text:
Using photos obtained from academic homepages in an ack. section in a public virtual event
I will be giving a talk in a virtual event and it will be recorded and uploaded on YouTube. I wanted to thank 2 professors who helped me during the preparation of it, I like to include photos with names in the slides, these 2 professors are going to be there at the event. It looks weird to ask them before the event, "can I use your photo in the ack. section of my talk?"
How to ask them for their consent in such a case?
The photos I used are on their public academic account.

Name a field? In mine people don't ask  - that's what public pictures are for

Why does it look weird to ask them? I don’t see what’s weird about it.

Maths @AzorAhai-him-

FWIW, the professors probably do not hold the copyrights of those photos, but whoever took the photos does. So, from a legal perspective, they may not even be the right people to ask.

Usually, you are free to thank whomever you want to thank. An exception would be a passive-aggressive thank you that is not meant as a thank you but as a reprimand. Including people's pictures is quite common when mentioning people in a talk, whether you thank them or just mention them for their contribution to the field. As this is academic use and the pictures are on their respective sites to represent them to the world (and thus are approved by them), copyright issues do not need to concern you. Thus, you can go ahead without asking.
If you are asking, which is not quite as awkward as you make it out to be, you actually put them into a small bit of a quandary. If they say yes, they might feel that they are self-promoting. If they say no, they seem to be pricks. I personally would not ask, but just use the photos and stop overthinking this issue.

copyright issues do not need to concern you – It is not that simple: The default copyright holder of a portrait is the photographer, not the subject. The photographer probably has not completely transferred the copyright to the professors (if that is even possible in the respective legislation) – most often, there is no written agreement about this whatsoever. And even than, just that the professors post the picture on their website doesn’t mean that it’s free to use in this context (whether this is an academic use is disputable: you are not discussing their photos scientifically). […]

[…] Mind that I am not saying, that you cannot make a good argument why copyright is not violated here or at least that one does not have to fear being successfully sued, but it’s not as simple as you depict.


text:
Missed the application deadline for a TA job. Should I contact them?
I missed the application deadline for a TA job by a day.
How should I contact the hiring committee while still looking professional and not make it awkward for anyone? Any suggestions?
The reason behind missing it is that I discovered it shortly before the deadline.

To answer the question in the title: there is no harm in contacting them in a humble and professional way to ask if they would accept a late application.
Whether they will is likely to depend on the rules of their institution (they may not be allowed to) and on whether they have good candidates already.
For the question in the body, of how to ask, this advice largely applies: be short and to the point.
Don't forget to mention why you are late. Try to contact an academic rather than HR if you can, eg if the job ad has "contact Dr Smith for informal enquiries" or similar, or if you know somebody involved in the process.

I would immediately apply, provided any application system is still active, and also contact them directly asking for consideration. If the system is now closed, I'd provide the material necessary for the application in the request for consideration.
Whether this is successful or not may depend on rules, as Flyto states, but it might depend more on whether they application pool is over or under subscribed. Universities need a certain number of TAs to manage the undergraduate program in many fields. In math it is a lot of people and things get hard to manage if there are too few.
It is probably enough to present your case as you do here. It is worth the effort and not applying or requesting an exception wins you nothing.
If your application to the doctoral (I assume) program is strong, they might be especially interested in making exceptions, budget permitting.

I strongly second the "immediately" part. It's not a question of etiquette; it's a question of whether there are still positions available. (And even as far as etiquette is concerned, telling them now while they still have time to process the applications is more polite than the most carefully worded message you might deliver when they're almost done.)

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text:
Can I get feedback on my dissertation from my lecturer before handing it in?
I'll be honest here I'm terrified by the idea of my final major project. I was wondering if it's acceptable or common practice to get feedback from my supervisor (lecturer) on my dissertation prior to submitting as I go along?
I'm from the U.K. if that helps.

Who will be grading the project?

Confused. What are you talking about? A dissertation is usually a major project to get a degree which your advisor should be involved in heavily.

@Azor Could be a final project for a master in the UK, something like a journal-club type paper.

@user What do you mean? IME "journal club" means people meet and discuss articles of interest. No theses or dissertations

Depends on the uni and institution. But generally, a lecturer will give general feedback, sometimes even detailed, on your work. How else would one learn? Why don't you ask them?

@Azor Guess I don't know much about clubs. What I meant was some kind of essay on a paper, a set of papers, or a topic.

Students at any level working on big projects learn best and produce better work when they confer frequently with advisors (and fellow students). Sharing drafts is crucial. It's how you reduce the terror you feel. Submitting a final product when you've seen no feedback courts disaster.
That said, I've no idea whether your advisor or institution allows, requires or forbids this in your particular case.

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text:
Is it ethical/acceptable to take courses for the sole purpose of getting a reference letter?
I am interested in going back for my masters.  While I have been accepted by a masters program (quite a while ago) previously, I am looking at another university and require a fresh set of references.  I have lost track of my previous advisors and am unable to get work references.
So I need to prove myself at this point to somebody.  There are some optional courses in the undergrad that I am interested in, but to be honest I could just read the textbook and save some money.
So:
Is it ethical/acceptable to take courses for the sole purpose of getting a reference letter?
and
Should I inform the prof before taking the class of my intent if this is a gray area?
Note:  I know that it is still the prof's choice if I get a letter and this method is nowhere near ideal.  Just the best I could come up with.

Students have lots of reasons for taking courses and I don't think I want to be in the business of telling students that there are right and wrong reasons to take a class. I certainly think it's a good idea for prospective PhD students to think about who might be good letter writers early on in their program and to make sure they work with some of them — not doing so can make the academic job market very difficult. I don't see this as being substantively different. If you take the class, do well, and then ask for a letter, you might get a good one. Or you might not. So I'd say go ahead.
That said, there is something very mercenary about the way you have phrased your question that makes me skeptical. Do you really think that working with faculty wouldn't teach you anything? If it's true that the only reason you want to take a class is because of the letter you might get, something seems off. Maybe your interests are different enough from the professor's that I'm skeptical that this person would be such a great letter writer for what you want to do.
Being able to excel in a Masters program means not resenting the idea that you may have to learn from professors when you could "just read the book." I think it's OK to take a class for a recommendation but you should use this as opportunity to learn something you are passionate about in ways you could not with just the textbook.
Talk to the professor. Let them know you are an advanced and passionate student. Get feedback on your work. Go beyond what is just in the book. If you do that, you will get more than you would otherwise. In the process, you will also earn a much stronger letter. If you can't get over that hump, I suspect that your recommendations — and your experience in grad school — will underwhelm.

My apologizes for the "mercenary".  My classes to this point have been limited by my peers and administration.  I found when I when I wanted to start a more interesting conversation it would be me, the prof and the rest of the class who didn't do the reading.  My interaction time (after class) with profs has been invaluable.  It just has been a rare instance where would get beyond initial topics and finish the book and get a point where the prof could be valuable.  This is a new university, if I get a C and learn something and miss my chance for a reference this would still be a success.

If the quality of your work surpasses those of your peers and you end up resorting to after-class conversations with the professors to push beyond what's on the syllabus, this is not a bad thing! It means you're passionate and learning! As a happy side effect, it probably means you'll get a good letter that reflects this.

@DarkSheep I received excellent letters of recommendation from professors whose classes I was required to take, even though I’d long-since mastered the material. Why? Precisely because I stayed late to speak with the professors, to get something meaningful to me from the class, and I tried to be helpful and useful to the professor in class (in one I effectively became TA for the class I was supposedly in, in another I was assigned to a group of struggling students for the big group project, and impressed the prof by helping them rather than just doing it all myself).

If you take a class for the express purpose of getting a letter, are you sure the class is to your interests ? If it isn't, and you aren't good at the material, you're not going to get a letter (or worse, you'll get a tepid letter).
If on the other hand you're taking the class because you like the material AND you hope that you can impress the professor enough to get a letter, then that's perfectly normal.

This is a completely personal decision. Is it ethical? Sure. People audit courses for all kinds of reasons.  You're not the first person that has needed to get references so if you want to do that then just make sure that you're ready to give that course 110% to ensure that you get a 'good' reference.
There is, however, another implied question in your post: 'If I just go back for one class to get a reference will it have any value?'.  Again, this is highly subjective.
(and here is why I didn't flag this question as being off topic)
Your references should provide the admissions board with enough relevant information about your work, accomplishments, intellect, and character, to support your admission to the program.  Taking one class, after a long academic absence, does not provide any frame of reference for your professor to make these types of assertions about you.  You may find it better to solicit references from managers or people that you've done research with.  Those people have the context to make a legitimate assessment of you and your work.
At the very least you should consider how your references support each other.  If you need to have an academic reference and you don't have access to your previous references then taking a class to get one should be fine, just don't forget to support that as appropriate.

Absolutely, this is ethical.
Life is about proving yourself, and if you want to take a challenge to make a statement, there is nothing unethical about it.
I would absolutely go ahead.
The purpose of a reference letter is for someone to make a character or professional evaluation of an individual.  The reason as to why the individual needs the evaluation should not make a difference.

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text:
Should a professor discuss his/her reviews (given by students) in class?
The question is inspired by this image posted on reddit. Would this be considered a constructive step towards improving the interaction with students and the teaching in general? To clarify, I am talking about the reviews that the department or college solicits from students towards the end of the course, aka student feedback.

Maybe you want to elaborate this question. I may be slow, but from these two sentences and the image, I cannot put to gather what you are asking. What kind of reviews are you talking about / what subject? Is it a "should" in the question, or a "can", or a "is it good idea" or ..? Also, "improving teaching in general" is one of the vaguest goal you can set ..

I have clarified my question.

Thanks. It may also raise ethical questions. My understanding is that reviews are in principle anonymous, therefore if one discusses review eg with the same class, it is inevitable that some info slip out from the reaction of the students. On the other hand, in general if someone address student feedback and open to discussion about criticism, I think it is a good practice (we are talking about higher education level, and discussion doesn't mean automatic surrender to "we want easier exams" voices ).

Are you talking about discussing reviews from previous semesters? At most places, you don't get the student evaluations until after grades are posted.

When I was teaching at a German university and we received course feedback, we were required to inform the students about the feedback. So while the feedback was anonymously given by each student (online), the students should get general feedback on how the course was evaluated. For some that meant simply sending the questionnaire summary to the students, but many discussed the evaluation in the last lecture.
For me it made sense to discuss the results:

You get an opportunity to thank the students for positive feedback.
You get an opportunity to clarify contradicting or unclear feedback (e.g., talks to fast vs. talks to slow).
You can also address 'below the belt' feedback. I think you can say anything if you do it with respect. And giving feedback -- even highly critical feedback -- with respect is something that students should learn, if only to prevent huge problems in the future where a lack of respect is ... less tolerated.
You can show students how to constructively deal with feedback (if you can deal with feedback). I think you should both take the feedback serious and add some humor (i.e., take yourself lightly but the job seriously). Otherwise, you are not only alienating the current students but also future students.
You can get feedback in the very last lecture. In some courses, the feedback was requested during the phase with the highest stress levels. Students only saw what they had learned and how they had benefited later.

Your question is still rather vague, but it depends upon the manner in which one approaches the topic.  The point is to make oneself inviting about student concerns rather than scaring them off.
It can helpful to show/mention some previous reviews at the start of a course to point out that there are certain issues the instructor is aware of and wants to avoid them being a problem.  For instance (from your linked image), the instructor may say something "Based on reviews, I know I sometimes get excited and talk too fast, so if you notice I start speaking too fast, please let me know."
I think once students know the instructor is aware of such issues and wants to address helps turn internal complaints (for students) or worries (for instructors) into productive conversations.  Discussing reviews can also be used as an opportunity to point out and correct common misconceptions of students.

Yes, though in my opinion the item about a classroom mass shooting is wildly inappropriate in today's sad climate.

I wonder whether it made sense in that class -- by which I mean it was actually seen and understood as humor. Reminds me a bit of this article: http://mu-warrior.blogspot.de/2014/01/marquette-professor-makes-flippant.html and how things can seem "inappropriate" from the outside when not knowing the lecturer and the class dynamics.

@DanielWessel If the end result of making a joke like this is the university telling you you can't teach but we'll still pay you, that's not a lot of motivation not to do it.

@Kimball I don't know. Working (or being paid by the university) but not being allowed to teach would be devastating for those people who love to teach. And frankly, if that prof has a more hands-on approach and does not shield the students from the ugly facts of life outside the safe campus bounds (and shows how to deal with them via humor), it's also a loss for the majority of students (who actually want to succeed later).

@DanielWessel That was tongue-in-cheek, but does represent my attitude to academia's tendency to reward people with greater responsibilities and punish people by taking away responsibilities.  Though I believe preventing professors from teaching (without termination) is usually a temporary punishment, for at most a few years.

@Kimball I guess the correct reply by a professor removed from teaching would be to loudly state: "Oh, joy. Now I finally have the time to write a blog." (If you thought I could damage in class, wait what I can do with an international audience.) ;-) Ah, this could lead to problems too: http://www.campusreform.org/?ID=6264

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text:
What does it mean "a dissertation submitted in partial satisfaction"?
It appears in thesis, e.g. "A dissertation submitted in partial satisfaction
of the requirements for the degree Doctor of Philosophy in Mathematics".
Does it mean the thesis is OK for a Ph.D, just some reviewers have comments? or does it mean that it's not good enough for Ph.D, and although the one summits it will not continue to work on the thesis, but still decide to submit it for, i don't know, archiving?

This is a standard bit of text that means that the dissertation is submitted towards one of the requirements for the PhD degree. There are other requirements (e.g. coursework, oral defense), so the dissertation alone is not enough to earn the degree.
It says nothing about the quality of the dissertation.


text:
Is it frowned upon to have a figure in the introduction of a Masters thesis?
Is it common practise/frowned upon to have a figure in the introduction chapter of a thesis?
The figure is not a 'picture', but a relatively small tree diagram that in my opinion shows the structure I am talking about more effectively than describing it in words.
I ask this question because I do not think it is common practise but also can't think of a good reason not to do it.

What does the style guide say? What did your supervisors say? What have recent theses in your department done?

Hi. i understand that these things often dictate what is allowed/not allowed. But at the end of the day it is my thesis that i need to feel proud about. My study leader clearly told me that all his guidelines are just that, and at the end of the day I decide what my thesis looks like. That may seem counter-intuitive as i asked the question here, but I was simply hoping to find other peoples view on the subject (-:

OK, but this isn't the place to solicit opinions.

I am sorry but I can literally not think of a more valid platform to ask such a question.

Whatever you do, don't do this :-)

@TobiaTesan: Maybe I'm misunderstanding something about the blogpost, but I'd have expected to find the images pointed out in the blogpost in the actual linked publications (as a "teaser image" maybe, or whatever "graphical abstract" is supposed to mean)? I opened a few of the papers from ScienceDirect, but none contained any of the graphics shown in the blogpost. Thus, it's not quite clear to me what "don't do this" actually suggests not to do.

@QRMapper: the images have since been removed by the publisher as a result of the controversy sparked, so that's probably why you don't see them in a freshly downloaded copy.

If a graphic clearly gets across the message then why not use it? Just check what the regulations specify though,
To elaborate a bit more you need to think about what the introduction is for. If it is  intended as an executive summary then a diagram that summarises the work could be very effective. If however it is setting the context of the work then I find it difficult to see how a diagram would help.

Having a figure in an introduction is a common practice, and one that I strongly recommend.  Images are very good at conveying some ideas and relationships, and are also good for catching the eye and helping pick out key elements of a document (i.e., the things the author thinks are important enough to illustrate).  There is nothing special about an introduction that means it should be image-free, especially in a thesis where there is a whole chapter dedicated to it.
Yes, some people do not put figures in their introductions.  Indeed, some people don't put any figures in their scientific writing, and I really hate reading the documents that they produce.


text:
Proper way to format computer code included in a thesis/dissertation
I intend to include my computational model code(s) in its entirety as an appendix in my dissertation.  I've gone through my university's formatting guidelines and haven't seen anything on the proper way to format the code in terms of size of font, text-wrapping, spacing, and so forth.  What's the best way to do this?
When I read code, while I'd want it to be a typical font size (12 pt), I'd also want the text-wrapping to be minimal, but given the traditional margin requirements, it can be pretty tough to accomplish this.  Having code trail off one line and onto the next is generally distracting.
Also, although comments in code are prevented from execution by using a character sequence like %or // or (* many compilers color-code this text to make it more easily distinguishable from executable portions of the code.  Is there any way to easily make comments distinguishable when putting the code into the text of your thesis/dissertation?

What text processing program are you using?

@DavidZwicker MS Office '08 Mac

@leonardo I checked the university guidelines and there was nothing on code formatting.  Advisor/committee members have no suggestions on this.

a monospaced font...is best to use for readability — [citation needed]!

Are you sure you need to "... include my computational model code(s) in its entirety as an appendix". Consider that, it's not read by many it would be; a) a waste of your money for the extra pages, and b) wasteful of paper. Maybe you can isolate the interesting bits and pieces only?

@JeffE For fixed-form codes, monospaced font is a practical necessity. I admit I sometimes write Matlab code in sans serif, but that's because it is free-form. Anything indentation-sensitive or with large, hard-coded numerical arrays is much easier in monospaced font. And in dead-tree format, when it's hard to count the column numbers, a non-monospaced font could cause ambiguity in indentation-sensitive code. Reference: the practical experience of my forebears.

@JeffE If you click on the word "monospaced", it was linked to the SE question/answer where I found that info.

I understand that typesetting code in a monospaced font is a common convention.  I'm disputing your claim that that convention increases readability.  @Moriarty: Consistent, readable indentation and array alignment does not require a monospaced font.

@JeffE I understand your point, and am willing to edit my post accordingly to add a citation, or remove the monospaced paragraph completely.  However, my main question was not about the font per se, but the font-size and text-wrapping.  Also, line indentation, font color or shading for comments, and the like.  Given your background and expertise, I would be very interested in your thoughts on this, especially since I am not in CS at all and my understanding of coding convention, formatting and archiving.  Thanks!

@posdef I've been asked by my advisor and dept head to include the code in an appendix in its entirety (even support files), even though they themselves (nor the college or university) had no suggestions on proper formatting for it.

@iwantmyphd i see... Well, I hope you find a satisfactory answer in that case, unfortunately I have no idea if there is a standard way to include that much code. :)

Put it on Github or your personal site or whatever and include a link to it in the thesis.

Might it be better to host it on a repository such as Github and provide a link to it in your thesis? That way, people reading the code would have many of the advantages of repositories (e.g. searching for files, syntax highlighting etc.)

In the bounty text you refer to "inconsistent indentation" and "commenting convention." Indentation and commenting conventions should be covered by the style guide for whatever language your code is in, regardless of what font face or size you use.

@ff524 And the style guides you refer to are exactly what I am looking for.  One code is MatLab, another is C, a third is Mathematica and a fourth G-Code (for CNC machines).

Those have nothing to do with thesis, though. See e.g. C style guides (pick your favorite), MATLAB style guide

There are a number of excellent LaTeX packages for typesetting code, made for just such occasions.  The listings package is one good example, which includes standardized formatting for a number of languages.
It does not provide a "definitive" way to typeset code (there is no such, since there are a number of competing conventions) but its defaults provide a standard and well-recognized formatting that is entirely appropriate for academic publications. Furthermore, it can be customized to follow any unusual requirements of your institutions thesis format.

Monospaced with syntax coloring and an appropriate description, see e.g.

from Appendix B of arXiv:1407.2432.

How is this typeset? By means of a LaTeX package like listing?

@EnthusiasticStudent You can lookup its source. I see knitrout environment, though I cannot spot a relevant package. So it seems that it is an export from knitr rather than hand-written LaTeX.

I would suggest a monospaced font, because that is the traditional method of displaying code. As a matter of putting all of your code into the appendix, I don't see why. Snippets of the relevant parts would be all you need. If you still feel the urge to include the full code, I would suggest referencing a link to the code through a Github repository instead of all of your code.
In addition, ask your advisor who the audience is. Do they have a background in programming? That would be the question to ask. If not, summarize the code, and walk the reader through the logical process of the code. Perhaps a flowchart would be useful.

If you aren't required to do it in a particular format, I'd recommend publishing the code online and using a nice LaTeX code formatting package for the parts you want to share in the print version. My personal favorite is minted . Very easy to use, beautiful formatting and coloring and no need to copy and paste anything, just use the \inputminted command.

I would argue that there are no real style guidelines, except maybe (the only one I've ever been given) not to drown your audience in lines of code, thus use excerpts and pseudo-code whenever possible.
However, to still put your code full-length on paper, you pretty much should have it readable on-screen already. You might have a little refactoring to do, if you expect people to actually read it.

Fixed font size are traditional in source code, which is due according to Joel Spolsky to it being easier to edit (say click on a specific letter) and to distinguish typos (e.g. rn/m vs rn/m) than when using a variable spaced fonts
A fixed width so you never scroll horizontally while your code is on screen. This, with a correct font size, will take care of line wrapping when on paper.
Modular code, so people know where (in which file, for example) they are : similarly to opening the interesting file, you want readers to be able to skip the pages of configuration, I/O and whatnot, to find wherever the core of your code is.
Be consistent, as you already noted, in all conventions: naming, indentation, comments...
include syntax Highlighting (maybe even colouring ?)

Your main options (most popular on a subjective scale of googleability) to achieve the latter are

in LaTeX, use a listing (with a language that it understands, hopefully). You can even input code from a file directly  \includecode[asm]{sched.s}
in LaTeX, use the minted package, an alternative whose code highlighting is done with Pygments
in MS Word, insert code in an embedded document as an "openDocument Text" object, copying your code from your usual IDE
in any WYSIWYG on Windows, use the NppExport plugin of Notepad++ to export your code, and then copy it into your document as RTF or HTML.
With any python interpreter, use  Pygments, e.g. :
pygmentize -f html main.c > main.c.html

The only guidelines I could find in the wild were on this random project report page, of rather small scale (4-6 pages), and they are rather succinct :

Format: Use [...] 11 point times font for the main text, and use 10 point courier font for computer code. [...]
Yes, your code should be in the appendix, monospaced, single column. You do not have to turn in all code used in your experiment; use your best judgement. You may want to include only relevent sections of code. For example, you should not include code that someone else wrote, unless you made major modifications. If your code is 100 pages, you should not print all of it. If your code is 6 pages, then you should print all of it.

The standard is to use 10 point courier font for computer code, monospaced, single column.
You do not have to turn in all code used in your experiment; use your best judgement. You may want to include only relevant sections of code.
EDIT
Usage of Courier is of my personal choice from the list of standard 10pt fonts usable for codes.

Do you have a source for this "standard"?

@ff524 Yes, I primarily use LaTeX Source Code Listing which is like the standard way of writing a Computer Science thesis, especially if you presumably have more code in it. Arial/Courier are the 10pt standards used by Carnegie for publishing thesis through PQ/UMI, my preference is to use Courier.

the best way to display the salient code of the key points of your algorithm is to write good code.
“Any fool can write code that a computer can understand. Good programmers write code that humans can understand.” -Martin Fowler, Refactoring: Improving the Design of Existing Code
the code itself should be readable with meaningful choice for variable names, sufficiently divided into meaningful functions or subroutines, and with a minimum of arguments passed around.  this means writing decent object-oriented or structured code and making objects or structures and using them.
i would split the code up into modules with a good comment on the top of the file describing what the callable functions do and who calls them.


text:
No mention of previous work = reject?
I am asked to review a paper for a fairly highly regarded conference.
The paper presents some 'novel' algorithms to do a particular job, but it fails to mention any of the various related previous work which address the very same issue.
Even if the algorithm is sound and their method is thorough I am hesitant to accept the paper, since there is no comparison to existing techniques; neither on a methodological level nor on the level of results.
Can I reject such a paper based on the non-existent comparison to related work, or should I focus more on their method and results itself?

Does it work, or does it not? And, are you competent to judge it? What is actually the question here? Is whether you should spend your tie on it? I can't see any other reason to ask us.

Would people attending the conference be reasonably expected to already know the related work, if so it may not be a good use of their time to cover it.

Just a minor point: the decision is not yours to reject or not. As a reviewer, you can only recommend.

Can you please explain what "paper for a conference" means here? There are a lot of conferences in a lot of different subjects and none of them is run in the same way. Talk? Poster? Conference proceedings? One, four, twelve pages? Paper is a useless slang term, correctly understood only in your little neck of the scientific woods.

This depends whether method is a replacement or complementary.
An improved compression algorithm needs comparison to others - it is one or the other. Well, unless it is radically different and interesting because of that. A physical simulation algorithm is likely an alternative to the current ones and will of course need many comparisons later on, but there is no need to have any in the first paper beyond mentioning those other methods exist.

One of the key questions for any piece of scientific work is this: how does this work contribute to human knowledge?
If a work fails to even discuss its relationship to prior work, then it is entirely appropriate to reject it. Likewise, if the authors mention algorithms that are directly comparable but fail to actually make a comparison with any of those algorithms. When I am given a paper that is entirely isolated in this way, I will not even bother to check the details of the algorithm's soundness, since the work already has a major disqualifying failure.
For many algorithms, however, the differences are qualitative and not quantitative, and thus a direct comparison would be unenlightening or pointless.  For example, if algorithm X tolerates a class of failures that prior algorithms do not, then it is enough to show that algorithm X tolerates those failures.  One does not necessarily need to re-prove or empirically demonstrate that the others do not.
Likewise, the number of potentially related prior works is often vast and complicated. No algorithm paper will ever compare to all of the other related algorithms, because "related" is a broad and fuzzy concept. You and the authors will generally not make the same judgements about which algorithms might be interesting to discuss in related work or to directly compare against.  Thus, the standard to which you should hold related work is not "Do I want to see comparison against Algorithm Y?" (that's Evil Reviewer #2 behavior) but rather "Does the comparison provided sufficiently support the author's assertions?"
Bottom line: be generous in your judgement of comparison to prior work, but papers with no meaningful comparison should be rejected.

Needs revision
There is a meaningful difference between asserting that a particular work is fundamendally not appropriate for this venue, or that it is unacceptable as it now stands. The former is a 'reject', the latter is 'accept with revisions required'.
You should recommend a rejection if the changes required to make it a good, appropriate paper would require to fundamentally change the paper itself or its conclusions. According to your description it's not necessarily the case - you claim that the paper needs a comparison to existing techniques on both a methodological level and also on the level of results. If the paper added these comparisons, would the paper be acceptable, or would it still be not good enough?  That's what the review should state.

From a conference paper I would expect at the minimum a comparison at a methodological level with  existing techniques, at the bare minimum stating why they are not a good way to solve the particular problem at hand.

You can write: the algorithm is sound and their method is thorough, however, there's no mention of the various related previous works (e.g., X, Y, and Z) which address the very same issue, without such discussion I cannot evaluate the work's novelty and I must reject the paper at this time.

I will add one important point not addressed in other answers so far: I consider that rejection criteria for a journal to be different from that for a conference, even for the same article. The most pertinent point I see here is that whereas journal articles have the time to request multiple rounds of revision (which could drag on to a year or two or even longer), conference reviewers must decide immediately whether the article can be quickly made acceptable, or not, since the conference review and presentation timeline is always very tight. In journal submission terms, a conference submission can give only one of two decisions: either it is "accept with minor revisions", or it is "reject". In particular, there is no option for "major revisions" as a decision.
With this understanding, the question is: whatever the revisions you think might be necessary, can they be done easily and feasibly in the space of just a couple of weeks? If so, you can accept the article and request those minor revisions. But if the revisions you consider essential cannot be done easily or quickly (in the timeframe of the conference, specifically, before the deadline for authors to submit the final "camera-ready" proofs), then you should recommend rejection.
Note that my answer is very general and does not even address your substantial question of whether or not the absence of a literature review is sufficient to reject the article. Rather, I ask you to reframe the question thus: do you have confidence that, in the tight timeframe of the conference, the authors can fix the literature review problems? Also, note that, unlike with a journal submission, you probably will not be given the opportunity to verify if they have done what you consider essential.
With this understanding, based on the details in your question, I think it might be unlikely that the authors would satisfactorily reframe the article in the literature, especially since you would not be able to verify this. If so, you should probably recommend a rejection. But, of course, explain to the authors what you would have like to see, so that they can hopefully do the revisions and submit to another conference or to a journal.

Conference papers are often submitted after the conference as well, and sometimes there are 3-6 months available for submission. Similarly, there may be ample time for review. I have been asked to review a conference paper where suggesting revisions was an option.

should I focus more on their method and results itself?

If you do this properly then you will have to do the comparison.
It should be the responsibility of the author to compare and contrast.
Of course if the new algorithms solve a previously unsolved problem this may be sufficient.

If it were me, I would say that it needs a substantial revision before being considered again for submission and that they need to add a thorough lit review making it clear that they are aware of the previous work on this problem and can explain the novelty of their contribution.


text:
What does it mean to change the required status of completed reviews from to review each week?
I submitted my article to a journal from Springer in September, two months later it changed the status to "Required Reviews Completed". Then within a week, it became "Under Review", and from then on every week it changed between "Required Reviews Completed" and "Under Review" to this day.
What could be the reason for this to happen and what does it mean?

Perhaps the editor rejected a review for some reason and asked for more. Perhaps the canonical question here can answer it in part: https://academia.stackexchange.com/q/55665/75368

Does this answer your question? What does the typical workflow of a journal look like?


text:
Can companies source paywalled scientific articles from authors?
I work for a company in the medical sector that, among other things, conducts literature searches and submits them to regulators for approval prior to product launch. The company currently pays for most articles and I was wondering:

If the authors are approached by employees and in turn send over free copies of their paper, can the company get in legal trouble if it uses the free copy for commercial purposes?
Does it make a difference if the author need not be directly approached but freely shares their paper on their own website or in sites like ResearchGate?

EDIT: I should point out that I will definitely not take advice here and apply it without legal consult - my objective with asking this question is merely to rule in the plausibility of such an approach to acquiring access to scientific literature based on other researchers' shared experiences.

If I worked for the company, I would make sure that all materials were sourced through the copyright portal we had a contract with. You say it is a medical regulatory field, so, really, the dollars/Euros/whatnot are peanuts. If you get a copy directly from the author and wish to use it for company purposes, get another copy through your standard process. As one further twist, where I work the articles we don't have direct access to come with a cover page that notes it is for 'Internal Business Use Only' - so, not for submission to another body.

@JonCuster So it's a non-starter - thank you for your input!

"The company currently pays for most articles"  I do not believe you have this right.  The company pays for a bundle of subscriptions, which is not quite the same as paying for individual articles.

@AnonymousPhysicist Maybe some companies...but in my brief corporate life, yeah, the company bought individual articles. No one was selling bundled subscriptions in a sufficiently narrow/targeted way to make any sense to a corporate customer - those subscriptions are for academic customers whose readers have very broad interests as a collective. Let's say an article costs $50 to access, 2 employees cost $100k each; that's 4000 articles. No pharma company is going to blink at that.

@BryanKrause "sufficiently narrow/targeted way to make any sense to a corporate customer" Are any of these companies familiar? Their activities are certainly not narrow. https://companiesmarketcap.com/biotech/largest-companies-by-market-cap/

"an article costs $50 to access"  plus hours of lost employee time required to organize a purchase in a bureaucracy.

What exactly does the company submit to the regulators? Is it a literature review that simply overviews the field and cites articles, or are the actual cited articles included in a larger bundle?

@AnonymousPhysicist Yes, they are very narrow compared to academic scholarship. Very very few papers are of interest even to a large pharmaceutical company.

@Anyon The company develops a product that needs to be supported by a scientific report that proves the concept behind its use is valid. This is where a literature review is needed - it provides evidence that similar implementations have been beneficial to patients in the past.

@AnastasiosTsarouchas Right, that much was clear to me from the question. I'm just saying that depending on what said reports include you might implicate copyright law as well as whatever terms and conditions the publisher applies to the accessing the material. E.g. attaching cited papers to the report (which I think some government agencies require) could make for a commercial use of a copyrighted work, whereas just citing ideas or results does not implicate copyright in jurisdictions I'm familiar with. But details matter and IANAL, so probably best to discuss that with your legal counsel.

As a company, you may want to consult a lawyer rather than collect opinions of random people on the internet (and IANAL, btw). Also, I am not sure the language in your question is precise enough. The copies that authors have are not "free", they can be used free of charge for particular purpose(s). Similarly, the copies made available via websites such as RG or personal pages, can be "freely downloaded" (meaning that there is no paywall), but it does not imply they can be freely used for any purpose imaginable. Even if you got a pdf, someone still holds the copyright and other derivative rights, and you need to carefully assess how your purposes agree with these protected rights.
In general, saying that your purposes are "commercial" may not be sufficient to make a judgement --- this is why you may need to consult a lawyer.  Regulations differ from country to country and from one area to another. For example, the way how medical regulators work in the US may be completely different from how, say, Engineering patents work in India. You may want to protect yourself and your company against consequences of an ill-informed decision. If you want to save money on article fees, contact a lawyer first to make sure this is safe and won't cost your company a fortune in fines.

"it does not imply they can be freely used for any purpose imaginable."  The question is pretty clear that the use is a "fair use" which is permitted in the USA.

"cost your company a fortune in fines."  This is a bit misleading.  Copyright litigation is usually civil litigation.  Criminal prosecution does exist, but is quite obscure.

@AnonymousPhysicist If the use is definitely fair use, then there's no issue. You don't need anyone's permission so long as you can acquire a copy by any lawful method.

@AnonymousPhysicist OP never said that they are in the USA. It is not at all clear to me that their purpose falls under fair use policy in their jurisdiction.

The company is EU-based but seeks to apply for FDA approval for some of its products as well.

If the authors are approached by employees and in turn send over free copies of their paper, can the company get in legal trouble if it uses the free copy for commercial purposes?

For recent, main stream publications, the agreement between the author and the publisher allows the author to do that.  Nobody will get in trouble.

Does it make a difference if the author need not be directly approached but freely shares their paper on their own website?

No.  For recent, main stream publications, the author is explicitly permitted to distribute works on their own website.  ResearchGate is a nuisance I won't address.
Even if the author has infringed on the publisher's copyright, simply receiving that infringing material is not a breach of the publisher's copyright.  Importing might be a breach.
Do not take legal advice from people on the internet.

This refers to US law.

IANAL but I don’t think you’re right, at least for paywalled papers.  IOP states explicitly here: https://publishingsupport.iopscience.iop.org/author-rights-policies/ that sharing is restricted (in particular but not exclusively to teaching purposes).  Likewise APS states here: https://journals.aps.org/copyrightFAQ.html#PDF that sharing pdf is also limited, this time for research purposes.  It’s a stretch to suggest either apply to the OP.  The copyright might not be practically enforceable, but my reading is that what the OP suggests is not in accordance with the copyright agreement.

@ZeroTheHero Your own links show you are wrong. "may use all or part of the APS published article, including the APS-prepared version (e.g., the PDF from the online journal) without revision or modification, on the author's or employer's website" "authors can share a preprint of their article anywhere and at any time"  I strongly disagree that the author is not conducting research.  Obviously distributing a research article for people to read is distributing it for research purposes.  Reading research articles is an example of research.

again IANAL, and wording in this situation is essential but that company is not the one doing research inasmuch as none of the people at that company are part of a research lab; presumably none of their names appear or is likely to appear on a grant or grant proposal; rather, they are explicitly contracted out for regulatory help.  So it might be legal for an author to share the paper to an MD actually doing the research (or another person doing the research), but it's not so clear to me that this extends to a company doing literature search on behalf of the researcher.  (I could be wrong.)

(The distinction here is with the use of the paper: I can't see how, in the context of the OP, the paper is used for research purposes but lawyers read things in their own ways and I could very well be wrong.)

Your reasons why the activity is not research do not make sense.   What the organization is called or who is an author just doesn't matter.

exactly.  what matter is the use of the paper, and it is difficult to argue that the OP is using it for research, since this is clearly not.

@ZeroTheHero These agreements are between the author and the publisher though. In what jurisdictions would third parties such as OP's company be bound by them unless they agree to the terms when receiving the PDF from an author? (Which seems unlikely if it's just hosted on the author's website, but I digress.)

@Anyon yes it may not be enforceable because of this type of issue but one could imagine that a publisher could refuse to publish work by this author.  But then again, how would a publisher know that the OP obtained the paper from the author?


text:
Finding dissertations as reference material
I'm a mathematician/computer scientist (my interests lie around the intersection of the two), and often when I want an introduction to a new research area I find that well-written dissertations are the best way to get up-to-speed quickly.
The problem is that I have no good way of finding these resources. I just Google "[subject name] dissertation" and look through the topics, or if I'm lucky someone in the field that I know will point me to a specific person's thesis. Is there any better resource for finding recent dissertations that are publicly available?

Find good paper on the topic from a year or two ago, from a university. Google that university's library listings of theses, and search on several of the initial names on the paper...

I'm assuming you know of the arXiv, you could try "[subject name] arxiv review/thesis"

The only comprehensive international compendium of theses and dissertations that I know of is ProQuest Dissertations & Theses Global. I think it is especially good in covering the United States and Canada, but I cannot personally vouch for its comprehensiveness in dissertations from other countries.
Other than that, most collections seem to be on a national level (e.g., HAL for France).

ProQuest is exactly the sort of thing I was looking for, thanks for sharing!

It is good to see which university is a powerhouse of your field and search for something like "University of XXX thesis repository". For example Eindhoven University is very good in photonics and they have a repository that looks like that
For most of the European universities there's DART initiative that offers a wide search.


text:
How should I reference the original work in a survey paper?
For example, if I want to dedicate a subsection of my survey paper to another research paper, I believe I need to reference the original paper. However, how should I do that? This subsection will have an interleaving of my observation and ideas and the original contents of the authors. Do I need to reference it whenever I try to talk about the original research paper?

How do people do it in the papers you read?

For the papers I read, most of them do not spend much time on reviewing existing techniques. They do mention and summarize those papers but there are usually several papers per paragraph which makes it a bit easier. But they do not reference the related papers for every sentence.

If you are devoting an entire subsection to discuss one specific original paper, then you should fully cite it at the beginning (e.g., AuthorA et al. [2]) and then refer to just the authors' names each time you subsequently refer to it (e.g., Author A et al.). This is particularly important since you will be interleaving your own ideas. It is very important to clearly distinguish your own ideas from those of the original paper. To do this, you must explicitly mention the original paper authors each time you refer to their work. Whenever you do not explicitly mention their names, then readers will understand that you are giving your own ideas.


text:
Is there a tool for finding or visualizing bibliographic trails between two sources?
As the questions indicates, I am curious if there is a tool that finds bibliographic trails ("cited by Y", "cites X") connecting two sources. I have found connectedpapers.com but this only works for inserting a single source.

Ask your local research librarians.

I don't know if one exists, but it could be made using the Scopus API: https://dev.elsevier.com/

Inciteful may be what you are looking for:

Select two papers and we will show you how the literature connects them together.


text:
How to differentiate between the author and a language editor?
I will translate a LaTeX document from English to Greek. How should I write who is the author and who does the language editing?
This is my first time doing a translation and publishing it in a scientific journal.
I mean, is something like this a good template?
\documentclass{article}
\title{}
\author{\thanks{%
Translator of this article: }
\date{}
\begin{document}
\maketitle
\end{document}
or do I have to write it in a different way?

Note that you need permission of any copyright holder (most places) to publish a translation.

What do you mean "how should (you) write"?

Maybe like this? https://tex.stackexchange.com/q/270283/128923

Have you talked to the journal about your plans? They probably have guidelines for such things. Further, getting some buy-in from a journal before spending the time doing a translation would probably be a good idea.

Welcome to Academia SE! I am not sure you will get a good answer for such a technical question on this site. You should probably check the LaTeX Stack Exchange. You can start there with a search on "translator"-related questions: https://tex.stackexchange.com/search?q=translator.

Publishing a translated article in a scientific journal is somewhat rare, especially if the original article is written in English, the lingua franca of much of science. Yours seems to be a rare case.  With machine translations getting better, the need for human translations is getting smaller, so that there is not a lot of precedence. Often, the translator does not appear (other than maybe in a foot-note). Some learned societies (American Meteorological Society, American Mathematical Society) publish translations of journals and articles from Russian and a few other languages. In this case, the translators are paid and their names do not appear. For books, the translator appears on the title page and is usually given in a complete citation. In the case of poetic works or classical literature, the translator becomes more important and is typically given. (Arno Schmidt's translation of English literature into German are read by Germans that are quite capable of reading the original because of the quality of the translation, which might even be seen as an enhancement of the original.) This is because translation has then many more artistic components than for a scientific article, which is supposed to be written in a bland language that demands less of a translator.
In short: There is precedence for leaving out the name of the translator as well for including the information on the translator. However, the name of the translator is -- as a rule -- not displayed prominently.
The rights-holder of the article (the author or the journal / conference / editor) might also have some ideas and some style guidelines. You probably should pose this question to them.


text:
Is it possible to bulk-download all citations for an entire field for analysis with AI?
I want to find a way to bulk-download citation data on (ideally!) all the papers published in my particular academic discipline. I want to analyse this large corpus of data using AI text classification tools, because I want to identify all papers that fit in a certain category. At the very least I want the basic citation info (title, authors, year, journal), and abstracts would be nice to have as well.
Are there tools for scraping the contents of literature databases that could achieve this objective? For example, one approach might be to compile a list of all journals that are relevant in my field, and use that list to download citation data for every single article in each of those journals. Or perhaps downloading citations of all papers that have certain keyword (even if there are very very large numbers of results).

I’m sure Web of Science would be happy to cooperate for a fee. But, talk to your local research librarians to get the right way to do it.

Could you be a bit more specific about what your actual question is? Is it about how to get the data? Or about about how to analyze the data once you have it?

@John Custer a hefty fee.

@henning - well, yes, but you get an actual dataset. And don’t violate various user agreements.

There are several fields that have abstracts journals. I only ever used Physics Abstracts. When I was doing that it was still on paper. I'm old! It should be digital now. Lists a metric-bunch-load of papers published each year in bunch of physics journals. I would not say all but a very large number.

@John Custer, absolutely correct. You don't just go about and scrape properietary data. (Not that I like Clarivate's, Thomson-Reuters' etc. business model too much, but still...)

Surely the basic citation details (and perhaps abstracts) should be freely available? The basic citation details can't be copyrighted, can they? It's not like I'm trying to illegally download the PDFs or anything! In the age of big data and machine learning, I would have hoped that there would be routes for accomplishing this sort of thing. I'm trying to do valuable and important science!

They are not exactly copyrighted, it is not a blanket ban on obtaining this data. You would not breach copyright law in this case, but ToS - very likely, as this aggregated data is at the very core of Clarivate's and the like business models. They did the hard part making sense of the bibliometric stuff with wildly different styles used in the text, and now you just want to just download it in a digestible, clean format. Not so fast.

Maybe this previous thread about a similar question (from 2017) could help https://academia.stackexchange.com/q/97777/164997. Please note that this question has been labeled off-topic and closed. Possibly Data Science Stack Exchange would be a better place to ask :)

First, get a corpus of all the DOIs that constitute the 'field' you are interested in. (One possible way to get the DOIs would be, first, to obtain all the relevant journals' ISSNs and then to find out all their DOIs in CrossRef's API. Here is an example.)
Second, filter these DOIs in the COCI (OpenCitations Index of Crossref open DOI-to-DOI citations) and fetch the DOIs that are cited by the former (citing) DOIs. Here is an example.
Third, use each (cited) DOI and loop them through CrossRef's API so as to obtain the data you need (title, authors, year, and journal will certainly be available, in some cases even the Abstracts). Here is an example.

This seems like a really promising approach. Two questions:

Do you know of an efficient API-friendly way to bulk-find ISSN numbers based on a list of journal names?
How can I return all the DOIs for each journal using CrossRef's API? The example you gave only returns 20 results.

(1.) Hm, not really... I sometimes used Web of Science's Master Journal List (or Scopus' source coverage lists) for finding the ISSN of journals of a given discipline, but that will be limited to the respective database's coverage. (2.) Oh, you can show more results by adding &rows=100 or so. But there's probably a limit, so you have to use paging/cursors. Look at the CrossRef API documentation of how cursors work: https://github.com/CrossRef/rest-api-doc

There may be tools that can do this on a small scale, but you will find that most publishers will block your attempts to download data in bulk using scripts. For example, ACM's usage policies of their websites explicitly prohibit the use of scripts. I happen to know because of a colleague's attempt at understanding what a subset of ~1000 articles in their journal I co-edit provides: The publisher promptly blocked his IP address from accessing any more article pages.
The issue at hand is not that citation data is copyrighted (it may or may not -- that's immaterial here), but that you are accessing a service that costs publishers money (namely, their websites) and there are service conditions attached to using their service. As a consequence, unless you have a specific agreement with publishers, you will find that trawling large numbers of websites is not going to lead to much success.

Not sure if it costs publishers much money, but it certainly makes them money (+1).

@henning How much it actually costs them is not the right question. It does cost them something, and so it is not unreasonable that they can set the conditions for your access to their service.

For this sort of work I strongly recommend looking into Dimensions.ai which is run by Digital Science. Dimensions is specifically designed to do what your looking for, and if you can get access to their API you will be able to efficiently pull and analyse large quantities of metadata/publications across entire fields. Ideally your institution will already have access to Dimensions and can help you out with an API key.
As for other options, it varies by database. Some subject specific databases will let you download bulk metadata but will often have an upper limit on bulk downloads (a few hundred for example).
I know Google Scholar does not like you pulling bulk metadata. If you are wanting to stick with Google Scholar your best bet is to use a plug-in like Zotero, which will let you quickly capture all the metadata (and potentially readily available .pdf's) of results on a page-by-page basis. If you start pulling too much metadata too quickly from Google Scholar you will trip their bot detection captcha's.


text:
I "lost" a paper: what can I do?
Half a year ago I stumbled across a noteworthy peer-reviewed article that was very relevant to my current research area. Being a noteworthy idiot, I didn't save it nor take a note (to be fair, I wasn't doing any relevant research at that point).
Fast forward six months, I really need to find this article again. I want to reference it and check out for more relevant information.
However, the problem is... it vanished.
It's been a week of non-stop trying, and I just can't find it. I've tried all possible combinations of keywords, google, scholar.google. I've checked every reference in all related articles that I could find. Not a trace. It even made me question my sanity: I'm starting to believe that I imagined or dreamed of it.
This isn't the first time I've run into such a problem. I've similarly lost at least two articles before. Same story: stumbled upon it at some point, found it interesting but didn't make a note (as it didn't seem important at that point) — only to never find it again.
Any advice on how I could find it again? I don't remember the title, the author, or the exact quotes from it. I only know what kind of point it made, and that I'll recognize it if I see it.

Comments have been moved to chat; please do not continue the discussion here. Before posting a comment below this one, please review the purposes of comments. Comments that do not request clarification or suggest improvements usually belong as an answer, on [meta], or in [chat]. Comments continuing discussion may be removed.

Your own Google search history might still have the link.

You could try a different search engine, like Bing or Duckduckgo. These use different indexing rules.

Ask the librarian at your institution. They are absolute wizards at finding information, and are also usually very happy to help.

Research librarians are worth their weight in gold. And are often more than happy to help because so many people think they know how to perform searches better than a trained experienced librarian. The more difficult the search is the more excited they get. Please, think of the librarians!

But OP might not be affiliated with any institution with librarians that she can ask

@user103496 that's fine, not all stackexchange answers have to apply to every single person.

@user103496 depending on the place, it may just be a matter of entering a university library and asking for help. No need to be formally affiliated.

Have you tried describing the paper to ChatGPT (version 4)?
I haven't used it to search for papers specifically, but I continue to be amazed at its awareness of obscure books and its ability to identify them based on incomplete/inaccurate information.

In contrast, I continue to be amazed by ChatGPT's (or Bard or any other similarly hyped AI) mistakes, hallucinations, and capacity to waste my time with false information.

@user103496 ChatGPT has a host of problems but using it as an intelligent search like this is playing to its strengths and avoiding its weaknesses. The only downside if it suggests the wrong paper is a loss of time, but I suspect our answer has already wasted a substantial amount of time looking for it.

This is definitely worth a try. I even recently used it to identify a couple of obscure shows. I’ve never really experienced any hallucinations to a large degree in GPT 4. I think the key is to properly formulate your prompts.

As an adaption of @leonos answer, try looking at the references in papers on a similar topic. They may reference this paper, or be cited by this paper.
Also can you remember anything distinctive about the paper's formatting, which may also help narrow down the journal/age? Details like was it a very long or very short article? did the text look a bit odd, perhaps being a scanned copy of an older work?

This might be too simple, but if you remember around what time you accessed the paper and if you were not using private browsing mode or disabled your history, you should be able to simply search your browser history around the relevant date or even manually go through it.
I've done it a few times and it has found me information I couldn't reproduce again by a search

Sometimes the downloads folder can be a helpful place to search, too.

As humans we're not great at remembering keywords, much better at remembering concepts.  And useful material can use different terminology in adjacent fields. Google of course tries to help, by including synonyms in search results, but they're overly broad, so instead of finding the needle, it merely increases the size of the haystack.  So quote marks around the keywords narrow things down - but you may have misremembered, and you narrow down to the wrong results.  A manually-generated set of synonyms helps.  I prefer a normal Google search over Scholar in this sort of case.
When you do search, you're likely to find near misses.  If these near misses are recent (try to remember how old your target paper was) look at their references.  If your near misses are old, look at what cited them
I suspect this happen to all of us at some point.  Quite often it's not interesting enough at the time to file in the "interesting, for later" folder/database, then happens to be of use to another project in the future.

Post a question on the relevant Stackexchange site, listing all the relevant details and clues you can remember.
(If there's no particularly suitable specialized Stackexchange site, I believe you can post here on Academia too.)
Try also other forums (e.g. the relevant Reddit forum).


text:
How to deal with demanding fees to accept the article
An author submitted a manuscript to a Scopus and a Web of Science Journal. Few months later, he received an email including the full name of the author, name of Journal and the title of the submitted manuscript. The email asking the author to pay $$ in order to accept reviewing the paper. Then, accept it for publication. The author immediately block the sender and report it as a spam. Then attached the spam email and send the case to the Journal asking for investigation. Should the author do any further action?
The sender was not associated with the journal. But how he got the information of the author? The sender ask for money to accept reviewing the paper and guarantee acceptance the paper. Hence, whatever the paper is, paying the money will result in accepting the manuscript.
The story in points:
1- Authour submitted the manuscript.
2- The status of the manuscript becomes "Reviwer invited" after about a month.
3- After 2 months the Author received unethic email. The email asked about the following:
● Gurantee accepting the paper for publication with one condition. The condition is to pay 200$ to the sender.
● before paying, the author must respond the sender with accepting the deal.
● Then, the sender accept the invitation to review the manuscript. Once this is apear in the system "Under review". Then, the authour pay the 200$.
● In 10 days, the paper will be accepted.
The journal is an open access journal. The author send the unethic email to the Journal asking for the investigation.  It is Ok to reject the paper for 100 times, but it is not ok to published it in an unethical way. This is completely unacceptable.
Thanks for your help.

Was the sender associated with the journal? Open Access journals are normally supported by author fees. Some other journals partially so. There isn't enough information here to suggest anything other than you may have a misunderstanding.

Should the author do any further action? -- It depends on the intent. What are you trying to achieve? Most people would likely agree that the sender's actions are unethical and do not align well with academic values. But not all academics agree on how much effort one should commit to protect those academic values, when it does not concern them directly. Some would delete email and do nothing else, some would contact sender's department and even police. This is largely a personal choice, and as such, your question may be considered off-topic here.

Sounds like someone (i.e. the journal) suffered a data breach and the scammers are trying to take advantage.

You appear to use "author" to describe different parties in this situation; can you please revise to clarify who is who.

@Buffy the sender seems not associated with the journal. However, instead of investigating in this case, the journal reject my paper. The last status was "Reviwer invited" then suddenly it becomes rejected??!! So this make me  feel that the journal is behind the unethic email.

@Buffy No there were no misunderstanding. The sender ask to pay 200$ to accept reviewing the manuscript. The payment must be done after accepting reviewing the manuscript. So, the authour (me) must first agree on this deal. Then, the reviwer accept reviewing. Then, the author pay, then the paper accepted. This is the story. So, it seems the journal involved.

It seems you think this journal is really demanding fees from you to accept the article. That's extremely unlikely (note the journal is indexed by Scopus & Web of Science). Far more likely that someone is impersonating the journal and trying to scam authors. In other words, if you had actually paid the "journal", your paper would still be rejected.
The odds are good your paper is rejected because it is not "good enough". This especially applies if the journal sent you reviewer reports that clearly say your paper is not good enough.

Should the author do any further action?

No, for the simple reason: what further action can the author take? What can the authors possibly imagine doing that will actually have an impact, beyond what they have already been done? I suppose they could file a police report, but it's the journal being impersonated, so the journal is the aggrieved party and they are the ones with standing. If they don't do anything then nobody else can.

Thanks for your nice answer.

You did the only thing that you could do: Involve the editor. It seems at first glance that the reviewer selected by the journal decided to get paid for their work of reviewing and then extended this by selling a positive review for a little money.
It could be that local laws were broken (maybe some type of fraud or bribery), so you possibly could bring this to the attention of the authorities.
If the reviewer is affiliated with an academic institution, you could (and should) inform their authorities since soliciting bribes for positive reviews is very unethical. You might have to leave this to the editor since they know more about what has happened and the identity of the reviewer.
Of course, you might be dealing with a predatory editor, in which case the reviewer might have decided to profit just as well.


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What happens if the second reviewer for a conference proceeding keeps missing their deadline?
I have submitted a journal article to a conference proceeding which will be held in June this year. Though I submitted it on time in December and the first reviewer accepted it in the first week itself, still I didn't receive a second reviewer's response. In the online submission system it appears as initial submission status, with the phrase "reviewer missed the deadline" repeated thrice in red color. If I cannot get a second guest editor what will happen to the article? Is it possible to accept an article without a second editor? How long would this usually take?

Have you asked the conference organizers?

Seems like that's entirely up to them and it might depend on the first reviewer's input. Someone else might come along here with more info on how these things normally progress, but I'm doubtful anyone will be able to give you a definitive answer besides the actual conference organizers.

Here is another opinion : ask the conference organisers...

Really, it seems that you are full of anxiety and so you want encouragement that there is still hope for your article. Sorry, but emotions aside, if you actually want a working solution, then do what the other comments are saying: ask the conference organizers.

This is not your problem but the conference organizer's one. They have to ensure a proper reviewing process.
Usually, they are contacting the reviewer and apply some pressure. It they still get no review, they acquire a third reviewer as replacement (or a program committee member does it by themselfes).


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How much modification in a manuscript is recommended after a major revision?
I've got three months to revise my manuscript I submitted to a journal a few months ago. I received two highly detailed reviews, from which it seems that the manuscript does not show the desired big picture of my work. Both reviewers pointed out similar deficiencies, and I must say, both of them are right.
According to the questions, remarks and advices, I rethought the entire paper and started to rewrite it (being attentive to the reviews), however, I am not sure if it is acceptable to completely modify the whole manuscript. Obviously, the background, the results, the theories and everything concerning the main content would remain the same with slight modifications, but I think the restructuring of the content and even a completely rewritten introduction would be necessary.
So my question is:
How much modification is acceptable after a moderate/major revision and after the decision of rejected with the chance of resubmission?

As corey979 mentioned in the comments, major may really not be major at all, and it depends on the journal. Either way, when I received review with major revisions I did not entirely rewrite the article, but addressed the concerns that the referees made. A poor rule of thumb I originally was told was to make one change per comment and resubmit.
The take away is that you should now evaluate your work having received feedback. If the edits are indeed minor (spelling, word order, grammatical) fix those and move on. If the major reviews are needed because of missing information that you have or can easily obtain you can add it as supplemental in order to preserve the original article.
If the general problem isn't framed well then maybe rewrite just a paragraph or two of the Introduction and the Conclusions. Often you can make the big picture more transparent with just a few changes to these sections.
It is acceptable to change figure order and sections, but I would caution from departing too far from the original. If it was sent back for revisions then revise, if it was rejected then you may consider rewriting. Remember that you are telling a story, and the ideas need to flow as such.


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Is it okay to restructure a literature review to fit a broad topic?
I'm aware that most literature reviews follow a similar structure, which is:

Introduce a topic
Discuss and cross reference papers that cover this topic

The literature review that I am covering is a very broad topic (medical applications for machine learning) and is interested in all the research covering this topic. Is it okay to write a literature review with the following structure?:

Introduce paper
Discuss paper
Move onto next paper and repeat.

This could be discussed in the methodology of the lit review.

What field is this in?

It's looking at medical applications for machine learning

This includes all medical applications, so the topics covered would be very broad

Given the breadth of the topic, do you plan this lit review to be several thousands of pages long?

@BryanKrause it is intended to be several thousand words

I take it that the comment by @BryanKrause is tongue-in-cheek, but it raises a very important point: the topic is so broad that it could be endless. You should seriously consider narrowing the scope of your topic until you have a narrow topic with no more than 100 articles that cover it. Otherwise, your review will never end and it will never be complete. (I speak from experience.)

The answer to your title question, “is it okay to restructure a literature review...” is yes. There is no one uniform way that literature reviews must be written. What is important is to make sure that your literature review does its job, which is to do a comprehensive review of the publications on a particular topic.
The only worry with the structure that you propose is the ability to do a completely comprehensive review (which is a difficulty in writing any given literature review, but is especially troublesome in your topic). By simply discussing papers and not cross referencing them within topical discussions, your literature review turns into a data-dump instead of a review. It is not necessarily bad to have a broad topic, nor is it bad to discuss and “rinse and repeat” through several papers, but it is essential that your review is well-structured and does not arbitrarily choose the pieces it is reviewing.
Restructuring is fine, but do not compromise the quality of the review because the topic is broad.

Given my original question, would it be better to do this for each topic present in the area? 1) introduce paper 2) discuss paper 3) repeat 4) compare and contrast that topic 5) move onto next topic

In principle, I don't think what you suggest is a good approach, assuming that your goal is to produce a helpful review of the literature (for yourself and for your readers). The reason for the "similar structure" of "most literature reviews" as you describe it is that it is a more useful format. It is far more useful to readers to understand what the literature says topic by topic than it is for them to read your paper-by-paper summary report.
An excellent explanation of the difference is presented in Webster and Watson (2002). Although what they cover is not exactly the same thing, it is pretty close: they call the recommended topic-by-topic approach "concept-centric"; as for the paper-by-paper approach that you propose, they condemn it as "author-centric". Very simply, it is not very useful for the readers.
If I understand your description correctly, you seem to think that "medical applications for machine learning" is one big topic, and so you have little choice but to then go paper-by-paper. On the contrary, every topic can be sliced into subtopics; that is very much so for a broad topic like yours. You could divide topics by different fields of healthcare; by different machine learning approaches (e.g. classification; regression; clustering; etc.); or by many other subtopics that present themselves in your reading of the literature.
However, I specifically recommend along the lines of Webster and Watson (2002) that you focus on theoretical concepts as your organizing principle. In machine learning, this would mainly mean that you would group studies based on similarity of the target variables (at least, that would apply for supervised learning studies), for example, grouping by targets that study predictors of the same kind of disease; targets of predictors of the effectiveness of certain procedures; etc. Unsupervised learning techniques might not be as readily amenable to this kind of grouping (since they do not have the causal structure of theory), so for those kinds of studies, other organizing schemes (such as those I listed in the previous paragraph) might be more suitable.
In my research on literature reviews, I have found that this kind of organizing principle (that is, based on theoretical concepts) is more useful to readers. (My most recent work is not yet published, but I have an earlier working paper on this topic that you might find helpful.)


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How to conduct an effective literature survey in mathematics?
Due to Covid, I am unable to go to my University and access the University server. As a result I am unable to use MathSciNet. Is there any other way to do a good and effective literature survey on a topic in Mathematics?
If someone could help me,  I would be  grateful. I am also interested to know how researchers working at Universities that don't have a MathSciNet license conduct research?

Indirect answer only (if that). Can your university librarian or department chair inquire about or arrange for remote mathscinet access?

I probably haven't used MathSciNet for over a decade. Google Scholar has been totally adequate for my needs. Is there some specific reason Scholar is not working for you?

It's unlikely that your university has no way for you to remotely connect to MathSciNet. Ask you reference librarian.

Simple answer: There are actually two good and well-known (at least, I had thought so) bibliographic databases for mathematical literature:

MathSciNet

zbMATH

The latter is freely available online as of 2021.
(Of course there are a few differences between them - for instance, the quality of the bibtex entries is a bit better in MathSciNet, in my experience. But anyway, for most purposes both databases do their job quite well.)
Historical Note: While MathSciNet is essentially based on Mathematical Reviews, zbMATH is based on the Zentralblatt für Mathematik - and both the Zentralblatt and Mathematical Reviews were founded by the same person, Otto Neugebauer. I would have called this a fun fact, but unfortunately the historically background (which is described in the previous link) is not particularly funny.


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Literature Review Tables: Plagiarism or Fair Use
I am in a debate regarding tables developed for a literature review which include Author, Year, Type of Study, Methods, and Results. I believe all components of the table should be paraphrased, but a colleague directly copied methods and results which has resulted in a debate. Is this direct copying of these materials plagiarism or considered fair use as it applies to a literature review?
Note: The copied material is anywhere from one to seven sentences total for each reference for methods and results.
Note 2: I should also note this was in a table we previously stated we created and there is no indication the material is directly copied.

Note that "fair use" is a concept from copyright law, and plagiarism is completely distinct from copyright infringement.

How much text are you considering copying from a given reference, given that it fits in a table? A phrase, a sentence, a paragraph, or more?

Hmmm. Likely you should say that you are quoting material when you do that. Otherwise it could be considered plagiarism - unlike my answer here.

First, please note that plagiarism is a different concept from copyright infringement/fair use. To summarize what I will explain here: as long as you put quotation marks around everything that is copy-pasted AND you clearly cite each instance, I don't think you have any problem with either plagiarism or copyright violation; this would be fully morally acceptable and within your fair use rights.
Here are my detailed comments:

Plagiarism: In general, as long as you properly cite your sources, there is no issue about plagiarism. (Plagiarism is strictly about copying words from other people without giving them credit. It has nothing to do with copyright violation.) However, your scenario is a bit tricky because even if you cite your sources, copy-and-paste almost always requires quotation marks; however, you might possibly get away without quotation marks in a table (if it were copy-and-paste into regular text, you would most certainly need quotation marks). To be safe, I would just put quotation marks around everything that you or your colleague copies-and-pastes AND also cite the source each time. If you do this, then there is absolutely no concern about plagiarism.
It is also very important to understand that "paraphrasing" does not let you escape from claims of plagiarism. If your paraphrase is still too close to the original quotation, some people might still consider it plagiarism, even if you quote the source. (I personally disagree that that would be plagiarism because you quote the source, but,  unfortunately, I know for a fact that some people do consider it to be plagiarism just because the paraphrase is still too close.) So, according to what you have described, I think paraphrasing would be a waste of your time: simply copy-and-paste, put quotation marks around each copy-and-paste, and cite each quotation clearly--if you do that, there is absolutely no concern about plagiarism.
Copyright violation and fair use: I'm not a lawyer, but as far as I understand, copying bits and pieces from several different articles (even entire paragraphs) and assembling them into a table is fully within fair use limits. Fair use will generally let you copy entire tables, so assembling your own table from various sources should definitely be within your fair use rights. (And note that fair use is your right; the copyright holder has no right to restrict people from making fair use of their copyrighted work--copyright is not unlimited.)

Quotation marks are probably not right when it comes to a table.
Better I think would be to include in the caption:  "This table is directly taken from table X.Y in CITE",   or "Rows 2-7 of this table are taken directly from the corresponding entries in table X.y of CITE".
In general for a table there is not much to paraphrase or quote, since it will be some numbers and a short method name I assume,

@LyndonWhite, what you say may be generally the case (as I said, "you might possibly get away without quotation marks in a table"), but my response is specific to OP's description, with OP's colleague copy-pasting "anywhere from one to seven sentences". This is not just "some numbers and a short method name", as you assume.

Unfortunately my fair use is her plagiarism is your copyright violation. Fair use was intentionally never very clear, but recently, IP rights owners have forced changes to laws, different in every jurisdiction, that have forced fair use to the margins.
What you describe is certainly not plagiarism as the words being used are correctly attributed to their creators. Dangerous ground if you use quotes without attribution, however. You shouldn't give the impression that words are yours when they are not.
But is it fair use?
Traditionally, I'm pretty sure that almost everyone would say yes. Fair to use the actual words in this way provided that they form an insignificant fraction of the whole work being quoted and proper attribution is given.
But now it is not so clear.
If you are at a University or other large institution, you likely have lawyers available that can give advice on this that is particular to your own situation (country, etc). There may also be a Research Office that has looked into this question and can provide guidance.
It might even be that paraphrasing is considered more troublesome than direct quoting.
But copyright is currently a moras. We are moving in many places toward unlimited and absolute copyright. Academics, especially, should work in the political realm to halt this trend before it makes some research fields impossible.


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How to describe affiliation in between college and grad school?
This question is similar to another one on here, but the details of my situation are not quite the same: Affiliation in the transition period between studies at different universities
I graduated college recently and applied to and was accepted to grad school. However, I deferred my admission for a year so I could complete a fellowship, which I have not yet begun.
1. How should I describe my academic affiliation now?
2. How should I describe my academic affiliation once I start my fellowship?
3. How should I describe my academic affiliation once I complete my fellowship but before I begin grad school?
It seems improper to list my former university, since I graduated and therefore should now be completely unaffiliated from them. Also an undergraduate has a tenuous academic affiliation to a department at best, at least in my opinion. On the other hand, the fellowship isn't really an affiliation with an institution either (even though I formally had to register at a university as part of the process, although I actually haven't completed the registration yet since this needs to be done in person). And for the grad school I haven't begun studies, and even though I was accepted and have an e-mail address there now, I feel like I would be counting my eggs before they hatched.
Honestly I know my situation is kind of strange, and maybe it would be best to say 'unaffiliated', but at the same time, for example if I posted something on ArXiv, I wouldn't want people refusing to take it seriously at all because I am 'unaffiliated', especially if they wouldn't think that way if they knew the specifics of my situation. That being said, they lack a snappy quick description.

Despite the differences in circumstances, I believe that the top answer in the linked question can be adapted  to your case as well.  Now, during the fellowship, and during graduate school, you will be registered with some university.
The fellowship period is a little odd, but they had you register with a university for a reason, and it seems that you will be affiliated at least tangentially---unless people with your fellowship list themselves as an affiliate of the institution giving the fellowship, which happens in some cases as well.  Check and see what other people with your fellowship have done, and it should be clear.
During the gaps, use your last affiliation on publications, since you will almost certainly have done at least some of the work there.  As for describing your current situation during the gap, you don't have to say "unaffiliated", you can just be clear, e.g., "I finished at X in June, and am starting at Y in September."