Wikipedia:Peer review/Phagocyte/archive2

===Phagocyte===
 * Previous peer review
 * A script has been used to generate a semi-automated review of the article for issues relating to grammar and house style; it can be found on the automated peer review page for February 2009.
 * A script has been used to generate a semi-automated review of the article for issues relating to grammar and house style; it can be found on the automated peer review page for February 2009.

This peer review discussion has been closed. I've listed this article for peer review because I would like somebody to point out mistakes (everything from grammar to readability) in the article and gauge its progress.

Thanks, Eulemur2008 (talk) 20:05, 14 February 2009 (UTC) :Note: Because of its length, this peer review is not transcluded. It is still open and located at Peer review/Phagocyte/archive2.
 * I've skimmed it and it seems generally excellent, with the caveat that it is centered on the role of phagocytes in handling infectious/foreign agents, but not their role in handling apoptotic cells. The latter is perhaps a greater proportion of phagocyte activity than ingestion of invading microorganisms, yet is not even mentioned in the lead.  Self-antigen presentation in the absence of inflammation is important for peripheral tolerance, and disruption of this process may be an important trigger of autoimmunity.  I can try to add some of this when I get a chance, but I have a lot on my plate and the links I've provided may help you do the same.  --Scray (talk) 00:31, 15 February 2009 (UTC)


 * Thanks, this is very helpful. Graham. Graham Colm Talk 00:36, 15 February 2009 (UTC)

Comments from Natural Cut: It is indeed a quality article. As a disclaimer, I am not a scientist so you could be explaining why the world is flat and my commentary would still consist of how to make it flow better. The lead reads very well until the last paragraph, which felt like things that weren't said yet but deserved a mention somewhere. I moved the etymology note to the first sentence; if you change the second sentence to 'Phagocytes have since been found in many species' it will tie in with the bit about discovery.

A brief elaboration of how/why the monocyte becomes a macrophage when it leaves circulation would help for laypeople like myself. If I'm reading correctly, it basically loses its granules. Keep an eye out for things like this that may have seemed obvious to the writer.

A peculiarity with one of the linked terms: Myeloid progenitor cells points to a different article than Myeloid progenitor cell.

I got called in to work mid-edit, I'll have to read the rest later. Natural Cut (talk) 21:14, 19 February 2009 (UTC)

Alright, I've read through it and must say the previous reviewer was correct about the article quality. The only major thing that stuck out at me was that the extracellular killing section is awfully short for a top-level section.

The article uses 'T cell' and 'T-cell' in different sections.

Under avoiding contact, I understand the following sentence but it sounds awkward in English: "Fourth, some bacteria can avoid contact with phagocytes by tricking the immune system into thinking that the bacteria are 'self'." Possibly a section you were already working on as I see an existing HTML comment that said "which does what?" Natural Cut (talk) 22:56, 21 February 2009 (UTC)

Comments from Brianboulton: This seems to be a thorough, carefully prepared article. I have thus far read only the first few sections.
 * General
 * The article is not very welcoming to those without special knowledege. To some extent this is inevitable, but has enough been done to justify the inclusion of this article in a general encyclopedia rather than in a scientific journal? My impression is that it is pitched a little too high to be accessible to the general reader.
 * For example, there often seems to be an assumption of "inside" knowledge; many terms which could be wikilinked are unlinked and unexplained.
 * The prose is not always 100% clear, and on occasion does not flow well.
 * Comments on specific sections
 * Lead
 * The syntax of the first sentence doesn't seem right as it stands. I assume the required sense is that phagocytes "ingest dead, dying, pathogenic or infectios cells, and other foreign particles." If this is the intended meaning, the sentence should be adjusted accordingly.
 * I find the verb to "phagocytise" a bit forbidding; could this be explained in non-technical English?
 * receptor could be linked
 * Awkward sentence: "When the phagocyte comes into contact with dying cells, they bind the receptors...". The proper from is "When dying cells come into contact with the phagocyte, they bind..." etc
 * The last lead sentence seems oddly placed, and looks like it might have come earlier.
 * History
 * Link or explain motile
 * Claus suggested the name "phagocyte", but it's not clear what he was actually naming.
 * You could avoid unnecessary repetition by rewording: "...and found that this organism could similarly be destroyed."
 * We have Mechnikov proposing something in the 1880s, and in the same sentence receiving a Nobel Prize in 1908. Could you link these two statements by, for example, adding after the words "primary defence against invading organisms" a phrase such as: "During the following years his findings were confirmed, and he and Paul Erlich..." etc?
 * The last two sentences seem out of place. The penultimate sentence is word-for-word repetition of a sentence in the lead; the last sentence would be better placed as an introductory sentence to the next session.
 * Monocytes
 * "bi-lobed nuclei" – is there any way of explaining what these are?
 * Links available for cytoplasm and antigens
 * Macrophages
 * "granulyte-monocyte precursors" Any explanation possible?
 * Link lysosomes, microglia, alveolar, cytoplasmic, IFN-gamma, TNF-alpha, phagosomes, cytokines, chemokines, enzyme, cationic
 * "they can even store iron..." Any significance of "even" in this statement will, I fear, be lost on the general reader.
 * Can "differentiation of CD4 T cells" be explained more simply?
 * "Activated" and "after activation" in the same sentence. One of these should be removed.
 * Neutrophils
 * First sentence: should there be a comma after "antibody"? And should this be "antibodies"?
 * Either way, antibody should be linked
 * Other links: proteolytic, Heparin, peptides
 * Dendritic cells
 * Links: Langerhans cell, MHC
 * Repetition to be avoided: "After monocytes have turned into immature dendritic cells, the immature dendriditic cells..." Use the pronoun "they"
 * Another awkward sentence: "How effective the immune response controlled by dendritic cells is, depends on their maturity", Suggest rewrite as: "The effectiveness of the immune response controlled by dendritic cells depends on their maturity" (or, "...on the cells' maturity")
 * Suggest explanation of "helper T cells", "killer T cells", if helpful links can't be found.
 * Mast cells
 * "toll-like receptors" Explanation possible?

That's as far as I've got, and I think you get the idea: more links required, more explanations required in the absence of links, and odd bits of dodgy prose to be sorted out. From now on I'll only deal with the prose issues and leave the article's writers to pick up the other issues. I'll come back to to tomorrow. Brianboulton (talk) 20:37, 24 February 2009 (UTC)

A few more comments (prose, mainly)
 * Non-professional phagocytes: no specific prose issues, but the first paragraph is a good example of what I mean by inaccessible language. The guideline in WP:JARGON is articles using academic or professional terms should contain more explanation at a more basic level than would be available in the typical academic paper or textbook
 * Phagocytosis: again no prose issues, but again severe readability problems
 * Initiation of phagocytosis: Prose issue – two successive sentences beginning with "These receptors..." Try and reword
 * Initial signaling: the SOS link is not appropriate
 * Endothelial and epithelial migration
 * Phrases in mdashes should not form a complete sentence. Dashes enclose interjections or interruptions within a sentence. Thus: "X—although Y says otherwise—was in complete agreement with Z"
 * The first para of the section seems light on citations. Second para also has uncited statements.
 * Oxygen-dependent intracellular killing
 * Avoid starting a new sentence with the concluding word or phrase of its predecessor, e.g. "...superoxide anion. Superoxide anion..." and "...hypochlorite. Hypochlorite..."
 * "The next type..." Type of what?
 * Oxygen-independent intracellular killing: Is all the material in this section verified by the single source cited at the end?

Will continue Brianboulton (talk) 18:52, 25 February 2009 (UTC)
 * Brian, thank you so much for this thorough review. This is just to let you know that I have read and noted all these very useful comments. Graham. Graham Colm Talk 21:07, 25 February 2009 (UTC)
 * PS. I left a note on my co-editor's talkpage (User talk:Eulemur2008), who has done most of the hard work on this article. Graham Colm Talk 21:15, 25 February 2009 (UTC)

Just a few more comments Time doesn't allow for a close reading of the remainder of the article. Here are a few further points:
 * Immunological tolerance: the term is somewhat over-repeated in this section. Also, the syntax of this extended sentence defeated me: "The second type of immunological tolerance is peripheral tolerance. Some T-cells that posses antigens that would cause them to attack self slip through the first process of tolerance, some T-cells develop self-attacking antigens later in life, and some self-attacking antigens are not found in the thymus; because of this dendritic cells again restrain their activity."
 * Avoiding contact: the meaning of "self" in this sentence should be made clear: "...some bacteria can avoid contact with phagocytes by tricking the immune system into thinking that the bacteria are 'self'". Also, there is a hidden "which does what" note in this section.
 * Survival inside the phagocyte:
 * "...enters phagocytes by coating its surface..." Either "a phagocyte", or "their surfaces"
 * "There are many methods of survival and stopping the fusion of a phagosome and lysosome into a phagolysosome is one." This doesn't sound very professional. I suggest: "One of many methods of survival is stopping the fusion of a phagosome and lysosome into a phagolysosome."
 * Defects of phagocte cell function: The sudden adoption of a bullet-point format goes against the style of the rest of the article. The section should be rendered into straight prose, for consistency.
 * Septic shock: "...this helpful chemical can produce hegative results" - negative, in this case, meaning good? Needs clarifying.

I think that sees me through. I can't guarantee that I've picked up every prose issue, but I hope my comments will help you to improve the article. Good luck with it. Brianboulton (talk) 19:51, 27 February 2009 (UTC)
 * Thanks again Brian. Graham Colm Talk 17:56, 28 February 2009 (UTC)