APS House Style :: Punctuation
Use commas only when breaks are needed for readability or to avoid confusion or misinterpretation.
APS style requires the use of the series comma.
To separate elements (words, phrases, or clauses) of a simple series of more than two. If any of the elements contain internal punctuation, then separate them with semicolons.
To set off an introductory clause beginning with a subordinating conjunction (e.g., "if," "although," "because," "when," or "since") or an introductory phrase ("To accomplish the task, we…") or participial phrase ("Using hippocampal slices from adult rats, we…"). Beware the dangling participle! For example, you may see "After performing the experiments, the rats returned to their cages…" This is both 1) humorous (well, to copy editors) and 2) a mistake that authors make frequently and should be corrected.
To set off a conjunctive adverb (e.g., "therefore," "still," "however," "accordingly," "moreover," "nevertheless," or "consequently") or a transitional phrase (e.g., "by comparison," "in contrast," "on the other hand," or "in fact") that introduces a distinct break in the continuity of thought.
To separate a separate phrase associated with the subject from the rest of the sentence. For example, "Raymond Turner, a biologist, described the species."
To replace the use of en-dashes within a sentence.
Before or after the word "respectively," depending on where it falls within the sentence.
After "i.e." ("that is") and "e.g." ("for example"), whether abbreviated or expanded.
After multiple adjectives modifying the same noun. For example: "monosynaptic, excitatory linkage" or "binocular, optokinetic stimulation."
Between superscripted letters in tables (but not between the * † ‡ § symbols).
To set off contrasted or antithetical phrases or clauses. For example, "the greater the risks, the more gratifying will be the results" or "…had an effect with A, not with B."
Before the word "and" when it connects two parallel elements, e.g., subjects, verbs, phrases, or dependent clauses. This is a frequent comma error. For example, change
I flew up into the air, and hovered like an insane butterfly.
to
I flew up into the air and hovered like an insane butterfly.
Before the phrase "compared with."
After the abbreviation "cf." ("compare").
After an introductory phrase directly referring to the subject. For example, "The GABAA receptor agonist muscimol did not influence the response of WDR neurons in normal or allodynic animals."
To separate two complete sentences joined by a conjunctive adverb (e.g., "however") rather than a coordinating conjunction. In this case, a semicolon should be used instead. The following sentence is an example: "We did not find that rats responded to the first drug; however, the second drug produced strong reaction."
A note on "which" versus "that." This is very common misunderstanding made by authors. Phrases beginning with "that" are restrictive clauses; they modify and describe the subject of the sentence and usually flow within the sentence. Phrases beginning with "which" are nonrestrictive clauses; they modify a noun that is not the subject and are set out by commas within or at the end of a sentence. Frequently, authors use "which" for both restrictive and nonrestrictive clauses; change "which" to "that" (or vice versa) when necessary.
Examples of "that" sentences:
The setup that we used in the experiment was very complex.
Animals that ate a high-fiber diet were more active and less irritable.
Examples of "which" sentences:
Rats were fasted for 4 h before each experiment, which was sufficient time to establish a steady state.
The animals, which had been fasted overnight, were then injected with 50 ml saline.
A note on "while" versus "although" versus "whereas." This is a complex one to explain. Basically, authors use the word "while" to denote several different things that should not be clumped together. The term "while" should only be used to denote that two separate processes are going on at the same time, i.e., "We applied the truth serum while the subject was questioned."
The term "although" denotes that two facts are being discussed in context with each other; if you can mentally substitute the phrases "Despite the fact that" or "Even though" in place of an introductory "While," then chances are the author really means "Although." For example, in the sentence "While other authors have found these results, the exact processes relating to these interactions were not investigated," the "while" is erroneous and should be "although."
"Whereas" is used to denote two conflicting statements, and the word "whereas" is preceded by a comma within a sentence. It can be used interchangeably with "although," but the use of "whereas" is most commonly used when conflicting results are presented. For example, "We found that control animals were really calm, whereas treated animals were spazzy" is a typical sentence illustrating the use of "whereas."