text:
What does "Associate Faculty" mean?
What does "Associate Faculty" mean, as used for example in this job advert headlined

FACULTY AND ASSOCIATE FACULTY POSITIONS

and this brochure from the Perimeter Institute in Canada:

In just 11 years since the Institute’s inception, PI has grown to
  include:
   - 16 full-time Faculty
   - 15 Associate Faculty

Given the adjective 'full time' above, perhaps 'Associate' just means 'part-time', but I've never heard that usage before.

Thanks Troy. I know what an associate professor is. So you're saying that under typical parlance, an associate professor is not "faculty", but only "associate faculty"? In the UK we don't have this distinction.

I used to work for some HK university as a research associate. In my case, associate means NOT permanent or tenured.

The two sense of "associate" are not related, at least in my observation in the U.S.: "associate faculty" (in dept X) may be full profs or assoc profs or assistant profs in some other department, and may or may not have tenure in that other dept. "Assoc profs" most often do have tenure (somewhere).

PI's associate faculty webpage says Perimeter Institute’s Associate Faculty members are jointly hired with a partnering university. So that's what they mean, but I think this usage is pretty non-standard in the US/Canada.

This usage of "Associate Faculty" may be fairly unique to the Perimeter Institute. They have a number of faculty with joint appointments at Canadian universities, who typically alternate between semesters with the usual teaching duties at the university and semesters at PI with no responsibilities except for research.
There is a list of such faculty here; you can see that they all have an additional affiliation outside of PI.

The Perimeter Institute may have its own idiosyncratic usage, but generically "Affiliate" and "Associate" faculty refer to faculty who have separate home departments (or universities) where their FTE line resides.
To give an example: many smaller programs such as Ethnic Studies or LGBT studies may have only one or zero FTE lines, and only consist of associate or affiliate faculty. These faculty might have their home departments in English or Sociology. From an institutional perspective, they are effectively volunteering their time into these other programs.

volunteering as in working for free?

As in, their work in the other program isn't being compensated by that other program.


text:
Is it petty to expect people to use your title in a professional setting?
As a general rule, I'm a laid back person and don't take life too seriously. So while I have a PhD, let's say, I don't wave around. (So much so that my PhD scroll hasn't been framed yet).
I work outside academia and for my job, I write governmental papers and submit to various committees. Yet despite members knowing I have a PhD, I always get referred to as "Mr" in conversations and minutes/agendas. Initially this didn't worry me but I see other staff who are PhDs as well do getting their titles acknowledged and titles seem to have 'sway', let's say.
Am I being petty to ask that official meetings/documents refer to my correct title? And what is the best way to raise this?

Let it go. I find using Dr in an academic teaching setting puts up a barrier between me and the students.

@user151413 - really, a PhD has nothing to do with academia?

@Mari153 Of course obtaining a PhD requires you to interact with academia... But whether or not you frame 'your scroll' or use your title in a non academic setting has nothing to do with academia!

@Mari153: It's not that a PhD never has anything to do with academia, it's the "I work outside academia and for my job..." (direct quote from your question) that has nothing to do with academia.

There are three basic modes of referring to people:

Formal: Mr. X, Dr. Y, Reverend Z, etc.
Full name: Andrew X, Bridget Emily Y, Cindy Z, etc.
Informal: Andy, Bridget, Cindy, etc.

It's petty to care about people using your title if people are not using title otherwise by using full names or using informal address. If everyone is calling each other "Tom" and "Suze" then demanding that they address you as "Dr. 153" is out of kilter but if people are referring to you in a formal fashion then it is entirely reasonable to expect people to use the correct form of address. The only reason for formality is politeness and correctness, and using the wrong title is impolite and incorrect. Doubly so if they're bothering for other people and not you.
Even so, making a big deal about it is probably not worth it. Ensure that your signature, email name, etc. use your formal name, and that when you're introduced that colleagues correctly identify you, perhaps gently correct from time to time. But starting a massive fight is unlikely to pay dividends.
You mention not being given your correct title in minutes, that's a good place to start. Contact the person writing up the minutes to discretely note the error, e.g. "I notice you're including people's titles in the minutes, just to make you aware: I also have a PhD."

Comments are not for extended discussion; this conversation has been moved to chat.

Outside of a university or a research institution, the only people routinely called doctor are medical doctors.  And their doctorates are MDs and DOs, professional degrees considered lower than a PhD earned through research.
If being called doctor is really important, you need a new job in academia or research where that will happen.  If you like the job you have, you will have to accept that it comes with being called Mr.  No one is disrespecting you.  They're simply behaving according to custom.
You could make a fuss and insist that people call you doctor and maybe they will.  But the most likely outcome is that they will think you're a petty and self-important asshat.  I think you should find a new job or let it go.
Added: I wrote all of that before OP clarified that other people with PhDs were getting addressed as Dr but OP was not. It wasn't about people with very different titles like Senator or General getting addressed by their titles.
It's caused me to reflect on the many times over the last 50 years in  industry and academia that I've worked on teams with some mix of PhDs and folks (like me) without.  I can only recall two places, IBM in the 70s and (now-defunct) Prime Computer in the early 80s, where people with PhDs were commonly referred to as Dr.
I think it mostly died out after that.  By the early 2000s at Microsoft, where they had lots of PhDs and lots without, I can't remember anyone being called Dr. Even at Michigan, where they had lots of PhDs and lots fewer people like me without, if someone got called Dr, it was on some kind of department press release.
Naturally, I can see why OP would feel disrespected.  But it's possible there are other reasons people do this that have nothing to do with OP.  For example, is it possible people are simply sucking up to people higher up the food chain?  Is it possible some simply aren't aware that OP also has a PhD?
Whatever the behind-the-scenes reasons this is happening, I'm going to stick to my advice, that OP could try to fix this case-by-case, perhaps by approaching people privately in their own offices (their territory) to request equal Dr treatment, starting with the worst offenders.  After one or two such requests, OP will quickly know whether this will work without creating hard feelings. If it can't be fixed, OP will need to find someplace else where they feel better respected, or get over it.

https://www.independent.co.uk/life-style/mansplaining-woman-doctor-title-arrogant-professional-name-twitter-fern-riddell-a8399076.html There's this, though.

@Allure  Hope she's happy.  She reports encountering 'mansplainers' who weren't.

I have a PhD in physics and I worked in the industry, first in research and then in a commercial role. In the research part it was understood you had a PhD so using your title was frowned upon. In my commercial role, I found that for some reason, it was better not to use it, including on business cards, as it seemed to create some kind of barrier. In fact, the only place I used the title Dr. was on booking planes. It was nice to be greeted by doctor, but I thankfully there never was a medical emergency on the plane. (this is continental Europe and UK fyi).

I would add to this answer, calling people with Doctor title is a little culture focus too. In some rare countries, people with PhD level are called Doctors and this is very important for them; and this is socially accepted and “Doctor Family Name” is a sign of etiquette. In some others, people with bachelors degrees are even called doctors.

I would agree with this answer if OP's employer didn't use doctoral titles at all (as is frequently the case). But my read of the question is that this employer does use "Dr." when referring to other PhD holders, but inexplicably does not do so for OP.

@cag51 And I'd agree with your comment if OP had answered Joel's question and said that.  But he hasn't.

@NicoleHamilton: How are you reading "Initially this didn't worry me but I see other staff do getting their titles acknowledged and titles seem to have 'sway', let's say." if not that other staff are getting their titles and others aren't.

@JackAidley Since he hasn't answered the question, I have no way of knowing.  But he mentions working with government committees.  So, maybe they have titles like General or Senator.

@NicoleHamilton It doesn't make any difference what the titles are. Either you acknowledge titles or you don't.

@JackAidley  Your opinion, not mine.  We'll have to agree to disagree.

@NicoleHamilton - sorry for late reply - different timezones This question (implied) just relates to the title of "Dr" after getting a PhD.

This seems directly contrary to my experience. In an academic setting nobody referred to colleagues as dr. something because everyone has a PhD. In an industry setting having a PhD is special and especially towards customers people would be refered to with their titles.

Nah, if you're referring to someone as   you should use the right honourific. If you're just using first names, then sure. I have no idea where you're from but what you're suggesting is certainly not custom in Europe

@Davor Aye, like I said, if you're referring to someone as their first name, then sure. What's not the case is refusing to use "Dr" in situations where you'd call people without PhDs "Mr". It's simply a matter of respect.

Outside of the university context, in formal settings, K-12 education folks with Ed.D. degrees are often called Dr.

@quarague Yes, I agree.  Titles are helpful and important with new customers because they quickly sell your credentials.  If you were consultant with a PhD, your business card would absolutely say that.  If you visited a new client with a team, you bet your teammates would call you doctor if they wanted the business.  If were at a startup looking for VC money, same deal. If you had a PhD, you'd be sure they knew.

It is not petty, but it may set you apart if it is not common in your company.

And what is the best way to raise this?

The first step is to change your email signature and your name in the IT system (chat, email...) so that it includes "Dr.". Depending on how your company is organized, it may be possible to ask HR to address you as Dr. in their communication with you (payslips and the like).
People will then gradually get used to the title "Dr." next to your name. For meeting minutes or other documents in which your name appears without Dr. and others' names appear with Dr., you can just ask the person who wrote the document:

Hey, can you add my title "Dr." to my name, to be consistent with other people's names in the document?

In conversation, it is trickier. Having your colleagues always address you as "Dr. Lastname" will create distance and may make spontaneous collaboration harder or more awkward. For example, I am in Germany (a country well known for "Dr." being an important thing and people being happy to be called that) and in my company many people are called Dr. in writing but no one wants it in speaking. It is probably a good idea to follow company culture in this case.

I think the difference is more between formal and informal. Written communication is just  formal a lot more often than oral communication. If you go to say a new customer, presenting yourself as Mr Smith and Dr Miller can be totally appropriate. If Mr Smith sends an email to Dr Miller afterwards he will probably start it with 'Hey Bob' and not with 'Dear Dr Miller'.

I feel it is important to point out that the context here is neither academia, nor business, but government, and the creation of government reports that may shape policy.
The creation of policy is a political struggle, and political struggles can be sneaky and childish. Folks will sometimes seek political advantage by referring to the experts that back their point of view as "Doctor", and those that oppose their point of view as "Ms." or "Mr.", undercutting their nominal expertise and standing to speak. It's a stupid trick of rhetoric, but that's the world you live in when you are politics adjacent. I believe this trick cropped up a number of times in hearings and reports on COVID policy over the last two years.
If you are giving formal testimony or preparing formal reports I think you absolutely want to get your qualification on the record. You also may need to stick to it when engaged with actual politicians on the job. Around the office with your co-workers, forget about it.

Very good point.

When I worked in industry, colleagues with PhDs had "Dr" on their business cards an in email signatures.  They were occasionally addressed as such by external contacts (even I was by mistake) and in paper mail auto-generated by internal systems such as payroll.
Apart from that, it was almost always first names, except where surnames were needed to disambiguate.  We normally reached that point pretty quickly when dealing with customers and suppliers as well.
Now I've got my own PhD and am in academia, titles of any kind are rarely used, except when formally introducing a speaker - even then, name and role ("Alice Jones, professor of Semiconductor Physics at...") would be a common alternative.  Outside academia I prefer not to be known as "Dr", when titles are used.  I'd rather not be confused with a medic, and it feels unnecessarily ceremonious.
This is in the UK; my understanding from the people I've met is that NZ should be pretty similar

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text:
I communicate a conjecture and a colleague/professor proves it; are we both authors?
Context: I have a (IMO, very interesting, and rather significant) mathematical conjecture. I communicated this conjecture to a professor at my university; he is a respected expert in the topic. He says he has not seen something like my conjecture before, that it is very interesting, and that he would like to share it with his close colleagues. I tell him yes, and that I have some related conjectures.
Now I'm shifting nervously on my couch wondering what will happen.
In the past, even single theorems on this topic (partitions) have been published in journals as high-roller as the Annals. My question: In the event that my conjecture is proven true (by my professor, or one of his colleagues which he sent the result to) and is sent to a journal, even if I did not majorly assist in the proof (I am a first-year undergrad student, I can only do so much!) is it reasonable to request I be listed as an author, since the conjecture is mine and I am the one who shared it?

@ssquidd OP should not necessarily be coauthor, but the conjecture should be named after them: "OP's conjecture".

I think it is quite reasonable to expect to be a co-author because without your conjecture there would be no paper at, so you basically found what to prove.

Why not just post the conjecture as a preprint?

I believe Tom Lehrer spells this  all out in "lobachevsky" : https://www.youtube.com/watch?v=UQHaGhC7C2E

@ssquidd it's not reasonable to request? Are you sure? I'm not that familiar with the norms in mathematics, but that seems fairly absurd to me.

@Nathaniel: As answers say, @ ssquidd’s assertion isn’t always true: sometimes a conjecture can warrant coauthorship. But in plenty of cases, a “conjecture” clearly isn’t a substantial contribution, and then as @ ssquid says it would be unreasonable to request co-authorship. E.g. I present my new theorem on left-abelian widgets in a seminar, someone asks “Does this work for right-abelian widgets?” and I say “yes, the proof is symmetric”; then I’d be shocked if they asked for co-authorship. (Of course with a student, it’s understandable that they may not yet know the cultural norms so well.)

@PLL here's what we know from the question: the professor said he hadn't seen a conjecture like this before and that it was very interesting, and he asked the student's permission before sharing it with colleagues. From this we can infer that the conjecture is not trivial and would quite possibly count as a contribution to the work if it leads to results. It may be that it wouldn't warrant authorship in the end, but the student could only possibly find that out by discussing it with the professor, and I think it's wrong to discourage them from bringing it up.

I think it also depends on the local university culture. At our research center, I think it would not be considered acceptable to take some one else's conjecture and publish a paper on it unless the person explicitly decides to "give the conjecture away".

Discovering a new and very interesting conjecture is a cool achievement and not an easy thing to do. Congratulations!
About your question, it’s quite possible that your having come up with the conjecture would warrant coauthorship. But it’s possible that it wouldn’t - it’s impossible to say until the conjecture actually gets proved. The issue is that for some mathematical discoveries, the mere statement of the theorem is the more difficult and substantial part of the discovery, in the sense that once the statement is known, finding the proof is not terribly difficult; whereas for other discoveries, it is finding the actual proof that is the difficult part that’s considered more impressive and worthy of recognition.
And sometimes it’s both: for some conjectures, both the people who discovered it and the people who proved it became quite famous for their respective achievements. One such example that comes to mind is the alternating sign matrix conjecture.
So, for example, if the professor and his colleagues spend the next five years working on a proof of your conjecture and come up with an amazingly complicated 100-page proof, I’d say your claim for being a coauthor is weak to nonexistent (although you should of course be credited for discovering the conjecture). But if your conjecture results in a relatively easy proof of a few pages, you can reasonably ask to be made a coauthor of the paper (or more likely than not you won’t need to ask, they’ll just offer you coauthorship as it would likely be seen as an obvious thing to do). A rather similar situation happened recently with a conjecture in linear algebra that was discovered by three physicists. They communicated their discovery to Terry Tao, and this ended with a joint publication by the four authors that was posted less than two weeks later. See this recent article from Quanta magazine.

One should also read the update at the bottom of the Quanta article for the puncline.

It seems that the fastest way to get any conjecture proved is to communicate it to Terry Tao.

@DawoodibnKareem Hmm...seems like a reasonable theory, do you have proof? Or should we pass it on to....oh

Dan Romik’s answer excellently addresses your title question.  I think it’s also elaborating on a couple of aspects of how the context you describe affects it.
Most importantly: I think the scenario you sound worried about — where the professor and/or colleagues solve the conjecture quickly and write it up, without your involvement — is extremely unlikely.  If that happened, it would be quite unethical of the professor.  If a conjecture has been publicly announced, then it’s certainly generally considered fair game for anyone to work on.  But if an interesting conjecture is communicated to you privately, especially by a student or a junior colleague, then it would be — at least — pretty bad form to work on it further without keeping the person who suggested it involved.
What I would be doing in your professor’s situation — and I think most academics would do something roughly along the lines — is something like the following:  First of all, I would try to figure out how hard the conjectures are.  Do I know them, or do I easily see that they follow from other results I know?  (Presumably not, based on the reply you received.)  If not, ask around some colleagues in case they recognise the conjectures, or see a clear relationships between them and known techniques/results; and also think a bit harder about them myself, and perhaps do a bit of literature search.  (It sounds like your prof. is at this stage.)  Depending on what I can find/figure out at this stage, then:

If someone recognises the conjecture as known, or as an obvious consequence of existing results (where “obvious” means roughly “if you show someone the results and the conjecture side by side, it’s easy to see that the conjecture follows from the results”), or, conversely, if the conjectures are false for similarly known reasons: Then I’d write back to the student to tell them, and congratulate them on (re)discovering an interesting fact, and suggest keeping in touch about research project possibilities in the future (depending on what kind of projects the department’s programme offers).  In this case, we’ve all had a fun problem to solve together, but nothing is publishable. This is honestly the most likely scenario — not just for a student suggestion, but for most questions anyone comes up with.  That’s just how research is!
If it looks like the conjectures are not obvious but are approachable using techniques within the student’s reach/background: I would suggest that the student works on this as a research project, under my or a colleague’s supervision.  (Again, this will depend partly on how “student research projects” fit into the department’s programme/curriculum.)  I’d aim to stay fairly hands-off, and giving no more guidance as the student needed.  If this goes well, it could well be publishable, with the student as first or sole author.
If it looks like the conjecture is best approached using deeper theoretical tools, beyond what the student can be expected to master in a short time-frame, but is reasonably approachable using those tools, then I might work on it myself or with colleagues, but certainly also keeping the student involved in the discussions (both to introduce them to the techniques involved, and give them the opportunity of contributing if they get up to speed enough on the techniques).  This might well result in a paper, probably including the student as an author.  (If the conjecture was interesting enough to spark such a project, then it’s most likely enough of a contribution to merit authorship.)
If I and colleagues can’t easily see how to approach the question at all, I’d congratulate the student on finding an interesting and difficult problem.  I’d keep it at the back of my mind, and if I later have an idea on how to approach it, I’d proceed as in case (2) or (3).  If it’s interesting enough, I might also mention it to colleagues further afield, and would mention that I got it from a student.  This is the only case that could reasonably lead to a solution without the student as co-author: if researchers one or two degrees removed from you hear the conjecture, see a solution, and write it up.  Hopefully, I would find out (directly or via the grapevine) that they had solved it, in which case I would suggest they at least acknowledge you by name, and possibly invite you as a co-author.  In this case, the criteria from Dan Romik’s answer for whether you deserve co-authorship or just acknowledgement would apply.

In all cases: if the conjectures are interesting and novel enough that a solution could be publishable, I would certainly make sure to keep the student in the loop about anything subsequently done with them; and I think most academics would consider it unethical if the professor didn’t do so.

Check out Beal's Conjecture.
The conjecture was formulated by an amateur mathematician named Andrew Beal who wrote to ~50 number theorists & journals. He got some responses affirming the novelty of the conjecture, and the conjecture is now named after him.
If someone proves (or disproves) the conjecture now, though, I doubt he'll be listed as the author. He'll certainly be cited, but if he's not involved in deriving the proof/counterexample, he won't be an author.

As the professor seems excited, your changes are high that you somehow get credit. I see three routes:

They will find some older source, stating (and maybe even proving) your conjecture. You don't get any further credit.
They will be able to find a proof or at least a partial proof. Then you should be co-author, as the initial idea is yours and similar as the proof, a building block of the paper.
They won't get a proof. Then you should consider to write a short paper and publish the conjecture. Then you get your name on a paper with your idea, the professor will probably help you writing, adding some flesh (citations, explaining the context, literature review) and publishing. They both of you should be author of the paper, too.

I mean if you can help prove the conjecture then it is a fair ask. I am a life-sciences researcher so I don't know a lot about maths. The more appropriate approach might be collaboration. If you can work with him and prove the theory then it's a win-win for both. Unfortunately one cannot claim authorship for merely asking the same question.

OP’s question is specific to pure math, where in fact it is not uncommon for people to get credit, including authorship, for asking a (sufficiently interesting) question.

Oooh okay. Good to know.

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text:
Lower division vs Upper division
In the United States, what is the difference between lower division and upper division in colleges and universities?

Closely related: What does “upper division” mean in the context of undergraduate classes?

"Lower division" courses are those typically taken by freshmen and sophomores (first and second year students at a typical 4-year bachelor's program).
"Upper division" courses are those typically taken by juniors and seniors (third and fourth year students at a typical 4-year bachelor's program).
Given that you've used the community college tag, it may also be relevant to point out that often community college credits are equivalent to lower-division courses and may be transferrable to a four-year school to substitute, as mentioned in answers to your previous question.
You could also possibly use the terms to group the students into 1st+2nd year and 3rd+4th year students, though these are also often referred to as "upperclassmen" and "lowerclassmen" (I'm not familiar with other gender-neutral substitutes - would appreciate an edit or comment if someone could add one).
There are not typically strong barriers to students taking upper division courses in their first two years (provided they meet necessary prereqs) or lower division courses in their second two years (especially electives outside their major).

Hm re: strong barriers, IME upper-division courses are often restricted to majors-only or majors-only for a a long time that can make them challenging to get into. One reason i didn't get a stats minor at my alma mater

@AzorAhai-him- - seems to vary. As a EE, I happily took upper level English and History courses - much nicer experience than the lower level classes, and there were no barriers to registration.

@AzorAhai-him- Yeah I would say my experience is more like Jon's. There tended to be more strict progression in sciences because of prereqs (with a lot of upper-division biology courses already requiring a year of physics and 2 years of chemistry). A lot of people majoring in those fields might have come in with pre-college credit in some of those courses so they might be ahead, but it would be harder for someone outside the major to break in. In contrast, I took upper-division courses in History of Science & Medicine that were available to me immediately.

@BryanKrause My school was famous for a PITA major system. But, I do know of similar problems in other places. Just adding info for our readers :)

Was, but still is.

@AzorAhai-him- Used to be. Still is, but used to, too. Bit of Mitch Hedberg?


text:
Maximum number of recommendation letters for assistant professor position
I am applying for faculty positions as assistant professor. I have two questions regarding recommendation letters.
(1) Is there is a limit for the number of references? For me, I have many research collaborators who I can ask them to write me a reference letter. Most of faculty positions ask for three reference. Is it a good indicator when more than 3 references sent their letters to the research committee?
(2) Is it okay to add one reference who is currently assistant professor and was my lab mate for two years? We also co-authored many papers together.

One question per post, please.

You will have to ask at the departments where you are applying. There isn’t a single worldwide standard on such things.

When reading references committee members evaluate them based on different evaluation criteria. Some place a lot of weight on the worst opinion voiced. In that respect, having more references than needed is a risky prospect. Another point to note is that you’re never 100% sure that all your referees write the most enthusiastic letter possible. For example, they have a student on the job market at the same time.
In my experience, additional letters carry little benefit and potentially expose you to a lot of risk.
While this varies widely by discipline (and by department I’d imagine), reference letters (in math/CS at least, but again YMMV) carry more weight when they’re from big shots. In that respect, a letter from a junior collaborator is not going to have as much impact, especially since this is a close collaborator who will most likely say only good things about you.

In many hiring circumstances, committees cannot and will not look at additional letters or any additional documentation that was not specifically asked for. If you send more than the required number or letters you risk having them selected at random, with additional ones tossed in the rubbish can. Your strongest and most relevant letter has a chance, then, of being thrown away.
It's not uncommon for applicants to have many possible people who could write strong references if asked. The posted application requirements are there to keep the playing field level for applicants and to not overload the hiring committee. You are not likely to benefit from going against the posted requirements. This would be an unwise risk to take.
Regarding your second question, who you ask to write your references is your choice. If that person portrays you in the strongest possible light, fine.


text:
New Journals on Springer Nature?
Springer Nature contains a large number of journals. It seems that the entry and the exit (or the archiving) of journals are dynamic.
How can I know about the recently added or new journals added to Springer Nature?

I guess they'll be happy to tell you if you ask them directly.

You can subscribe to a newsletter type of e-bulletin that will keep you informed about their new titles.

They are not offering it right now. See here.

Ok, I did not click that far. But this seems like an issue that will be dealt with in the forseeable future and once it is fixed this is a simple way to keep track of the new journals.

Thanks a lot, anyway!


text:
How to respond to journal suggestion we get a native-speaker editor when writing seems reasonable and one author is a native English speaker?
I've seen this question on suggesting someone get a native speaker to edit and check. But my situation is rather different.
Several colleagues and I wrote an article for a special volume of a journal. The initial review was R&R with some pretty severe changes requested. We've made those changes. After that we received an odd e-mail from the editor for the special volume (via her assistant -- but via subsequent e-mail confirmed to be under her direction):

We have carefully read it over, and in order to move forward, we highly recommend that you kindly consider seeking out academic editorial services in order to meet ... standards.

Then later in the message:

We recommend that authors have their manuscripts checked by an English language native speaker before final approval of their submission; this will ensure that submissions are judged at peer review exclusively on academic merit.

The publisher and journal are not known for being predatory.
As a native English speaker, I was rather surprised that the journal said this. So I reread the article and there aren't any gaping grammatical or structural issues (I actually edit papers for others who are non-native speakers in addition to my own publishing, so I'm rather accustomed to the sorts of mistakes they make).
What is a good way to respond to this request?

Edit to make clearer, I absolutely agree that part of what one should do when told find an editor is to find and get some objective checks done on the writing itself (non-author parties and other forms of third parties competent to check). My question is assuming you've cleared that hurdle and have received this sort of comment.

Perhaps ask for specifics? Is there a possibility that the journal expects a different dialect of English from the one you are used to? For example, English vs. American. Spellings, and to a lesser extent punctuation, are different.

From what you describe, this does not look like good editorial practice at this particular journal. The only thing I can think of is that some or all of the message from which you quote is "boilerplate" material, which may have been used thoughtlessly without paying attention to the revised manuscript.

I agree with @YemonChoi in that it's standard boiler plate stuff.  The journal may not have a budget to hire editors or someone to look over stuff.  So they put the onus on the authors.

I had one manuscript criticized by a reviewer for the large amount of typos, and a few examples given. They were all perfectly fine British English.

Does the quoted text come from a reviewer, an editor or the journal office? Who sent this e-mail? This seems important information, and it is missing. I am downvoting for now.

Their own first sentence is incorrectly punctuated so I'd find another journal.

Having another person read something is always valuable. We all make mistakes. Your edited-in paragraph says "to find get", for example. Not to say the journal is truly right, but perhaps there are things that you missed?

@FedericoPoloni editor's assistant for the special volume (not the regular editor). But it looks like it's clearly some sort of boilerplate.

I have received similar comments lately.  My response now is to note that grammatical and typographical errors are not exclusive to non-native speakers.  Also I remind reviewers that a name that does not sound western does not imply an author is not a native speaker; yes, this implies that the reviewer is racist!

While one should avoid antagonizing editors where possible, I think it would be reasonable for you and your coauthors to respond with a matter-of-fact email that includes the following points:
(1) one of the authors, namely yourself, is a native English speaker;
(2) said author has re-read the revised manuscript, and did not find obvious defects in the grammar or idiom;
(3) it would be greatly appreciated if the editors or the referees could point out the exact places in the revised manuscript, where it is felt that further correction is needed to meet the desired standards.
If they are being picky in good faith, point (3) should not cause a problem. If they stall or ignore point (3), then at this point it might be worth asking other people in your field or related ones if they have had similar experiences with this journal or its editors.

In #3, requesting the exact places where there are problems may be asking too much. It's much better to ask for a sample of places that are in question. As a reviewer who has written such a demand for English usage help, I always give a sample of the problems first.

I disagree with this answer, because you might be right, but you'll just get rejected with a different story. Obviously the reviewer doesn't like the English, so you should change something (rewrite for clarity). Stating that one of the authors is a native speaker is just rebutting one of the wrong assumptions the reviewer made while helping you, it doesn't do anything about the main problem (bad English).

@VonBeche It is far from clear to me that there is any bad English, and -- having refereed many articles and published quite a few myself -- it seems much more plausible, given the passages quoted by the OP, that the paragraph concerning English is part of standard boilerplate. Furthermore, if concrete instances are not given of where the English is regarded as deficient, authors have every right to ask for clarification.

@BillBarth Good point. I do think that it is important to ask for specific places or instances where improvements are sought, because this is the place where an editor or referee might reconsider, or back down. (I speak from personal experience.)

@VonBeche You suggest to the OP that he or she "... should change something (rewrite for clarity)". Let us assume that the OP knows what they are talking about when it comes to the clarity or otherwise of the article; then how can one "rewrite for clarity" without knowing what is sought? House style and referees' predilections can vary quite widely; some people seem to really care about the use of the subjunctive, while others view it as often being an archaism; some people forbid prepositions placed at the end of a sentence, despite Churchill's caustic rejoinder; and so on.

@VonBeche The comment is coming from the assistant to the editor for a special volume (based on clarifying e-mails, this is a request from the volume editor) -- rather than a comment from one of the reviewers. Didn't want to make it the focus, but assistant for the volume editor and the volume editor do not appear to be native speakers of English themselves.

In some cases reviewers have nothing to say about the content of the manuscript, so they request general language editing. In other cases the language you choose may be grammatically correct, but very distracting. I've read papers with perfect grammar, but the word choice was so bizarre that it distracted from the idea.
In this case you should:

Re-read the paper yourself - fix any problems you see (there must be some)
Have another, non-author, academic read the paper.

If your colleague could understand the work, and the language was not
distracting, then email the editor for clarification. For example "My work has been reviewed by native English speakers, and no major issues were found. Can you please elaborate on what changes you would like to see to this manuscript."
If your colleague could not understand the work, rewrite or use an editing service.

While I take your point on a certain level, for the purposes of the question, we'll make the assumption that the problem isn't with the style of my English. Do you have an answer that addresses how to respond to an off-base request that one use an editor or find a native speaker?

You should never assume there is not a style problem, that is why I recommend having one of your colleagues read your work to see if they find anything. If they see no problem, then the issue is likely with the reviewer/editor, at which point you should request clarification. A simple reply to the editor saying "My work has been reviewed by native English speakers, and no issues were found. Can you please elaborate on what changes you would like to see." I'll update the answer to be more specific.

I would also like to say that this happens to me about once every 1 - 2 years. Sometimes it is a problem with my editing, sometimes it is just a reviewer trying to find something. Having a quick peer review can usually sort out which one it is.

I'm not making the assumption in my own life. I'm just explaining that I'm not asking for advice as to how to check my writing.

I can see that you're not asking for advice on how to check your writing. However, given your situation, I think "check your writing" is a necessary step to resolving the problem you've outlined, and an independent check is probably the best way to do it. Personally, I think your best bet would be Nos. 1 and 2 in this answer, followed by No. 3 in the answer by Yemon Choi.

I completely accept one should do something like #1 and #2 when you get told "find an editor."Maybe I was insufficiently clear in my question, but I'm asking assuming one has cleared the hurdles related to doubts about the writing itself.

@virmaior You say "assuming one has cleared the hurdles".  Have you actually cleared those hurdles and have had your article looked at by a different native speaker?  (Without meaning to nit-pick, your phrase "I'm not making the assumption in my own life" in an earlier comment does not come across as one "a native speaker" would use).  If you have (and they found no problems), you should probably explicitly state this in the question (in which case the answer is they're boiler-plating or don't understand English themselves, so change journal).

@virmaior: if you've already cleared the hurdles, i.e. you've already done the thing they asked you to do, then all you can really say to them is, as Joshua indicates, "our academic editing service, who is not just me in a different hat but an actual different person, is absolutely stumped as to what problems you might be talking about". Bluntly, the fact that one of the authors is a native speaker is completely irrelevant if you have a native-speaking non-author editor already. The problem (and I don't know whose fault this is) is that neither you nor your editor is producing prose they like.

@TripeHound I'm saying for the purposes of the question, assume that hurdle is cleared. I'm not saying we won't do due diligence on that front -- just that it's completely not what I'm trying to ask about in this question.

@SteveJessop I'm sorry. My expression was not supposed to mean that we hired an editor (i.e., the thing they asked us to do). It was meant to indicate that for the purposes of the question, I'm asking what one should do taking as an assumption that the writing is not in need of a native check / edit. (Again, it's not that we won't do due diligence in checking it to make sure but that there's no question there worth asking -- any time I've ever been told to do a better job editing or get someone to look over something for style, I've done it).

@virmaior: I really think you are too hung up on this idea of a "native" check. They say it needs editing. You say it has no "gaping grammatical or structural issues". These things can both be true, because "no gaping grammatical errors" is an absurdly low threshold for a competent edit. So, OK, it's had a native check. Ignore that paragraph. Concentrate on the paragraph where they said it desperately needs a better edit.

... but if you insist that the problem is, "the journal says X about my paper, and X is false, what should I do?" then I suppose you either build a case involving independent opinions that X in fact is false, and present it to them, or else you withdraw the paper from consideration and submit elsewhere. If you believe it meets their standards for quality of prose, and they believe it doesn't, you're kind of stuck. If they really did intend to hint darkly that your text isn't even at "native speaker" level, that just shows how deep the disagreement is.

@SteveJessop your latter comment focuses precisely on what I'm asking (or intending to ask) -- journal says X about our paper and X is false where X is something that seems askance in both timing and merit.  The specific X is "consider using an editing service" spelled out as premised on the authors not including a native speaker. (Note the timing is also odd: this is after it has already been sent to reviewers 1x  and we've tried to address the issues they raised (primarily content-related but 1 or 2 structural issues) but before being sent to the reviewers again).

@SteveJessop Maybe the editors or other editorial staff have simply dropped the ball on this one. It happens from time to time

It could be that the second quotation is simply boilerplate that is sent to every submission. In particular, it is written in the abstract "We recommend that authors", rather than "you" or "the authors". The journal may find it easier to send this to everyone rather than trying to work out the native languages of the authors.
The first quotation is more direct, and may indicate that there are issues of style (perhaps relating that particular journal's house style), rather than a problem with the level of English.

This. They recommend academic editing services (because, rightly or wrongly, they think the paper badly-written). Furthermore, they recommend that the editor (or anyway someone who checks the paper) be a native English speaker.

+1.  I add that the boilerplate text could possibly have been an error.  Sometimes people may be using "copy&paste", or even clicking on a button which causes text to be added.  Or one person may have reviewed the paper, and told another typist what feedback to provide.  I'm not saying that I have strong cause to believe that an error did actually occur.  I'm saying that it's better to presume such a thing is a possibility (rather than to feel offended).

It's for a special volume of the journal, so I'm not entirely certain the person sending the e-mail would have access to all of the boilerplate they use, but it's a fair and interesting point.

This happened to me but by one of the peer-reviewers. I am a native speaker and as it happens I also have a masters in English Literature as well as a medical degree. What we did was to write a concise response to that comment which said we confirm that the manuscript has been checked by a native English speaker with a masters degree in English. We did not mention that this person was one of the authors all along. I think that the reviewer just saw non-English names in the author list and fired off that comment quickly as it's no drawback for him/her to say it and it then ensures the authors make really sure their language is up to standard.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
Why are some sources cited twice in a bibliography, once with DOI and once with arXiv?
Just to clarify what I mean, I have seen some review articles that have bibliography items like this:

Bloggs, J., "The Paper that has Been Written", The Journal Title,
  Series Number, page number(s), (year). [DOI] [arXiv link]

where both [DOI] and [arXiv link] are hyperlinks to the paper, the former to its webpage on the journal website (with which it was published), the latter to its arXiv webpage.
Does the author cite twice just in case someone is reading it who might not have access to journals? Or is there another reason?

I imagine it is the case that the authors want to make sure that readers can access the paper.

I have seen mathematics papers cited with paper publication info, DOI, Math Reviews review number, Zentralblatt review number, and ArXiv ID.

You're right that access is an issue, since many readers may not be able to download the published version.  But there's more to it than that.  For example, I prefer citations to my papers to include the arXiv link even when the published paper is freely available, since I view the arXiv version as being the primary one.  For example, I can fix typos in it or add bibliographic information (for example, for papers that were only preprints at the time of publication).  It's important to point to the official published version, but for my papers the version on the arXiv is better.

In the example quoted, the paper is only cited once. The citation includes two links to online versions of the paper.

I agree with Dave Clarke.  I think the primary purpose of a bibliography should be to offer the reader a way to read the cited material.  A version of the paper on the arXiv achieves this goal better than any other means I know.  However, it's also important that the cited material has been verified.  By citing the journal version of the paper, the author communicates that it has been.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
How to mark/cite text that you only translated?
In my thesis I included some pages of a foreign specification. To improve the reader's convenience I have translated them as they are vital to my topic and I can't paraphrase them.
How do I properly cite these five pages/mark them as not my own?

Indentation, quotation marks, italics.

For entire five pages?

Most style guides (MLA, Chicago, APA) suggest indentation as the solution for long quotations. I'm sure this could apply to translated text.

Were they reproduced with permission? Then, preface the section with a notice like, "The following section was reproduced with permission from (citation) and translated by (your initials)." If the item is in the public domain, alter your notice to include a statement about public domain. If the passage is not in the public domain and was not reproduced with permission, you have a second, copyright-related, problem.

If this section of the thesis contains only the translated passage, then it is silly to use one of the quotation notifiers. As I said in my comment, preface the whole section with a notice about the origin of the passage. Then, present the passage unaltered (except for the translation). The contents of that notice will depend on which of the following categories the original passage falls into:
Public domain
The original passage is in the public domain (for example if it was written by a government employee in the course of their normal duties or if the author released into the public domain or if the passage is old enough that any possible copyright has expired) - then say something like

The following section is was translated by (your initials) and is reproduced without any further alterations from (original source). This passage is in the public domain (rationale if possible).

Fair Use
Since a thesis is a document created in the course of obtaining an education, you can claim fair use for educational purposes. The passage represents less than the fair use maximum set for the original document (typically around 5% or less of the original work), then you can state something like

The following section is was translated by (your initials) and is reproduced without permission and without any further alterations from (original source). Since this passage represents a minimal part of the original document, it constitutes fair use.

Public License
The creator of the document could have released the document under a license that allows reuse for non-profit purposes with appropriate attribution. See Creative Commons Licenses and GNU General Public Licenses. Licenses like these generally allow you to reproduce the work if you include the appropriate statement. Make sure the license allows derivative works (because that is what your translation is).

The following section is was translated by (your initials). It is reproduced from (original source) under the  Creative Cmmons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0) License. The original copyright is held by, and all other rights are reserved by, (original copyright holder).

Express permission
If you have obtained written permission from the copyright holder to reproduce the work in your thesis, then you would state something like the following. You should include the evidence of written permission in your appendix.

The following section is was translated by (your initials). It is reproduced from (original source) with permission of the copyright holder. The original copyright is held by, and all other rights are reserved by, (original copyright holder).

None of the above
Without permission, a license, fair use, or public domain, you are violating copyright by reproducing the passage, even if you translated it (translations count as derivative works, which are still a no-no). Get the appropriate permissions or reduce the length of the passage so that it becomes fair use and see above.
US Copyright
Note that this answer primarily to US Copyright Law, with which I am most familiar. The copyright laws in other nations, as well as international copyright law, will vary, but many have similar provisions. However, some parts of my answer will be inapplicable in some countries. In these cases, behave as if the material is copyrighted. The concepts of public domain, copyright, and license are fairly similar in most places. Generally, the existence of a license supersedes copyright, with the exception that a license cannot supersede the public domain status of a work. Fair use may not exist in all jurisdictions. If you are unsure whether your nation has a fair use or similar exception in its copyright law, act as if it doesn't. Better safe than sorry.

The advice regarding "fair use" above appears to have been written from a US perspective. Other countries have similar provisions. In the UK it is referred to as "fair dealing". Note that the conditions for the use of copyrighted material for educational purposes may vary between jurisdictions.

I agree. I will update my answer.

You say "Make sure the license allows derivative works" and then give an example of a "NoDerivs" license. Is this intentional?


text:
How should a job title be translated?
When you introduce yourself to an international audience and come from an non-US system, there always is an awkward moment of translating your job title into a form recognizable by the people you introduce yourself to. Here are the options I see:

using the title in your native language: completely honest, but probably not understandable by anyone who does not know the system
replacing it by the closest US title: complete localization, completely understandable, but some nuance in the function might be lost
translating in a literal way: something in-between

I'll give a specific example here (from my own system, the French one). CNRS is a research-performing organization, in which permanent researchers hold the title of chargé de recherche (junior staff) or directeur de recherche (senior staff). I usually see these titles translated into “research scientist” and “research director”, but I those terms aren’t really self-explanatory. In particular, I don't think it's clear from “research scientist” that this is a permanent position, because that term could also be used in other places for post-docs.

What sort of situation are you introducing yourself in? Is it at the start of a talk, for example, or something more formal, like a job interview?

I am not a big fan of using titles. What is wrong with "I work at CNRS" or "I am a researcher at "CNRS"?

@DanielE.Shub: One item would be if someone wants to introduce you at a departmental seminar. Normally, they'll want to say "X is a Y at Z."

There's no single right answer here. You should provide the information that you think is most salient in the given situation. In your case, you probably want to say something like "tenured research scientist" or "staff scientist," as those terms normally give the idea of permanence in a way that "research scientist" or "research associate" might not.
If you are writing a CV in English, on the other hand, you could write "Junior research staff (permanent position)," as that gets your title more accurately. In this circumstance, it's probably better to go with a literal translation (or as Federico Poloni suggests in a comment below, the job title in the original language) plus explanation, rather than try to find the "closest equivalent."

Seconded, but I'd go with original French + explanation instead. This will be more helpful than a botched-up translation to both native speakers and people that try to get more information through a search engine.

Literal translation may be very misleading. For example, part time lecturers in Spain are called "professor associat" in Catalan or "profesor asociado" in Spanish. Literal translation of that title as "associate professor" would be very uninformative, since associate professors in other countries are full time senior faculty. To make things worse, protocol rules in the University of Barcelona used to state that in formal events the title "professor" should be used for teaching staff members who are not doctors, just making "professor" a lower title than "doctor", which is just the opposite of the usage in English speaking countries.
Therefore, I would not use literal translations. If I would need to be very precise about my role (for example, in a CV) I would give my official title name in its original language and a short explanation of what it means, for example with the rough equivalent in the destination language. However, in most situations we don't need to bother the audience with such details. If we are going to give a talk on any subject, the audience is supposed to be interested on what we can tell them about the subject, not about what kind of position we have, and saying which institution or department are we affiliated with may be enough.

There are two times that titles are used. One is when referring to yourself, which seems to be the case the question is focused on, and the other is when referring to someone else.
I suggest that you do not use titles when referring to yourself. If you are in a situation where you need to use titles (e.g., on a CV), then go with the correct, but possibly less informative foreign language.
When referring to someone else it is perfectly acceptable (and in my opinion good fun) to butcher the title and then give a general vague translation of it.

Personally I would translate the title as literally as possible or derive some half-translation i.e. chargé de recherche would become something like 'research manager' (one who is in charge of research) and directeur de recherche would becomre 'research director'.
This is more of an educated opinion though, as I believe that people benefit from learning small bits of other languages when applicable, and it helps to aid cultural understanding.
That's also often how borrowed words come about. Take the word 'halal' for example, it translates into English as 'lawful' or 'permissible', but it has been adopted by the English language because of its specific context when describing food. Titles are the same, they describe what people do, so they should remain as close to the original context as possible.


text:
Should my withdrawals be included on my transcripts for graduate admissions?
When I first started college out of high school I attended a university for a few months before withdrawing. I received all W's on the transcript from that school. I am now about to graduate from a different university and am applying to different graduate schools.
Do I need to send the transcripts from this first school where I received the W's or do I only send transcripts from schools where I earned credit?

This will depend on the schools that you're applying to. The best bet is going to be to call the admissions office and just ask.  Every application I've sent in has specifically stated all colleges attended, but I suspect that your mileage may vary.
House-keeping note: Welcome to Ac.SO! Your question is fairly specific to your circumstances and so would be generally frowned upon as it doesn't really adhere to the format of the site. Check out the FAQ for more information on what a good SO question looks like.
Best of luck with your applications.


text:
How to share a scientific dataset with the research community
Background:
I am a PhD student and am one step away from graduating. I have created a dataset in 3D microscopy vision, particularly 3D surface reconstruction from scanning electron microscope images, and the work has been already published in a highly respected journal. I would like to share the dataset with the research community to draw attention and possibly evaluate the contribution(s).
Question:
I am wondering what are the typical channels that scholars use to share datasets?

That's very broad - there are lots of channels. Questions that ask for recommendations for a particular resource (aka "shopping questions") are  off-topic, as are big-list questions.

I find this question pretty useful.

@Dirk: It certainly is useful, but I doubt it is a question that can have one correct answer equally valid across all fields. For example, in some fields, providing a dataset is considered a kind of a contribution of its own that warrants a particular type of article. For fields that do not have this kind of a channel, answers will be very different.

@O.R.Mapper I share your view that there is not a single correct answer. However, as the answers indicate, there are standard ways to share scientific data and even platforms that are used by many different fields. As I perceive the usage of this site, questions with answers depending on the field are usually welcome (even more if the field is specified, but also otherwise).

@O.R.Mapper From this answer I understand that questions asking "Is there a good way to do X?" (in contrast to "Can you list options for X?") should be ok here.

You may be interested in this related question on OpenData SE: http://opendata.stackexchange.com/q/980/190

It may depend on the order of magnitude of your dataset: <1 GB, [1 GB, 100 GB], [100 GB, 10 TB], >10TB.  The larger, the harder.

Although I think the first thing is to talk to your institute, and if they already have a platform or webpage to share data, use that one in the first place.
You also could use figshare, datahub, or zenodo to share your data.
Actually the OpenData SE site opened a datahub site for OpenData SE, see this question:
How do I share Open Data with others on this SE site?
Furthermore, Open Data commons has some good information on how to share data, and what licenses to use.
Also see:
How can I Share my Data Sets Without Worrying About Copyright Issues?

+1, particularly for the first point. Even when your institute does not have a service, they may have an existing agreement with a trusted third party which won't cost you anything. In addition, talk to your funder - some funding bodies maintain their own data hosting services or have existing arrangements.

For people who care about this kind of thing: Figshare is commercial, Zenodo is run by CERN and thus noncommercial (and they also have a plan about what happens with your data should they ever shut down). DataHub is in alpha as of August 2017 and seems to have an early access program going - they are run by Open Knowledge International and also seem to be noncommercial, but not geared towards scientific data specifically.

You could just host the data on your own university homepage but I would not encourage this. You can not guarantee stable a URL or long-term support. A website of your institute or a project website would be a bit better but still, long term support is not guaranteed.
You may want to check out Harvard Dataverse at https://dataverse.harvard.edu/. It seems to cover many different fields and provides dois (i.e. permanent links) which make the dataset citable.

I've would prefer ResearchGate to make datasets publicly available in addition to your publications. ResearchGate also has the option to generate a DOI for the same. This would hence also increase the visibility of your research.

There is actually an old ResearchGate question about this suggestion.

Why would you prefer ResearchGate? They have a terrible reputation for shadiness and spamming.

No.  No, no, no, no, no.  Absolutely not.  Do not post your data set on a site that spams its user base.

@JeffE: Could you explain more about the spamming, I'm intrigued to know.

ResearchGate are a commercial company with no clear method so far for making money. At some point, they're going to make a grab and try to monetise whatever you do there, and it'll be a mess; there's no guarantee that your content will remain there or remain accessible. This is leaving aside the spamming problems that Jeff alludes to.

@Andrew: no clear method so far for making money... monetise whatever you do there... no guarantee your content will remain there...; all your statements seem to be primarily opinion based. There seem to be sufficient number of researchers from various parts of the world actively participating in the RG community. I find many useful Q&As that are present there that are otherwise out of scope in StackExchange. I doubt many would agree to your claims on this matter.

@ÉbeIsaac well, let's come back to this one in ten years, if you're so confident! For the time being, I think recommending someone publish data in a commercial project with no apparent long-term preservation plan, which can limit or prevent access at any time for any reason, is somewhat naive. Yes, lots of people use it today (though probably less than they imply) - but lots of people have used other services that got closed when they didn't make any money.

@Andrew:  I agree to your last claim. Many have been closed in the past. But recent terminations  are not close-downs per se. It may even be bought by a bigger company or just turn community driven. Whatsapp was bought by Facebook; Nokia mobile was bought by Microsoft. Why leave it at that: StackExchange itself was bought by StackOverflow (check history for details). Whatever the management may be the content should remain intact.

You have also Kaggle.com where you can publish your datasets. It allows users to find and publish data sets in a web-based data-science platform. On an early post you can find more debate regarding a more specific question to it.


text:
Repetitively citing studies in a literature review
I am writing my first literature review (not using a systematic methodology) and I am trying to put some thought into the underlying structure of the literature review. I have considered these two structures:
Structure 1

Study A does this...
  Study B does that...
  Study C does this...
  My study does this...

Structure 2
In this structure, (at least early on in the review) I write about how the papers that I have gathered vary based on their collective characteristics as parts of a greater whole, e.g. general modelling approach, spatial and temporal scale, problem framing:

These studies differ based on their general modelling approach.
  These studies differ in their spatiotemporal scale.
  These studies differ in their framing of the problem.
  My study is similar in characteristic XYZ, but differs in characteristic ABC, and advances the field through characteristic EFG.

I personally think that Structure 2 is more interesting in terms of content layout and synthesis of the material relative to Structure 1, but at each point of discussion it requires me to talk about mostly the same papers, just in different contexts.
So I am concerned that repetition in Structure 2 could be a problem as compared to Structure 1.
Are my concerns justified and are there any further arguments for one of the structures?

You should definitely go with Structure 2. It is far more helpful to you (that is, it forces you to engage more deeply with the literature) and your readers (that is, it gives them a more useful review of the literature).
The article that is probably the most seminal in my field (information systems) on literature-review methodology is mostly famous because they clearly addressed precisely this distinction. Webster and Watson (2002) argued that author-centric literature reviews (your Structure 1) are not very useful. They are simply an extended bibliography. (When you think of it, all that does is little more than summarize the abstracts of each article, which are already summaries of the articles.) They argued instead for what they called a concept-centric approach to reviewing the literature.
The concept-centric approach is not quite the same as what you describe in Structure 2: what you describe, I would call a topic-centric approach. Webster and Watson’s concept-centric approach identifies the theoretical concepts in each article and then presents them as the structure of the review. Your Structure 2 identifies common topics in each article. While not as useful for developing theory as the concept-centric approach (and maybe developing theory is not your goal at all), it is far more useful than the author-centric (or more accurately, article-centric) approach of your Structure 1.
Reference
Webster, Jane, and Richard T. Watson. Analyzing the past to prepare for the future: Writing a literature review. MIS quarterly (2002): xiii-xxiii.


text:
I conceptually understand a result, but not its mathematical implementation – how can I defend using it?
There is a particular result from another author that I wanted to use in my research which is a central component to my research question (it’s an animal’s growth rate). However, deriving the results computationally requires an understanding of some areas of mathematics that neither I nor my supervisor have had training in. The nature of my work draws heavily on objects from mathematical biology, and I’ve recognized that this is a weakness in my education portfolio I intend to fill when I do my PhD.
I was making some progress in learning the math on my own, but I occasionally needed to reach out to the authors for clarification because I had nobody else I could speak with. In the end, the authors volunteered to give me their code so that I could produce their results and allow me to proceed with my research.
I find myself in the conundrum that I don’t know how to reconcile or could defend when pressed by a committee: conceptually I understand what the authors are doing, but I lack the training and time to do the computations entirely on my own. Yet I have the tool I need to continue on with my research.
I feel like this scenario is not entirely uncommon, particularly for graduate students, but I’m wondering if a reasonable defence can be formed for using another’s work (given the context above) if pressed by a committee.
I only have an analogy that I would offer as a defence if pressed today.
How can I approach this issue?

Reaching out to the authors is a good plan.

I’m definitely not shy when it comes to cold contacting, but once the initial relationship was established I didn’t want the email chain to converge to a point where I was always asking them questions - I don’t want to become their burden. I think the authors also recognized that, hence why they offered to just let me use the code they made.

Ask them to point you to resources they know of that can help you get up to speed.

It's hard to say without knowing the details, but I would challenge the view that you understand the mathematical tools/concept if you cannot actually manipulate them (not having time/energy to re-derive them is another issue). That said, it's often fine in most field to not really understand some of the tools used.

When it comes to applying mathematical results, it is the norm that you do not understand all the nuts and bolts of what you are applying. This is nothing to be ashamed of. Instead, it’s the only way that modern science can work – it is too vast and intertwined to be understood in its entirety by one person. The crucial part is that there is a clear interface between theory and application where everything is communicated clearly.
To give an illustrative example: I recently wrote a paper where I derive some rules for building ecological models from basic principles. I did my best to describe said principles as well as the rules and their consequences so that those applying my work can use them. However, I expect that the vast majority of my readership cannot understand the mathematical proofs that go in between. I must expect that they treat this as a black box. On the other hand, in order to perform my proofs, I in turn relied on theorems whose proofs I did not understand.
Mathematical theorems are great interfaces. They give you some statement of the form: “If X, then Y.” You only need to understand the statements X and Y, but you do not understand why one implies the other. That’s what mathematicians are for. On the other hand, the mathematicians who proved the theorems I use have no particular expertise in ecology as far as I know.
Now, there may not always be a clear interface. In that case, I suggest to create one yourself (and not only for yourself but also for your readers): Write a passage for your thesis that describes what you understand and need the tool to do. Then back up everything with references from the relevant publications and documentation. If necessary, ask the authors again.

I really appreciate that analogy with theorems. Gonna keep that one in my back pocket for a rainy day.

(Good) Mathematicians themselves don't always understand the proofs of results they rely on.  Some things are above one's weight class; a deep result relying on complex abstract nonsense and crossing across multiple fields may be very difficult for most people to grasp, but still relatively easy to utilize, as you describe.

@zibadawatimmy: I wouldn’t use the term nonsense here. If it’s nonsense, you obviously should not rely on it.

@Wrzlprmft "Abstract nonsense" is a term in the mathematical community conveying the highest respect for difficulty and achievement, actually. Loosely speaking it refers to a high level of mastery/deployment of categorical concepts (often to achieve potent results in non-categorical fields/contexts). The proof can can be quick and concise (see the example on the link), but the density of the information content quite high, and it can be very difficult to see the "abstract nonsense" solution without having already been given it.

@zibadawatimmy: I see. Mathematicians really have a talent for unfortunate terminology.

@Wrzlprmft It was originally used as a self-deprecating term, but quickly got repurposed as slang for categorical arguments.  As category theory is the pinnacle of most of modern mathematics, both in complexity and utility, the utilization and mastery of such arguments is currently a highly valued skilled.  The subject matter is indeed very abstract, as category theory generalizes huge swathes of mathematics and subsequently provides fertile ground for connections between seemingly disparate areas. It can thus seem like nonsense to those unaccustomed to it.

@Aksakalalmostsurelybinary: Well, I am only almost a mathematician, so that’s okay. In general, at some point you cannot understand the methods you are applying all the way down, because that would take more than a lifetime.

@Aksakal: Your example was a mathematician using mathematics theorems that they don't understand. – My example was literally me. — generally mathematicians can follow the proofs of almost everything they use – Depends on your scope of can here. I guess if I invest a week, I can understand the proofs of the theorem in question. I strongly doubt that it would be worth the effort though. I also strongly doubt that other researchers on a similar appliedness level (many of which are mathematicians) do this.

@Aksakal: if you're using the results from your own field, you better be able to understand them too – What do field borders (wherever they may be) have to do with this? There are several fields out there which are so vast on their own that this is impossible and I am pretty confident that this also applies to mathematics.

@Wrzlprmft, ok, I'll remove my previous comments after clarifications you gave

@Wrzlprmft: At least "abstract nonsense" conveys a roughly correct impression to another mathematician. "Monstrous moonshine" does not even do that.

Imho what matters is whether understanding the theoretical background is crucial for your own research: for instance if your research focuses on analyzing the outcome of this system in a new context, then you're just using this system as a tool in your research. Obviously it's always better to understand the tools you use very well, but you probably don't need to be able to re-implement their tool for using it correctly. On the other hand if your research goal is for instance to modify this system for a new application, then clearly you must acquire an in-depth understanding of it.

If I understand correctly, you have a problem which is described in a mathematical model. You need to solve this model for some conditions and what you care about are the results.
If so, you do not need to understand how the calculations will be done, you can treat is as a black box. The same way as you do not need to understand assembler when using Python pandas.
There is however a very important thing you must understand: the conditions/limitations of the numerical recipe you will be using. You can have 20 methods to solve one problem (say, a differential equation) but some of them will be better, worse, unusable or plain wrong for that specific equation.
You can say: "I used method ABC to solve the equation in the model because it is a stiff equation and this and that. This allowed me to get a results with 10% precision in a reasonable time".
You do not need to explain how that method works (if you have no love for these methods, they are horribly complicated), but you must show you understand the limitations and therefore the implications on the result.