User talk:Boghog

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Variability in PSA Measurement[edit]

I have edited it just because it is a very common problem occuring in practice. The review artcile may not be upto date but it is addressed considering routine problem of clinicains and lab professionals.

Disambiguation link notification for April 24[edit]

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I am not[edit]

…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[edit]

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 [1] 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)

Reference errors on 30 April[edit]

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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) 00:38, 1 May 2015 (UTC)

Disambiguation link notification for May 1[edit]

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Proteasome complex[edit]

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 (talkcontribs) 22:05, 2 May 2015 (UTC)

Interview for The Signpost[edit]

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[edit]

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)

Congrats[edit]

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)

Cite PMID[edit]

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:
Boghog (talk) 18:46, 21 May 2015 (UTC)

Butyric acid[edit]

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 ) 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:CHEM 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 ) 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 ) 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.