User talk:Boghog

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PK pathway enzymes[edit]

Hey Boghog, I figured it wouldn't hurt to put this in the pharmacokinetics section of the amph page, but I'm not sure what the common abbreviations are for these enzymes. I'd rather not put the full names in the drugbox.

Benzoic acid is metabolized by butyrate-CoA ligase into an intermediate product, benzoyl-CoA,[1] which is then metabolized by glycine N-acyltransferase into hippuric acid.[2]

I'm guessing the 2nd is GLYAT, but I have no clue about the ligase. Would you happen to know of a contraction or where to find one for it? Seppi333 (Insert  | Maintained) 01:21, 8 May 2014 (UTC)


References
  1. ^ Substrate/Product. "butyrate-CoA ligase". BRENDA. Technische Universität Braunschweig. Retrieved 7 May 2014. 
  2. ^ Substrate/Product. "glycine N-acyltransferase". BRENDA. Technische Universität Braunschweig. Retrieved 7 May 2014. 


Hi Seppi. PMID: 12616642 refers to this enzyme as a xenobiotic/medium-chain fatty acid:CoA ligase or XM-ligase for short. Benzoic acid in this context is a xenobiotic, hence I believe XM-ligase would be an appropriate abbreviation. For CoA:glycine N-acyltransferase, ACGNAT (PMID: 7833837) would be an appropriate abbreviation. Boghog (talk) 20:00, 8 May 2014 (UTC)
Hey again Boghog; I just updated the articles with that information, but I noticed glycine N-acyltransferase has a duplicate at GLYAT while making redirects from the shortened names you provided. Should we merge these two? Seppi333 (Insert  | Maintained) 23:28, 21 May 2014 (UTC)
Sorry for not responding sooner but I have been really busy in real life. It is appropriate to merge protein and enzyme articles if there is a one-to-one correspondence (i.e., only one human gene that encodes an enzyme that catalyzes a specific rxn as designated by an EC number). Digging into this further, there are the following enzyme/protein correspondences:
Whereas the UniProt entry for GLYAT (Q6IB77) lists EC numbers 2.3.1.13 and 2.3.1.71 as entries. Because there is not a one-to-one correspondence, I think it would be better not to merge glycine N-acyltransferase (EC 2.3.1.13) with GLYAT. Boghog (talk) 16:28, 26 May 2014 (UTC)
Ah, alright. Thanks for pointing that out. Seppi333 (Insert  | Maintained) 00:48, 28 May 2014 (UTC)
One other thing - since you've made major contributions to the article (half the images were made by you) and have already done a ton of work to help address issues at the FAC, would you be interested in being a co-nominator at the next FAC for amphetamine? I figure you deserve credit ({{FA user topicon}}) for all you've done to help attain the Featured article rating. In any event, I'm going to open the 3rd FAC for it in 2-3 days since I need to do copyedits to address Shudde's issues first.
Best, Seppi333 (Insert  | Maintained) 03:17, 23 May 2014 (UTC)
Thanks for asking but I think you are overstating my contribution ;-). In any case, I might be interested in co-nominating the article, but this would obligate me to devote a significant amount of time to address reviewers comments, time that I do not have at the moment. If you could hold off on the nomination for a week or two, I would be able spend significantly more time on improving it. Cheers. Boghog (talk) 16:39, 26 May 2014 (UTC)
I seriously mean it - your help has been indispensable in copyediting and expanding the chemistry portions of the article. Thanks to you, it puts chem sections in other drug articles to shame. Face-wink.svg The best I could have hoped for had I written it myself is to make it merely not suck, so I mean it when I say you've done a lot for the page!
In any event, I actually wouldn't need or expect you to help out at the FAC with anything but technical issues related to the physical/chemical properties sections, since you're familiar with those sections and way more knowledgeable than me in that area. I'm perfectly fine with handling all the basic copyediting and technical issues in the remainder of the article myself. That said, feel free to address any issues outside phys/chem if feel comfortable editing the section and have the time. Seppi333 (Insert  | Maintained) 00:48, 28 May 2014 (UTC)

Hey again Boghog. I've been off Wikipedia for nearly 2 weeks due to a broken laptop; I have a working one now though, so I intend to renominate the article at FAC very soon. Are you still interested in being a co-nominator? Seppi333 (Insert  | Maintained) 22:08, 13 June 2014 (UTC)

Sorry to hear about your lap top but I am glad your connected again. I have a bit more time now for the co-nomination, so bring it on! The biggest unsolved issue as I see it is to make some of the more technical sections more accessible. I will see what I can do to help. Boghog (talk) 22:49, 13 June 2014 (UTC)

Deleting the message is fine[edit]

Your Talk page is yours to do with as you please. Message was intended just for you, in any case. Sad that you can see only nonsense, and nothing worth your consideration, but that is the state of things. Cheers. Le Prof

Not touching anything at the Nat Product page[edit]

…not synthesis or anything, until the matter of the "course of the ship" is settled. And I heard and acknowledged Smoke, both halves of what he said. I see one ambiguous statement, leaning as much my way as yours. So there is no decision possible based on it. You are the one that wants to run with half a vote, in your prescribed direction. That, my friend defines self-serving. I am staying put until (given summer, and busy life) others have time to respond. The WP standard seems (with merger proposals, and other higher order proposed changes), to allow 30 days. That is at least what I am looking at. And sorry, no longer playing your WP:THIS and WP:THAT game. You do not seem to care to hear that you, perhaps unconsciously but nevertheless self-servingly, limit your purview when you do this, so I've ceased arguing in such ways with you. Good news, no more walls of text. Le Prof Leprof 7272 (talk) 08:45, 12 June 2014 (UTC)

Too much to ask[edit]

but I will do it to avoid confusion when folks start responding. I would appreciate it if you would, in good faith, sandbox the last three edits that you did, since they directly bear on the questions of the discussion that were ongoing, and then revert to the version that I linked to and discussed (immediately prior to your last three edits). If you are confident in your case, you should be confident without any changes, with the form that stood for the 6 mos. of your absence. Reverting will ensure that people see what I was describing at the time, and not some muddle of old and new. Don't expect it, but in integrity, and to give you the chance, I have to ask. If you do not, say by end of day Saturday, I will have to review my opening description of the history and argument, and make sure it still makes sense (fixing links and anything else that your edit will have muddied). But as I said, the simplest is to return the matter, in good faith, to what I was talking about before those three edits. Le Prof Leprof 7272 (talk) 08:56, 12 June 2014 (UTC)

I really do not see how my recent edits would fundamentally change the course of the discussion. If you disagree, you can always provide a link to the previous version on the article's talk page. In the meantime, this article is like any other, and unless there is persistent edit warring or vandalism, anyone should feel free to edit it. Boghog (talk) 20:34, 12 June 2014 (UTC)
Thank you for the clarity of your response. I will do what I have to do, to make this work. Le Prof Leprof 7272 (talk) 04:09, 13 June 2014 (UTC)

My closing word[edit]

Not engaging with you further at NP, sorry. In your most recent spate of unscrupulous actions, you have shredded any last basis here for AGF from me. I will work around you, if possible alongside you, but any chance for real discourse or collegiality is gone. Please do not post to me, or refer to me anywhere that you can help it. Cheers, best of fortunes in our shared, difficult day to day, as we try to do something real. Le Prof Leprof 7272 (talk) 05:37, 14 June 2014 (UTC)

@Leprof 7272: unscrupulous actions? Is asking a response to a simple question unscrupulous? Boghog (talk) 05:48, 14 June 2014 (UTC)

Wikipedia talk:Articles for creation/p3 peptide and P3 peptide[edit]

Hello, Boghog. Some time ago you made some improvements to the draft article above, and it turned out that it was a copy-paste remnant. Was there anything that you wanted to move over to the mainspace article before the draft is deleted? —Anne Delong (talk) 01:37, 16 June 2014 (UTC)

Hi Anne. Thanks for the heads up. I have compared the draft with the mainspace article and it doesn't look like there is anything additional that needs to be moved over. Please go ahead and delete the draft. Boghog (talk) 05:59, 16 June 2014 (UTC)

NFkB in neurons[edit]

Hi Boghog,

In April of 2011 I updated the the section on NFkB in neurons and I see that user Neuroglider has made substantial changes to the section that I don't agree with. Neuroglider states that s/he talked with you on 11/23/2013, though I couldn't find the talk on either of your talk pages, about removal of synaptic components as gene targets of NFkB. Could you fill me in, or point me to the correct talk page? I feel that these should be in the article as the support the idea that NFkB is important in neurons, not just glia. Which brings me to my main point. I believe that the NFkB field in neuroscience does not hold to Neuroglider's views that NFkB is primarily important in glia and not in neurons. In 2011 I specificially removed sections stating these points as I believed them to not be representative of the thoughts of the field. Specifically Meffert et.al. 2003 (citation #7 in NFkB article) [1] demonstrated that NFkB could be activated in biochemically isolated synapses (synaptoneurosomes) and was unlikely to be confounded by glia. Additionally, there are many studies that support the idea that NFkB function is important in neurons, such as studies that show cell autonomous roles for NFkB in neurons related to synaptic function and regulation of genes that are also important to synaptic function. While Neuroglider does make a good point that we should all think about heterogeneity in our systems, I believe s/he has given too much weight to this idea and the paragraph is now larger than the rest of the section. I would like to rebut Neuroglider's addition to the section, but do not wish to turn the article into a discussion of the merits of Neuroglider's v.s. other perspective. While I do not agree with Neuroglider, I'd be okay with his/her opinions to remain, but with more balance. If you have any thoughts on the best way to proceed, please let me know.

P.S. Thank you for your time and effort looking after these wikipedia articles. 16:24, 16 June 2014 (UTC)Aventre3

Hi @Aventre3:. I believe that the link to the relevant discussion is here. I must admit that I am not an expert on neuronal molecular biology nor have I read these citations very carefully. My interest in NFkB mainly relates to its cross talk with nuclear receptors. I suggest that you continue the discussion with @Neuroglider: at the above link. In cases where there may be controversy, it is especially important to cite secondary sources (please note PMID: 12947408 is a primary source). I will follow the discussion and jump in if I think I have anything constructive to add. Cheers. Boghog (talk) 18:26, 16 June 2014 (UTC)

Simple matter in re steroids[edit]

For you to consider. Colleague looked at WP steroids on an iphone, and said the article opened with three structures in a row, and it seemed off-putting as a way to open an article for general readers. I checked his report, and it is true. Because of the way the image markups are inserted relative to the lede, the article opens on small screen handhelds with the three images appearing 1-2-3 that show up to the right of the lede for a standard laptop or PC viewing. Your call, but perhaps the markups could be moved down a bit, with no change of appearance for computer viewing, but resolving the negative reported by this handheld user. No RSVP necessary. Completely your call. Cheers. Le Prof Leprof 7272 (talk) 02:10, 17 June 2014 (UTC)

Image for signaling cascade in addiction[edit]

The current (incomplete) schematic; the receptor labels are temporary.

Hey Boghog. I was wondering if you'd happen to know of any any information resources (e.g., databases) that would have content on on signaling cascades / communication networks between receptors and gene transcription factors.

I'm working on an image (File:ΔFosB.svg - a DA neuron/synapse in the nucleus accumbens) for the addiction section in amphetamine at the moment to illustrate how the NDMA receptors, calcium channels, and ΔFosB are related, since it's not entirely apparent in the text. This KEGG diagram (the bottom pathway) and my molecular neuropharmacology textbook are the only 2 resources I'm working off of at the moment. Unlike the KEGG pathway, I'm just doing the synaptic cleft and postsynaptic neuron since the schematic for the presynaptic half is exactly what's shown in pharmacodynamics. I know all 5 DA receptors are present in accumbens DA neurons, so I'm planning to add the 4 other DA receptors into the KEGG schematic that I recreate in order to show their influence on the cAMP cascade. Seppi333 (Insert  | Maintained) 02:50, 17 June 2014 (UTC)

Also if you have any suggestions or feedback for me on the diagram itself, feel free to chime in. Face-smile.svg Seppi333 (Insert  | Maintained) 03:42, 17 June 2014 (UTC)
Update: I just realized that I saved a few papers on this topic on my website in a subpage that I forgot I made around 2 months ago. I unfortunately lost a large number of research papers when my laptop died, but at least I still have these signaling cascade models. In any event, I probably don't need more information resources for the model, but I'm always open to feedback! Seppi333 (Insert  | Maintained) 00:42, 18 June 2014 (UTC)
Hi Seppi. Sorry for not responding sooner. Your graphic looks great! One minor issue. Shouldn't the arrow between ΔFosB and DNA be reversed? According to the KEGG diagram, CREB regulates the expression of ΔFosB (i.e., CREB transcription factor → DNA (ΔFosB gene promoter) → ΔFosB protein). Also the transcription factor NFKB is a heterodimer of Fos and Jun. The KEGG diagram suggests that Fos (through the NFKB heterodimer) up regulates the expression of c-Fos. It appears that part of the diagram needs to be adjusted as well. Boghog (talk) 17:27, 21 June 2014 (UTC)
Ahh, alright. I'll make those tweaks when I work on the image within the next couple of days; several of the resources I used as a cross reference had a differing schematic inside the nucleus, so I wasn't really sure how to model that part. I don't expect to be done for another week or 2 since I'd like to look for additional reference models in reviews and on reactome first - assuming I can find anything relevant.
Thanks for the feedback by the way. Seppi333 (Insert  | Maintained) 11:44, 22 June 2014 (UTC)
Ignoring all the off-center text (wikipedia hates rendering svg text), how's it look? I'm probably going to replace all the image text with an overlay from my annotation template. I imagine it would help to wikilink most of the terms. In any event, I still need to put in a legend somewhere; the only notable difference between this diagram and KEGG's legend is that I noted expression/repression with +exp and -exp. Seppi333 (Insert  | Maintained) 06:06, 25 June 2014 (UTC)

I am reverting you at NP Talk because you changed more than the shading[edit]

You also changed my words in several of MY TALK ENTRIES.

If you want to revert something in particular, it is YOUR responsibility to do it selectively, and not change my words. You have no right to change my words.

And if you had a modicum of decency, you would also leave the shading in place, as it is intended to call attention to the words of individual other than ours.

If you revert again, I will ask an admin to adjudicate.

Le Prof Leprof 7272 (talk) 15:03, 19 June 2014 (UTC)

@Leprof 7272: First of all, you redacted refactored other peoples comments in the same edit that you changed your own comments. If you don't want edits to your own comments reverted, don't combine edits to your own comments with edits to other editors comments. Better still, don't redact refactor other editors comment to begin with. Second, I did restore the edits to your comments in the next edit. Please more carefully look at the edit history before you jump to conclusions and assume good faith. Third, your excessively long talk page post are drowning out other voices. If you posts were more concise, it would not be necessary to highlight text. Finally mature editors try to work out differences between themselves first. Only in extreme cases is admin intervention required. Boghog (talk) 15:24, 19 June 2014 (UTC)
Redact means to "edit (text) for publication. censor or obscure (part of a text) for legal or security purposes." I redacted noone's text, and in shading, censored and obscured nothing. If you look closely, you did not capture all of my changes to my own text. I did look carefully at the edit history, and changed it back as I had it the first time. Go ask Pad and Smokefoot, et al, if they object. It is not your right to object for them. Leprof 7272 (talk) 15:27, 19 June 2014 (UTC)
@Leprof 7272: You have it completely backwards. It is your responsibility to first ask if it is OK, not my responsibility to ask for you. Boghog (talk) 15:31, 19 June 2014 (UTC)
Neither Smoke nor Pad have issues, and I have asked Doc for his permission. Stop warring with me. The shading (highlighting) of other editors' comments serves a clear positive purpose. Your response is knee-jerk negative against me. Plese, stop warring. As you say, focus on content. Leprof 7272 (talk) 15:34, 19 June 2014 (UTC)
@Leprof 7272: I stand behind what I state above. Stop highlighting other editor's comments without their permission. Boghog (talk) 15:38, 19 June 2014 (UTC)
And I by mine. The only thing approaching an edit of another's text that can be asserted, is my adding another editor's name in square brackets, where a less than careful interspersed reply from you had made unclear who had authored the original comment. Otherwise, apart from shading (highlighting), there is no change, and highlighting of a whole section, without change in content or emphasis, and indeed with elevation of attention, cannot be considered a redaction. This is a
redaction
. Permissions are in place as they need be. Others see merit and AGF. Le Prof Leprof 7272 (talk) 15:49, 19 June 2014 (UTC)
@Leprof 7272: The only significant change that I missed was Pharmagognosy to Pharmacogn abbreviation. Stop highlighting other editor's comments without their permission. Boghog (talk) 15:53, 19 June 2014 (UTC)
Reread what I just said. If you revert again, you will be subverting not only my will, but others, and I will involve adjudication. There is a page of content issues in play. Deal with the real matter at hand. Le Prof Leprof 7272 (talk) 15:58, 19 June 2014 (UTC)
@Leprof 7272: One editor already objected to your highlighting of their comments. Did you receive permission from the other editors? Your selective highlighting of other user comments (unless you quote them in your own post) is bad practice and needs to stop. Boghog (talk) 16:04, 19 June 2014 (UTC)
Leprof, rather than WP:REDACT, I think what Boghog means is WP:REFACTOR. Flyer22 (talk) 16:24, 19 June 2014 (UTC)
Thanks Flyer22, that is indeed what I meant. Boghog (talk) 16:58, 19 June 2014 (UTC)
You're welcome. Wikipedia:Talk page guidelines#Others' comments states: "Refactoring and archiving are still appropriate, but should be done with courtesy and reversed on protest." Flyer22 (talk) 18:41, 19 June 2014 (UTC)

In reply to your talk my page also appearing immediately above[edit]

I have no clue as to who Flyer22 is in relation to the question of highlighting Talk text to make minority voices clearer, or what "refactoring" or "archiving" are, and what they have to do with highlighting. Here, brevity is your enemy; I am not chasing possible meanings down for you. This you need to clarify, significantly, to simply be understood. As for Padillah's statement, I have asked him to make clear what he wants, and when he does, I will act. As for your "protest", you can assuredly speak to what I do with your comments, but—as far as I see in the WPs, and as far as I have been counseled—not about what I do with other others' comments. I have highlighted none of your comments. I have queried all others, and will respond to their requests. It is, I understand, up to them, individually. (There is no overriding, firm policy, whatever you might think; this is what I am told.) So for now, I will await Padillah et al's replies, and yours if you care to say more. (But no action taken until.) Cheers. Le Prof

Got your note and[edit]

first, no problem about it being the weekend before a response to the outline. But, did it not strike you that I might find a bit odd, so many Talk edits fitting schedule, but no "the outline looks fine, go get started"? And, for all that, in future, don't presume regarding your refactoring either (or whatever it's called). Whatever my sins, your rejiggering the whole of the Talk — appearance, order of entries, what appears on the current page, etc.—was not appreciated mate. For one, I've several incoming links, now broken, to the archived Talk. (For another, your perceived "I'm in charge here" persona is still an issue.) Effectively reading one another's minds—a point we're clearly not at yet. Nor is empathy a natural product between us. Ask first, still. (And so, to be clear, I expect to see Talk about the NP outline/changes, before any editing starts.) No reply, please. Respectful actions, enough. Le Prof Leprof 7272 (talk) 03:33, 21 June 2014 (UTC)

It is recommended to archive or refactor a page either when it exceeds 75 KB, or has more than 10 main sections.
— WP:TALKCOND

At the time that I had archived the talk page, it had grown to 133 KB and had 15 main sections. Based on length alone, it was time to archive. Furthermore TenOfAllTrades had specifically stated that (s)he thought that the talk page was a mess and needed to be cleaned up. Padillah agreed and indicated that (s)he would archive some of the discussion. If I had not archived the discussion, Padillah probably would have done it for me. Breaking links is an unfortunate side effect of archiving talk page discussions. However one of the reasons there has been very limited engagement from other editors was it was becoming impossible for anyone to follow the discussion. Creating links into this complex discussion is not likely to generate a much of a response. I was also having trouble reading the talk page and as a consequence, it was interfering with our recent productive discussions and improving the article. It is time to put the past acrimonious discussion behind us and move on to improving the article. Boghog (talk) 06:46, 21 June 2014 (UTC)
You seem particulary incapable of perceiving what sort of treatment of others will put an end to acrimony. Try respect. Asking prior to acting significantly is respectful. Acting without asking, is not. Wrong impetus mate. I have not another word to say on this. Le Prof Leprof 7272 (talk) 00:32, 22 June 2014 (UTC)

If my mind serves me[edit]

here are some ketone-containing drugs: acetohexamide, befunolol, daunorubicin, ethacrynic acid, haloperidol, ketoprofen, metyrapone, loxoprofen, naloxone, and naltrexone. Le Prof Leprof 7272 (talk) 04:27, 21 June 2014 (UTC)

Not sure what you are getting at here or if this message was meant for me. Are you suggesting we create a new Category:ketone containing drugs or mention these in the ketone article? Boghog (talk) 08:19, 21 June 2014 (UTC)
Misplaced, and since moved. You can delete this entry if you wish. Cheers. Le Prof Leprof 7272 (talk) 00:33, 22 June 2014 (UTC)

IL-23 subunit alpha[edit]

I think that the IL-23 subunit alpha page needs to be reduced. Right now it is a mixture of pages about IL-23 subunit alpha and the IL-23 heterodimeric cytokine. There should be a separate page for IL-23 subunit alpha, and for the cytokine itself. The page re the subunit will by definition be shorter because little is known about its function, outside of functioning as a heterodimer. What do you think? That's how it is now set up for IL-12, you can read about the cytokine IL-12 and then about each of the subunits separately. — Preceding unsigned comment added by Exiledscientist (talkcontribs) 19:33, 26 June 2014 (UTC)

Agreed. Interleukin 23 which is now a redirect to Interleukin 23 subunit alpha should be converted into its own article. BTW, thanks for your contributions. You clearly know the subject and I do appreciate your contributions. Cheers. Boghog (talk) 19:43, 26 June 2014 (UTC)
Per your suggestion, I went ahead and converted Interleukin 23 to an stand alone article. Please edit and expand as you see fit. Cheers. Boghog (talk) 20:00, 26 June 2014 (UTC)

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CASK article[edit]

Hi, You removed a lot of my entries from this page. https://en.wikipedia.org/wiki/CASK This information is critical for children (like mine) who suffer from CASK gene defects. How can we manage that this information reaches the general public and the parents of the children affected with this rare disease. Can you provide me with some tips on how to integrate this information more wisely into the article ? — Preceding unsigned comment added by Reachme A (talkcontribs) 14:59, 2 July 2014 (UTC)

Hi. Thanks for your note. Simply stating a journal article is about the subject of a Wikipedia article is generally not sufficient reason to include it. One also needs to understand what the journal article says about the subject and write some prose to go along with the citation. To start with, I will re-add the citations into the further reading section. As I have time, I will try to integrate a few of these papers to better illustrate what I mean. Cheers. Boghog (talk) 15:36, 2 July 2014 (UTC)


Cite error: There are <ref> tags on this page, but the references will not show without a {{reflist}} template (see the help page).