Talk:Polyclonal B cell response/GA2

GA Review
This review is transcluded from Talk:Polyclonal response/GA2. The edit link for this section can be used to add comments to the review.

Hello!

I have renominated the article after addressing the issues raised by Narayanese on the talk page of the article, and also making other changes as thought appropriate by me.

Regards.

 —Ketan Panchal  t aL K   18:43, 27 May 2008 (UTC)

I will be reviewing this article over the next couple of days to see if it adheres to the GA criteria. At first glance, I am doubtful of this. The most obvious issues that I see thus far include:

3 B cell response
 * Numerous violations of the manual of style. For starters, the 'explanation of difficult terms and concepts' is not a section normally included in wikipedia articles, and the use of the two templates combined with the small font text do not adhere to the WP:MOS either. Templates such as those two should only appear at the bottom of an article, at the very end. Difficult terms and concepts should be presented in a more user-friendly manner in the article itself, not with a bold and blatant warning like this, which is really going to do little more than discourage less advanced readers from reading the article. The proper way is to explain these concepts in the article text itself, and use internal wikilinks to let readers learn more about specific terms as they go along.
 * You are very right about the violation of manual of style, in particular, because of incorporating a section of difficult terms. It has been a great challenge to explain the terms within the article as firstly this breaks the flow on many occasions, and secondly, it would be quite beyond to explain certain terms within the main body of the article, say for instance, host and pathogen. Both the terms will find repeated mention in the article, but it would be very weird to actually explain the meanings of these terms, which can usually be taken so much for granted by those even remotely related to the field of biology/medicine, but might confuse those who are unrelated to the field. I can think of totally doing away with explaining them, but that might interfere with their understanding by the so called lay person. Likewise, if I try to explain the functions of the antibodies within the article even in the briefest possible fashion, it would be very much out of scope of the article, and also conflict with the subject matter of the article antibody. But, without doing so, a person unaware of their functions might simply respond like "so what?". I'd be very happy to make the article adhere to MOS to the greatest degree, but not at the cost of intelligibility to a general audience. It is in this respect that I'd like to quote the opening of the WP:MOS—"This guideline is a part of the English Wikipedia's Manual of Style. Editors should follow it, except where common sense and the occasional exception will improve an article." I am not using that as a shield, but, I genuinely feel that the concept inherent in the article cannot be explained (to a general audience) without initial introduction to the terms to be encountered in the article. Of course, I'm most open to suggestions. I'd be very glad if a compromise could be reached between intelligibility of the matter and rigid adherence to the WP:MOS.  —Ketan Panchal  t aL K   23:01, 27 May 2008 (UTC)
 * The names of subsections in the article are very long, and combined with the use of multiple subsection headers, make the table of contents look very "scary" and unhelpful. Section & subsection headers should be short and concise, and should not use the article title (e.g. 'Polyclonal response') in the name of the header (see WP:MSH). Try to minimize the use of subsection headers and only use them where absolutely necessary. A reorganization of some of these sections may be in order; try to somehow "tell a story" -- each section should help the next one out, and lead into it. It's difficult for me to see that that's actually happening here, as it appears to be more bits and pieces of random facts.
 * I have tried to shorten the length of a few section heads, but, I personally felt that in some cases, it is the longer heading that made better sense. Like, "Significance of polyclonal response" would put things much better in context rather than simply "Significance". I also agree that some concepts might be appearing as "bits and pieces of random facts", that's because that's what they are in the context of the article. For instance, how a B cell gets stimulated and costimulated has nothing to do with somatic hypermutaion or affinity maturation. It has also got nothing to do with the concept of original antigenic sin. But yet, it appears in the article because polyclonal response is, after all, all about the B cells getting stimulated. I've maintained a pattern—first, I have introduced the concept at a gross level, and then introduced the subtleties like the original antigenic sin, autoimmunity, affinity maturation, etc.  —Ketan Panchal  t aL K   23:01, 27 May 2008 (UTC)
 * I am very concerned about the 'verifiability' requirement of the GA criteria here. I see lots of information that is not cited with an inline citation, and at least half of all citations provided appear to come from the same textbook. It would be good to not depend so heavily on the same source.
 * A few pieces of information were introduced in the article today, so citations for them didn't appear. The text book I have quoted is a standard one, and actually supports the information I've included in the article. Wherever, some relatively unconventional concepts are involved like the original antigenic sin, or the antigen and antibody slightly altering their conformations to make a better "fit" have been backed by research articles.  —Ketan Panchal  t aL K   23:01, 27 May 2008 (UTC)
 * I see several subsections that have very little text in them (e.g. 'T helper cell stimulation and B cell costimulation', 'Costimulation of B cell by activated T helper cell', most of the subsections under 'Basis of polyclonal response', the entire main section of 'Diversity of B cell clones'), which could either be issues with the completeness criterion of WP:WIAGA, or issues with organization (combine these short subsections into a larger main section).
 * That is because, they are merely expanded explanations of the steps enumerated in the opening of the same section. If you'd see the same sections in the table of contents, it'd make much better sense--


 * 3.1 Recognition of pathogens
 * 3.2 Antigen presentation
 * 3.3 T helper cell stimulation
 * 3.4 Costimulation of B cell by activated T helper cell
 * 3.5 Proliferation and differentiation of B cell

It shouldn't matter if the text serving as explanation of the step is very short because the concept to be explained itself is short.  —Ketan Panchal  t aL K   23:01, 27 May 2008 (UTC)


 * On the bright side, I don't see any issues with WP:NPOV or stability, so those two criterion are ok. The images are also tagged with appropriate copyright tags.

I'll go ahead and change the GA status to on hold pending revision. Dr. Cash (talk) 19:27, 27 May 2008 (UTC)


 * I'd be very grateful if apart from pointing out the points in which the article departs from the WP:MOS, I'd be also told how to effectively make them reconcile with it. Surprisingly, I had almost the very same points pointed out to me in the past (especially regarding the long section heads), which I'd altered then, too. But the outcome of those modifications wasn't satisfactory. I think that's because whoever quite used to the usual Wikipedia articles, at first only notices how the article has departed from the guidelines, but not that it'd be very difficult to convey what could be conveyed in the present form of the article, by strictly adhering to all the guidelines.


 * The fact that article has done well to explain the inherent concept to even a person unrelated to the field is of great satisfaction.


 * Lastly, I feel, it's the long headings only that can give it a feel of a "story". Still, I assure, am not being adamant. Will try my best to meet the WP::MOS criteria. Looking forward to some help from you and others, too in this regard.


 * Regards.


 *  —Ketan Panchal t aL K  23:01, 27 May 2008 (UTC)

Re-review by Dr. Cash
The changes that you've already made to some of the subsection headers seem good, and are MOS-compliant. It seems to make sense. The conversion of subsections in 'significance of polyclonality' isn't MOS-compliant, and should probably be converted back to subsection headers. The 'main article' links go at the top of subsections, not at the bottom, per MOS. I don't like the bulleted list there at all.
 * I'm not sure if any other title for the said section would adequately convey what is to follow. So, if you have any ideas, I'd like to change it yourself or discuss it over here.  —Ketan Panchal t aL K  16:43, 6 June 2008 (UTC)

The 'historical' section is very short. Usually, this section is simply titled 'History', not 'Historical'. I see some definite issues with completeness here, though.
 * To be honest, I wasn't aware of the contributions of the named scientists; I found them in the article clonal selection. But, I've confirmed the accuracy of the statements I've made in the section, so I don't feel there are any issues.  —Ketan Panchal t aL K  16:43, 6 June 2008 (UTC)

The external link the the 'see also' section needs to be moved to an 'external links' section. It is not necessary to put a 'retrieved on' date for links in this section; just put the link. The retrieval date is only necessary for links used as inline citations.
 * ✅  —Ketan Panchal t aL K  16:44, 6 June 2008 (UTC)

The 'Explanation of difficult terms and concepts' needs to be removed. It's redundant, and the use of the drop-down templates is bad form, and not consistent with WP:MOS. As far as difficult terms and concepts are concerned, this is the exact reason to have internal wikilinks to other articles! If a reader needs more information, they click the link to the other article to get it!
 * Almost ✅ I think I've explained all the important terms in the sections to follow. Converted the entire section into a hidden comment.  —Ketan Panchal t aL K  16:43, 6 June 2008 (UTC)

I'm not complaining about the use of your textbook to help build the article -- this is good! But make sure you're not just copying text directly from the article word-for-word, that's plagiarism. I still think it's a good idea to use multiple sources. Do you have any other textbooks? Have you checked PubMed for some of the latest journal articles or studies on the topic? Dr. Cash (talk) 16:55, 28 May 2008 (UTC)
 * Well, I do have another textbook, but that's a textbook of microbiology, and certainly less detailed than the current one. Plagiarism is almost not an issue, as I'd written the article first, and then tried to look for the corroboratory statements from the said book. But, again don't worry about the accuracy of the concepts I've included&mdashI've made sure they're accurate (even though that was a lot of hard work). The problem with PubMed is that their results usually show articles containing recent research, and not review articles that could serve as sources for the article at hand. Thanks for the suggestion, though.  —Ketan Panchal t aL K  16:43, 6 June 2008 (UTC)

Re-re-review by Dr. Cash
I'll look over this article in more detail over the weekend, but I have to say I see a huge improvement! I think we're getting close. There's still an 'expand' tag in the history section, which is a red flag for GA status. The 'Significance of the phenomenon' section is also a little scarce of citations. There's also some "for more details" tags that are at the bottom of sections, which should be moved to the top. That's all I notice right now -- I'll look at it a little more closely tomorrow. But overall, I think we're getting close. Cheers! Dr. Cash (talk) 19:05, 6 June 2008 (UTC)
 * Thanks for the comments. I'll remove the "expand section" tag, though I personally never felt that much more of historical background is required for such a theoretical topic.
 * It's not exactly the "Significance of the phenomenon" article that is lacking in citations, but only the first ("Increased probability of recognizing any antigen") that is. I'd tried to find to citation, but couldn't find a reliable one. I also feel that, it is kind of self-explanatory, and further with the analogy I've given, it should not be considered to be "controversial".
 * Well, now I've added a citation for that piece of claim, too the only problem being, the support for the fact is not the main subject of the citation, and hidden somewhere in the middle-paragraphs. Though some citation is better than none.  —Ketan Panchal t aL K  21:07, 6 June 2008 (UTC)
 * I've tried to maintain a pattern with regard to the main and details templates. The subjects, which are not required in their entirety, but only aspects of which have been discussed, have been incorporated in the main template, and placed at the top of the paragraphs. The subjects which have been sufficiently explained in the discussed article, and the core concepts of which HAVE been discussed in the article in sufficient details, and which are particularly important in the context of the article have been incorporated in the details or details3 template and placed at the bottom of the sections. This ensures that, the discussion of the "core" concepts is not interrupted by a tag. Well, do tell me if this is also against the WP:MOS.
 * Thanks for all your time. Regards.  —Ketan Panchal t aL K  19:49, 6 June 2008 (UTC)

Section-by-section discussion
I am introducing a new head for section-wise discussion of polyclonal response. Any one interested in the improvement of article may kindly leave comments under the relevant section heading. If a certain section is deleted, merged or altered in any way, I will try to make corresponding changes, here too, but should that not be possible, I request any one noticing a discrepancy to make the required changes. I have made reading the sections from the article simple. If you are a registered user, and have popups, on, simply point to the relevant section, heading, and you'll see a preview of the same section from the article. Depending upon your browser, and its settings, you can also, simply Ctrl+click on the section heading/subheading and open it in a new tab/window. So, happy assessing!  —Ketan Panchal  t aL K   21:55, 28 May 2008 (UTC)

Article in general
Added the templates main, details and details3 at relevant places in the article.  —Ketan Panchal  t aL K   13:48, 28 May 2008 (UTC)

The lead
I would suggest removal of the "This article deals with...", unless the polyclonal response is not unique to mammals. If its presence is necessary, then it probably ought to be formatted using dablink (to standardise text size) or one of the other disambiguation templates (to point to another article). Rephrase "a very important component of this response" to "a central component of this response", "a key component of this response", or something similar to avoid using the generic phrase "very important". Link to "soluble". –Black Falcon (Talk) 16:40, 29 May 2008 (UTC)


 * The immune system may respond in multiple ways to an antigen; a very important component of this response is the production of antibodies by the B cells (or B lymphocytes).
 * I'm sure we can find a much more concise way to say this, but I'm not sure exactly what it is right now. Perhaps "One way that the immune system responds to an antigen is the production..."?  WhatamIdoing (talk) 20:39, 31 May 2008 (UTC)


 * Well, I've employed the dablink. The problem is I don't know about the immune system in other divisions (hope that's the correct taxonomic term) like the aves and reptiles is similar. I'd feel that it must be similar in them too, but am not sure, so I felt the need for clarification. To remove ambiguity with "very important component", I've replaced it by "a key feature". Hope this change should be satisfactory. I didn't follow the suggestion of WhatamIdoing as I thought the repetition of the word "respond" in two contiguous wasn't "sounding" right.  —Ketan Panchal t aL K  14:31, 6 June 2008 (UTC)

Explanation of difficult terms and concepts
The fate of this section is undecided. Might have to be removed as Dr. Cash has objected to its existence.  —Ketan Panchal  t aL K   12:54, 28 May 2008 (UTC)

Infection
Added this new section, which basically elaborates upon the concepts of host, infection, pathogen, etc. It's a bit short, but expanding it might just make certain info in it irrelevant. But, if any one feels more info in it would do justice, you are welcome to add it.  —Ketan Panchal t aL K  14:49, 6 June 2008 (UTC)

Re:Inoculation and colonization
It does not mean what you use it for in the article. Just have a second read of the ref you gave and you'll see that, or just read the inoculation article (organisms don't inoculate by themselves). Colonization is anoather word you aren't using right, it's not the same thing as infection. Narayanese (talk) 19:31, 10 June 2008 (UTC)
 * Hi Narayanese! I believe I understand your concern about the usage of the term, but I have added a note for its usage in the article. The term is indeed used in vaccination and culture techniques to imply an active act, but in discussing pathogenesis of an infectious disease, it is generally absolutely alright to call the entry of organism as "inoculation". Like you might read about a chancre that it is found at the "site of inoculation", i.e., the site in the body from which the causative organism (Treponema pallidum in this case) would have entered the body. Quoting the said article on inoculation from Wikipedia: "'...but also can be used to refer to the communication of a disease to a living organism by transferring its causative agent into the organism, to implant microorganisms or infectious material into a culture medium such as a brewers vat or a petri dish, to safeguard as if by inoculation, to introduce an idea or attitude into someone's mind, any placement of microorganisms or viruses at a site where infection is possible such as to increase soybeans' nitrogen fixation one can treat soybeans at planting with Rhizobium japonicum inoculant.'"
 * As you can see even the Wikipedia article supports this usage of inoculation.


 * As regards "colonization", I realized the sentence wasn't properly framed, and have added notes and citation even there. Please do see if you're satisfied by them.


 * Nice to see you're still having an eye on the article.


 * Regards.  —Ketan Panchal t aL K  21:05, 10 June 2008 (UTC)


 * I have never seen it used as a synonym for transmission, always as artificial transfer, and I don't see the the beauty of using a word in an unusual meaning. And while pathogens can be said to colonize, infect is the more common word as colonize can be understood to mean the organism is harmless there. I don't think the section belongs in the article anyway (too far off the topic, let the wikilinks provide background). Narayanese (talk) 21:41, 10 June 2008 (UTC)


 * Firstly, the usage of the term "inoculation" is not at all unusual in the given article, just a bit less used than in immunology. Secondly, as regards colonization, I have provided the definition almost verbatim from the best known textbook currently in Internal medicine on the globe. Moreover, I don't see why a section consisting of just 6 lines and 5 sentences should pose so much problem that it has to be removed without any consensus? If you see it from a layperson's perspective their response would be like "so what?" without that opening section. I definitely don't feel, it was unrequired. So, I have restored it. You can of course wait for some consensus to build. Sorry, that I'd to revert two of the deletions you'd made to the article. Regards.  —Ketan Panchal t aL K  22:48, 10 June 2008 (UTC)


 * Here, I will cite some instances of inoculation being used as a natural, spontaneous event in the pathogenesis of some infectious disease or the other, as against using it only to imply deliberate introduction of the infectious agent to induce acquired immunity:


 * "... an incubation period of three weeks, the classic chancre of primary syphilis appears at the site of inoculation ... days, the macule ulcerates, producing the typical chancre (Figure 1). The chancre is usually solitary and consists of a painless"Dermatologic and systemic manifestations of syphilis.
 * "Local skin reaction (chancre) induced following inoculation of metacyclic trypanosomes in cattle by tsetse flies is dependent on CD4 T lymphocytes" Title of article appearing in "Parasite immunology" journal
 * "The number of malarial inoculations experienced, and the intervals between them, are all-important to the malaria immune status of an individual."Evolutionary and Historical Aspects of the Burden of Malaria. Here even though it might appear like one is talking of vaccination, if one reads the article, it will be sufficiently clear that the authors are referring to natural "inoculation".
 * "The intense malaria transmission conditions found in many parts of tropical Africa, the much lower malaria inoculation rates currently sustained in areas of southern Asia, and the epidemic outbreaks of malaria occasionally seen on both continents, present highly contrasting patterns of malaria-related mortality."Malaria Mortality Rates in South Asia and in Africa: Implications for Malaria Control
 * "Pathophysiology (of Tuberculosis): A single cough can generate 3000 infective droplets. Fewer than 10 mycobacterial bacilli may initiate a pulmonary infection (Sherris, 1990). TB inoculation can result in latent infection or active disease. Depending on the population, 10-30% of inoculated individuals progress directly to active primary disease. More commonly, however, TB inoculation results in an asymptomatic latent infection. Skin test conversion and identification of a Ghon complex on chest radiography are the only means of identifying such cases."Excerpt from Tuberculosis. Please note: here they are talking inhalational route, and obviously without any reference to vaccination or immunization of any sorts.
 * "Mycobacterium   tuberculosis    is an intracellular pathogen. On inoculation (usually inhalation into the lungs),    it is phagocytosed by monocytes."Aetiology of tuberculosis
 * "Natural barrier in primary tuberculosis inoculation: oral mucous membrane."Title of an article from "Int J Tuberc Lung Dis."
 * "Rabies develops with three main phases: prodromal period, acute     neurological period, and coma.  The onset of symptoms follows these     general stages:
 * 1. 	Prodromal stage. Prodromal or premontive 	  symptoms are mild and nonspecific.  They include:  a slight fever 	  (100 F to 102 F), chills, malaise, headache, 	  anorexia, nausea, sore throat (the beginnings of 	  hydrophobia), photophobia, musculoskeletal pain, and a persistent 	  loose cough.  This stage usually lasts 2-10 days. 	   A specific early symptom is local or radiating 	  pain, burning, or itching, a sensation of cold, and/or tingling 	  at the inoculation bite."TKH Virology notes-Updated!


 * Moreover, I'd like to point out that the difference between transmission and inoculation is subtle, but it exists: in the case of former, one is talking of transfer of the infectious agent from a source to the certain tissue of the susceptible host, whereas when talking of inoculation (in context of pathogenesis of an infectious disease), the infectious agent is introduced into certain tissue of the susceptible host somewhat ignoring the source for the time being. So, the important difference between the two is of the "source", which is not to mean that inoculation of does not require a source, but that that aspect of transmission is being overlooked to draw attention to specific aspects of agent-host interaction, say "inoculation of Leptospira icterohaemorrhagicum is more likely when the skin is moist or there are cuts on it", as against "Leptospira icterohaemorrhagicum can be transmitted from rain water contaminated with rat urine when flooding occurs". As you can see in the statement containing inoculation the source is not important, whereas, in the discussion of transmission, the actual step that results in introduction of the bacterium into the body is somewhat unimportant. So, this is how subtly transmission and inoculation differ. If you'd want, I'd be glad to cite a few other instances of inoculation as a step in natural pathogenesis of infectious diseases.


 * Regards.  —Ketan Panchal t aL K  08:21, 11 June 2008 (UTC)


 * Well, you seem certain, so I'll have to assume you know what you're talking about and let the section be. But it would be nice if you could pull all the section that aren't directly about polyclonal response and put them as susections in a section labeled Background. Narayanese (talk) 20:34, 13 June 2008 (UTC)


 * Thanks for the suggestion, but the logic of putting the section there is that "first there's an infection, and then only the immune system requires to respond against it". But, if there are more people against the section where it is, it can certainly be moved. Regards.  —Ketan Panchal t aL K  16:59, 15 June 2008 (UTC)

Body's response to invading pathogen The immune system
Combine the last two sentences of the first paragraph, by placing the explanation of the term "specific" (i.e. the content of the second sentence) immediately after the word "specific". Or, rephrase the second sentence to avoid the passive voice. (For instance, change "By these responses being specific it is meant that two different pathogens..." to "Specificity means that two different pathogens...".) –Black Falcon (Talk) 16:40, 29 May 2008 (UTC)


 * I've changed the title as I've added some content, and with it, the current title seems more appropriate. I don't remember if I changed the sentences in passive voice to active voice, or if some body else made those changes, but somehow the issue has been taken care of someone or the other has taken care of the issue.  —Ketan Panchal t aL K  14:37, 6 June 2008 (UTC)

Recognition of pathogens
I am tempted to expand the title to "Recognition of pathogens by APCs", but that would make it longer. Comments?  —Ketan Panchal  t aL K   12:53, 28 May 2008 (UTC)
 * Keep the shorter name, especially when APC is an abbreviation not seen outside the field. Narayanese (talk) 17:20, 6 June 2008 (UTC)

You've fixed the bit about TCR and BCR I complained about before, good job. Narayanese (talk) 17:20, 6 June 2008 (UTC)
 * Thanks for your comments. Yes, I have made many other changes. What do you feel about its status regarding GA? Regards.  —Ketan Panchal t aL K  18:53, 6 June 2008 (UTC)

Antigen processing
Started this new section as antigen processing is an important step before antigen presentation.  —Ketan Panchal  t aL K   12:51, 28 May 2008 (UTC)

Proliferation and differentiation of B cell
The section now explains well memory B cells are involved in affinity maturation. But it leaves out selection, mutation by itself can never result in a shift toward stronger affinity. And it calls mutation itself the maturation, which is a close but not quite right. Narayanese (talk) 17:11, 6 June 2008 (UTC)


 * You're certainly right. I've added the point in brackets in the sentence: "Some of the newly created paratopes bind more strongly to the same epitope, which is known as affinity maturation. And others bind better to epitopes that are slightly different from the original epitope that stimulated proliferation in the first place". But, I had any way discussed the subject in greater details in one of the following sections. Thanks.  —Ketan Panchal  t aL K  21:59, 6 June 2008 (UTC)

Clonality of B cells
"Memory and naïve B cells normally exist in relatively small numbers. As the body needs to be able to respond to a large number of potential pathogens, it maintains a diverse repertoire of B cells."-->"Memory and naïve B cells normally exist in relatively small numbers. As the body needs to be able to respond to a large number of potential pathogens, it maintains a pool of B cells with wide range of specificities." Thought that the word repertoire would be complicated for many, and the sentence explains the concept better in its present form.  —Ketan Panchal  t aL K   13:44, 28 May 2008 (UTC)

Recognition of epitope by B cells
"Epitope recognition by B cell": changed the section heading to the current one.  —Ketan Panchal  t aL K   21:55, 28 May 2008 (UTC)

Historical History
Added this new section as I found additional information from another Wikipedia article clonal selection.  —Ketan Panchal  t aL K   16:13, 28 May 2008 (UTC)

Significance of polyclonality
Expanded the title to "Significance of polyclonality" form just "Significance" as this better provides the context to read the text that follows.  —Ketan Panchal  t aL K   14:45, 28 May 2008 (UTC)

Support
I think it meets the GA criteria now. While most is from a single source, there are no obvious differences from my book The Immune System by Peter Parham (which covers all but affinity maturation and original antigen sin). I intend to write out some three-letter abbreviations though (APC, WBC, TCR). Narayanese (talk) 22:43, 6 June 2008 (UTC)
 * Thanks for the support. You can of course expand the above-mentioned abbreviations. Though, I've tried to make sure that first usage of each term is in its expanded form. Well, I'd be very grateful, if you could find some more information on the historical aspect and to support the fact that polyclonal response widens the capacity of the immune system to recognize antigens. Thanks again. Regards.  —Ketan Panchal t aL K  23:32, 6 June 2008 (UTC)

Article promoted
The article now meets all aspects of the Good Article criteria, and will be listed. Nice work! Dr. Cash (talk) 21:54, 17 June 2008 (UTC)


 * Thanks a lot!
 *  —Ketan Panchal t aL K  05:47, 18 June 2008 (UTC)