text:
What is facultyawards.org?
I recently received an unsolicited email from https://facultyawards.org. I tried Google to get a better sense of just what this group intends, but I couldn't find much insight. My question is simply this:

What is the origin of this group and do their awards carry any merit towards a typical promotion for faculty tenure, etc?

I did not know this site either, but I'll be damned if what boils down to a popularity contest ("cast your votes for your peers") holds any relevance for tenure review or promotion.

Buried deep in the web site is a description of a "high-quality leather-bound volume" for each discipline that they plan to produce and offer for sale.  It's a typical "Who's Who" scam.

If it appears too good to be true... it usually isn't true.

What is the origin of this group

Nobody knows.

and do their awards carry any merit towards a typical promotion for faculty tenure or promotion?

No.
At least, I certainly hope not.  Nobody in their right mind would trust an award of completely unknown provenance.
I wouldn't be the least bit surprised if everyone who signs up is selected for an award and then immediately offered a high-quality leather-bound archival book listing your achievements and those of other winners, all for the absurdly low price of $500, but only if you reply in the next fifteen seconds with your credit card information.  See also "Who's Who".

Yup, definite scam site. Avoid like the plague.

Thank you for answering my question. I only hope this shows up on Google as prominently as the tripe the originators of the spam have plastered there.


text:
How to identify the publications that cite two specific papers?
Finding the citations of any particular paper is straightforward.
But how do you identify the set of publications that cite two specific papers?
The reason I am asking this is because I am trying to write a review article to resolve an issue in the literature. There are 2 papers that adopt opposite views regarding that issue. To check if any similar study to mine has been attempted before, I am trying to look for any papers that cited those 2 papers together. Any way to do this?
Each paper has hundreds of citations, so looking for common citation is not practical!

@DSVA That would have been easy if each paper had a few citations. Unfortunately, each paper has hundreds of citations. So you want me to cross reference hundreds of citations? I am also curious, is that your down vote?

LIBRARIAN ... Are you at an institution that has an academic library?  They will have "reference  librarians" on the staff ... consult them.  The fact that we have computers nowadays does not mean you have to do everything on your own.

My procedure was simple but worked for me. It is similar but different to that suggested by tripartio.

Look up article A in Google Scholar.
Click the link for articles that cite that article A.
Check "Search within citing articles"
Type the details of article B in the search bar (e.g. authors or title)
Explore the results

This is not as systematic as would be ideal, but should help to give a first-cut idea.

One can use the API of OpenCitations. Here is an example code in R based on two DOIs as visible in the form of https://w3id.org/oc/index/coci/api/v1/citations/[DOI]:
library(jsonlite)

work1 <- jsonlite::fromJSON("https://opencitations.net/index/coci/api/v1/citations/10.1017/s0020818313000337")

work2 <- jsonlite::fromJSON("https://opencitations.net/index/coci/api/v1/citations/10.1177/1354066106067346")

citingworks <- intersect(work1$citing, work2$citing)

Then, citingworks lists 32 DOIs that have cited both work1 and work2:
> citingworks
 [1] "10.1017/9781108644082"                 "10.1017/9781108644082.001"
 [3] "10.1017/9781108644082.002"             "10.1017/9781108644082.003"
 [5] "10.1017/9781108644082.004"             "10.1017/9781108644082.005"
 [7] "10.1017/9781108644082.006"             "10.1017/9781108644082.007"
 [9] "10.1017/9781108644082.008"             "10.1017/9781108644082.009"
[11] "10.1017/9781108644082.010"             "10.1177/1354066119889401"
[13] "10.1093/jogss/ogy021"                  "10.31338/uw.9788323542988"
[15] "10.1080/13533312.2020.1753513"         "10.1080/13569775.2020.1795372"
[17] "10.1007/978-3-030-51521-8_1"           "10.1007/978-3-030-51521-8_2"
[19] "10.1080/13600826.2020.1828298"         "10.1057/s41268-018-0147-z"
[21] "10.1146/annurev-polisci-040711-135425" "10.1111/pops.12616"
[23] "10.1093/isq/sqz055"                    "10.1093/isr/viy006"
[25] "10.1093/isr/viz002"                    "10.1017/s0260210516000176"
[27] "10.1017/s026021051600019x"             "10.3384/cu.2000.1525.1572479"
[29] "10.1177/1354066117745365"              "10.1163/24056006-12340008"
[31] "10.1177/0010836716653161"              "10.1080/09662839.2018.1497985"

But note that OpenCitation's data sample is CrossRef, which is not the same as Google Scholar.

I haven't done this myself, so I can't give specific details, but here's a general algorithm:

Look up Article A in Google Scholar. Click the link for articles that cite that article. Extract all the results as a list of articles. (This is where I can't give details, since I haven't done it myself.)
Do the same thing for Article B.
Compare the two lists to identify common articles.

Indeed, this could work. Library software can check for duplicate references (super easy in Endnote) and could thus simplify step 3.

For biomedical publications you can use Europe PMC citation network (I work for this database). Here is an example of a search to find a publication that cites two particular papers: https://europepmc.org/search?query=CITES%3A24240771_med%20AND%20CITES%3A24036476_med. You can also do that programmatically (https://europepmc.org/RestfulWebService#cites)

I've made a website that searches publications that cite all specified ones: onthecitesof.info.
Edit: Quotes from its 'about' page:

It uses the OpenCitation API to get the list of publications citing the submitted ones, and the Crossref API to get info from DOIs.

This website is designed to search for subsequent publications that have a high chance of mixing the subjects of the submitted ones and increase the chance that they are specifically related to them.

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.

I came across Inciteful recently.
Its literature connector enables searching link between two papers.
[Extract]
How are the links made between papers?
A link is established through citations. Two papers are linked if either one cites the other. So starting from the seed paper we recursively search through all the papers that are cited by the seed paper or that which cite the seed paper.
How many hops will it search?
The largest number of hops right now is six ...

This can be done with reasonably high accuracy using Scopus and it is much easier than the other methods suggested here. Just do an advanced search for
"title of paper 1" AND "title of paper 2"
The idea is that publications that cite the two papers will have their titles listed in their references sections.
This might not give completely accurate results, because:

It will fail if a journal does not give the title of the
publication in the references list (I think Nature just gives
journal, volume, and page numbers).
It will fail if one of the titles is not distinct enough and appears by coincidence in the main text of a publication that does not cite it.

You might be able to get round these problems by including the author names or page numbers and doing a more complicated search. See https://www.scopus.com/search/form.uri?display=advanced.
Of course you need access to Scopus and your institution might not have this. But something similar might work with Google Scholar.

Using OpenCitation's API in Python would look like this:
import requests
import pandas as pd
import numpy as np

link1 = "https://opencitations.net/index/coci/api/v1/citations/10.1017/s0020818313000337"
work1 = requests.get(link1).json()
df1 = pd.DataFrame.from_dict(work1)
link2 = "https://opencitations.net/index/coci/api/v1/citations/10.1177/1354066106067346"
work2 = requests.get(link2).json()
df2 = pd.DataFrame.from_dict(work2)

print(np.intersect1d(df1['citing'].unique(), df2['citing'].unique()))

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text:
Is it okay to incorporate a block of citations from a review paper into my own paper?
I'm currently writing a paper on a certain topic for which a review article was recently published. Of course, I want to contrast my new approach to existing techniques. For that purpose, I have identified the relevant prior work with the help of the above-mentioned review article.
However, in my current version, I simply reuse the whole block of citations from the review article with no change at all. I have consulted each reference individually and they do seem appropriate for citation.

Is taking a pre-existing block of citations and using it in my own manuscript considered plagiarism?

Relevant: M.V. Simkin, V.P. Roychowdhury "Read before you cite!" arXiv:cond-mat/0212043

I'd say not if you also cite the review paper. It sounds like it's worth explicitly acknowledging its value in text, as well. Gracious over-acknowledgement isn't really a wound.

You must cite your source every time you use someone else's intellectual contributions.
A review article contributes curation of sources (among other things) as its intellectual content. If you use that intellectual content, you must cite the review paper (in addition to the individual sources). Otherwise you are misleading the reader into believing that you've done all that work (reading very broadly in the literature, identifying the most relevant and useful sources) yourself.

Yeah. Needed to say, it also common to write something like: For a wider context, we refer the reader to [ReviewPaper] and the references therein. Of course, you still also cite the most important ones yourself.

+1 for "Otherwise you are misleading the reader into believing that you've done all that work"

@ChrisWhite it's somewhere between what's described in this post and what's described in this other one. Like most things having to do with plagiarism and theft of ideas, the exact bounds of the line can be pretty fuzzy.

I do not see why that would be plagiarism at all. Taking references from other papers, reading them, and citing them in your own paper is a regular process. If you copy & paste the sentences that refer to those citations along with the references, then it would be considered plagiarism, but no, not in your case.

Indeed as long as you read them. This is called the snowball method of literature research

"Taking a whole block of citations" from somebody else's paper is using their work (the compilation of a comprehensive bibliography for a review paper), which requires acknowledgment in the form of a citation. It is just as intellectually dishonest to use the excuse "Oh, I could have compiled that list myself" to justify copying a bibliography as it would be to use the excuse "Oh, I could have written that paragraph myself" to justify copying text.

@David Richerby: I can't see that this is any more intellectually dishonest - assuming you actually read the papers! - than using Google Scholar to find relevant papers, then automatically capturing the citation information in BibTeX format.

Then just do the google scholar search. The fact that you found the review succumbs useful is because it involved scholarly work.

Mmm, in retro spec, I do have to agree with David a bit. Acknowledging the review, also as a starting point for the lit review, would be good practice.

Perhaps your choice of the word "steal" to describe the inclusions of  block citations reveals your feelings on the matter.
If you are copying text verbatim, and I assume it is by saying "block of citations," then you should provide a citation to the source. That is my take.
However, by altering your conundrum slightly, does it lead you to a difficult question or an unknown?
As in, had you found these papers 12 months ago and the question of copying the citation block wasn't applicable, would you have cited the paper in which you discovered these additional sources?

I've noticed many papers deal with this problem by doing:

time-travel has long been known to be possible [17, 18, 4].

Where 17 is an older research paper, 18 is a recent paper with more comprehensive results, and 4 is the review which may or may not have pointed the authors to 17 and 18 in the first place.
I suppose this way, you both cite the original source (which you have to do) and credit the review (so as to not be plagiarizing their collection of sources). Perhaps you could argue that this does not explicitly indicate that the first two are taken from the review, but it does deal with the matter using the fewest characters.

I'm sure this is field-dependent, but to me that sticks out as an example of sloppy editing. (Not much of an issue in a preprint, but in a published paper that has presumably gone through proofreading, that'd be a different story.) Based on my experience I'd expect simultaneous citations to be ordered by number. And this is the first I've heard of any convention that assigns meaning to the order in which multiple papers are cited. So I guess what I'm saying is, know your audience and their expectations before you decide to do this.

@DavidZ I didn't mean to say that there's a formal convention. I just noticed that this is how others seem to deal with it. Re: Order - I think citations are usually numbered by order of first appearance. In this case, [4] could have been cited elsewhere, in the beginning of the paper.

Sure, I understood that you didn't mean there's a formal convention, but someone else reading this answer might think so, or at least might apply your advice to a context in which it doesn't hold. I thought it would be useful to clarify that for other readers.

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text:
How to responsibly apply for more than one PhD position?
My Master thesis is under review, may be it will finish in a week. I had a discussion with my thesis supervisor about a potential PhD position. He applied for a 1 year grant, with my name as student beneficiary. Together we decided to apply for some more grants once I graduate.
In the mean time, I got an interview for PhD in another much better university. If I clear the interview, this employer would contact my supervisor for reference and my supervisor might think that I am playing a double game. Did I do something unethical? How to handle this situation?
I will inform my supervisor about the interview sooner anyway. I am extremely worried about this scenario that I could not focus on preparing for the interview at all.

Did I do something unethical? Absolutely not. How to handle this situation? Tell your advisor now.

When you tell your advisor, you could say something along the lines of, "If this falls through, I'm hoping we can still arrange something here. I've enjoyed working with you." That might make the situation less awkward for you, particularly if your words are heartfelt.

By the way, note that as a PhD student, you're not typically an employee, so this other university would not be your employer.

No reasonable person can fault you for exploring different options since

there isn't a guarantee of a job
you haven't committed to this job.

Definitely tell your advisor so that you'll be in the right frame of mind for your other interview and can excel there as well !

And one year's funding isn't nearly enough to do a PhD.


text:
How to cite a previous single-author paper by oneself?
Suppose my name is John Smith, and I am writing a new (single-author) paper which wants to cite a previous (single-author) work by myself.
What is the best style for this?
(1) As we showed in [1], the following condition applies ....
(2) As I showed in [1], the following condition applies ....
(3) As Smith showed in [1], the following condition applies ....
(4) As [1] shows, the following condition applies ....
I would prefer to avoid (4) because it is easier for the reader to follow a discussion where names (rather than numbers) are associated with certain concepts. This leads me to prefer (3), because a specific name is attached.
The problem with (1) is that it can be difficult for the reader to distinguish two meanings of "we" in the context of a (math) paper: first, there is the impersonal use of we as in "we define a group as a set with an operation + etc.", and second there is the use of we as in the actual human writing the paper.
The problem with (2) is that it draws attention to myself as opposed to my ideas, which is the opposite of what I'd like in a scholarly paper
Does it matter if this is in the middle of a paragraph citing a wide variety of authors, only some of whom happen to be equal to myself? For example,
"As Jones showed in [2], ...., As Doe showed in [3], ...., As Smith (or we) or (I) showed in [1], .... "

You can also consider: "As the author showed..."

I've always used the "as we previously showed" construct; it seems more straightforward and clear.  (If I had relevant solo papers I'd say "I" rather than "we'.)  I don't know if there are specific guidelines, but clarity should be a general goal.

Other alternative: As shown in [1]. Passive forms sometimes get a bad rep, but they are not forbidden by the grammar police yet.

In my field of psychology, it is normal to treat any previous citation as if it was another person. In a sense it is the article that presents the point. This convention is also related to the use of double blind review in many journals.
So you'd just write:

Smith (2015) showed that ...

or

Smith (2015) conducted a study and found that ...

This is uncommon (or unheard of) in Theoretical Computer Science, from my experience.

@einpoklum How does theoretical computer science handle blind review?

By not pretending it's possible when you follow up your own work? Anyway, the limited number of reviews I've written have been single-blind, i.e. the submitter is known, the reviewers aren't (which is a situation I disapprove of actually).

The TCS reviews I've done have been single blind as well.

Your institution or publisher probably wants you to use a specific style guide.  Most of what I've seen other places is consistent with the style guide here:  Same citation format as for anyone else, typically inline, surname date and maybe page number; full citation also same format as anyone else.

I don't think that this is what the OP is asking for. It looks like his citation style is by numbers in square brackets.

To me (3) sounds strange (i.e. to refer to yourself in the third person). Also (1) and (2) are rarely used and may sound odd to some people (to me only to a mild degree). I would certainly prefer (4).
I must admit that I do not see how names of persons would make it easier to me to follow the discussion. Names of concepts would certainly do (and often concepts are named after people you don't want to call your own method "Smith's method) but author names are quite irrelevant to me.

"Here" we don't exactly refer to  ourselves in third person.  We just quote (with quote marks) or paraphrase (without) and put the citation afterward in parens, hence, "Same citation format as for anyone else" (Groleau 2016).  But again, the organization surely has a style guide.

"I do not see how names of persons would make it easier to me to follow the discussion" Seeing author names is often useful to me. Many times the author's name and surrounding context will be enough for me to recognize right off what the reference is without having to look at the bibliography, and other times knowing the author adds context to me (e.g. if "Mauldin", the paper probably doesn't involve high-powered set-theoretic notions and is likely something I could understand; if "Shelah", the result is probably something whose precise statement I wouldn't even understand).

I have sometimes seen (multiple) authors referring to themselves as "The current authors" and would like to suggest another option:
(5) As the current author showed in [1], the following condition applies ....
It is similar to option (2) but draws a little less attention to yourself, in my opinion.


text:
Ethics behind using external excel freelancer to help with my thesis?
I have been working very hard on my thesis and I have reached a point with my data where I am required to code.
I am no where near experienced in coding, and there is also not enought time left to learn it.
Simply, the coding is required to re-format the information and figures I already have.
I have used an external source (freelancer) to re-format my data and provide instructions as to how he has done it. I asked for instructions so I could carry out the task myself, and the reformatted data so I could  check this against my work. Now, I am not sure if this is ethical and could compromise my degree?
I have not used the re-formatted data or instructions yet - as I am now unsure. I want to ask my supervisor about the ethics of using external assistance but I am unsure if this is a good idea?
In order to re-order my information and make it easier to process my initial formula instead of the manual way which I have been doing (there are close to 980,000 rows), the excel freelancer constructed a macro to essentially do the same work (which I still have not completed manually). I 100% want to give credit, and of course do not want to do anything unethical which is why I am asking here for advice.
What I mean by reformat is creating a macro/code  that performs a process. I have been doing this manually and have not scratched the surface considering the large volume of data. The creation of the macro gives the same answers I have been getting manually. So essentially it is not creating anything new, except for the macro. I hope this clarifies things. Again, I do not want to pass any work as my own so I would appreciate any more advice!
What concerns me is that I paid this freelancer to create the macro, a very small fee. Nonetheless, it does not sit right with me. So, What exactly should I explain to my supervisor? Should I mention I have already found someone? Or will this raise suspicion?

What do you mean by "re-format"? Has the coder essentially just made aesthetic changes to your figures (and restructured the data to allow this)? I largely suspect that there's no problem here, but I'd be hesitant to tell you that it's fine when the details are a little vague. It would be perfectly fine to ask your supervisor for clarification though. As you've said, you've not used the figures yet, so if there is a problem then you know now not to use them.

What's not ethical is passing (explicitly or implicitly) other people's work as yours. That being said, as long as only cosmetic changes (e.g. changing the style or labels of your figures, renaming table headers, switching the order of columns in a table, etc) have been made, you should be okay. But if this reformatting included some sort of analysis, or non-trivial modification, of your data, then you need to give credit where credit is due.

Raise suspicion of what?

If you have to do some arithmetic for your thesis, is it any different if you do it by hand or if you use a calculator? What if you buy the calculator especially? I'm not sure I understand your concern that paying a fee for this help changes things.

You can respond to mine (or anybody's) comments by clicking the Add Comment link below your question. If you specifically want to reply to me then including @Ian_Fin in the reply will ensure I'm notified of your response.

Maybe I'm under the impression that I cannot seek external advice, let alone pay for it - hence why I am worried I've done something wrong or worst yet, cheated. This is my ultimate worry/concern as I have worked incredibly hard for my masters until now. Is my assumption about paying for assistance wrong then? @Ian_Fin Also, do you have any advice how I should approach my supervisor about this? Many thanks,

@JaneDoe It's perfectly acceptable to seek external advice. Seeking advice from people whose expertise is different to your own is an extremely common part of academic work. Where it becomes problematic is when you don't acknowledge that the advice came from someone else, and you (even inadvertently) pass it off as your own. I don't see that the fee changes this at all. As for how to approach your supervisor, see the final paragraph of my answer.

Hi @Ian_Fin ok thank you very much. my last question is, should I mention in my email to my supervisor that I have already reached out, paid and obtained instructions how to create the macro and know would like to confirm whether it is acceptable to use this or not? My main concern is if he says no it is not acceptable to use it, then does this leave me in a bad situation where if I actually end up working out the macro myself, how is my supervisor to know if I honestly did it myself or used the macro provided by the freelancer?

I think it would be okay to write an email asking whether doing what you've described is acceptable. You don't need to say that you've done it, but don't make it sound like you haven't done it either, and if your supervisor asks whether or not you've done it then be prepared to be honest. In the event that it is against the rules, and you manage to produce the macro yourself, your supervisor may have difficulty proving that you didn't (or did) write the macro yourself.

Hi @Ian_Fin, thank you. I have put together an email saying exactly what I have on this thread and ended with '
So my question is, I would like to know what the ethics are in seeking assistance with the coding of the excel sheet (which is what I have done, but not yet used)?  I have not used the information as part of my thesis and if it is something that should not be used then I am happy to continue carrying this out manually, as I am conscious of carrying everything out ethically as I have continued to do within all of my academic studies. '. I think it might be better to be honest.

@Ian_Fin when I think about it, There is no way I will be able to create the macro on my own. So I feel there is actually no reason to worry about my supervisor proving my macro later on, as I would not be able to create it myself. Do you think this is a good approach? I really appreciate your help with all of this.

In that case, you might as well tell them what you've done and ask them if it's okay.

Possible duplicate of Is it ethically questionable for me (an undergraduate) to hire "research assistants"?

@CapeCode Hi, I dont think this is anywhere near the question you have tagged.

Thank you ever so much @Ian_Fin . I have emailed my supervisor and will see what he says. Thank you!

One thing to note is that if this analysis done by an outside person actually affects your data, beyond cosmetics, you are still the one responsible for the accuracy and any validation necessary to verify the program is working as expected. If this type of analysis is commonly used in your field, you at least need to understand it well enough to know it's working properly, even if you are slow/inefficient at doing it yourself. Finally, if your data contains any protected content - from human subjects, for example - then you are likely against IRB protocols and very much in trouble.

From what you've said in your question, it doesn't sound like there's a problem here. You said the information and the figures are your own, you've just had some assistance with making the data easier to work with.
It doesn't sound like what's been done is much different than if someone had pointed out that Excel already has a function that does what you were doing in a more streamlined fashion. Of course, this would be perfectly fine.
It's quite common for a student to have had the help of someone else in the course of working towards their thesis. This is particularly the case in technical matters like coding. You just have to make sure that you acknowledge their assistance appropriately (typically, by saying in your Acknowledgements that they provided assistance with your data). It's perfectly acceptable to get help from other people in your work. Seeking advice from people whose expertise is different to your own is an extremely common part of academic work. Where it becomes problematic is when you don't acknowledge that the advice came from someone else, and you (even inadvertently) pass it off as your own. I don't see that the fee changes this at all.
If you want to know for certain that this is acceptable then you should obviously ask your supervisor. Just explain the situation in full and ask "Is it okay to include this work in my thesis?" The thesis has not been submitted yet. So in the case that what you have done is inappropriate then no damage has been done. You would just ensure that the figures that appear in the thesis were not those that the freelancer produced.

When in doubt, give credit.
As Ian_Fin states, this doesn't sound like an ethical problem. But it never hurts to be explicit in stating, either as a citation, or as an acknowledgement, that you had assistance.
There are two cases here. Either there is no problem, and giving an explicit acknowledgement changes nothing to do with your thesis, or there was a problem, and you've made the ethically correct decision by being honest about it.
Unless you're getting a degree in Excel formatting, and showing that ability was the point of the thesis, I don't see this as a likely problem.

If you can manipulate a smaller dataset, say 20 rows, to reach the same stage of data manipulation, which you reach after the excel help, there is no new subject matter content added by the excel helper.
It might hurt if you mention it, verbally or in writing, because one can never be sure how much the reader would understand about the extent of help received.
But be sure to not use the excel file directly provided by the excel expert. Use the given instructions and generate it yourself, so that you can ensure repeatibility of the analysis as well as instruct others, if need be. If you cannot do it without help from that person, there would be no option than to acknowledge the assistance.


text:
Is offering to use personal funds for research a good idea?
I'm at an engineering department at a public US university, and I'm somewhat new to writing proposals. The call I'm submitting to wants know if the project budget is higher than the amount of the grant, what other sources of funding the PI will use, presumably to ensure the success of the project.
First, I'm not rich. But this leads to me to think, is it okay to use personal funds to do research? For example, if a piece of equipment costs $4000 and I only have $3950 left, can I supplement it with personal funds?
What might end up happening is that I might convince a colleague to lend me his instrument. But I don't want to say this in the proposal. Also, I'm not sure saying the project will be "supplemented by personal funds" is a good idea.

I'm confused. Why don't you just apply for $4000 instead of $3950?

@DavidRicherby, He is saying if something costs N dollars and he only has N-1 dollars left, can reach into his pocket and use $1 to pay the difference.  It is independent of how much he initially received in the grant.

@user1717828 One can imagine the answer being very different if the question is about N-1 dollars, rather than N-50 or N-5000.

@DavidRicherby At which point one might ask at what point N-n' does the answer change, but now we have a problem for mathematics stack exchange I think...

@Michael We might ask that but it would be futile and unnecessary.

I think you shouldn't offer private fund to supplement a research budget, and I also think people won't let you for the two following reasons (among others):
1. It's not your private responsibility to fund your research. For the sake of your own self respect, you shouldn't pay to work. It will give a bad signal, even subjectively, about the quality of your work. It's important for an academic career to be able to show that you can secure complete funding for your research.
2. Personal funding is not reliable:
People reviewing your application will see that the project is underfunded and will doubt that you will effectively be able to compensate with your own money. There will be no ways for the institution to enforce a funding commitment like "the project will be supplemented by personal funds". Funding is generally secured via contracts or other forms of legal documents.
Besides, any institution that relies on researchers breaking their piggy banks to pay for equipment is doing a sloppy job and it's going to hurt its reputation.

Absolutely I agree with the answer when we're talking about substantial sums of money, or contributions to larger purchases. But small and relatively incidental purchases shouldn't be a problem if you get some personal benefit as well. e.g. if you want a nicer notebook than what's in the department's stationery cupboard, I think it's fine to buy a Leuchtturm on your own dime.

+1 Never mention that you are going to use your own funds, even if you decide doing it.

If I have a $40 pen that I just love, it seems like using that (or perhaps even getting a second one) while working would bring much greater satisfaction while working than if I were to use the institution-provided good, but just not quite right for me, pen to make the same markings on the same papers. If I needed a $4000 piece of equipment to get started... well, that's a different matter. Now, you could argue that using my own pen isn't "offering private funds to supplement a research budget", but it's obvious that just like in all walks of life, there are shades of grey here too.

The call I'm submitting to wants know if the project budget is higher than the amount of the grant, what other sources of funding the PI will use, presumably to ensure the success of the project.

Almost certainly the answer to that is not "my private money". I can see three "correct" answers from the point of view of the funding agency:

The PI will make sure that this does not happen. Optimally, you will attach a detailed cost planning that is well within the grant amount to substantiate this point.
The host institution is co-funding the project. This is often quite popular with funding agencies, as it shows commitment from side of the host institution.
Another funding agency is (potentially) paying for it (see info on other submitted or accepted grants). This one is a bit iffy, as relying on another submitted grant is high-risk. Also, depending on the concrete setup, you may involuntarily raise the suspicion that if your current project is not accepted, the "other" agency may fund it in full - and as you can imagine this is an impression you want to avoid at all costs.

For example, if a piece of equipment costs $4000 and I only have $3950 left, can I supplement it with personal funds?

You can definitely do that, and in practice this can sometimes happen (maybe subtly - for instance by going on self-paid conference travels, using your own laptop, etc.). However, the project proposal is certainly not the right place to mention this.

#2 in your list is usually called "voluntary committed cost-sharing" and is basically forbidden by the NSF in the US except where it is explicitly required. Cost-sharing gives large institutions with deep pockets an advantage over smaller ones with smaller budgets since their projects can propose to do more. Out of fairness to everyone, NSF has basically banned it. It used to be popular until the smaller schools complained enough about the well-endowed universities buying their grant opportunities out from under them.

@BillBarth I was not aware of NSF's stance on this, but it's definitely not uncommon here in Switzerland. Not so much for the NSF-equivalent, but for various smaller foundations. The grants they provide are usually not that big, so by themselves they are not sufficient to fund ambitious projects. Hence, commonly one proposes a big project, says the host uni finances 50% of it, and only asks for the other half from the foundation.

When NSF or another federal agency wants to do something bigger than it can, they can demand cost-sharing so that the overall size of the pot gets bigger. It's pretty uncommon to do these days here, but I have seen it.

Not sure about the US, but over here in Europe (Britain to be specific) we usually ask the university to top-up the grant as to fill the gaps.  If a researcher succeeds to get 90%, the institution that gets credit for the research should give something in return in the form of 10%.


text:
What is the limit on reimbursement of indirect expenses due to attending conferences (e.g., baby sitting, winter coat, etc.)?
Going to conferences induces some costs on a researcher's personal budget. In all places I know, expenses directly related to travel and accommodation are usually covered (travel, hotels, food), but there are also some indirect expenses that aren't typically covered.
I'll only give one example, that is directly applicable to me: when I'm away I have to get a baby sitter for the kids (for the days where my wife can't pick them up, say). However, I'm sure there must be other examples.
Are there institutions that cover these “hidden” (or indirect) expenses? What rules do they follow? It must be difficult to know where to put the limit… (“hey, I'm going on a conference in Sweden in December, which means I have to buy myself a new coat! can I get it reimbursed?”)

As far as I know, there is no such thing as "general" rules which things can (or cannot) be refunded. In my institute, there are unwritten differences even among different groups. And not to be overly pushy... I think this question fits more a polling question, see http://meta.academia.stackexchange.com/questions/336/a-place-for-open-ended-discussions-about-academia :).

Let me add another conspicuous example: tips in the US. You can't avoid tipping, and often they don't show up on receipts.

I'd be very surprised by any answer other than "They follow whatever rules their accountants have decided to impose on themselves."

The usual solution is very simple: you will get a daily allowance ("per diem"), which is a lump sum of money that covers all small costs related to travelling.

A concrete example: a researcher at a Finnish university, travelling to a conference in Germany. You will get a daily allowance of 61 euros per day, tax free. This should cover food and all other small expenses related to travelling.
Direct costs related to travelling (conference fees, hotel, transportation, etc.) are covered based on the receipts. However, lunch & dinner is not covered, as they are included in the daily allowance. Corner cases have special rules (e.g., what if lunch & dinner is included in the conference fee).

I have more experience in industry than in academia. Per Diem is the usual answer in industry.

At my university, I have two options:  (1) Don't submit receipts, and receive the standard per diem.  (2) Do submit receipts, and receive the minimum of the receipts and the standard per diem.

Several of my past universities have had the complement of @JeffE 's situation: submit receipts and receive the maximum of receipts and standard per diem.

@JeffE (3) come back from Japan and submit receipts in kanji up to a total of whatever you're allowed to get without regard for what purchases they represent (booze, cool Japanese elctronics you can't get in the states, ...) because the fool university bureacracy insists on reciepts even though the grant adgency specifies per diem.

@dmmckee No, I can't do that; my university insists on receipts in English.  And no, I can't get reimbursed for the cost of translation services.  (Fortunately, my per diem for international travel is larger than the state-mandated limit for domestic travel.)

I would strongly recommend against this procedure suggested by @dmckee . Even if no-one in the expenses department can read Japanese, they will find someone if they suspect you of the financial fraud you describe, and the gain from what you saved will probably a lot less than what you lose by the ensuing disciplinary (if not legal) action.

A "per diem" is - AFAIK - not supposed to cover anything and everything, just some kinds of expenses. Babysitting your children is not one of those.

@Jeffe What incentive do you have then to submit receipts (besides possibly an ethical one)? In addition to being tedious, your universities solution implies that you always get more money from per diem.

@Miguel Precisely. And that's why I don't submit receipts.

@einpoklum Wouldn't a per diem be exactly for those costs that you aren't going to be reimbursed for when you show a receipt?

@sgf: The thing is that a per diem can be used for whatever you like, since nobody checks the actual expenses. So the question of what's it for is not entirely clear. However, it's often calculated using prices of food, drink and lodging; and you can report some additional expenses over the per diem.

@Miguel Maybe the university decided the tradeoff of having to pay someone for double checking the receipts and the person handing in for collecting and submitting them are worth just making it easier to get the full per diem. On topic: In Germany you get the receipts (not food, but travel and fees) plus the per diem (which is more than just covering food would be).

Usually, if an "indirect cost" will be reimbursed by the university, it must be a cost that would normally be allowed if it weren't occurred on travel.
So, for instance, something that would be considered an "equipment" purchase—such as a battery for a laptop to replace one that dies—might be allowed, but babysitting costs might not.
However, most institutions do have a "travel manual" or regulations that cover what costs are permitted for travelers to have reimbursed. If you have any questions about the policy, you should consult your institution's travel office for guidance. (These regulations often change, usually in response to someone else going overboard and exploiting loopholes in the regulation, which are then tightened for everybody.)
My instinct, however, tells me that such policies are probably quite rare for any institution that accepts government financing for its operations. Usually, those funds have significant restrictions on what sorts of expenses can be associated with travel, and thus it's easier to adjust the institution's policies in accordance with that. For institutions that are privately financed, it's a lot easier to institute policies that are more liberal. But you'd probably have to go to an extremely "progressive" institution (maybe a Google?) to find one that will reimburse you for these sorts of costs.

Oh, I am perfectly aware of my institution's policies: only very specific (and listed) costs are reimbursed, for the rest I get zilch. I am specifically asking if there are academic institutions out there that have employee-friendly policies regarding expenses created by the travel. (Maybe hidden costs is not the right term for it, though… I'm thinking about stuff that would not happen unless one traveled.)

Upon checking “hidden cost”, it appears it have a more specific meaning than I thought… so, I'm editing my post to remove this term. Sorry about that! I meant to inquire about indirect expenses linked to travels.

Given your answer here, would you mind having a look at this question of mine?

Disclaimer one. I'm from a big Japanese University with lots and  lost of Money.
Here, like Juka suggests, travelers get paid a daily expense, for example, I went to Australia last year, and I got paid the exact sum for the airplane and a daily allowance that is supposed to cover meals and lodging. The thing is, unless you eat like a king and sleep in a 5 star hotel, you'll usually end up with extra money. (around 200 USD-300 USD more).
I ask my adviser and he told me that this was normal, and postdocs and profs get even more money, because they consider they have families.
I think is a good practice, but then again, if your University does not have a huge endowment, it may get tricky.

Just curious — why do they suppose having a family means needing more travel money? Do they suppose the family joins in the travel, or do they suppose the family needs to make additional costs because one family member is not there (e.g. extra childcare costs)?

Here in Japan they like to be very inclusive, and the logic goes, if you are a single parent, you may need to pay child care, but then it would be unfair to those who are not single parents, so they pay them both.
Is like the child allowance the government gives, everyone receives 200 USD per child a month, regardless whether you need it or not.

Are there institutions that cover these “hidden” (or indirect) expenses?

Yes, but not necessarily all such expenses, and specifically I don't know about babysitting costs.
To give some concrete examples, I have had the following expenses covered:

Personal insurance having to do with my travel
Laundry during travel (although that was from a commercial research outfit so might not apply)
Membership in a professional society which enables reduced registration fee for a conference
A tube for carrying posters (as opposed to an actual poster which is a direct expense)

What rules do they follow?

Individual institutions have their own rules, and if these are not in writing - people in charge of budgets have some set of rules in their heads which you would need to query...

It must be difficult to know where to put the limit… (“hey, I'm going on a conference in Sweden in December, which means I have to buy myself a new coat! can I get it reimbursed?”)

Actually, I just asked a related question. I would actually think that if you live, say, around the equator and need to be at a conference in Sweden you should indeed be reimbursed for the cost of coat - either partially or fully. After all, you're unlikely to need that kind of coat in your daily life and perhaps not even when you travel.

Sometimes conferences actually organize child care services or provide support of child care that you pay yourself. See examples: https://www.hr.cornell.edu/life/support/conference_care.pdf and http://www.aps.org/programs/women/workshops/childcare.cfm  The last one says:

Examples of Allowed Expenses

Daycare expenses at the March Meeting
Extra daycare expenses incurred at home because the primary caregiver was attending the March Meeting (e.g., cost of a sitter)
Expenses incurred in bringing a babysitter (or grandparent) to the March Meeting

Other than that I don't think many employers explicitly reimburse those costs. People tend to consider that they are part of the "package" that you accept when you start a career in research (I am not saying it is a good thing).


text:
Is transferring to another university an option for an unhappy PhD student?
I've heard of people transferring between graduate schools because of their advisor moving to another school and taking their students with them.
Do students ever transfer for other reasons? If a student isn't happy at the school they choose, could transferring be an option? Presumably they would frame it as something positive such as "turns out I really want to work with Professor X" rather than "I hate my school", but does this ever happen? Is there a certain timeframe in which this is possible? (Assume it's a 5 year PhD program.)
If the answer varies by subject please mention the subject in your answer.
(Context: many friends have told me that if it turns out I'm not happy with my choice, I can always transfer. My impression is that this is actually difficult since many schools don't accept transfer students and in any case not being able to stick with a program looks bad -- but I don't have evidence either way so wanted to ask people who are in academia. Of course the ideal would be to pick a school one is happy with in the first place!)

I know "transfers" of two kinds: 1) starting a new PhD program 2) formally being enrolled and one place but de facto collaborating a lot with another place. Sadly, one of the biggest pains in doing PhD is that when things aren't working you cannot just change places.

Related: https://academia.stackexchange.com/questions/23170/my-department-is-not-concerned-with-publishing-is-this-a-valid-reason-to-move-t

Mathematics
Let me specify that by transferring, I mean moving to another university in the middle of a graduate program.  Switching universities between undergrad and grad or between a master's degree and a Ph.D. is very different.  Basically, those are the only mainstream opportunities to move, and anything else will require an exception.
Transferring is certainly not unheard of, but there are some serious caveats:

It's difficult to transfer to a substantially more prestigious department.  It can happen, but the admissions committee will be very skeptical, and it's just not going to work out unless the application is outstanding.  In particular, many committee members specifically do not want to reward rolling the dice again and seeing what happens, so for transfers the question is not "Does this application look better than our weaker students?" but rather "Is this application so obviously wonderful that we would be shooting ourselves in the foot if we accepted someone else instead?"
Expressing any unhappiness will make it much harder to transfer.  You may think you'll be happy at the new school, but they will worry about ending up with an unhappy, unproductive grad student on their hands.  And they are right to worry about that: the best predictor of future happiness is past happiness, and many unhappy people have unrealistic beliefs about what would make them happy.
It's hard to transfer once you start seriously working on a thesis.  If your work isn't going well, then that's a reason not to accept you.  If your work is going well, then that's a reason you should continue working with your current advisor.  Unless your advisor has died or left, it will be tough to convince anyone you are a good candidate for transferring.
No matter why you say you want to transfer, there will be some suspicion that your goal is to end up in a stronger department or a more desirable location.  If you have another reason, you'll have to make a powerful argument for it.

I've heard of people transferring between graduate schools because of their advisor moving to another school and taking their students with them.

Sometimes they transfer officially, and sometimes they still get degrees from the previous school but complete their theses while in residence at the new school.  The latter is generally easy to arrange when an advisor moves.

"No matter why you say you want to transfer, there will be some suspicion that your goal is to end up in a stronger department" -- assuming the candidate is suitable for the "stronger department", why would the admission committee see this motivation as something negative?

@Pandora: It's not so much that it's negative, but that the committee may not believe other reasons.  Applicants sometimes outline personal or intellectual reasons why they feel a certain department would be a much better fit for them, only to have the committee basically ignore the stated reasons on the grounds that they are just an excuse.

@AnonymousMathematician what if they accepted you and offered you an assistantship, but then you wound up choosing somewhere else? Would the place you turned down be more inclined to accept you as a transfer?

I have transferred during my PhD to a far better institution and it was one of the best decisions I've ever taken. On points 1 and 2 above:

I agree that the admission committee will likely to be skeptical. Get in touch with a potential supervisor first or detail why you are transferring in a cover letter.
If you share the reasons you're unhappy we can help you formulate them. Remember that the potential supervisors likely know your current one and no supervisor wants to be known for stealing other people's PhD students. Balancing transparency and political correctness is key here.

Computer Science
Yes, PhD students transfer for many reasons besides moving advisors.  Sometimes the reasons are purely professional; for instance, I've seen several students successfully transfer because they  discovered a passion for a subfield that didn't match the interests/experience of the local faculty.  Sometimes they're more personal things like two-body problems (especially when they become three-body problems).  Sometimes advisors die or leave academia.  Sometimes it's because of an irreconcilable disagreement between student and advisor/committee.  Sometimes the student just thinks they can do better than their current department (and has the publications to prove it).
Probably the most painless time to transfer is immediately after completing a master's degree.  (I did this.)  That's a natural time to switch research directions, and many PhD programs allow their students to pick up a Master's degree along the way, even if they don't have a separate Master's program.  (Mine didn't.)
Still, applications from MS students in PhD departments will face skepticism, especially if the applicant already has a good track record with their former advisor.*  (Why do they want to leave their current advisor?  Shouldn't we offer this slot to someone who doesn't have one?)  So it's important for the applicant's research statement to explain why the new department would a better match, without disparaging the old department.  It's also important to have a strong and supportive recommendation letter from the former advisor, to address possible concerns about technical weaknesses or personality conflicts.
(*And if a PhD applicant doesn't have a good track record with their MS advisor, they're not likely to be admitted anyway.)

Computer Science
It's not uncommon for a student to transfer, usually earlier in the program. The reasons can be as you mentioned, and often there are non-academic reasons as well.
You do have to apply again from scratch, although its possible that admissions committees will look more generously on the application. You might be able to apply out of cycle for spring admission as well - there are fewer applicants and each application gets more careful scrutiny.
But in any case it is important to have a reason relating to the desired destination. If you want to work with professor X it will help immensely if professor X can speak on your behalf by writing a letter. In other words, don't think of transferring out, but think about transferring in to maybe one or two targeted placed.

Field: Mathematics.
Transferring is possible although you might have to 'start over' at your new university. For example, perhaps you have completed the first year sequence of courses in University A and passed some prelims before transferring to University B. At University B you might either be required to go through their first year sequence, or take (and pass) the relevant prelims to have the courses waived. This can be difficult since first year courses and topic and prelims tend to vary across departments. In addition, depending on how much prior experience you have before coming to University B, they might require you to finish your degree in less than usual time (say, 3-4 years instead of 5). In particular, folks with Masters degrees applying to PhD programs are often required to get a second Masters in their second university.
Source: A friend of mine transferred from Rice Mathematics to UW Madison Mathematics; additionally this was a topic of conversation at a Nebraska Conference for Undergraduate Women  in Mathematics where a breakout session leader had transferred universities mid-PhD.

In particular, folks with Masters degrees applying to PhD programs are often required to get a second Masters in their second university. — Interesting.  My university explicitly forbids duplicate degrees.  If you have an MS in mathematics, you cannot get another MS in mathematics (although you can get an MS in, say, computer science).

I haven't heard of being required to get a second Master's degree (many programs don't even require one in the first place), but prelims/required courses can definitely be an issue.

The specific instances I have seen of students being required to get a second Masters degree are not in mathematics. In particular, the students in question had masters degrees from India and were required to get second masters degrees as part of their (5 year) PhD programs in Psychology and Engineering - possibly in part because the masters degree is somewhat synonymous to candidacy and/or skepticism about degrees from other countries.

I am currently trying to transfer too. My story isn`t the nicest neither. I met one guest speaker at my current university and just loved her work. My lab is stacked in old technologies and I feel we aren't innovative at all.
I talked with this guest speaker and her answer was very positive regarding getting me as her student. However she asked me to tell my supervisor before applying: bad idea.
Maybe because I am in Asia and here the culture is that your professor is a God, he was really unpleasant and rude with me. He even said he would write bad recommendation letters for me if I change universities. For me that was harassment. His main reason was the money invested and how bad this looks for him and for the university.
My advise is: be sure you can move and then talk with your adviser. The only positive thing was that after talking with him, I was certain that I was at the wrong place. I am positive I can change. So if you aren't happy or the program isn't aligned with your future goals and perspectives, change! Don't waste your time.

I see the anecdote and its connection, but I'm not entirely sure that I see this as an answer to the question.

I transferred during the first year of my PhD program successfully. My project at my original department was fully funded and my adviser was also great. However, I did not like the department and my PhD major was not in line with my interest. Thus, I applied for another major which I liked more.
One problem that may arise is recommendation letter. I asked my MS adviser (in another school) to write letter. I also asked my PhD adviser for recommendation letter. This part is a bit tricky, but I suggest to be honest and tell the truth and provide detail explanation for your decision.
I talked with 4 faculty members about my application in a conference. Three of them did not have any problem whatsoever with the fact that I am a PhD student from another school, and they recommended me to apply whereas one of them told me that the department does not accept transfer student. I finally got admitted into one school. I applied from a mid-rank school to top rank schools.
My personal view is that there is nothing wrong with transferring from one school to another, but you should have a good reason for doing that. In any case, some faculty members understand that a student could have many reasonable reasons for moving away from a school and joining another one while others are not very open-minded and think that it is wrong.

Selection of graduate students is hard.
It's fine to switch programs, but it's a lot like switching jobs after a short period.  If you start a job somewhere, then immediately leave it, you need a decent reason in your narrative.  The program you're applying to needs to believe that you're interested in sticking around when crunch time comes, or you're not worth the investment.
It helps if you have a legitimate-sounding reason in your personal statement that makes it sound like the reason you left the previous institution is unlikely to recur.  It definitely helps if you have an LOR from your former advisor.

What about, say, transferring from a Math Education PhD program into a regular Math PhD program, because you realize that doing research in pure mathematics is where your heart really lies, and not in doing research on how best to teach it to other people?

I realize this is an ancient question, but I think it's a lot more defensible if you are changing programs entirely like you mention. It's not uncommon for someone in the grad-school path to shift gears because they discover something they are more passionate about, and passion is exactly what your selectors want to see evidenced. If you can convince them "I like this even more" rather than "I'm bored", then that is a positive.

Science (chemistry).
It is very hard, up to impossible, to change PhD program in science after you started one, as well as starting over after a failed attempt.
The only option is before you enroll in any.
Even if this is not directly stated in requirements, selection comity will be very suspicious and very unlikely to admit such a student.
For the most part already enrolled applicants or applicants that were enrolled and quit are not considered eligible be programs and in almost all cases you are not eligible to apply for a scholarship.
I now as I am trying to change the PhD program.

Molecular Biology
The only time I can think of when PhD students changed universities was on the unexpected death of their advisor.  In that case, former students of the advisor who had since started their own labs took on the students, in some cases temporarily until they could find a better fit, in other cases until graduation.  For the "better fit" cases, I believe both student and new supervisor approached the better-fit lab and explained the situation.
In the case I'm thinking of, the deceased advisor was very well known, came from a highly prestigious university, and had many former students in strong positions.  I don't know how well it would have worked if all those points were not the case.
Aside from that instance, it's very rare for PhD candidates to move locations without your advisor moving as well.


text:
Appropriate to mention using a lab's dataset when seeking grad student position in that lab?
I'm in the scenario where I'm approaching my final year of undergrad and am looking for a potential advisor for grad school; I've done my research on their research, including reading through several of their papers and have a pretty good handle on what they're doing.
Now, obviously I'm interested in this research, and I find that some of these papers have some great datasets that I could use in (potentially) interesting ways (that the paper did not do). So I take this data and start playing with it, and let's say that I serendipitously arrive at an interesting find. In the eventual e-mail that I send to the researcher asking about the possibility of him/her taking me on as a graduate student, where I talk about their research and what interest I take in it, would it be appropriate to mention that I have worked with a dataset they had published in a previous paper?
I'm not sure how this might be taken, and I'm afraid of appearing disrespectful or full of hubris; just generally where it hurts instead of helps my case.
Potentially (?) Relevant:

In this scenario I'm just playing around on my own and my results aren't published or in the process of being so.
By 'playing' I mean in a bioinformatics sense, just manipulating the dataset.
Would the answer to this question be impacted if I didn't find anything interesting?

There's always a chance that they've played with the data in the way you've done/plan on doing, found whatever it is that you find, and decided it wasn't interesting enough to pursue. That does not mean you shouldn't try anyway if you find it interesting - after all, what is learning if not "throwing science at the wall and seeing what sticks"? ;)

It sounds to me like you have a couple of ideas regarding how you can use the data and what you might find: why not speak with this individual about your thoughts one-on-one? That way the advising process can begin informally prior to grad school! Additionally, the advisor may be able to help you refine your ideas (one of the pivotal roles of an advisor in the first place), or help you avoid pitfalls (e.g., "We've already tried X, and that didn't work, but maybe we could try Y!"). This should also be a good opportunity to see whether this potential advisor's style is a good match!


text:
Why do companies fund academic research?
I noticed that a lot of big companies are actively funding research at universities. I was wondering why they do this, as opposed to say funding in-house research as the knowledge ends up in the public domain.
Do they get actual patents out of it?
Do they just want to keep in the loop of the research (and if so why not just read the papers)?
Maybe they want to influence the direction of research?

There is a variety of reasons, as someone who has worked on such projects, here are a few that come to mind:

Access to research facilities. It's often far more rational to fund a study in a university than to invest in building your own wet lab/cleanroom/animal testing lab, etc. In some fields and countries, there are also regulations that limits certain area of research to university institutions (example: research on human tissues).
Highly educated, relatively cheap human resources In the subsets of projects where academic researchers actually do the work from the project description, it is generally cheaper and bears fewer risks than hiring people directly.
Great way of recruiting scientists by establishing a close collaboration, the company has the opportunity to meet and see potential hires in action.
In some fields, it can be a form of advertisement. In particular for companies that have scientists or research labs as customers. Example: lab equipment manufacturer, metrology tools, lasers, etc.

Do they get actual patents out of it?

Yes. It's frequent for industry-funded projects to result in patents. The patents are usually owned jointly by the company and the academic institution. Sometimes the technology is already patented and the study is only about testing an application. Publishing a technology in the scientific literature can also be a way to prevent other companies from claiming ownership, since you can't patent something that is already published.
Note that industry implication in academic research might diminish, as it becomes evident that they aren't always getting good research for their money. See: http://blogs.nature.com/news/2011/09/reliability_of_new_drug_target.html

Another note on patents: often company funding gives the company the option to take out an exclusive license to any university IP developed with their money.

A few other reasons, which are less glamorous:

Often provides tax incentives for companies
Very cheap way of training potential future employees who are experts in their research
Inexpensive way to explore new ideas. If a company has financial issues, far better from a PR perspective to stop funding research at a university than it is to lay off some of their employees
Speaking of PR, it provides them benefits and can get their name EVERYWHERE within a University
Some US companies are obligated to spend a certain amount of money on domestic research (our institution had several grants of this nature)
Easy and cheap way to stay informed of latest technology/research trends. A research project for a year is a much cheaper way to generate a literature review than paying a fulltime employee, for example

as opposed to say funding in-house research as the knowledge ends up in the public domain.

This is not always true.

Can you clarify "Some US companies are obligated to spend a certain amount of money on domestic research" ?

How is any of this 'less glamorous'?

@usεr11852 it might be cheaper but the productivity is also lower, because PhD students and their advisers have other priorities and are usually free not to do what the company paid for. The vast majority of industrial research is still done in-house for good reasons.

My significant other has been involved in the startup world for some time. Big companies do this for the same reason that they will take high risks on acquisitions... It's cheaper labor for R&D. The thing that always perplexed me is that Pfizer report from a few years ago that essentially said they couldn't come near replicating many of the findings in academic journals. So, at least in biotech I'm perplexed by this behavior, but it seems to happen less in that field based off of my personal experience with lots of professionals at small and large companies.

There is an organizational problem with doing long-term research internally in a high tech company: it is almost always more cost-effective to divert the researchers into solving some short-term problem related to a current project.
Outsourcing the research via a long-term commitment to funding an independent organization that has its own priorities (e.g. a university department awarding PhDs to its student "employees") is a good way to resist that short term pressure.
My employer (a multinational engineering company) doesn't have any delusions that every university research project will produced something "useful." It's more like investing in Broadway shows were one big hit pays for all the flops, but you can't predict in advance which show will be the hit.
The conflict between open publication of results in academic papers and PhD theses, and the commercially sensitive application of those results to benefit the sponsoring company, needs to be managed, but that isn't an insuperable problem. For example new analysis techniques or computer algorithms can usually be demonstrated using well-known problems addressed in earlier academic papers, or using sanitized data, while the "real" application remains confidential to the sponsoring company. If a competitor decides to learn how to use the research starting from what is openly published, it's their choice to fund the costs of that task, both in money and elapsed time.

Answering this as someone who works in public health, and whose work has been funded by industry in the past:

"as the knowledge ends up in the public domain" is not necessarily true, as some others have noted. It is fairly common for corporate funders to require their approval of a study before publication - something I usually pretty vigorously oppose. But it is not safe to assume that it automatically ends up being publicly accessible.
They can get patents for the work or otherwise receive IP rights to the results of the study, but again, this isn't universal.
It is a good way to recruit scientists, or recruit scientists short term. Research funding means you can get a "burst" of productivity to answer a particular question without having to hire and maintain an employee. It's also a good way to add expertise that the company lacks without having to build a whole group around it.
Funding steers the direction of research. If a company thinks there's a topic that needs more exploration, making funding available is a good way to foster that research.
It adds credibility. While industry-based research isn't inherently biased, there's often an assumption that it is. Funding independent university-based groups means having studies done in different settings, and with researchers with their own free-standing reputations. It's much easier for them to point to "Dr. So-and-so's Study..." if they don't work for the company.


text:
Do my articles published in local newspapers count as publications?
I'm applying to Columbia's journalism school and it asked me if I have any publications. Since I worked as a reporter before for the local newspaper, and I did write a few headline stories, I thought this might help my journalism application. But since they're nor academic, I'm not sure if I should put down my news articles as "publications."

Rule of thumb: is it relevant for your application? put it in. Is it irrelevant? leave it out.

It's not uncommon to have subheadings for different kinds of publications. "Peer-reviewed journal articles", "Proceedings", "Monographs" and so on. For a journalism program, "Newspaper articles" seems like a completely appropriate subheading.

Or "popular press"  -- this kind of publication is highly prized in some circles, it shows the author's abilities to make complex ideas clear and relevant for a broader audience of non-specialists.

This seems particularly relevant given that the OP is applying to journalism school.

If that's a school which teaches journalism, then definitely, but like @rturnbull suggests, list them separately from anything else, since they're not academic publications about journalism.
If it's a graduate program for the study of journalism, then possibly, but only to a minor extent - and still it's the same practical advice: List them separately from anything else.


text:
Adding pictures to mathematical academic papers
I was wondering if there is this "universal" program that generates a picture of a graph (you make), then exports it to SVG form. The SVG is because I want to export my whole project to PDF, so I need everything to be scalable vectors.
I was really curious how do people add different style of graphs, from regular "circles connected with lines/arrows" to graphs of automata like so (Apologies, I cannot make this picture view from the front as I don't have enough reputation):
Picture of Automata for example
My question is basically if there are some good (free) softwares to create graphs (any time of graph), so that it would look nice in a PDF, and not pixel-y.
Or do they make these on photoshop alone?
I was really trying hard to find some, the closest thing I found is XMIND which costs money for SVG, and on top of that, I did not see how to make this automata style.
(The automata is just an example of a "bizarre" graph/image, but I really mean all styles)
Thank you very much!

In my experience, these kinds of pictures are usually created using the LaTeX package TiKZ. An example collection of what can be done with TiKZ and how is available here: https://texample.net/tikz/examples/

See also the associated package, pgfplots. One can also embed gnuplot code in that way, which can be more flexible in some cases. In general if you don't have a 'closed form' expression for your graph, you will need to use data files.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
General Guidline in making a index for a textbook
I am currently writing a textbook in some mathematical area and now I am at the point of creating an index of words.
Are there some general rules in academia on this, like there are for citing references?
For example, if I have some mathematical theorem, like "Theorem of BlaBla", should I then include it to "T" or to "B"? And also if there is some general definition, like a "norm" of a space and then there are some specific examples, like "p-norms", should I then order the latter separately in $p$ or together wth the general concept at "n"?
Thanks!

https://www.overleaf.com/learn/latex/indices

I know how to make an index with latex thats not the problem. I am asking if there are some general rules for making them.

I don't think there are general rules. My experience is many of them are a mess. Personally I'd have an entry under both "T" and "B" for the "Theorem of BlaBla" because some readers may look in one place and others in the other one. I think asking yourself what is most reader-friendly is a good guideline.

Okay, thanks a lot @Lewian !

@Udalricu S Your question is specifically about mathematics and I don't have an answer.  Wiley publishes many technical books.  They have a detailed and excellent guide to indexing that might be useful.  https://authorservices.wiley.com/author-resources/book-authors/prepare-your-manuscript/indexing.html


text:
Asking another Professor for available PhD-position within the same research group
I am currently looking for a PhD-position and I am in touch with a professor already for some weeks. We had two zoom meetings and discussed about possible topics. The official call for the application starts soon. The professor now also said that he helps me writing the research proposal.
Now, within the same research group, there is also another professor, which is doing research in quite some different direction. I also wrote him an email some time ago (before I become in touch with the prof mentioned above) and he said that he has a free position. Now, I would like to ask him for a meeting in order to discuss about possible topics.
Obviously, I can only apply once for the same university, but still I would like to know about all possibilities. Now, my question is the following: Is it "impolite" or "ungratful" to ask the second professor for available topics? I do not want to give the first professor the feeling that I do not like his topic and I am looking for something better, because in fact, I really like his research program. As I say, I just would like to see all possibilites before applying.

I think it depends on how you approach the situation. For example, if you talk to the second professor about your "shared research interests" and mention openly that you have also been in touch with the first professor, it is probably all right. Professors from the same research group/department can talk about their applicants- and so better that they hear it from you. Another possibility is that if you like the topics from both professors, you could explore being co-advised (if there is any way to find common ground between the topics, or that one of the professors later serves as a committee member). I think it is very important to pursue what you find the most interesting, but also to communicate openly about your options, and usually professors know (and understand) that at that stage you are exploring your options.

agree with above. Would add that of course they (the professors) would (/should) assume you are scoping out options, as no future is secure in academia.


text:
Citing article with number AND issue
I stumbled over some journal which uses, next to volumes, numbers AND issues. I am wondering how one cites articles in this journal. For example, if some article is contained in a journal having only a volume and a number (OR issue), then usually one writes
Author: Title. Volume(Number):FirstPage-LastPage
But what should I do if the article has a number AND an issue? Are there any rules for this case?

So the Journal of Old Dits and Dahs, often abbreviated ODD, has decided to use volumes, numbers, and issues. Perhaps this eccentricity is related to the focus of the journal, the history of Morse code. And (somehow) there is an article there which you want to reference.
First step: look through articles in ODD to see how references to other papers in ODD are formatted. This is how that particular journal prefers things. If you are submitting your article to ODD, copy this format. If submitting elsewhere, also use this format unless ruled out by step 2.
Second step: look through any style guides available for your (non-ODD) target journal. Perhaps they have some guidance. Lacking that, check articles in your target journal that may have referenced an article in ODD. For example, you could look at the citations for the ODD article you are looking at. Copy that format.
Third step: (probably not needed if you can find any info above) - use a more conventional citation style, making sure there is enough information to uniquely identify the ODD paper in question. Submit as usual and see if the editorial staff complain at some point. It is highly likely, particularly with electronic databases, that given the authors, journal, and some variety of volume/number/issue/page that the article in question can be found even if not cited as the ODD journal would prefer.


text:
Do Springer, IEEE, Elsevier charge a fee for non-open-access journals?
My PhD advisor and lab colleagues think that Springer, IEEE and Elsevier journals non-open-access charge authors for publishing a paper. (They usually only publish in local journals.) All the info I've found points to the contrary (except for "gold" open access journals, which do charge authors), but all I've found are people commenting on particular journals saying that they do not charge.
Nonetheless, I've found very few journals that explicitly say "submission and publication is free of charge". For example, JAIR mentions that there aren't any submission fees, but does not mention publication fees.  Frontiers of Computer Science does not mention charges at all in their instructions for authors.
I'm sorry if it's a stupid question, but I can't for the life of me find any definitive yes/no information online. (I don't have a concrete journal in mind since this all started because we are looking for one, but it'd have to be a machine learning/artificial intelligence journal.)
Do Springer, IEEE and Elsevier journals generally charge an author fee for their non-open-access journals? It may include submission fees or post-acceptance fees as well as page or figure charges.

Sorry, but I don't think it's in the spirit of the website to ask people to do Google work for you, in order to resolve a trivial dispute.

I did search; but given that: my research advisor and 4 other researchers in a research group I've recently joined (my first) were convinced there were charges; and that none of the journals I checked explicitely said there were no fees whatsoever to publish, it wasn't trivial to me.

Surprising that publication charges would keep a lab group from submitting to a journal. The publication cost is trivial compared to other lab expenses (e.g. postdocs), while publications in more prestigious journals help secure future grants -- and boost the careers of the authors. Even if no current grant pays for it and the university offers no funds, as long as the journal is more prestigious than free alternatives, it'd even be sensible to pay for it out of pocket. (May not apply to people in developing countries, but they tend to get fees waived anyway.)

Check te web sites of the journals looking for "instructions for authors", if that doesn't clear up the doubts, email the contact.

@user289891 In Argentina, phd candidates and postdocs are supported by scholarships from universities and other government agencies, so basically a research group or the institute it belongs to doesn't pay their salary. The same goes for full time researchers/tenured professors. This means that you can have a research group with few or no grants in some fields (ie, cs). Even if you have a grant, you need to take into account how exchange rates affect the cost of publishing.
Paying a journal $500 when that's basically half your monthly salary isn't always an option.

@ff524: submission fees are only one type of article processing charges (APC), which also include, e.g., post-acceptance publication fees; did you restrict the scope of your question intentionally? If not, the question should be editted for clarity.  For background, see https://en.wikipedia.org/wiki/Article_processing_charge#Submission_fee

@FelipeG.Nievinski I've edited it.

I agree with the other answers, but they are anecdotal, and you asked for some "definitive" answers to help you convince your colleagues and advisor. Here's what I found:
IEEE
None of the IEEE journals has a required charge for non-open access publications.
The publication FAQ says:

For a detailed listing of paper charges by publication, download the List of Voluntary and Overlength Paper Charges (PDF, 287 KB).

Here is the current version of that list. You will note that some journals have voluntary "sustaining" charges for "normal-length" manuscripts. In fact, IEEE policy specifically states that those charges are not obligatory:

IEEE Policy 6.9 permits some types of periodicals to levy page charges. If your publication is one of these, it is your company or institution, not you, which is being asked for support. Payment is not obligatory nor is it a prerequisite for publication.

In the statement above "page charges" refers only to charges for not-open, not-overlength, not-color-print articles. Many IEEE publications do have "overlength" page charges, which are mandatory - if your paper exceeds the "normal" length then you must either reduce the length of your paper or pay the overlength charges. The length of a "normal" paper depends on the journal and publication type (normal-length "letters" may be as short as 1 or 2 pages, for example.)  Some also have charges for color figures appearing in print, although there is no charge for online-only color.
More definitive info is available for each journal in the IEEE Xplore site, at the "About Journal" page, section "Author Resources", link "Additional Information", which opens a PDF with detailed "Information for Authors" (see an example).
(The document also does not include the recently added IEEE open access options, which do have required charges, which are listed here.)
Springer
The Springer author FAQ asks

HOW MUCH DOES IT COST TO PUBLISH IN A SPRINGER JOURNAL?

The answer there is:

For the majority of Springer journals, publishing an article is free of charge.

If a journal requires page charges, you will find them on the journal's springer.com homepage or in its Instructions for Authors.
Charges might apply e.g. for color figures or over-length articles. The information on these extra costs will also be available from the journal's homepage or its Instructions for Authors.
Charges for open access articles: If you choose to publish an open access article ("Springer Open Choice" article or in a "SpringerOpen" journal), there will be an Article Processing Charge (APC) to be paid by the author. As a consequence, the article can be freely read, downloaded or distributed from SpringerOpen.com and SpringerLink.com by any internet user.

Furthermore, even for open-access journals, Springer advises:

SpringerOpen journals routinely waive charges for authors from low-income countries; and individual waiver requests are considered on the grounds of hardship on a case-by-case basis.

Another Springer FAQ titled Why publish with Springer? claims:

Page charges do not exist.

which I think is as close to "definitive" as you can get.
Elsevier
Some Elsevier journals do have author charges, and by searching the Elsevier site I did find a (very) few non-open journals with required page charges.  I did not find any in CS with author charges, though.
The official policy I found is:

I am submitting my paper to one of your journals. How do I find out if there are page charges associated with this journal?
Page charges are journal specific. Many journals do not have page charges for submitted papers.
To determine whether the journal to which you are submitting has page charges, you will need to find the homepage for the journal and check it's specific submission instructions.

So if you're looking for a definitive "No page charges," Elsevier is not the answer.  In practice, however, there are literally only a handful of non-open Elsevier journals that charge author fees.

Looks contradictory to me: "If a journal requires page charges, you will find them" and "Charges might apply e.g. for color figures or over-length articles" vs "Page charges do not exist." (well, logically these are not mutually exclusive, but why mention the possibility if they do not exist?)

@DavidRoberts  I was just collecting all the policy statements I could find to go alongside the "experience" answers, I really don't know more than this. In practice I couldn't find a single non-open Springer journal with author charges.

@DavidRoberts This is one of the reasons why I asked the question; if you go and look in particular journals, they instructions for authors never say something like "Publishing in this journal is free for authors" or "Publishing in this journal is free for authors for articles of less than 10 pages".

@facuq The Springer journals do not usually say anything about charges, but the Springer policy is that "If a journal requires page charges, you will find them on the journal's springer.com homepage or in its Instructions for Authors." - so if there are no charges listed in those places, then the journal is free.

@facuq and the IEEE journals with "voluntary" charges often list them on their websites, but in any event none have required charges.

@ff524 Thanks, I read that, but I still don't get why it says no page charge; why qualify the word charge if there's no other charge other than the page charge?

@facuq There are "overlength page charges," "color images in print version charges," and for open-access, "article processing charges." Hence the qualifier, "page charge" - which is the only charge that applies to not-open, not-overlength, not-color-print articles.

@facuq In general any reputable publisher make any fees apparent up-front - if they do not clearly describe any author charges (as most don't, because they are free) then you can assume there are no charges.

@ff524 Yes, thanks again, I understand that now. And given the prior that they don't charge, it makes sense. But if your prior is that they do charge, like mine was, it's not immediately clear that they don't; I kept thinking that maybe there were other charges besides those for page, color and openness. You have to asume they don't because they don't say they do and consider those three the only possible charges. You can't find instructions that say "Authors can publish articles for free as long as they are not-open, not-overlength, not-color-print".

@facuq Agreed, they really should be more specific :)

You're accepting as "definitive" Springer's statement that "Page charges do not exist" despite Springer's own acknowledgemnt that over-length charges might apply.  Similarly, your summary that "None of the IEEE journals has a required charge" flies in the face of the sentence "Many IEEE publications do have overlength page charges".  You're underestimating the prevalence of these charges.  The declared page limit is set much lower than the average article length.  Below in my own answer I present statistical evidence demonstrating this point.

I have never paid for the publication of any journal paper, including papers in Springer, Elsevier, IEEE, ACM, SIAM, and AMS journals.
Some of those journals do advertise "page charges", but in my experience these are strictly voluntary.  I've never paid them, and my papers were published anyway.

Colored images in print sometimes have a fee as well.

The papers I have published in various IEEE journals have had voluntary page charges up to a certain page count, say 9 pages, after which you paid some per page fee which was mandatory. If I recall correctly, it was about $175 per page.

"Voluntary page charges"? Wow, I had never heard of such a thing. (I am in mathematics.) Does anyone pay them?

@Anonymous: I have heard of such a thing, typically at non-profit open-access journals.  (I am also in mathematics.)  They ask that authors pay page charges to subsidize the operation of the journal, but if and only if the authors have grant money to use for that purpose.

An anecdotal opinion based answer with zero evidence.

@FelipeG.Nievinski Really? Is this not direct evidence that the Springer (and other) journals that I have published in do not charge for publication?

@JeffE: your statement was vague: we have no idea how many papers you are talking about, in what field of research, etc.

@MarkMeckes Open Access "Article Processing Charges" are distinct from "page charges" at traditional journals.

To be certain, you'd have to check the specific journal's author instructions.
However, I've published in two Elsevier and one Springer journal (in mathematics) and never paid an author fee. The Springer journal had an open access option, which would have had a fee, but we didn't choose that option.

Around half the titles from the major commercial publishers (Springer, Elsevier, etc) have (potential, & effectively optional) colour charges (Kiley). [Wiley is listed as "no data available" here, but I can confirm from experience that some Wiley titles do have colour charges, and have a very tedious paper-based process for paying them].
Very few of the commercial journals have page charges - usually for historic reasons - but they are still reasonably common among journals published by US scholarly societies (Curb & Abramson). Other fees (eg submission fees, revision fees, supplementary material fees, "picture on the cover" fees...) are generally rare but not unknown.
As a result, they're a significant issue in some fields, where page-charge journals are still common, but in others, you can go your entire career without ever encountering them. Hence the wide variation in answers...

Edit: I finally wrote up and published my notes on this - "Considering Non-Open Access Publication Charges in the Total Cost of Publication'", Publications, 2015, 3(4), 248-262; doi:10.3390/publications3040248
My estimate is that overall these charges (page, colour, submission, etc) are equivalent to around 2% of subscription costs, which is relatively small but (given the cost of subscriptions) substantial in cash terms. The costs appear to be very variable among disciplines (and institutions), and aren't very well recorded by our existing ways of tracking spending on scholarly publishing. Which is concerning...

I find your "total cost of publication" (akin to "total cost of ownership") a useful concept to assess hidden charges, especially in non-OA publications.

@FelipeG.Nievinski It's not mine, but I agree :-). The main focus of current work is (understandably) on calculating TCO/TCP for OA material (taking into account APCs, double-dipping, offsets, and so on), but my feeling is that page/colour/submission/etc fees are overall a noticeable & yet badly-documented cost. They used to be fairly well understood, but as they've grown rarer people tend to forget about them...

Beside the above mentioned some journals (not necessarily of the above publishers) require a fee before reviewing your submission (sometimes only if you are not part of a society).
For instance the American Sociological Review charges a "$25.00 Non-refundable Manuscript Processing Fee."

I think the common name for them is "submission fees": https://en.wikipedia.org/wiki/Article_processing_charge#Submission_fee

It's not uncommon for charges to come in disguise, e.g., this is from the IEEE:

A mandatory Excessive Paper Length charge of $200.00 per page (beginning with page 7 and beyond) is required for papers in excess of six (6) printed pages. The author will be notified of the estimated paper length upon receipt of the original manuscript. The author will be requested, conditional upon favorable technical review, to pay an optional sustaining page charge of $110 per printed page to cover the cost of publication of the first six pages and will receive 100 black/white (no color) reprints of the paper if this charge is honored. There will also be mandatory charges for color figures.

Now comes the catch: the average paper in this periodical is more than six pages long and has at least one color figure. So in effect the majority of authors did end up being charged.
Here is some evidence that IEEE charges authors in excess of a thousand dollars per article in some of its journals.  I picked IEEE JSTARS because I have experience with it, both as an author and a reviewer.  I looked at the four issues published so far in the current year.  I scraped the page range of each numbered contribution; there were 151-7=144 articles, after removing 7 editorials, forewords, or tables of contents.  The typical article length, 12.1 pages +/- 3.2 pages (mean and standard deviation, respectively), is more than twice the nominal normal length (6 pages).  Multiplying $200 times the excess number of pages gives the sought-after figure.  IEEE charged authors US$ 1,213 on average as mandatory over-length fees in this journal.  That's effectively an article processing charge in disguise.  (I've shared the spreadsheet online.)

I don't know where you got this. But I have published several papers in IEEE journals and was never charged and my papers were up to 14 pages in IEEE Transactions. This charge is probably for some very specific journals.

Re: where I got this, there's a link above in "this is from the IEEE".  The over-length article charges start after various page numbers, between zero and 14, depending on the journal or magazine, see details.  As for anecdotal counter evidence, I was once charged US$800 in payment for publication of a 10-page article in an IEEE Transactions journal, and another time US$600 for a 9-page article.  Apparently some titles are more lucrative than others.  And these were non-open-access titles -- double dipping?

http://www.editorialmanager.com/homepage/DOCS/Author_Tutorial.pdf
Starting on page 35 of this pdf, this Springer journal details how there is a fee for paper submission ($75 charge for members; $100 charge for non-members) and the paper will not be forwarded to the editorial office until the payment has cleared. Additionally, there are other charges when they go to production (e.g., $50 per page for the first 5 pages, $35 per page for pages 6-10, $20 per page for 11+ pages).
I find this very odd as I've never had a journal request payment to submit or publish a paper.

The linked document appears to be a tutorial for software used by journal publishers including Springer, not a "Springer journal". The tutorial includes, starting on page 35 a description an optional feature of this software, which as far as I know, Springer's editorial process does not use.

authors: أبو عبدالله ابن يعقوب