Commas often make a difference in meaning, but also help to make reading smoother by clarifying the relationship between ideas. They should not be inserted randomly in a phrase that expresses a single idea. This often occurs in some papers before prepositional phrases, especially beginning with “with”, and should be avoided unless there is a very clear and definable reason for that comma.
“We used both, X and Y” should be “We used both X and Y”
“Two important physical features that are to be constrained by the model are the extent of the disk, and the presence of a halo.” (The list only has two items.)
“…model are the extent of the disk and the presence of a halo.”
“Smith detected five sources, with strong X-ray signals, with one confirming that…”
“detected five sources with strong X-ray signals, with one confirming that…” (The comma signals that a dependent verb phrase follows.)
3.1.1 Commas between two separate thoughts in one sentence
Use a comma between two separate thoughts in a sentence (i.e., each thought has its own subject and verb) that are joined by connecting words: and, or, nor, but, for, so. You can omit the comma if these thoughts are short and the relationship clear because of the connector.
“Superficially interpreting statistics may lead to false conclusions, but altering any statistic or leaving out contradictory evidence is much worse.”
“It becomes optically thick and the adiabatic phase sets in.”
The comma is left out when the two sentences share the subject:
“We depend on statistics but do not always know how to use them.”
Omitting the connecting word creates run-on sentences (especially if there is no punctuation between two thoughts) or comma splices (splicing two thoughts together with only the punctuation: commas or semicolons), which might confuse readers because they cannot tell where the first idea ends and the second begins, or else they can only guess at what the relationship between those ideas might be. [http://grammar.about.com/od/rs/g/runonsentenceterm.htm]
“Superficially interpreting statistics may lead to false conclusions, altering any statistic or leaving out contradictory evidence is much worse.” (See the example above with “but”, or divide this one into 2 sentences.)
3.1.2 Commas after introductory phrases
It is clearer to use a comma after introductory phrases of more than three words. If the phrase has fewer words, the comma is optional, but the final sentence must not be ambiguous. It is also needed when there are several numbers and symbols in that part of the sentence.
“As previously emerging radiation spectra are calculated for a radius of the scattering cloud equal to the Bondi radius."
Does the author mean "As previously, emerging radiation spectra are calculated…” or "As for previously emerging radiation, spectra are calculated…”; or could this be a fragment that introduces the next sentence?
“For the magnetic spot distribution with rsp = 10◦ illustrated in Fig. 2 nz gradually increases.” Does the comma belong after “spot” or “Fig. 2”?
Inverting the normal order of the English sentence is acceptable if not used too often. There should be a reason for it, such as for transition or rhetorical emphasis, rather than simply for varying the syntax. A comma is also required in this case, even if it is technically part of the main idea, precisely because it is not in its normal position. See Sect. 6.2.1 for a warning about dangling participles (modifiers using verb forms: present or past participles).
“The value of nz gradually increases for the magnetic….”
3.1.3 Serial commas in lists
At A&A, as for most technical and scientific writing, a comma precedes the “and” or “or” before the final item in a list of three or more to avoid ambiguity:
X, Y, and Z
X, Y, or Z
W, X and Y, and Z
3.2 Punctuating dependent clauses and phrases
3.2.1 Nonessential sentence parts (i.e., nondefining or nonrestrictive)
Commas are generally used around parts of the sentence that are not essential to the main idea (e.g., additional information about what the idea refers to) or parts that have been added for emphasis or as a transitional indicator. In contrast, a comma should not be used randomly in the middle of a sentence where it can lead to confusion (e.g., before a prepositional phrase that is part of the main idea of the sentence, see Sect. 3.1 above), and they are never used within the structures “either X or Y” and “both A and B”.
“The S/N is higher when, as shown above, the…”
“The Galaxy, which is rich in metals, has a thin disk.” (The information between the commas is not the topic of the sentence even if it is useful in the wider discussion.)
“plotted above the original, with colors brightening with time.” (This gerund clause with “with” needs a comma, whereas “with” as a preposition for a simple noun does not use a comma: “…plotted above the object with the bright colors” as in the examples under 3.1. above.)
“The HeII and OIII lines in ε Ori do not vary, while HeI 4026 and HeI 4713 do.” (“While” is used for contrast here before another full sentence, so there is a comma. However, if the intent is to say they do these things at the same time, as in the example in 3.2.2--one varies at the same time as the other does not--then there'd be no comma, since they go together.)
“Discovering whether the polluted population appears redder than the counterpart, depends on the photometric filter combination used.” (The comma separates the subject--the noun phrase “Discovering...counterpart”--and the verb “depends on”).
“The halo temperature is between a few 10K and 100K, which is warmer than the molecular cloud but colder than the diffuse ISM.” (If you can change “which is'' to a new sentence beginning with “This is”, then it is neither defining nor restrictive.)
3.2.2 Essential sentence parts (i.e., defining or restrictive)
Commas should not be used around dependent clauses that are essential to the main idea of the sentence, for example, when the dependent clause contains the information required for identifying the noun it refers to (defining or restrictive, see an explanation of adjective phrases in http://grammar.about.com/od/basicsentencegrammar/a/adjclause.htm).
“The Galaxy has a thin disk that is rich in metals.” (Metallicity is the point of the sentence, so using “that” implies that there are disks that are not metal-rich.)
“The observations were secured while the object was in eruption.” (The adverb phrase is essential to the meaning.)
“This occurs because there is often more than one way to construct a sentence.” (This guide, Sect. 1)
“We thank the anonymous referee for the useful comments that improved the manuscript.” (Grammatically speaking, the comments improved the paper, but using “which” and a comma implies that some comments did not improve the MS.)
For the relative pronoun, A&A prefers “that” over “which” to make the defining adjective connection to the subject very clear, even in MSs using British conventions. There is never a comma before “that” as a result, unless the reason comes from something else in the sentence or it is being used in another sense. [http://grammar.about.com/od/punctuationexercises/a/Practice-In-Punctuating-Adjective-Clauses.htm]
3.3 Colons and semicolons
A colon is a way to introduce one or more illustrative examples, especially in a list. It should not be used for any other connections between ideas, as a semicolon might be. To separate the items in the list, use commas between simple items (no commas in the phrase) and semicolons between complex ones. If a capital letter follows the colon, it signals that what follows amplifies the first sentence and is another full sentence.
“… as follows: the Earth, the solar system, and the Galaxy.” The complex formulations look more like “… as follows: the Earth, but not the Moon; the solar system and all its planets; and finally the Galaxy, which is a member of the Local Group.”
Use a semicolon between two related sentences when one or both of them is complex and contains one or more commas.
“The optical/UV spectra of FSRQs are characterized by the presence of prominent broad and narrow emission lines; instead, BL Lacs are dominated by continuum emission in the optical band.”
3.4 Punctuation with equations
Punctuate all equations according to their function in the sentence, whether in the running text or separated in the layout. If the equation ends its sentence, then it is followed by a period (full stop), even if separated in layout.
A colon is only used when it is the illustration of what is in the sentence and when the sentence ends after the equation or just after the explanation of the variables. Since equations are part of their sentences, there is never a colon after “as”, a verb, or a preposition, because the equation is the object of each.
“The sum is calculated as follows: A+B=C.”
“The sum is calculated as
A+B=C. Eq. (2)”
3.5 Parenthesis (brackets)
Placing additional information in parenthesis is acceptable as long as it is not done frequently. Excessive use of parenthesis in one sentence often indicates that the sentence should be split up into two sentences or more, and it is awkward to have more text in parenthesis than in the main sentence.
Likewise, placing essential information in parenthesis is counterproductive to your message, and this includes when more precise information is given there rather than in the sentence: “This percentage is high (> 40%)” is more precise, hence clearer, when written as “This percentage is higher than 40%”.
Avoid parentheses when using a comma or including it in the main sentence would suffice.
“We observed these stars for 24 hours (which did not include breaks to eat and sleep).”
“We observed these stars for 24 hours, which did not even include breaks for eating and sleeping.”
You may use the same phrase but as a second sentence in parenthesis, punctuated as
“We observed these stars for 24 hours. (This did not even include a break for eating and sleeping.)”
Avoid parenthesis within parentheses, except when it is part of a formula. This includes the year in a reference that is placed in parenthesis, where we also prefer no comma between the name and year, but do expect the period after “et al.”: (Johnson et al. 1999). When the name is in the text, only the year is placed in parenthesis. See the author information pages for more on citing in A&A.
This sign is used first and foremost to indicate a ratio and secondly to replace “or”. Using it instead to imply “and” or even “and/or” is incorrect and leads to greater ambiguity: Which of the three is really meant? In the main text of formal writing, precision requires avoiding its use altogether except for the ratio, and then if used, make certain that “or” is the only possible replacement if written out.
“This shows asymmetry between red/blue” is therefore incorrect because clearly “and” is the intended relation, not “or”. This is much too informal, note-taking style for the running text.