 January

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Please check this page and fix the errors highlighted. If you think this is a false positive, you can report it to my operator. Thanks, ReferenceBot (talk) 00:25, 25 January 2015 (UTC)

tools.wmflabs.org/citation-template-filling isn't running

Manage link if it should be & something has expired. RDBrown (talk) 04:19, 31 January 2015 (UTC)

 Fixed Thanks for the alert. I have no idea why it was no longer running. I stopped and restarted the citation-template-filling webservice and it now runs again. Boghog (talk) 08:17, 31 January 2015 (UTC)

Nomination for merging of Template:Infobox nonhuman protein

Template:Infobox nonhuman protein has been nominated for merging with Template:Infobox protein. You are invited to comment on the discussion at the template's entry on the Templates for discussion page. Thank you. Andy Mabbett (Pigsonthewing); Talk to Andy; Andy's edits 16:33, 31 January 2015 (UTC)

Arachidonate 15-lipoxygenase vs ALOX15

Hey Boghog - I started working on an eoxin article (from my userspace for now... User:Seppi333/Eoxin) and noticed an issue with the naming convention of the associated enzyme articles for these compounds. Arachidonate 15-lipoxygenase (15-LOX) has 2 subtypes: 15-LOX-1 (located at ALOX15 - this is the eoxin producing enzyme) and 15-LOX-2 (located at ALOX15B).

Our other lipoxygenase articles use the longer name (e.g., the most notable lipoxygenase is 5-LOX; this contraction and ALOX5 both redirect to Arachidonate 5-lipoxygenase), so I'm assuming the ALOX articles should be moved for consistency:

Do these moves seem appropriate? Also, should the general 15-LOX article be converted to a set index of these two, or just remain as is?

Seppi333 (Insert 2¢ | Maintained) 00:59, 5 January 2015 (UTC)

Some refs for context:

Hi Seppi333. The usual convention is to gene/protein articles using the approved HUGO gene symbol or recommend UniProt name. According to this convention, the two articles should be renamed as follows:
The complication is Arachidonate 15-lipoxygenase already exists as an enzyme article and IMHO should remain as is. Furthermore since ALOX15 and ALOX15B share the same EC number, it would not be appropriate to merge ALOX15 with Arachidonate 15-lipoxygenase. We could label the two isozymes "A" and "B" respectively, but ALOX15 is not normally referred to as the "A" isozyme. So I guess your proposal is the most reasonable, since these names correspond to the UniProt "expanded short names", 15-LOX-1 and 15-LOX-2, respectively. Boghog (talk) 01:26, 5 January 2015 (UTC)
Thanks for the clarification. So, should we use 1 and 2 or A and B following "Arachidonate 15-lipoxygenase" in the page names?
I also have a chemistry question that I need some clarification on. Most papers I've read indicate 5-LOX and 15-LOX metabolize along distinct but analogous pathways following synthesis by the associated 5-LOX or 15-LOX enzyme (see page 122 of the "15-LOX-1 review" pdf located here). However, reactome is indicating that EXA4 is produced from LTA4 via 15-LOX-1 in humans (the mostly complete series of reactions along arachidonic acid pathways is also located at special:Permalink/641335373#Biochemistry). I'm confused - wouldn't 15-lipoxygenase-1 action on LTA-4 create a completely different compound than EXA4 (aka 14,15-LTA4), or is that posible/correct? Seppi333 (Insert 2¢ | Maintained) 01:17, 7 January 2015 (UTC)
@Seppi333: Sorry for not responding sooner. You are asking interesting but challenging questions. Also arachidonic signaling is somewhat outside my area of expertise. Finally, I becoming somewhat burned out lately ;-) Regarding your first question, the existing nomenclature used by UniProt unfortunately does not provide a clean answer. In analogy to the 15-LOX-1 and 15-LOX-2 short names that are already in use, my suggestion is to use 1 and 2 following "Arachidonate 15-lipoxygenase" in article names. Regarding your second question, the "15-LOX-1 review" (secondary source) is correct and the reactome (tertiary source) is incorrect. It looks like the reactome misinterpreted PMID 18184802 (Figure 3) which was trying to distinguish (i) "5-LO-derived cysteinyl LTs" from (ii) "cysteinyl 14,15-LTs (EXs)". This distinction is important in interpreting mass spectral data but in no way should be interpreted as the two species interconverting as apparently the reactome database did.

Nevermind, I'm not going to edit these pages further since I lack the background chem knowledge to really understand what I'm writing about. And on that note...

The Science Barnstar
This is for all the work you put into expanding and improving amphetamine's chem content and citations; you helped a lot with getting through the FA process and I appreciate the assistance. Seppi333 (Insert 2¢ | Maintained) 01:48, 2 February 2015 (UTC)
Nada. My contribution was very minor. Kudos to you for your enormous hard work and determination in promoting amphetamine to FA status. Boghog (talk) 18:40, 2 February 2015 (UTC)

Microscale thermophoresis

Hi! Sorry, I edited again since I thought I just missed to save... — Preceding unsigned comment added by SciMarie (talk • contribs) 16:30, 5 February 2015 (UTC)

No worries. Thanks for your note. Boghog (talk) 16:34, 5 February 2015 (UTC)

looks good! Thanks for you help and input! — Preceding unsigned comment added by SciMarie (talk • contribs) 16:36, 5 February 2015 (UTC)

NAD(P)H dehydrogenase (quinone 1)

The article is a stub so expanding the article with new information is necessary. If you delete new information you will prevent a coverage of the whole area of interest. If something is unclear or could be improved just expand it yourself or correct it. — Preceding unsigned comment added by 190.57.232.111 (talk) 18:28, 6 February 2015 (UTC)

@190.57.232.111: Your latest edit is much better since it emphasizes what the publication say about the enzyme and not what the enzyme says about the publication, but per WP:MEDRS, secondary sources are strongly preferred to support medical claims. The source that you have supplied (PMID 21034357) is primary and needs to be replaced. Per WP:COI, Wikipedia is not the forum to promote your own publications. Boghog (talk) 20:06, 6 February 2015 (UTC)

Thank you for your help. It was the paper containing the crystal/NMR structure and the analysis of the data for the variant so it is the source for this specific data. I could not find another structure yet. Perhaps the other sources should be audited as well since there are two other primary sources too. Maybe all of the sources could be fortified (but not replaced) by this review :The NQO1 polymorphism C609T (Pro187Ser) and cancer susceptibility: a comprehensive meta-analysis [[2]]? — Preceding unsigned comment added by 190.57.232.111 (talk) 21:10, 6 February 2015 (UTC)

Fine points of formatting citation template fields

Hi, Boghog,

I see you have been in the thick of editor discussions about how to format citation templates. I just saw your recent edit of Chikungunya on my watchlist, and looked up your wikilinks to editor discussion about the doi templates and other templates. Here on your talk page I see you are also discussing templates. I'd like my practice to human-readable, not subject to willy-nilly reversion by people running bots, and consistent with the practice of more experienced Wikipedians, so I'd appreciate hearing from you your thoughts on why (or why) to include whitespace between the equal sign that distinguishes a field label from field content or whitespace before or after the pipe character that shows the beginning of a new field. I have a habitual pattern in using whitespace, which I think I picked up from the documentation of the citation templates, but maybe I can change my habits if I see a rationale for doing so. For an example of how I do citation template, I invite you take a look at a Intelligence citations bibliography I keep in my user space. What do you think about the mark-up style there, which I tend to copy and paste into articles as occasion arises? Thanks for any thoughts you have about this or any pointers you can give to Wikipedia documentation on the issue. See you on the wiki. -- WeijiBaikeBianji (talk, how I edit) 00:14, 1 February 2015 (UTC)

Hi WeijiBaikeBianji. Thank you for your message. Concerning whether or not to pad template parameters with white space is purely a personal preference and is subject to WP:CITEVAR. There is a tradeoff between readability and compactness. Arguably the most readable templates have each parameter on its own line (vertical format). On the other hand, compactness is important if the citations are included in-line. Vertical formatted citations overwhelm the surrounding wiki text making it harder to edit. My personal opinion is that padding parameters with white space while retaining horizontal format is a good compromise between readability and compactness. Others may disagree. The reason I included white space in my recent edit to Chikungunya was that the script that I was using rebuilt the citation templates from scratch. The advantage of this is approach is consistency, the danger is that it may run afoul of WP:CITEVAR. Making edits only to add/subtract white space is generally frowned upon. Another concern that I have is the use of first1, last1, first2, last2, ... parameters which starts to become unwieldy if there are many authors. The advantage of using these parameters is they allow generation of clean metadata and allow the use of |display-authors=, |author-link=, etc. parameters. To permit the storage of author data in a more compact comma delimited list while retaining all the advantages of first1, last1, first2, last2, ... parameters, I created the {{vcite2 journal}} template (see also rationale). Boghog (talk) 06:51, 1 February 2015 (UTC)
Perhaps I might offer a comment? I suspect many editors prefer horizontal format (one long line) because it is more compact, does not split the text as much as vertical format does. What I would add here is that all the bibliographic detail that is proper for a full citation is always intrusive in the text, regardless of how it is formatted. There is much to be said for collecting all that detail in a special section, and linking to it from the text with "short" citations. This makes it a lot easier to edit the text, and a lot easier to edit citations (such as for consistency, etc.), because these two kinds of "text" are no longer intermingled. ~ J. Johnson (JJ) (talk) 22:53, 3 February 2015 (UTC)
Yes we had consensus to switch citations over many lines to citations over one line at WPMED. Doc James (talk · contribs · email) 04:02, 4 February 2015 (UTC)
I see this discussion has attracted more interest than I expected. I'd appreciate comments from all of you (knowing that you tend to work on articles in disciplines other than psychology, which is what I'm best equipped to work on) on my new guide to brief inline citations to specific pages in reliable sources used multiple times in one article. I learned that style from a much more experienced Wikipedian, and I'm looking forward to refining the style--with your advice--to improve many more high-page-view articles about psychology. -- WeijiBaikeBianji (talk, how I edit) 05:31, 4 February 2015 (UTC)
I use cite journal rather than Harvnb as I am not sure if the latter works in other languages.
But this is a personal preference. Doc James (talk · contribs · email) 07:03, 4 February 2015 (UTC)
In "other languages"? Why not? Perhaps you are thinking of special characters used in names? {{Harv}} was modified for those several years ago. I don't know if Unicode encodings work (may have to try that) but I believe Harv is compatible with all European names. ~ J. Johnson (JJ) (talk) 22:13, 4 February 2015 (UTC)
Because all these templates have not been installed in most languages. Doc James (talk · contribs · email) 11:40, 5 February 2015 (UTC)
Ah! That's not a language problem, but a problem with the wiki of a some language. More particularly, an incomplete installation of needed templates. ~ J. Johnson (JJ) (talk) 21:57, 5 February 2015 (UTC)

@WeijiBaikeBianji: Concerning the guide to brief inline citations, there are two methods that are in use in your example, both of which have distinct advantages and disadvantages. The is no one "best" way to organize citations. A lot depends on the type of citations and how they are used. Individual editors may also have their own preferences and which style is used is subject to WP:CITEVAR. In your example, the first citation style is {{harvnb}} and the second is List defined references. I think harvnb makes most sense if the citations are to books and different pages of same book are cited in different parts of the Wikipedia article. The disadvantage of this method is that it is more complicated and generally not needed if most of the citations are to journal articles. If different pages of the same source need to be cited, {{rp|page number(s)}} is an alternative. The advantage of list defined references is it separates the clutter of the citations from the text. The disadvantage is that it is separates the text from the source that supports that text make it somewhat more difficult to compare the two. List defined references make the most sense if the same source is used multiple times while less sense if each source is cited only once. Boghog (talk) 20:42, 5 February 2015 (UTC)

As Doc James mentioned above, another potential disadvantage of both techniques is that they may not be supported in all foreign language Wikipedias making it more complicate to transfer a English Wikipedia article's citations into a foreign language article. Boghog (talk) 21:06, 5 February 2015 (UTC)

I've already run into a wiki that runs Media Wiki software but without all the extensions used on English Wikipedia, so now I have a lot of interest in what minimal mark-up that might transfer to lots of different wikis would look like. I'd be best off looking at the Media Wiki documentation to understand that, I suppose? Thanks for the very interesting comments here. -- WeijiBaikeBianji (talk, how I edit) 21:32, 5 February 2015 (UTC)
Yes, identifying the extensions necessary for doing proper citations would be good. But should also look for any reason why these don't get installed. Starting to sound like a project. [Whoops! I thought I had signed this.] ~ J. Johnson (JJ) (talk) 00:25, 7 February 2015 (UTC)

Replacing Cite PMID with Cite Journal

Can we have a bot do this on all medical articles and than do so again on regular basis?

Consensus is here [3] Doc James (talk · contribs · email) 05:26, 25 January 2015 (UTC)

Let me know if you are able to take this on? Happy to help with the bot approval process. Doc James (talk · contribs · email) 09:51, 31 January 2015 (UTC)
Sent you an email. Let me know if you are able to work on this? Doc James (talk · contribs · email) 04:03, 4 February 2015 (UTC)
@Doc James: Yes, I can start to work on this. However it would really be helpful if USER:Citation bot in the future would insert the full citation within the article instead of creating additional {{cite pmid}} templates. That way, we would only need to run the substitution bot once. Per consensus, we would seem to have the authority to request this. The problem is that USER:Citation bot is no longer actively maintained. I filed this bug report bug report last October and still no response. Thoughts? Boghog (talk) 20:55, 5 February 2015 (UTC)
A solution is we block USER:Citation bot and replace it with a bot that does what we wish. What do you think? Doc James (talk · contribs · email) 01:22, 6 February 2015 (UTC)
Blocking citation bot is not a good answer. The RFC linked above applies only to medical articles. A solution that better addresses the RFC would be to create a new bot that carries out the RFC's result only on medical articles. The new bot could also tag articles within the project to prevent citation bot from editing those articles if there is consensus within the project to do so. – Jonesey95 (talk) 03:10, 6 February 2015 (UTC)
This consensus was not limited to medical articles. One thing that bot approval group doesn't like is conflicting bots. I can bring this issue up with them when I apply for the approval of the new bot. Boghog (talk) 09:18, 6 February 2015 (UTC)
Perfect. Doc James (talk · contribs · email) 11:39, 7 February 2015 (UTC)

Citation error introduced by substing

You appear to have introduced a citation error into Tobacco smoking when you replaced a cite PMID template with a cite journal content (see the last citation). I don't know how that could have happened if you were simply substing the templates. Be careful out there. – Jonesey95 (talk) 15:44, 8 February 2015 (UTC)

@Jonesey95: There were author parameter inconsistencies in the {{cite pmid/9862656}} and {{cite pmid/2136102}} templates that were substituted and the script I am using to do the substitution did not anticipate these inconsistencies could exist (these templates contained "author" + "first" + "last2" + "first2" parameters, huh?). I will modify the script so that it checks for inconsistent author format input and outputs a consistent author format. Please note that this script does a lot more than substitute the templates. It rebuilds the templates from scratch using the data supplied by the templates and supplements with data from PubMed if missing in the template. The script also checks to see what the predominate citation style is (multiple authors assigned to a single "author" parameter vs. "first1, last1, ..." parameters) and maintains that style in the substituted template. (Of course, it would be much cleaner to use the more compact {{vcite2 journal}} template and store the author list in the |vauthors= parameter ;-) Boghog (talk) 17:23, 8 February 2015 (UTC)
Thanks for updating the script. As far as I know, there are no cite doi or cite pmid templates with CS1 author-related errors; I try to keep the template space free of CS1 errors, although it is currently cluttered with "chapter= ignored" errors that will be fixed with a CS1 module update at the end of this week.
If your script is going to upgrade and improve the citations, not just subst them, you might want to scroll to the end of each article when it is in Preview mode after applying the script, then do a quick check for citation errors before you save. That's how I perform script-assisted edits, since editors put all sorts of crazy things into citations, and GIGO can lead to unexpected results. It just takes a few extra seconds. – Jonesey95 (talk) 18:29, 8 February 2015 (UTC)
That is the reason I am running the script for the time being manually to catch these sort of errors. I do visually look at the end of the article in preview to catch these errors, but for some reason, I missed this one. Eventually the intention is to have a bot run the script after it is sufficiently debugged. Boghog (talk) 18:36, 8 February 2015 (UTC)

Protein nomenclature

In light of your comments about the protein template merger, I figured you might have some thoughts on a protein naming problem. We currently have an article ribonuclease A, and another, skimpier one at pancreatic ribonuclease, to which RNase I redirects. Fine, except RNase A and RNase I and pancreatic ribonuclease are all accepted synonyms for the same thing. Worse, the UniProt recommended name for these in eukaryotes is the clunky "ribonuclease pancreatic". The RNase A article (the most common term in the literature by a long shot) focuses mostly on the well-studied bovine form (UniProt).

The technically correct resolution seems to be: merge the general content in ribonuclease A to pancreatic ribonuclease, redirect, and move what remains on the bovine protein to bovine ribonuclease pancreatic, but that's awful. Is there any compelling reason (broken bots?) not to put the bovine form at bovine pancreatic ribonuclease, even though that breaks the convention a bit? Opabinia regalis (talk) 07:35, 5 February 2015 (UTC)

@Opabinia regalis: Thanks for your note. I agree with your suggestion of merging ribonuclease A into pancreatic ribonuclease (the Enzyme Commission accepted name). WP:COMMONNAME would argue for a merger in the opposite direction, but I think consistency with the names of other enzyme articles which for the most part also use the EC name shifts the balance toward the EC name. Per WP:COMMONNAME, I would also support using the name bovine pancreatic ribonuclease since that is the one that is most commonly used (see below) and is less awkward sounding. Compare:
Boghog (talk) 20:09, 5 February 2015 (UTC)
Thanks, I'll sort these out when I get a chance. I noticed this when investigating some Pfam/Wikipedia mapping problems. (I do now think there are issues with the multiple infobox templates, but the problem seems to be using Template:Infobox enzyme, which has no Pfam parameter, for articles whose subjects really are families.) Opabinia regalis (talk) 00:09, 6 February 2015 (UTC)
@Opabinia regalis: As you are no doubt aware, the information contained in {{infobox enzyme}} which is based on Enzyme Commission numbers represent an enzymatic reaction, not an evolutionary related family of proteins. As a result of convergent evolution, two completely different protein folds may catalyze identical reactions and hence would be assigned the same EC number (see non-homologous isofunctional enzymes). As a consequence, the relationship between EC numbers and pfam families is not always one-to-one. Where they are one-to-one, I think it would be appropriate to add both an {{infobox enzyme}} and {{infobox protein family}} to the same article. When there is a single human gene that encodes an enzyme with a given EC number, it may also be appropriate to add a {{GNF Protein box}}, although this starts to become very messy and it may be better to keep the articles separate. One could think of some sort of a merged infobox which would have separate sections for a protein fold, evolutionary related genes that encode that fold, and enzymatic reactions catalyzed by that fold, but I think this merged box would be even more confusing for editors to create and maintain compared to using separate infoboxes. Boghog (talk) 11:21, 7 February 2015 (UTC)
PS: Good to see you back. We have missed you. Boghog (talk) 11:24, 7 February 2015 (UTC)
I was thinking along the lines of the switching parameters suggested in the merge discussion, as a way to streamline the display and encourage filling in as much information as available rather than just what's suggested in one set of infobox parameters. Right now it looks like most articles stop at one box (or where they do have two, as in ribonuclease H, there ought to be [at least] three). But you're right that that could create other confusions. For the time being I mostly just want the enzymes in common laboratory use to have accessible annotations.
Thanks, I don't know that I'm back for the long term, but might as well make myself useful. Strange how little has changed really. Opabinia regalis (talk) 23:29, 8 February 2015 (UTC)

Image

Top: this graph depicts the acute expression of various Fos family proteins following an initial exposure to an addictive drug.
Bottom: this graph depicts ΔFosB expression following repeated drug exposure, where these phosphorylated ΔFosB isoforms persist in neurons for up to 2 months.

Hey Boghog, just wondering if you have any feedback before I paste this image into FOSB.
It came from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC58680/figure/F1/. Seppi333 (Insert 2¢ | Maintained) 07:18, 8 February 2015 (UTC)

Hi Seppi. The figure itself is fine. There may be a problem with copyright however. I noticed you raised the question here and did not get a clear answer. I don't think the X-ray example is a good analogy. A closer analogy can be made with chemical structure drawings that was discussed here. The conclusion was chemical structure drawings that are not "traced" are OK to used because of the merger doctrine where the "expression is considered to be inextricably merged with the idea". In your case, you are using an exact "traced" copy. The safest option of course would be to redraw the figure. The simplest way to draw the curves would be to use a Bézier curve which some versions of PowerPoint have (see for example [4] echosvoice). Another possibility is if you have a mathematical function that approximates the curves, one could plot it in Excel. I will play with this a bitl.
I also see that you have uploaded this figure to commons with the {{cc-by-3.0}} license. Because copyright laws differ between different countries (see Commons fair use), it would be safer to upload figure into the English language Wikipedia and claim fair use under US copyright law (rationale is that you have only copied a part of the figure). Alternatively you could ask permission from the publisher and submit a WP:OTRS. Boghog (talk) 10:04, 8 February 2015 (UTC)
@Seppi333: OK, I misunderstood and now see that you have redrawn it. However you use the word "trace" in the summary description. This description is problematic. If it is an exact trace, it does not get around the copyright issue. If it is redrawn without tracing, I would suggest that you change the word "trace" to "redrawn". I know this seems like a small semantic issue, but it can have legal repercussions. Boghog (talk) 10:11, 8 February 2015 (UTC)
I traced some the lines in the top graph - the rest I reproduced differently from the journal graphs. E.g., there are differences in the axis marks, text ("exposure"), text location, and graph cutoff point on the x-axis. I'll revise the description I guess. Seppi333 (Insert 2¢ | Maintained) 10:48, 8 February 2015 (UTC)
Edit: when I say "traced" I mean "manually fit a bezier curve through it until they lined up", in the event that's ambiguous. I can make some superficial tweaks if this is an issue though - just let me know. Seppi333 (Insert 2¢ | Maintained) 10:52, 8 February 2015 (UTC)
The change in the description is probably sufficient and I don't think any changes of the figure are needed. Boghog (talk) 05:54, 9 February 2015 (UTC)

Removing information

I'm sorry I've felt it necessary to revert your recent edit to Hyperbaric medicine. I'm very sympathetic to the desire to do away with {{cite doi}} and removing access dates from journals, but your edit went far beyond that. You changed dates with month and year to just the year. You merged multiple author parameters into a single author parameter. You replaced the full name of a journal with an abbreviation. In each of these cases your edit removed information, or reduced data granularity, or obfuscated information. The data in our references is available for third parties to use via data dumps and removing pieces of information or lumping together multiple pieces of information simply makes it more difficult for those third parties to extract information from the dumps. Someone had gone to the trouble of separating individual editors when writing the reference and you ditch that hard work when you pull all of it into the author parameter - not to mention that you make the reference less amenable for re-use in other articles that use different citation styles because you've hard-coded the separators. Finally there's a long-standing consensus that because this is not a paper encyclopedia, it's better not to use journal abbreviations (Wikipedia:Scientific citation guidelines #Citation format); many readers won't know the abbreviations and supplying the full journal title is a service to them. Again, somebody went to the trouble of finding the full journal title and using it. Setting it back to an abbreviation is a retrograde step and you ought to avoid doing that. --RexxS (talk) 01:08, 11 February 2015 (UTC)

Should be fairly easy to use the full journal name and the year and month yes? Doc James (talk · contribs · email) 05:50, 11 February 2015 (UTC)
Also for the ref width can we go with 32 rather than 35? 35 just gives me one column rather than two. Doc James (talk · contribs · email) 06:31, 11 February 2015 (UTC)

@RexxS::

  • multiple author parameters into a single author parameter – The original consensus stated that the substitution of {{cite pmid}} templates should comply with WP:CITEVAR. Concerning the author parameters, my edits were completely consistent with WP:CITEVAR. The Hyperbaric medicine article had a mix of author formats but by far the predominant (and the originally established style) stored a Vancouver style comma separated author list in a single |author= parameter (70 citations). In addition six citation used "first, last, author2, author3, ..." format, four used a deprecated "coauthor " format, and one was a transcluded {{cite pmid}} citation that used a "first1, last1, first2, last2, ..." format. WP:CITEVAR also states that consistent a citation style within an article is desirable. Before my edits, there was a mix of styles. After my edit, there was a consistent style. The reason for using "first1, last1, first2, last2, ..." parameters is that it generates clean metadata. However the value of this metadata is highly dubious. First, how often is this used? Second, Wikipedia is not a reliable source and this includes citations that may suffer from accidentally or intentionally introduced errors. The vast majority of this citations in this article came from PubMed. The only metadata one really needs is the pmid where one can download a fresh, error free copy using RefToolbar or some similar tool. The best long term solution might be to use a parameter like |vauthors= in {{vcite2 journal}} that would generate clean metadata without the character overhead of explicit "first1, last1, first2, last2, ..." parameters (see rationale).
  • Someone had gone to the trouble of separating individual editors when writing the reference – that someone was Citation Bot (diff) as a followup to an incomplete citation added by an ip (diff). This bot edit was in violation of WP:CITEVAR.
  • reduced data granularity – I reduced excessive unnecessary data granularity. The Vancouver style comma separated author list is trivial to parse.
  • simply makes it more difficult for those third parties to extract information from the dumps – again, before my edit there was an inconsistent mix of formats. After my edit, there was a consistent format that makes it easier to extract information.
  • your edit removed information – some of the citation author lists were incomplete and my edit added the missing authors. Again, why would anyone want to reuse incomplete error prone citation data extracted from a Wikipedia article? Wikipedia is not a reliable source of citation data. PubMed is.
  • full name of a journal with an abbreviation – again, the reason for doing this was consistency. The majority of citations before my edit used abbreviations. I can modify the script so that full journal names are used throughout. However the danger of doing this is that occasionally a journal has a very long name in which case other editors might complain.
  • month and year to just the year – once again for consistency. I can modify the script so that a consistent |date=MMM YYYY format is used.

I hope this explanation is sufficient. Would it be acceptable to use a consistent (1) Vancouver style author format, (2) full journal names, and (3) |date=MMM YYYY throughout this article? Boghog (talk) 15:13, 11 February 2015 (UTC)

I understand your rationale, but I still think it's sub-optimal in respect of the author parameter.
I often reuse citations in related articles, but sometimes find that the citation style is different. Using the last1, first1 format allows any citation to be immediately reused and has absolutely no disadvantage compared to the hard-coded author format which requires changing by hand.
You also may call this level of data granularity "unnecessary"; I say it's not and I don't think you have any evidence that supports your assertion.
Similarly, questioning the value of our data to third parties doesn't favour your change to author format as that is just as prone to error, yet requires an extra stage of parsing that isn't needed with the first, last format. First, last has nothing but advantages over author format and I repeat that it degrades the quality of the information to move away from that. Google is known to make extensive use of our data dumps, for example, despite the occasional error, because it's the largest, decent quality source of both structured data and free text. If you ever find a hour to spare, I'd recommend viewing "Intelligence in Wikipedia" as you may be surprised at what uses our data is put to.
WP:CITEVAR is much misused to bolster one side of a disagreement, so it may be worth examining what it actually says. It says that citations should not be changed between two equivalent styles - this is to stop back-and-forth edit wars between say API and Vancouver simply because of editor preference. It does not prohibit upgrading the references; the extreme case of from bare urls to citation templates being an obvious example. In addition, the method of determining which style to consolidate to when there is a mixture of incompatible styles is to be determined by the style used by the first major contributor, not by taking a numeric count (even though the latter is more convenient). In brief, if you're going to ignore CITEVAR anyway, why not simply consolidate all cites to the superior last, first format which is at least defensible as an upgrade?
Finally, I'd like to express my appreciation of the work you're doing in improving references here. My dissent over the detail is meant to be wholly constructive as I think there is an opportunity to do an even better job. I won't revert you further whatever you decide in going forward. Cheers --RexxS (talk) 16:49, 11 February 2015 (UTC)
Thanks for your thoughtful reply. A couple of thoughts in response:
  • Copying a "last1, first1, ..." formatted citation into another article that uses Vancouver style citations introduces formatting inconsistencies.
  • The disadvantage of the "last1, first1, ..." format is parameter bloat and the increase in size of the template. This makes it harder to spot and edit prose that the citation is imbedded into.
  • Extracting the pmid from a citation and inserting the same citation with RefToolbar is less error prone than copying a citation from one article into another. As a specific example, the Hyperbaric medicine article had several citation templates that had missing authors (PMID 22592699, PMID 11558483, PMID 16299259, PMID 18643783, and PMID 19485935) and one that contained a misspelled journal name (PMID 6159432). By copying these citation templates into another article, these errors would have been propagated. By inserting the pmid into RefToolbar to create the citation from scratch, these errors would have been corrected.
  • First addition of citations to the Hyperbaric medicine article in the were in this edit, which itself was internally inconsistent, but at least half were in Vancouver format. First in-line citation were in this edit. The first templated citations were added in this edit and used Vancouver formatted authors in single |author= parameter. Hence not only the current predominate format, but the first established format used the Vancouver system. This is probably true of most older medical articles that used Diberri's template filling tool to create citations.
  • Module:ParseVauthors that is used by {{vcite2 journal}} is strong evidence that "last1, first1, ..." data granularity is not necessary. This is a very efficient Lua module that rapidly and accurately parses |vauthors= parameter contents with appropriate error checking to produce clean author metadata and is fully compatible with |author-link= and |displayauthors= parameters. Furthermore its use is completely transparent to both Wikipedia editors and content consumers.
  • Which citation format is superior is a matter of opinion. IMHO, the best long term solution would be to add |vauthors= support directly into Module:Citation/CS1 so that it can be used in the standard {{cite journal}}, {{cite book}}, etc. templates. This parameter would have all the advantages of "last1, first1, ..." parameters without the character overhead which can become significant for citations with a large number of authors. Boghog (talk) 20:57, 11 February 2015 (UTC)
And thank you for your thoughtful response. Sadly my principal interest is in scuba diving (and thence hyperbaric medicine), so I don't always get sources with a pmid. The one remaining issue that I'd comment on is the problem of citations obscuring the text where they are embedded. I'm a strong advocate of using list defined references once an article has stabilised to "de-snot" the text as a wiki-friend of mine was fond of calling it. Obviously once references are placed in the References section - where they belong - you don't have to worry about bloat. One day we'll use just the {{sfn}} and {{r}} templates within the text and editing scientific & medical articles will become easy again. Regards --RexxS (talk) 23:31, 11 February 2015 (UTC)

about my link

Hi, boghog I did read the guidelines and policy and I must have missed a few things, when you pointed me in the right direction I saw that the like that I posted did in fact violate the terms and conditions.

That was not my intention as I thought it was relevant and is except for the fact that it's also there to sell which is the part that violates the terms and conditions.

I do apologize for this and will try to pay more attention to what is allowed and not allowed as I am new here.

Sincerely, Matt6648 — Preceding unsigned comment added by Matt6648 (talk • contribs) 18:43, 15 February 2015 (UTC)

Thanks for your note and welcome to Wikipedia! I do appreciate that you carefully read the terms and now understand them. I wish more people had your constructive and positive attitude. Cheers. Boghog (talk) 20:16, 15 February 2015 (UTC)

Tagging as reviews / primary

I like this a lot. Thanks for doing it. Doc James (talk · contribs · email) 20:57, 18 February 2015 (UTC)

@Doc James: Thanks. I noticed someone else included these designations in the original non-templated citations and I wanted to preserve these. You might be interested in this discussion when we tried to decide the best {{cite journal}} parameter to use this purpose. The discussion got side tracked on whether including such a designation is original research or not. I obviously don't think so, but others disagree. I would appreciate you input. On practical matter the |department= parameter is both a non-obvious (i.e., the name of a "department" in a magazine or newspaper) and not ideal since it doesn't automatically include parenthesis. Boghog (talk) 16:21, 19 February 2015 (UTC)

Spam?

I appreciate where you are coming from. However, the entire goal of an open source reference is to encourage individuals to add material where they have specific knowledge. I sincerely hope that you and others will edit, remove and improve what I have tried to add, however, a blanket declaration of 'spam' is not right, nor an accurate description. — Preceding unsigned comment added by Jon33dn (talk • contribs) 23:25, 20 February 2015 (UTC)

@Jon33dn: Repeatedly adding citations authored by one research group to a number of articles in a short period of time is definitely ref spam. If you have any connection to the authors of these citations, adding these citations represents a conflict of interest. Please note that excessive self-citation is strongly discouraged. Thank you. Boghog (talk) 23:32, 20 February 2015 (UTC)
@Boghog: I would ask that you and any other future edits focus on the actual content added. Good faith addition of content is not spam, nor a conflict of interest.
@Jon33dn: To reiterate, you have added a number of citations from the same research group to a number of articles:
Extended content
This strongly suggests to me that you have a conflict of interest. Futhermore secondary sources (i.e., review articles) are preferred over primary. Even though primary sources may have been peer reviewed, secondary sources are generally preferred over primary because it is an independent verification that the source is notable, and is a second check as to the reliability of the conclusions as a disturbingly large number of research results cannot be reproduced. Boghog (talk) 23:39, 20 February 2015 (UTC)
@Boghog: I think we shall simply disagree. Respect for your efforts. The content added is obviously the same set of results in the various appropriate locations where it is topical. Suggestion to add to the talk page is a welcome piece of information.
@Jon33dn: The issue here is more than a disagreement between two editors. WP:SELFCITE is a Wikipedia policy that states in part Using material you have written or published is allowed within reason, but only if it is relevant, conforms to the content policies ... is not excessive ... and should not place undue emphasis on your work. When in doubt, defer to the community's opinion. I am part of the community opinion. You have only added citations from one research group to a number of articles which clearly qualifies as excessive. Furthermore all the citation you have added are WP:PRIMARY (reliable primary sources may be used in Wikipedia; but only with care, because it is easy to misuse them). Citing only your own papers is neither acceptable in scientific publications nor per WP:UNDUE, in Wikipedia. Finally the material that you have added appears not central to the subject of the article. In short, the purpose of the material that you have added appears more to promote the work of one research group rather than improve Wikipedia. Boghog (talk) 00:08, 21 February 2015 (UTC)
@Boghog: Actually, I think a disagreement it is exactly what it is. I am also a part of community opinion and I believe the content I have added is valuable to the topics where they were posted. I also assert that my use of citations are within reason and relevant. Nor are they excessive as they support the statements made. Addition of more and diverse citations by yourself would not be amiss.

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ERCC6

Hello Boghog,

I just want to let you know I will be editing the ERCC6 page quite a bit in the next few days. I will make sure not to amend any of the content you have written.

I am a Stanford University junior majoring in chemical engineering; the reason for my edits of this page stem from a project I am doing for biochemistry 2 class here (ChemE183). As part of my grade, my edits must be able to be seen (obviously). I just wanted to let you know, and ask that if I put any information on the page/formatting that you don't agree with, please let me know and I will fix it immediately. I don't want to step on the shoes of any other editors; yet, I also want to make sure my content that I am taking quite a bit of time to post doesn't get deleted.

Thanks so much and let me know if any other concerns arise.

Ajit Vakharia Stanford '16 — Preceding unsigned comment added by Ajit Vakharia (talk • contribs) 23:38, 2 March 2015 (UTC)

I appreciate this.

Useless generalization deleted. I am sure that you have become aware that sulfur in cysteine is quite different from that in ITC, so that the change was also an implausible generalization. In other words, the change was about sulfur-containing phytochemicals, about which nobody can make useful generalizations in effect on life, and the article is restricted to about three specific categories. Thanks. 70.74.198.226 (talk) 09:40, 3 March 2015 (UTC)

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TFA blurb

Hey Boghog, as you probably already know from the edit notification/echo ping, I've nominated the amphetamine article for TFA. I was wondering what you thought about the blurb I wrote for it at Wikipedia:Today's featured article/requests/Amphetamine. I basically just took a couple sentences from the first 2 lead paragraphs and condensed them to meet the ~1,200 character limit (I just made sure it had fewer characters than the featured article blurb for today, which is over 1,200).

Is there anything you think we should change in it? Seppi333 (Insert 2¢ | Maintained) 03:49, 9 March 2015 (UTC)

@Seppi333: Thanks for nominating the article and including me as a coconspirator ;-) Looking over the blurb, I think it could be simplified a bit and reorganized to place first what most people are interested in, namely its use. Below is a suggestion. Cheers Boghog (talk) 20:55, 9 March 2015 (UTC)
Amphetamine is a potent central nervous system stimulant of the phenethylamine class that is used in the treatment of attention deficit hyperactivity disorder and narcolepsy. It is also used as a performance enhancer and nootropic, and recreationally as an aphrodisiac and euphoriant. Amphetamine increases neurotransmitter activity in the brain, with its most pronounced effects on norepinephrine and dopamine. At therapeutic doses, this causes emotional and cognitive effects such as euphoria, change in libido, increased wakefulness, and improved cognitive control. It induces physical effects such as decreased reaction time, fatigue resistance, and increased muscle strength. Amphetamine exists as two enantiomers, levoamphetamine and dextroamphetamine, and normally refers to a 1:1 mixture of the two enantiomers in its free base form. It is a prescription medication in many countries, and unauthorized possession and distribution of amphetamine is often tightly controlled due to the significant health risks associated with uncontrolled or heavy use.
I've updated it per your suggestion, though I made a small revision to the 1:1 mixture clause since I'm not sure if the average reader will realize it's referring to a ratio vs something else. Since it was below the word limit, I just rewrote that part as "and normally refers to an equal parts mixture of the two enantiomers in its free base form." Regards, Seppi333 (Insert 2¢ | Maintained) 21:15, 9 March 2015 (UTC)

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hi

Boghog you have a minute--Ozzie10aaaa (talk) 19:31, 19 March 2015 (UTC)

@Ozzie10aaaa: Hi. I do have a minute. For ? Boghog (talk) 19:34, 19 March 2015 (UTC)
Boghog...a week ago Bluerasberry approved #3 criteria for Dyslexia for GA nomination however he told me I needed someone else to finish and close, interested?--Ozzie10aaaa (talk) 19:38, 19 March 2015 (UTC)
Hmm, this is a bit outside my area of expertise. But I will take a look at this over the weekend to provide my opinion if the missing recommended MEDMOS content is required or not. Cheers. Boghog (talk) 19:45, 19 March 2015 (UTC)
ok...thanks--Ozzie10aaaa (talk) 19:47, 19 March 2015 (UTC)

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ERCC4 entry

Hello Boghog - thank you for your guidelines on formatting this page. I will be working on this entry and that for ERCC1 under the direction of Andrew Su and Ginger Tsueng of the journal GENE (Elsevier Press) who have asked us to edit this entry in addition to writing a review article on ERCC1 and ERCC4 that will be published in GENE. HumDNARepair (talk) 21:20, 24 March 2015 (UTC)

Thanks for excellent contributions! I hope you don't mind, but I changed back the protein name to ERCC-4 (the recommended alternate UniProt name, see Q92889) while leaving the ERCC4 gene symbol (the approved HUGO gene symbol). Gene and protein names often differ. Boghog (talk) 21:32, 24 March 2015 (UTC)

Hippocampus

Your edits introduced multiple "Vancouver style errors" - perhaps something has changed in the cite templates. Regards. Materialscientist (talk) 12:26, 29 March 2015 (UTC)

@Materialscientist: Those are not errors. See Help:CS1_errors#vancouver and discussion. Right now, any author name that contains a diacritical mark is flagged as an error. The consensus is that should not be marked as error. Trappist the monk will fix. Unfortunately it may be several weeks before the fix in Module:Citation/CS1 is rolled out. Boghog (talk) 12:32, 29 March 2015 (UTC)
Right now there are 683 pages with these Category:CS1 errors: Vancouver style errors. These will go away once Module:Citation/CS1 is updated. Boghog (talk) 12:36, 29 March 2015 (UTC)

I'm sure you'll see on WP:MCB, but I thought I'd ask personally here too. Given how excellent the enzyme FAR was, it'd be great to have your help in overhauling the gene article a bit. T.Shafee(Evo﹠Evo)talk 10:08, 31 March 2015 (UTC)

The gene article

I'm sure you'll see on WP:MCB, but I thought I'd ask personally here too. Given how excellent the enzyme FAR was, it'd be great to have your help in overhauling the gene article a bit. T.Shafee(Evo﹠Evo)talk 10:08, 31 March 2015 (UTC)

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Re-added PMC links

Thank you. — Preceding unsigned comment added by Silverfox369 (talk • contribs) 20:23, 22 April 2015 (UTC)

Reference Edits in Sandbox

I would like to inform you that it was not the wrong pmid number. Rather, the Pubmed Central number was listed, which I double checked and is correct. I will be watching any further edits carefully. — Preceding unsigned comment added by Silverfox369 (talk • contribs) 20:17, 22 April 2015 (UTC)

I agree that the PMC IDs were correct. The problem is that the PMC IDs were copied into |pmid=. PMC ≠ PMID. The script that I used to reformat the citations assumes that the PMIDs were correct, but this in case they were incorrect. Boghog (talk) 20:33, 22 April 2015 (UTC)

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I am not

…going to rekindle old conflagrations by deeply engaging you on the question you left at my talk page. This once, I'd reply that the content moved to footnote in the article in question was all there before I arrived, was moved to the footnote so that it could be retained and not deleted, was corrected for the same reason, and was tagged as it was to make clear that someone had said those things (that were in the original content), and that that very someone needed to be identified. So, yes, I called attention to the shortcomings still present after the editing I had done. This, I have found for the most part, results in good longterm consequences for articles, at least with people who AGF with regard to my editing. Leprof 7272 (talk) 21:47, 24 April 2015 (UTC)

Another article is yours. Goodbye. Leprof 7272 (talk) 21:52, 24 April 2015 (UTC)
@Leprof 7272: I have what I think are legitimate objections to your edits which I outlined on your talk page. I have now moved them to the article's talk page. If you disagree, please respond there. Boghog (talk) 21:57, 24 April 2015 (UTC)
@Leprof 7272: the content moved to footnote in the article in question was all there before I arrived. – False. You have tagged your own edits. @Leprof 7272: tagging own edits diff Boghog (talk) 22:19, 24 April 2015 (UTC)
As I explained, yes, I tagged my own edit, to call attention to the fact the bulk of that content—that discussing the component kinetics and thermodynamics governing ligand association—was moved from text to footnote, and was unsourced. It is one of my practices, that when an editor says something unsourced, to add a bit of text making clear that someone in some source somewhere had to have said what is being written in by the editor, and so a source is needed. The added bit of text I inserted, was to allow the [who?] tag to be added, to draw an editor in, to provide a source. As always, you have the wrong end of stick, and baby went out with the bath (mixing of metaphors intentional). Last word is yours, I am out. Leprof 7272 (talk) 22:41, 24 April 2015 (UTC)

inappropriate comment

Boghog, one is not supposed to comment on neutral notices of discussions elsewhere---but far worse is that your comment is misleading, as it appears to point to a discussion in which a consensus had been reached, when in fact it links to the very discussion of the notification. Please demonstrate your good faith be removing your misleading comment. Curly Turkey ¡gobble! 17:47, 28 April 2015 (UTC)

@Curly Turkey: One never, ever is supposed to revert a some one else's comment on a talk page unless is it a personal attack, libelous, etc. The proper way to respond to a perceived error is directly on the relevant talk page. Please demonstrate your good faith by following standard talk page guidelines. Thank you. Boghog (talk) 18:52, 28 April 2015 (UTC)
If "One never, ever is supposed to revert a some one else", then, of course, you would never, ever do such a thing, would you? Curly Turkey ¡gobble! 19:31, 28 April 2015 (UTC)
@Curly Turkey: You clearly are confused. You collapsed others comments. That is a revert. I reverted your reversion. Boghog (talk) 19:38, 28 April 2015 (UTC)
@Doc James: Do you agree? Curly Turkey ¡gobble! 19:41, 28 April 2015 (UTC)

The important discussion is that concerning cite ISBN generally not the talk page issue. Doc James (talk · contribs · email) 19:46, 28 April 2015 (UTC)

This is not allowed though [5] Doc James (talk · contribs · email) 19:49, 28 April 2015 (UTC)
@Doc James: Is this allowed? Curly Turkey ¡gobble! 20:02, 28 April 2015 (UTC)
That is adjusting formating. The other is removing someone's comments Doc James (talk · contribs · email) 20:04, 28 April 2015 (UTC)
@Doc James: Then collapsing the discussion itself is not a problem? Curly Turkey ¡gobble! 20:06, 28 April 2015 (UTC)

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Proteasome complex

Hello Mr. Boghog,

I have been editing the pages of subunits of proteasome complex. I noticed that the structure of my content has been edited by you. I want to share my consideration with you.

Proteasome is a very complicated subject to discuss. I noticed that there is a page dedicated to proteasome and have been trying to connect my page to the main page as much as possible.

For the Gene Wiki page of each individual subunit, I think it should contain the following information as following,

1. Intro: basic information regarding the gene and protein, and their brief function. 2. Structure: I think it should started with "protein expression". It includes the information regarding the gene and its process for translation. It should also contain information regarding the protein itself, including MW, PI, and amino acids. As a component of a complex, the "complex assembly" is an important part within the structure section. 3. Function: I started with evidence provided by crystal structure. In my humble opinion, the major function of a subunit is its interaction with other partners and its contribution to form the complex, which needs strong evidence from crystal structure analysis. And the function of proteasome as a whole, including protein degradation and MHC class I precessing, is less important since it is about the complex instead of this particular subunit.

As a long term process, I am trying to search information regarding this individual protein, such as its unique interaction with other enzymes, or their contribution to gate opening or complex assembly. These information will come back later.

If you may kindly share your thought regarding the structure and content of these particular subject, I would be really appreciate it.

Best,

Heartbd2k DingWang (talk) 20:26, 1 May 2015 (UTC)Heartbd2k DingWang

Hi. Thanks for your message and thanks for all the great content you have been adding. One thing that puzzled me however was the organization of the content. To me, structure should included the primary (amino acid sequence), secondary (alpha helices vs. beta sheets vs loops), and tertiary structure (3D arrangements of atoms) as for example determined by X-ray crystallography. It would also be appropriate to say something about the quaternary structure of the proteasome (how the subunits fit together) in this section. The number of amino acids and MW are a consequence of the primary structure and hence should be part of this section. On the other hand, expression data is not structure and therefore IMHO should be placed in a separate section. Placing the crystal data in the function section is also puzzling. This should be placed in the structure section, not the function section. The function is what the protein does, i.e., it is part of the proteasome and in turn the function of the proteasome is to degrade other proteins. In summary, I think the following sections are appropriate for a Gene Wiki article:
  1. Structure – primary, secondary, tertiary, quaternary structure as determined by X-ray crystallography
  2. Function – what the protein does
  3. Expression – how the protein is produced
  4. Mechanism – how the protein accomplishes its function
Does this make sense? Boghog (talk) 21:40, 1 May 2015 (UTC)
@Heartbd2k DingWang: I realize that structure and function are closely linked and therefore it may be difficult to separate the two. However I still think it is confusing to included information about expression in the structure section. In PSMB6 I tried a different organization:
  1. Gene – where it is located and exon organization
  2. Protein – basic properties (size, MW), post-translational processing
  3. Complex assembly – quaternary structure
  4. Function – including aspects of quaternary structure that directly determine function
Is this any better? Boghog (talk) 08:01, 2 May 2015 (UTC)

Thank you for spending time to share your thought. I agree for most of your idea. I just started to write those pages and multi-subunit complexes is quite a complex concept to cover. I will try to adopt your structure in my future writing.

  1. Intro
  2. Gene
  3. Protein Structure
  4. Complex Assembly
  5. Function
  6. Clinical Significance
  7. Pathways & Interaction (if any)

I will revisit those subunits when I have filled most of them with basic information. I will add more specific info regarding subunits themselves instead of the whole complex. the complex has its own page which should provide more detailed information regarding the complex info.

Best,

Ding — Preceding unsigned comment added by Heartbd2k DingWang (talk • contribs) 22:05, 2 May 2015 (UTC)

Interview for The Signpost

This is being sent to you as a member of WikiProject Molecular and Cellular Biology The WikiProject Report would like to focus on WikiProject Molecular and Cellular Biology for a Signpost article. This is an excellent opportunity to draw attention to your efforts and attract new members to the project. Would you be willing to participate in an interview? If so, here are the questions for the interview. Just add your response below each question and feel free to skip any questions that you don't feel comfortable answering. Multiple editors will have an opportunity to respond to the interview questions, so be sure to sign your answers. If you know anyone else who would like to participate in the interview, please share this with them. Thanks, Rcsprinter123 (express) @ 16:10, 9 May 2015 (UTC)

Your recent reverts

Hi Boghog, thanks for catching the extra periods that were being added; not sure why WPCleaner is doing that, I'll have to file a bug report. However, you really shouldn't revert the entire edit, especially when it would be so incredibly easy to remove the extra periods. Please undo your reverts and manually remove the extra periods. (Or, if you really don't feel like manually removing the periods, undo your reverts and let me know so I can remove the periods.) Each of the edits you reverted contained more than adding a period. Thanks, --L235 (t / c / ping in reply) 04:34, 15 May 2015 (UTC)

Sorry, too quick on the draw. I have selectively reinstated all the rest of your edits. The punctuation issue is slightly more complicated than adding an extra period. This script moved a period from before the citation to after (WP:CWERRORS, #67 which is deactivated). It should be doing the reverse per WP:CWERRORS, #61. Boghog (talk) 05:01, 15 May 2015 (UTC)
@L235: The script is working correctly. I was confused by the edit summary which stated "Reference before punctuation" which refers to the error that is being corrected. I thought it was saying, this is how it should be. Sorry for the confusion. Boghog (talk) 05:08, 15 May 2015 (UTC)

Cite PMID

Hello,

I just noticed that you reverted Cite PMID to the old style. Cite PMID is very convenient. PMID is the record number we use in all references in the biomedical sciences. If Cite PMID has been deprecated (as you wrote) why it is still mentioned at http://en.wikipedia.org/wiki/Help:Citation_tools

Hi. A link to {{pmid}} was and still is included in all the citations. Further more, cite pmid and cite isbn have been deprecated and should no longer be used:
Warning banners
{{cite pmid}} and {{cite doi}} {{cite isbn}}
Boghog (talk) 18:46, 21 May 2015 (UTC)

Congrats

On your writeup in the Signpost. Doc James (talk · contribs · email) 05:53, 21 May 2015 (UTC)

Thanks. The most important thing of course is to attract interest in the project and Wikipedia as a whole. Cheers. Boghog (talk) 18:52, 21 May 2015 (UTC)

Butyric acid

Hey Boghog - since I'm planning on merging the content from the other 2 articles (butyrate + sodium butyrate) at some point this week, and since this is basically a drug which is MOS:CHEM, MOS:MCB, and MOS:PHARM/MOS:MED, I was wondering if you'd be interested in lending a hand in organizing it accordingly. I have no idea how significant any of the 3 compounds are from a chemist's perspective, but from a medical POV, butyrate-producing microbiota are essentially the symbiotic equivalent of toxoplasma gondii (in mice, toxoplasmosis induces DNA hypomethylation in amygdalar AVP-related genes) - they're bacteria that can+do modify the host's neuroepigenome - and can drive subtle long-term changes in behavior in healthy hosts as a result. (e.g., PMID 25401092)

Is any chemistry-related data in the chembox worth retaining/incorporating in the chemistry section if a drugbox is used instead? Seppi333 (Insert 2¢) 11:08, 23 May 2015 (UTC)

Hi Seppi33. I think we are in general agreement about consolidating the biological information into one article so we can start with that. However as I explained here, I don't think replacing the chembox with a drugbox is appropriate. Butyrate is a pharmacologically active metabolite, not a drug per se. Furthermore since the information in drug databases on butyrate, many of the links in the drugbox would remain unpopulated whereas some of the links in the current chembox would be lost because they are not supported in the drugbox. To me, the subject of this article falls more within the scope of WP:CHEMS and WP:MCB than WP:PHARMA or WP:MED hence IMHO the chembox is a more appropriate infobox than drugbox. Finally butyrate should be left behind as a disambiguation page and sodium butyrate should be retained as a chemical that is distinct from butyric acid. Boghog (talk) 11:52, 23 May 2015 (UTC)
I didn't see your reply on WT:MED until just prior to my reply - I'm okay with going that route. I actually wasn't aware of the half-life being unusually short in relation to other HDACs used as research compounds though; would you happen to know of any databases/papers that cover half-life data in rats and mice as well? Seppi333 (Insert 2¢) 12:22, 23 May 2015 (UTC)
OK, no problem. I don't know much about the half-lives of these compounds. I will see what I can dig up. Boghog (talk) 12:48, 23 May 2015 (UTC)
@Seppi333: Table 3 in Elaut et al.[1] lists the metabolic stability of a variety of HDAC inhibitors. According to this source, the half-life of sodium butyrate is less than 5 minutes in mice and less than 30 seconds in humans. In comparison, the half-life of valproic acid is 8–16 hours. Boghog (talk) 14:08, 23 May 2015 (UTC)
I think the author just misspecified the half-life; I noticed a few clinical studies with the ~5±2 minutes half life, while another (first one below) said something different, as quoted.
  1. Pharmacokinetic study of butyric acid administered in vivo as sodium and arginine butyrate salts.
    - "In man, the butyric acid elimination curve can be divided into two parts corresponding to two half-lives: for the first (0.5 min), the slope suggests an accelerated excretion, while for the following (13.7 min), a slow plateau is observed. The rapid elimination of butyrate is a limiting factor for practical applications. However, the lack of toxicity supports its use in human therapy."
  2. Phase I Study of the Orally Administered Butyrate Prodrug, Tributyrin, in Patients with Solid Tumors
  3. Clinical pharmacology of sodium butyrate in patients with acute leukemia.
  4. Butyrate and phenylacetate as differentiating agents: practical problems and opportunities.

I'm sure some researchers/authors realize the current limitations of butyrate, but the doses used in addiction research are generally at least half or less that of what I've seen covered in those cancer papers... I remember seeing ranges of 100mg/kg - 300mg/kg when specified as oral or "systemic", the latter end of the range corresponds to the sodium butyrate dose used in their original paper on amphetamine/HDAC1/c-fos to restore c-fos once it was repressed by ΔFosB. That not really that bad IMO. Seppi333 (Insert 2¢) 22:47, 23 May 2015 (UTC)

References

  1. ^ Elaut G, Rogiers V, Vanhaecke T (2007). "The pharmaceutical potential of histone deacetylase inhibitors". Current Pharmaceutical Design. 13 (25): 2584–620. doi:10.2174/138161207781663064. PMID 17897003.

Hey there!

Just wanted to extend my thanks for your formatting help on the MAPK15 page -- I'm pretty new to the editing process, and really appreciate your updates! — Preceding unsigned comment added by Sasanit (talk • contribs) 22:55, 29 May 2015 (UTC)

Reference errors on 3 June

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Mail call

Dropped you a line. WormTT(talk) 07:49, 19 June 2015 (UTC)

Nomination for deletion of Template:PMID3

Template:PMID3 has been nominated for deletion. You are invited to comment on the discussion at the template's entry on the Templates for discussion page. Magioladitis (talk) 12:29, 20 June 2015 (UTC)

Question about NF-κB signaling

Hey Boghog - I know you're knowledgeable about this topic, so I figured I'd ask. I expanded a table (NF-κB#Addiction) yesterday based upon a new review, but I made an assumption about an effect of NF-κB when I replaced "regulation of cell survival pathways" with "NF-κB inflammatory response in (structure)". Am I correct in assuming the former statement could entail the latter as a functional consequence? I'm not entirely sure on that since NF-κB makes a distinction between an inflammatory response and a cell survival response in the text.

I'd need to add that entry back into the table otherwise. Seppi333 (Insert 2¢) 20:56, 22 June 2015 (UTC)

Hi Seppi. I am less familiar with the role of NF-κB on cell survival compared to inflammation. I do know that inflammation can trigger apoptosis, especially in neurons. Hence apoptosis could very well be secondary to the inflammation. However the various NF-κBs regulate the expression of a large number of genes, hence I would not at all be surprised if there was a direct effect on cell survival as well. I will have to dig into this. More later. Boghog (talk) 05:07, 23 June 2015 (UTC)
Yup, there is a direct effect as well. See for example PMID 16397579, PMID 16187223, and PMID 16997282. Boghog (talk) 05:15, 23 June 2015 (UTC)
Ah, thanks for clearing that up. :) Seppi333 (Insert 2¢) 05:42, 23 June 2015 (UTC)

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Aebp2 Help

Was adding a citation for the AEBP2 article to this publication but I think I messed somerthing up. Can you help add the correct parameters? Thanks. — Preceding unsigned comment added by 159.39.34.12 (talk) 19:04, 16 July 2015 (UTC)

Barnstar

The Barnstar of Good Humor
To Boghog, for pointing me to AXL receptor tyrosine kinase. Axl ¤ [Talk] 13:59, 28 July 2015 (UTC)

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Reference errors on 11 August

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If the rest

For the record, bold, italics, and all caps cannot all mean shouting here, so I took your down-dressing on that matter as particularly weak. Perhaps work to have these tools disabled in Talk? Since others have allowed, but since you they so offend? Meanwhile, you may use no textual tools for emphasis, but I do. You will not change me, at least not in the limited ways you seem willing to try.

That is to say, if the rest of your life experiences have not taught you this, hear this once from me: beating peers is not a winning strategy of persuasion. Your way of relating/communicating with me does absolutely no good, whatsoever, toward the ends that you seem to be aiming for (compliance, respect, etc.). It smacks of overwhelming personal frustration (enough so that it has led me to offer up an occasional passing prayer for your work and family).

Otherwise, when I make a knee-jerk mistake and initially misunderstand another editor's effort, I most often correct myself, editing out prose regarding my misunderstanding, especially if it has led me to misjudgment and criticism. While I will never again touch your words, anywhere, I would offer you might do the same with your own words at the other page.

Whether you decide to leave them in, a testimony to your "shoot first, ask questions later" approach to me, is up to you. But, again, just this once: Besides doing me no good at all—only tempting me to reply in kind, a temptation which I committed some time ago to deny—I suggest they do you no good either. Note italics, no bold. (To the extent that I understand the less collegial, more vitriolic forms of our natures—imagine losing temper with wife or colleagues—these self-indulgances, when they occur, damage not only the receiving party, but also ourselves.)

However, note, when you respond "against interest" (I take based on precedent that a significant interest of yours has been attempting to belittle me), that is, when you actually find some point on which to agree with me, it is so bloody remarkable as to be breathtaking and thought-provoking. Then, then, you are truly admirable, and I am responsive. (A word fitly spoken is like apples of gold in a setting of silver… or again, To make an apt answer is a joy to a man, and a word in season, how good it is.) Do whatever you will, there, at the Infobox issue. I won't respond to that matter, further. Le Prof Leprof 7272 (talk) 05:07, 12 August 2015 (UTC)

Review request

Hi,

Could you have a look at the optimum temperature you gave in the Lactase article? There is a discussion here which claims that the reference you added gives 37 and not 25 as the optimum. --Raziman T V (talk) 08:38, 20 August 2015 (UTC)

Ref spam?

Hi, I wanted to know exactly what aspect of this edit constituted "ref spam". Thanks. Everymorning (talk) 02:18, 20 August 2015 (UTC)

Because of the way the text was written. A 2015 study in Cell Metabolism detected irisin in human plasma using tandem mass spectrometry. Why is the year in which the study important? Why is the journal in which this study was published important? Why was the detection method important? This sentence tells more about that study than what the study says about the protein. When I run across contributions like this, it is frequently due to some one trying to promote their own publications, and if so, this is a form of WP:REFSPAM. Combined with earlier studies, the paper suggests that "human irisin exists, circulates, and is regulated by exercise". This is far more relevant than the year, journal, and detection method. Unfortunately this is a primary source supporting a medical claim which is strongly discouraged per WP:MEDRS. I think it better to wait until this finding is supported by an independent secondary source. In sort, I think it is too soon to include this statement in a Wikipedia article. Boghog (talk) 02:55, 20 August 2015 (UTC)
Thanks. I suspect that the problem here may lie in that I did not read the whole abstract, just the highlights section. Everymorning (talk) 11:22, 20 August 2015 (UTC)

Reference errors on 27 August

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Consistent citation formatting?

Hey, this refers to [6]. What tool did you use to make those changes? I get why vauthor is preferred, but I tend to use the citation generator a lot, and that won't spit out the vauthor, nor will it make the other changes you made... So if there's a way to fix that myself without manually going over each ref or having others fix it (not my intention at all!), I'd prefer that. Thanks. Garzfoth (talk) 09:51, 25 August 2015 (UTC)

Hi, thanks for asking. You can use the User:Diberri/Template filler (tool link) to create vauthors style citations. Right now, it generates {{vcite2 journal}} templates, but since {{cite journal}} now also support the |vauthors= parameter, there is no longer a need for {{vcite2 journal}} (just replace "vcite2" with "cite" ). When I find some time, I will make a change to the tool so that it outputs "cite" instead of "vcite2". Cheers. Boghog (talk) 11:57, 25 August 2015 (UTC)
I have modified the tool so that now outputs {{cite journal}} instead of {{vcite2 journal}} while retaining he |vauthors= parameter. Boghog (talk) 17:08, 29 August 2015 (UTC)

Reference errors on 29 August

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Template

Per this edit here [7] the discussion is for deprecation rather than deletion yes? Wondering if we can change this? Doc James (talk · contribs · email) 21:37, 7 September 2015 (UTC)

Just to be clear, I was not the one who nominated this template for deletion, GeoffreyT2000 did here and here I understand what you are saying, but I don't think we can change it. Similar to an article, once a template has been nominated for deletion, the notice should not be removed or changed until the discussion closes. Furthermore, there is no established mechanism for "templates for deprecation" discussions other than the current ongoing RfC. In any case, It looks like this deletion discussion is close to a snow close for keep and the deletion template will soon be removed. Boghog (talk) 03:34, 8 September 2015 (UTC)

Curious about comment on behavioral epigenetics, please give more detail

Your edit summary; "Not WP:MEDRS compliant nor does it directly support the corresonding text." ... where in MEDRS?

References:

99.109.126.40 (talk) 05:53, 16 September 2015 (UTC)

Hi. Thanks for your message. I generally reply here, not on the simple English Wikipedia, especially when the article is question (Behavioral epigenetics) is in the regular English Wikipedia, not the simple English Wikipedia. In any case, the reason I reverted your addition was two fold. First, the citation that you added is a primary source. Per WP:MEDRS. generally secondary sources are required to support medical claims. This is because I surprisingly large percentage of medical research simply cannot be repeated or the association is less strong than initially claimed. The conclusions needs to be reviewed by a third party and put in context in order to increase the confidence that the results are real. Second, the citation that you inserted is about a very specific epigenitic genetic result (the effect socioeconomic status on epigenetic aging) whereas the text you inserted it after was about a general mechanism (epigenetic changes on neuron structure and function). Hence the citation didn't really fit there.Boghog (talk) 07:32, 16 September 2015 (UTC)
The IP is evading blocks (apparently global blocks, as well). See User:Arthur Rubin/IP list for some of the history. — Arthur Rubin (talk) 16:04, 16 September 2015 (UTC)

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FNDC5 unreliable medical source

Hi Boghog, I would like to know why you think that PNAS journal is an unreliable medical sourse. Thank you. — Preceding unsigned comment added by Mnemonic1975 (talk • contribs) 16:18, 19 September 2015 (UTC)

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FAT gene wiki page

Hi,

Thanks for fixing up my edits concerning the FAT gene wikipage. I am very new to this and am learning the syntax on the fly. In particular the referencing, which I get wrong all the time.

Concerning the wiki entry. FAT is not really correct anymore. The accepted name is now FAT1 (see also http://www.genecards.org/cgi-bin/carddisp.pl?gene=FAT1). Problem being that FAT (without the 1) is an alias for CD36.

Is it possible to rename the entry to FAT1 instead of FAT. Will this then alter any links made from other pages?

Your help much appreciated.

Best. — Preceding unsigned comment added by SkiNaki (talk • contribs) 18:23, 11 October 2015 (UTC)

Hi. And thank you for your great contributions to the FAT1 article! As the accepted name is now FAT1, I took the liberty of renaming the page. One doesn't need to worry too much about links from other pages after a page rename since a redirect is left behind. If you haven't seen this yet, check out User:Diberri's Wikipedia template filling tool (instructions). Given a PubMed ID, one can quickly produce a formatted citation that can be copied and pasted into a Wikipedia article. Cheers. Boghog (talk) 19:09, 11 October 2015 (UTC)


Hi,

Thats great. Thanks for renaming the page. I do note that if you do a google search, it still comes up FAT (gene) as a hit, rather than FAT1 as the page name. But I guess this will change with time?? Will the redirect page ever disappear?

Thanks also for the link on how to insert citation links for the wiki page. Much appreciated.

Best, — Preceding unsigned comment added by SkiNaki (talk • contribs) 06:57, 12 October 2015 (UTC)

Mesna

Could you take a look at the merge proposal on this page when you get a chance? No crisis, but another opinion would be welcome. --Smokefoot (talk) 17:47, 12 October 2015 (UTC)

H3F3B

Joylandrews (talk) 05:48, 10 October 2015 (UTC)== Crucial to leave the only link in the internet available to help find other kids with H3F3B mutations. Not "spamy"! ==

Why have you called my edit "spamy"? It is absolutely relevant and crucial to get information to parents of kids who have mutations in H3F3B. What type of reference would you like in order to publish the link to help these families get their kids the medical attention they deserve? I can provide you with a genetics report if that is helpful.

Thank you.

Joy — Preceding unsigned comment added by Joylandrews (talk • contribs) 03:51, 10 October 2015 (UTC)

Hi. Thanks for your contribution to H3F3B. However, there were a number of problems with it:
  • Per the Medicine-related articles manual of style, Don't use external links to web-based or email-based support groups for patients, professionals, or other affected people (even if run by a charitable organization).
  • The material that you added mentioned Genedx, a for profit genetic testing and diagnosis company. If you have any connection to this company, you may have a conflict of interest.
  • Statement in Wikipedia need to be backed up by reliable sources. For biomedical information, this normally means peer-reviewed articles, preferably reviews (see WP:MEDRS).
  • Per, WP:EL, External links should not be placed in the body of an article. Boghog (talk) 04:12, 10 October 2015 (UTC)

How would you recommend this be re-written to meet the criteria? Or are you saying that Wikipedia cannot publish information about medical theory when it is emerging? Can I phrase it in a different way that would make this admissible? — Preceding unsigned comment added by Joylandrews (talk • contribs) 05:39, 10 October 2015 (UTC)

Also, I have no connection to Genedx other than that they are the company that did the exome sequencing for four of the five known cases where a child has a known mutation in H3F3B. I am fine leaving the company name out of the article. — Preceding unsigned comment added by Joylandrews (talk • contribs) 05:40, 10 October 2015 (UTC)

Also, please note that the website is NOT a support group - it is a place to find other patients so that medical studies can be done and these children's lives can be improved and maybe even saved. And, the Facebook page already found one medical researcher in Germany who found it in an online search. Please be a part of the search for information and help me find a way to write this section in a way that complies with the standards! — Preceding unsigned comment added by Joylandrews (talk • contribs) 05:45, 10 October 2015 (UTC)

Thanks for the clarification. When I first tried the h3f3b.org link, it didn't respond so the only information that I had access to was the Genedx web site. Now the h3f3b.org link is working. I now understand better what the issues are and apologize for characterizing your contribution as spam. I am very sympathetic to your situation but at the same time, we need to follow relevant Wikipedia guidelines and policies concerning external links. I have added back an edited version of your contribution. I hope this is OK. The problem is that this particular condition has not been well documented in the published biomedical literature (see for example H3F3B disease associations). It would be much better if we could cite a description of this specific condition in a peer reviewed publication. If such a article is published in the future, it should be added to H3F3B. Boghog (talk) 10:12, 10 October 2015 (UTC)

Thank you so much for this. I do understand that Wikipedia has strict guidelines. Is there a way to edit the section so that it more clearly calls out that the site exists? For example, could I add "There are ongoing efforts to locate individuals who have genetic mutations in H3F3B, such as at www.H3F3B.org, so that they can connect to the researchers who are currently studying this condition"? This is accurate. Neurologist Elliott Sherr at UCSF (http://brain.ucsf.edu/) is writing a paper on these variations. Thanks again - I really appreciate it.167.246.62.1 (talk) 23:58, 13 October 2015 (UTC)

If this information belongs anywhere, it should be in the external links section and not in the body of the article as I have done in this edit. I think it is great that you are in contact with Elliott Sherr and are reaching out to other families with children with this condition. Once Elliott Sherr's paper is published, it should definitely be added as a citation to the H3F3B article. Boghog (talk) 11:55, 17 October 2015 (UTC)

BQUB15-Alara

The synthesis of this enzyme is the same to all enzymes... what can I do? — Preceding unsigned comment added by BQUB15-Alara (talk • contribs) 18:33, 20 October 2015 (UTC)

Steroid

Hi. I'm copyediting this article at the request of LT910001 on the Guild of Copy Editors request page. Since we're edit-conflicting, I'll put their request on hold; please let me know when you're done, so I can continue. Thanks and all the best, Miniapolis 20:19, 21 October 2015 (UTC)

@Miniapolis: Sorry for the edit conflict. I think your edits are a definite improvement. I will hold off from further edits until you are done. Cheers. Boghog (talk) 20:23, 21 October 2015 (UTC)
No problem; I should probably use {{GOCEinuse}}, but don't like to because I can hardly ever finish a copyedit in one go (certainly not in this case :-)). I began another requested article, but it shouldn't take more than another day or so and then I'll get back to this (and should finish in a day or so; my cruising speed is about 2,000 words a day). I'll ping you when I'm done. Thanks for removing those tags and all the best, Miniapolis 22:25, 21 October 2015 (UTC)
I've finished the copyedit. Thanks for waiting and all the best, Miniapolis 15:57, 23 October 2015 (UTC)
@Miniapolis: You have a real talent for making articles more accessible. A huge improvement! I am impressed. Thanks for your edits. Cheers. Boghog (talk) 17:38, 23 October 2015 (UTC)
Aw, thanks for the kind words; FWIW, I wasn't good at chemistry in school :-). All the best, Miniapolis 23:23, 23 October 2015 (UTC)

iL-1a

I just made some edits to the 1L-1a page that were rejected in whole. I can see if the wording is an issue, but having reviewed the page referring to primary sources, I do not think that ClinicalTrials.gov, Elsevier, or the numerous PubMed links could be problem. If you want the name of the drug used removed, that would be fine, but it is no lie or mistruth to say that there are more iL-1a agonist pharmaceutical applications being examined than currently listed. If there's a change in wording you'd like, let me know. In my text, I attempted to try to limit talking too promotional a tone by taking the wording from the "Purpose" sections in the case of currently running clinical trials. In hindsight, I think that I should have used the exact wording from the findings/results sections in the PubMed and if you want to talk about what that would look like, that's fine. That said, it is not an untruth that the pharmaceutical applications are being examined. Moreover, I maintain that the sources are legitimate. The sources are (in order) as follows. Let me know which one would count as a primary source.

— Preceding unsigned comment added by Jmccargo (talk • contribs) 22:05, 27 October 2015 (UTC)

Hi. Thanks for your message. The problem is that all the sources you have added are primary. PMID 25484055 which briefly mentions MABp1 is secondary. Primary sources can be used to document that a drug is in clinical trials, but they cannot be used to state that a drug is effective. Secondary sources (review articles) are needed to support efficacy claims. Also per WP:PHARMOS, drugs should be referred to using their nonproprietary names (MABp1) and not their trade names (Xilonix). Finally leukocyte Interleukin (Multikine) is a mixture of 14 cytokines, only one of which is IL1A, hence it doesn't really belong in the the IL1A article. I have restored a part of your additions replacing primary with secondary sources. Boghog (talk) 07:10, 28 October 2015 (UTC)

I don't know if this is how you respond on here (as you can tell I'm about as new as they come), but thanks for the thoughtful response. It seems fair. (Though the Multikine wasn't me, I thought the same thing, but I didn't want to touch it.) I'm going to be honest, I don't see myself showing the same commitment to editing here. (Some are editors and some are readers) Would it have been better to just put a message up on the talk page for IL-1a and let someone else do it? — Preceding unsigned comment added by Jmccargo (talk • contribs) 13:30, 28 October 2015 (UTC)

Human Alkyladenine DNA Glycosylase

Hello. You have recently merged Human Alkyladenine DNA Glycosylase with DNA-3-methyladenine glycosylase. We are 4 students of a Medicine University and we have just realized that our contributions are not visible. This is a problem because when the teacher will correct our work won't know where to find what we have done. All the article you emerged with DNA-3-methyladenine glycosylase is our work and we want you to do something about this. Please answer me. We are waiting an early answer to this. — Preceding unsigned comment added by BQUB15-Arafi (talk • contribs) 09:31, 29 October 2015 (UTC)

Hi. Thank you for your contributions. The content fork that you created is still visible in the article's history. Since content forks are by definition redundant and result in repetition of content, they are to be avoided. If it is essential for your course that your material is undisturbed before being graded, I strongly suggest that you use a sandbox instead of creating new articles in Wikipedia mainspace. Wikipedia is encyclopedia that anyone can edit at any time. Boghog (talk) 09:50, 29 October 2015 (UTC)

Human Alkyladenine DNA Glycosylase merger

Which is the reason for the merger? Both terms, DNA-3-methyladenine DNA Glycosyalse and Human Alkyladenine DNA Glycosylase, are different concepts, being DNA-3-methyladenine DNA Glycosyalse an enzyme in E. coli and Human Alkyladenine DNA Glycosylase a different enzyme that, despite sharing the function, have considerably different structure and mechanism, as well as another function (ODG activity) that DNA-3-methyladenine DNA Glycosyalse lacks of. — Preceding unsigned comment added by BQUB15-Salmeron (talk • contribs) 10:50, 29 October 2015 (UTC)

Hi again. Actually there were three different articles. Previously there was DNA-3-methyladenine glycosylase II (enzyme) and MPG (gene) (gene/protein) articles. As Gene Wiki articles are not only about human genes but also orthologs in other species, the Human Alkyladenine DNA Glycosylase that you created was a fork of the previous MPG (gene) article. I renamed MPG (gene) as DNA-3-methyladenine glycosylase and merged material from Human Alkyladenine DNA Glycosylase and DNA-3-methyladenine glycosylase II. There is only one human gene, MPG, that encodes a EC 3.2.2.21 enzyme, I thought it made sense also to merge the enzyme and gene articles. As you point out, the bacterial and vertebrate enzymes, while catalyzing the same type of reactions, have different folds:
  • EC 3.2.2.21
    • vertebrate DNA-3-methyladenine glycosylase (MPG; P29372) that contains a single protein domain:
    • E. Coli DNA-3-methyladenine glycosylase 2 (TAG II; P04395) that contains two protein domains:
      • Pfam PF06029 – AlkA N-terminal domain that is responsible for 3.2.2.21 activity
      • Pfam PF00730 – HhH-GPD superfamily base excision DNA repair protein
So, in summary, DNA-3-methyladenine glycosylase should include material from MPG (gene) and Human Alkyladenine DNA Glycosylase but the material from DNA-3-methyladenine glycosylase II (enzyme) should be split out again as a separate article. Boghog (talk) 11:47, 29 October 2015 (UTC)

Good morning Boghog, we are the creators of the wikipedia article that you merged with yours:" Human Alkyladenine DNA Glycosylase". We are 1st-year students of Medical School in Barcelona (Spain) and this article was a project for our Biochemistry Class which has a agreement with the local offices of Wkipedia. Because of the modification that you made, our article doesnt exist anymore and the project is due tomorrow so we want to ask you to undo the merge until November 10th and then you can do whatever you want. This project counts a 30% of our final grade and we would appreciate if we can restore our work. Thank you, Martín Marzabal — Preceding unsigned comment added by BQUB15-Mmarzabal (talk • contribs) 11:40, 29 October 2015 (UTC)

Hi. This is becoming a real mess. Undoing and redoing my edits will create an even bigger mess. I request that you use your sandbox for further work on the article. I have taken the liberty of creating a sandbox in your user space (see User:BQUB15-Mmarzabal/Sandbox) that contains your version of the article. Please note that the history of the edits that created this version may be found here. Boghog (talk) 12:14, 29 October 2015 (UTC)
In retrospect, I should have merged MPG (gene) into Human Alkyladenine DNA Glycosylase and then moved the merged article to DNA-3-methyladenine glycosylase. This would have preserved the original edit history of Human Alkyladenine DNA Glycosylase. Sorry about that. I have unmerged the DNA-3-methyladenine glycosylase II enzyme article and added a new Evolution section to that article which mentions the two different protein folds (bacterial and vertebrate) that share the same enzymatic activity. Boghog (talk) 13:21, 29 October 2015 (UTC)

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Drug discovery

I reverted an edit you made at drug discovery because the link involved was spammed rapid-fire to many articles - WP:REFSPAM. If you feel the reference was indeed appropriate at this article, please feel free to add it back. Since you seem to be active in editing in this subject area, will you please examine the other articles where I reverted this addition and revert me if you think I was wrong to remove it? Thank you. Deli nk (talk) 15:00, 14 November 2015 (UTC)

Have a look at my contribution history to see what articles I'm referring to. It should be fairly clear. Deli nk (talk) 15:02, 14 November 2015 (UTC)

Did not know

...that you were an expert on the inflammasome, but your work at the NALP3 article was a distinct improvement over what appeared before. I am glad your periodically disrespectful commitments regarding this editor occasionally point in a constructive direction. Le Prof Leprof 7272 (talk) 01:25, 16 November 2015 (UTC)

Not sure that you should not leave the primary sources that appeared in the Further reading, where they are appropriate. They may not be useful as citations in the article, but they reflect a lot of work, and represent expertise, and so could be of value in the directions they point, so others can find secondary articles to draw from on those subjects. Perhaps paste them into talk for the time being, if not back in to the article? Leprof 7272 (talk) 01:34, 16 November 2015 (UTC)
Thank you for your kind words. I am not at all an expert on the NALP3 inflammasome, but a search of PubMed quickly lead me to several good review articles which I used to update the article and learned a lot in the process. This activity is a far more productive and rewarding than adding attention banners to articles ;-)
Concerning the further reading section, I was the one that originally added it in this edit. This citation list was created by User:ProteinBoxBot as part of the Gene Wiki project and I just copy and pasted the bot generated output into the article. The bottom of the protein infobox contains a PubMed link where an up-to-date citation list can be regenerated at any time. The purpose of the including the bot generated further reading list and the public domain Entrez text was to provide seed material that could later be expanded by human editors. Since this article has now has a significant number of in-line citations, the need for a further reading list is diminished. Boghog (talk) 06:25, 16 November 2015 (UTC)
Bog, I did an edit adding further secondary sources to the lede, not that they (and the content to which they sre attached) should remain perfectly as they are, but that the additions are a starting point that the information find its way in at appropriate places. The move around of the definition of the acronym (and its demotion from bold) was to reduce bold in the lede, and to move understandable information on definition and function up. I even think an insertion of what an inflammasome is, is in order, given our mandate to reach non-specialist audiences. I also firmly believe, as the lede rewrite tag indicates, that even with explanations of the acronyms, the lede is still to jargonist, and without enough on structure, mechanism, and path. (Imagine a run of the mill grad school or new industrial medi-chemist reading this, before having years of human and microbial gene and protein name experience under belt. Then take a step further toward undergraduates, sixth formers, etc.) I hope it can evolve further as you have began, and that all my contributed explanation and sources will not be tossed. Lede tag can go as soon as you see fit. Le Prof 73.210.154.39 (talk) 08:36, 16 November 2015 (UTC)

Photosynthesis

Maybe you can help out at photosynthesis. Its not a lot of work. An editor is angry with me and I dont agree with them, so someone else should look over their work. Hydrogen per se is not involved in photosynthesis unless it is coupled to a hydrogenase and even that is rare. But whatever, the main thing is to make the text right and clear, independent of my or their mood swing. --Smokefoot (talk) 15:24, 23 November 2015 (UTC)

ArbCom elections are now open!

Hi,
You appear to be eligible to vote in the current Arbitration Committee election. The Arbitration Committee is the panel of editors responsible for conducting the Wikipedia arbitration process. It has the authority to enact binding solutions for disputes between editors, primarily related to serious behavioural issues that the community has been unable to resolve. This includes the ability to impose site bans, topic bans, editing restrictions, and other measures needed to maintain our editing environment. The arbitration policy describes the Committee's roles and responsibilities in greater detail. If you wish to participate, you are welcome to review the candidates' statements and submit your choices on the voting page. For the Election committee, MediaWiki message delivery (talk) 16:19, 23 November 2015 (UTC)

Reference errors on 23 November

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Reference errors on 25 November

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Included a summary of SUCLA2-mtDNA depletion syndrome with references

I saw you reverted a lot of the changes I added to the page. These were all referenced with decent evidence base. All of the added information is of interest to patients (or typically their parents). As a reference source do you not think this material should be available on wikipedia? B A Thuriaux (talk) 16:11, 29 November 2015 (UTC)

Included a summary of SUCLA2-mtDNA depletion syndrome with references part 2

And another thing...

I object to the idea that I added primary material on the site. There was no primary material there.

Finally, I have read the notice in "medical advice" to which you helpfully provided a link... nothing in that notice states that wikipedia has a policy of not giving advice.

If you wanted to add material that is fine, but you should consider carefully before removing existing material with decent references. What I mean is that it is fine to add references to baclofen and other drugs which are used to treat seizures etc. but it is not fine to remove references to CoQ10 and other anti-oxidants as this is typically the only "medication" that patients are given.

@B A Thuriaux: Per WP:MEDRS, we generally require secondary sources (review articles) to support medical claims. PMID 17287286, 26475597 are both primary sources. (Note peer review ≠ secondary). Primary sources may be OK for rare orphan disease where suitable review articles have not been published. Fortunately this is not the case with SUCLA2-mtDNA depletion syndrome where a number of review articles have been published ( PMID 23385875 and SUCLA2 GeneReviews). Also per WP:MEDMOS and especially MEDMOS citing sources, we generally avoid mentioning details about individual studies. Simply state the conclusion of the studies. I have marked the primary sources as unreliable. These sources should ideally replaced with review articles. Concerning CoQ10, there is a review article that covers it PMID 17486440 which is currently not used as a source. Boghog (talk) 16:59, 29 November 2015 (UTC)
I am not sure how you define primary sources and why you would think that the 2015 would not qualify since it expands on the material gathered by Ostergaard in 2007 (you site the 2009 material which is effectively the same but is apparently a secondary source). Since the 2015 study includes the original patients and also significantly expands the number of SUCLA2 patients from those reported in the 2009 secondary source (from 13 to 50), why would the 2015 not be considered a secondary source? Confused. B A Thuriaux (talk) 17:57, 29 November 2015 (UTC)
What makes a source secondary is that it reviews primary sources. When in doubt, PubMed lists publication type. For example, PMID 22513923 under Publication Types, MeSH Terms, Substances, Grant Support lists this paper as both a Meta-Analysis and Review. Hence this source is secondary. Ostergaard 2007 publication is primary while her 2009 publication is secondary. I know she reviewed her own work, but the review article also places this work in a wider context and is also subject to another round of peer review, hence the review should be considered more reliable. In any case, I have retained the conclusions of the material that you added about the founder mutations while trimming some of the unnecesary detail. Boghog (talk) 20:37, 29 November 2015 (UTC)
According to PMID 19891905 At present, the evidence of [vitamins and cofactors] effectiveness does not rise to the level required for universal use., if we mention CoQ10 and antioxidant therapy, we need to also mention that evidence that this treatment is effective is lacking. Boghog (talk) 17:12, 29 November 2015 (UTC.

I made not comments on the efficacy of the treatment, simply that that treatment with cofactor q10 is the most frequent form of treatment (this is the case for any kind of Mitochondrial disease). I will revert but happy to insert a source that says that there is conflicting evidence on the efficacy of CoQ10 suplementation in MDS (and certainly no evidence of an impact in the case of SUCLA2 - but because no one has investigated this for SUCLA2). B A Thuriaux (talk) 17:57, 29 November 2015 (UTC)

OK, fair enough. I have readded a statement that CoQ10 treatment is used but evidence for clinical efficacy is currently lacking. Boghog (talk) 20:37, 29 November 2015 (UTC)

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Reference errors on 4 December

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If you don't know the material, then stay out of it

Not everything needs a reference. That material I added is a statement of the obvious; obvious to anyone that knows something about the subject. If you knew the subject matter you would recognize the material was correct and improve it with the reference you think it needs rather than resort to the mindless nonsense of reverting an edit at the behest of your friend and inciting an edit war. Please read from this article to gain a basic understanding of the process.

From the wikipedia article on Photosystem II : "The hydrogen ions (protons) generated by the oxidation of water help to create a proton gradient that is used by ATP synthase to generate ATP." https://en.wikipedia.org/wiki/Photosystem_II

An edit that is insightful, reasonable, and well written should remain; improve it rather than revert it. I don't need your permission nor anyone else's to perform edits here. Zedshort (talk) 13:12, 24 November 2015 (UTC)

Responded here. Extraordinary claims require extraordinary proof. Requesting a citation in this case is consistency with Wikipedia policy. Boghog (talk) 05:46, 26 November 2015 (UTC)
Also hydrogen ≠ protons. Even to say protons are generated for later use is also highly misleading. Boghog (talk) 19:07, 26 November 2015 (UTC)
There are no extraodinary claims made by saying hydrogen is released with the splitting of water. The material I added in the introduction is supported by material within the body of the article. Not every claim requires a reference, especially if the material is supported within the article. For the point about the freeing of hydrogen to be left out of the intro is a glaring error. You are splitting hairs in saying that I was claiming free hydrogen is created vs hydrogen ions. I am sure you understand that but are simply squatting on what you believe to be your territory. Zedshort (talk) 15:25, 5 December 2015 (UTC)

Notice of discretionary sanctions and 1RR on Glyphosate

Hello. I don't see that you have been properly notified that Glyphosate is under discretionary sanctions and is subject to a 1RR restriction per the temporary injunction in the Arb case. Please do not edit war in the GMO topic area, or elsewhere. Please disregard this notice if you have already been notified. Thank you. Minor4th 23:09, 5 December 2015 (UTC)

Pesticides

FYI, herbicides are a type of pesticide. It's a common mistake for people to think herbicides are not a kind of pesticide. That being said, I'm hoping to leave the article be for the time being until the ArbCom case closes, which should be in a few days from the most recent update. I may not agree with everything you've said so far over at glyphosate (really more minor things best left when the dust settles from the case), but I'm glad to see editors not involved in the case are willing to work on the page. Kingofaces43 (talk) 21:37, 7 December 2015 (UTC)

Thanks for your note and pointing out the definition of pesticide includes herbicides. I am more of a pharma than farma guy ;-) It becomes difficult to find the right balance between Wikipedia policy and common sense and I find it nearly impossible not to comment on the methods used by studies if I see glaring deficiencies. Hopefully we can get back to more producitve activities once the dust settles. Cheers. Boghog (talk) 06:30, 8 December 2015 (UTC)

Consistent formatting

Hi Boghog I noticed that you are having to fix some of my edits for consistent formatting after I made deprecated (co-authors)parameter fixes. I hope that hasn't been too frustrating for you. I have been individually listing the authors as described in the fix here which is obtained by clicking on the (help) link such as this example ref 3 here. I usually use the doi generator to generate the new cite parameters. Regards CV9933 (talk) 11:31, 21 November 2015 (UTC)

Hi. Thanks for the message and no worries. I have a script for these Gene Wiki edits that fixes several other things in addition to adjusting the citation format. Replacing |coauthor= with explicit |first1=, |last1=, ... author parameters is a legitimate way to fix the deprecated parameter error. I prefer to use the |vauthors= parameter since it preserves the original formatting style. Boghog (talk) 11:43, 21 November 2015 (UTC)
There are literally dozens of those that need fixing, a script is the way to go - I'll give them a miss. Regards.CV9933 (talk) 15:31, 21 November 2015 (UTC)
There are more than a few dozen but probably less than 100. I have gotten up to the letter M and will try to fix the remainder over the next week as I find time. Cheers. Boghog (talk) 19:02, 22 November 2015 (UTC)
Whoops -Irisin - that doi generator can get one into bad habits. Regards. CV9933 (talk) 18:35, 18 December 2015 (UTC)

References to PUBMED articles

I noticed that you changed the format of the references on the page for SCNN1A that I edited as part of the Gene Wiki project. Your revisions are acceptable to me. But, I generated the references using the Wikipedia's own CITE application that is available on each page. If you really want your style then could you please contact whoever is responsible for the CITE application to change the format that is automatically generated. This will save you time and will save the author time to recheck the page.

Genewiki1 (talk) 07:44, 11 December 2015 (UTC)

Hi. Thanks for your note and for your contributions to SCNN1A. One guiding princple in Wikipedia WP:CITEVAR which states that once a citation style has been established in an article, other contributors should try to maintain it unless there is consensus to change it. Vancouver author style had been previously established and my edits were intended to maintain that style. I assume that you have been using RefToolbar to create your citations. As RefToolbar only supports only one citation style, it goes against the spirit of CITEVAR. Unfortunatley it has been difficult to get the maintainers of the RefToolbar to add Vancouver support. There are other citation tools avaiable such as the User:Diberri/Template filler (tool link) that can be used to create vauthors style citations. I hope this makes sense. Cheers. Boghog (talk) 19:56, 13 December 2015 (UTC)
Thank you very much for your corrections. The style you set is better than the automatically generated output. I will follow this style. I tried the link you provided and it did not work for me. I would appreciate if you could refer me to a citation generator(s) that works. Thanks again.

Genewiki1 (talk) 09:16, 14 December 2015 (UTC)

Hi. These are not really corrections, but rather preferences. Doesn't the tool link work for you? I just tested it and it seems to be fully functional. Boghog (talk) 18:47, 18 December 2015 (UTC)

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Citation formatting thanks

Thanks for your Serpin edits! I always appreciate your citation formatting blitzes! T.Shafee(Evo﹠Evo)talk 09:10, 21 December 2015 (UTC)

Yo Ho Ho

Doc James (talk · contribs · email) is wishing you Seasons Greetings! Whether you celebrate your hemisphere's Solstice or Christmas, Diwali, Hogmanay, Hanukkah, Lenaia, Festivus or even the Saturnalia, this is a special time of year for almost everyone!

Spread the holiday cheer by adding {{subst:User:WereSpielChequers/Dec15b}} to your friends' talk pages.

Thanks for all you have done this year :-) Doc James (talk · contribs · email) 22:53, 21 December 2015 (UTC)

Gene stubs

There are a lot of long articles about genes, enzymes etc. marked as stubs. They turn up at Wikipedia:Database reports/Long stubs, a place I monitor. I'm afraid I don't understand much of the content, and I am certainly not competent to decide how complete they are. I wonder if anyone in the projects you are associated with would be prepared to monitor them?Rathfelder (talk) 12:17, 26 December 2015 (UTC)

Thanks for the link. I have been performing maintenance edits on Gene Wiki articles so I could go through this list and remove the stub templates if appropirate. There must be thousands of these, so it will take some time. Cheers. Boghog (talk) 12:43, 26 December 2015 (UTC)

Reference errors on 26 December

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Reference errors on 28 December

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Amine oxidase article

Hi Boghog. The amine oxidase article has some issues and I was wondering if you could help me figure out how to address it.

The main problem is that the article content (text, infobox, and citations) is entirely about the AOC1 gene (UniProt link) and the protein that it encodes (the diamine oxidase/histaminase enzyme: EC 1.4.3.22), while the article title spans a much broader scope. A more correct title for AOC1 would be amiloride-sensitive amine oxidase (copper-containing) or amine oxidase (copper-containing), although the latter term includes AOC2 and AOC3 as well.

A second issue is that several enzyme articles (e.g., Flavin-containing amine oxidoreductase) include text along the lines of "xyz's are a family of various amine oxidases". There's a very large number of incoming links to the amine oxidase article in large part due to its inclusion in various navboxes, so finding these articles isn't particularly easy to do to remove such links.

In order to address this, I think the current amine oxidase article (Special:permalink/697409496) should be moved to AOC1 and then a new amine oxidase article should be written to cover the topic with the correct scope. The only issue with this is that "amine oxidase" technically refers to a huge number of enzymes since it's an ambiguous name. In a nutshell, I'm not really sure how to address rewriting amine oxidase after moving the current page to a more appropriate title. Should that article just be a stub which states something along the lines of "Amine oxidases are a family of enzymes that catalyze the oxidation of amines" and then lists a few examples like the ones below?

A few human "amine oxidases"

For example, some of the enzymes that I can find listed as an "amine oxidase" in a database (ExplorEnz or BRENDA) include: amine oxidase (flavin-containing) (alternate name for EC 1.4.3.4), amine oxidase (copper-containing) (alternate name for EC 1.4.3.21 and EC 1.4.3.22), flavin-containing monooxygenases (EC 1.14.13.8), renalase (EC 1.6.3.5, spermine oxidase (EC 1.5.3.16, N1-acetylpolyamine oxidase (EC 1.5.3.13), Protein-lysine 6-oxidase (EC 1.4.3.13), and other enzymes classified as an "amine oxidase" (e.g. epigenetic enzymes like KDM1A).

Seppi333 (Insert 2¢) 00:42, 31 December 2015 (UTC)

Hi Seppi. I agree that the amine oxidases articles are a mess. Similar to what you have suggested, I have moved Amine oxidase → Diamine oxidase and replaced the protein with an enzyme infobox. I have also converted the resulting Amine oxidase redirect into a more general article about amine oxidases but restricted the content to the EC 1.4.3.- family which is the way at least one reliable source (PMID 7124512) classifies these enzymes. I have also modified the {{CH-NH2 oxidoreductases}} navbox to be consistent with the classification now contained in Amine oxidase. I hope this is OK. Boghog (talk) 10:59, 31 December 2015 (UTC)
Much better now; thanks for fixing it! Seppi333 (Insert 2¢) 20:40, 31 December 2015 (UTC)

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Parathyroid hormone article

Hi Boghog, Thank you for all your useful edits to the Parathyroid hormone article.

Would you mind having a look at the Calcium_balance.jpg diagram (which can be viewed in the Calcium metabolism article) to see whether it should not replace the current Calcium_regulation.png. The current diagram is inaccurate in that it shows blue arrows (which represent PTH's effects according to the legend) pointing only to the kidneys as target organs. PTH's effect on bone is unclear in the diagram (being indicated in unexplained pink, which seems to suggest that PTH causes bone resorption via 1,25 dihydroxy-vitamin D. This is incorrect). The purple arrows are also undefined. It is, in my opinion, a very confusing and misleading diagram.

The two diagrams do not display exactly the same information. Calcium_balance.jpg is about the movement of calcium from one body compartment to the other, and indicates how each of these movements is regulated. The Calcium_regulation.png diagram attempts to illustrate PTH's target organs, but clutters it with the effects of 1,25 dihydroxy-vitamin D and of calcium ions, in a blaze of colors with undefined points of origin or end-points, or explanations in the legend.

Cheers Cruithne9 (talk) 11:45, 31 December 2015 (UTC)

Hi Cruithne. Likewise, thanks for your edits to the parathyroid hormone article. Great team work! I am more familar with how nuclear receptors work and in particular the vitamin D receptor and less familar with parathyroid hormone. I agree that both File:Calcium_balance.jpg and File:Calcium_regulation.png are problematic. The effect of vitamin D on calcium homeostasis and bone resorption is complex. The File:Calcium_balance.jpg figure does correctly depict the role of vitamin D on calcium absorption and excretion. The effect of vitamin D on osteoclast regulation is not specified in this figure. The active metabolite of vitamin D does regulates the expression of RANKL (see for example PMID 24605212) which in turn activates osteoclasts which results in bone resorption. The net result of vitamin D action is to increase the rate of bone remodeling (both resorption and rebuilding). Hence the figure should be updated to include the effects of vitamin D on osteoclasts. Does this make sense? Boghog (talk) 19:02, 31 December 2015 (UTC)

Hi Boghog. Let me give this some thought. I think that what you point out about the action of calcitriol on bone is important, as it would explain why calcitriol can be used as replacement therapy in patients who have had parathyroidectomies. If I managed to fit in an purple arrow going from 1,25 dihydroxy Vit D3 running parallel to PTH's purple arrow to the bone resorption calcium-flow arrow in the File:Calcium_balance.jpg diagram, would that be an acceptable summary of the physiology of calcitriol? The alternative would be to mention it in the legend; but that is too long as it is already - and I am not too sure that that would be be adequate, as the picture speaks a thousand more words than text does! Cruithne9 (talk) 06:15, 1 January 2016 (UTC)

Hi Boghog. Try File:Calcium balance 2.jpg to see how you like it. Cruithne9 (talk) 09:26, 1 January 2016 (UTC)

Parathyroid hormone continued

Hi Boghog. I'm not sure that you were notified that I had added comments to the end of the Parathyroid hormone article section, above. It is about a new diagram I have created.

My apologies if you have seen the comments, and are busy evaluating the diagram etc.

Cheers (and best wishes for 2016). Cruithne9 (talk) 16:03, 2 January 2016 (UTC)

Your modified diagram is a big improvement. Much more informative than the previous one. Likewise, best wishes for 2016! Cheers. Boghog (talk) 08:50, 3 January 2016 (UTC)

Many thanks. Cruithne9 (talk) 13:25, 3 January 2016 (UTC)

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