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Choosing appropriate words for lay summary of a health research project
The lay summary of a research proposal is often needed to secure grants and get wide public support and engagement, especially in health research.
I understand that the more a scientist understands her research, the more her ability to explain it to the public and to write an excellent lay summary. It should be easily readable, and should use everyday words instead of complex terms and scientific jargon.
Problem
Apart from structuring the whole summary, the word choice could be challenging, especially for non-native speakers who don't directly work or have sufficient contact with the public.
One could:

ask for help from relevant patient and public engagement (PPI) groups or native colleagues: they can even help revising the whole document, but I think scientists should improve their own public writing skills in the first place
look for synonyms in dictionaries: this could help, but general dictionaries don't tell which synonyms are understandable by the average people
read related articles in websites that provide health information to the public: this is potentially very useful for familiarisation with non-jargon language, but may be time-consuming.

Questions:

Other than asking for help from others, what are (other) effective ways of finding out whether the words and phrases I use in a lay summary are appropriate to the public audience, and if not (which is more important), finding better alternatives?
Is there something like a "dictionary" to translate common or domain-specific jargon words/phrase to simple English (similar to 'academic word lists')?

Ways of finding out whether the words and phrases you use in a lay summary are appropriate to the public audience:
One approach is to put your text into something like simplewriter.
http://xkcd.com/simplewriter/
It highlights words which are not part of the most commonly used 1000 words in English.
That specific program is a little bit limited, more for an audience of children but there are similar text editors which can highlight complex or rare terms.
If you limit it to the 20000 most commonly used english words things should be readable by most laypersons.

This is not enough: there are many common words that have a common meaning for a layperson, but a very specific one in jargon; or are composed by simple words. From the top of my head,  "profile", "contact", "sequence", and "secondary structure" look pretty harmless words; but have a very different meaning for a protein scientist.

True but it's better than nothing for a foreign speaker trying to figure out which words are most likely to be unknown to a lay-reader.

Hand it in to some friend that isn't working on what you are doing, and learn about your mistakes from their feedback. In a few iterations, you will see a pattern, and hopefully, be able to correct it. For example, you may notice that you use "p-values" without explaining what they are.
Academics on a different field are a good target, since they are used to proofreading papers and specifically, looking for things that are introduced without explaining.
This will also help you not only with the vocabulary, but also the flow of your explanation. Even if a layperson understands a certain concept, it doesn't mean they are as familiar using it as you, and you may need to add more background or more careful explanations when using them.

Try to think about how you would explain what you want to do to a friend who may have a college education, but not in your field. This is roughly the level you should shoot for. If you have trouble evaluating whether what you wrote meets that standard, field test it: give what you have (or read it) to not just an imaginary friend, but to a real person, and let them comment on it.
I practice this in my writing intensive math courses with my students by letting them write a dialog. In a dialog, you write one person's statement and then have to turn around and wonder how someone else would perceive this. If that other person is a layperson, would they understand what the first speaker just wrote?


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How does copyright work on screen captures?
I am writing an article comparing three pieces of software. I have taken screen shots of all of them and would like to use them in a non-open access article. Given the intended journal, there is a reasonable chance of the images being on the cover. What are the copyright issues associated with screen shots?
Specifically, one of the pieces of software is free and open source (GPL v2), and two are free as in beer, but closed source with unknown licenses and no EULAs. To further complicate matters one of the closed sourced pieces of software looks and functions very much like a proprietary piece of hardware produced by a massive company. Three years ago I contacted the developer of the software and asked about using a screen shot and he said it was fine. The software is still widely available, but the direct download from the developers site now has text indicating that the massive company has "requested" that it be taken down. I own the physical hardware and am not aware of any crazy licensing restrictions. I could use a photo of the physical hardware if that is better.

You need legal advice. Talk to an attorney.
Perhaps your institution has one that you can take advantage of. Everything from here on out is rank speculation, and even your attorney's advice may not protect your from suit.
If you can, get permission from each source you want to take a screen capture of. There may be copyright protectable elements in those screen shots. There may also be trademarked elements.
If you cannot get permission for whatever reason, you may have to rely on fair use. Fair use is a defense to an infringement suit not a get out of jail free card. By using a copyright or trademark protected work without a license, you run the risk of lawsuit. Your institution may not be willing to rely on a fair use defense. Also, your publisher may not be willing to rely on a fair use defense (since they will be the lawsuit target).
I personally think your use is without question a classic and canonical example of fair use, but that doesn't mean that you will prevail in publishing without permission. Many venues require that your sign a form saying that you have the copyright or permission to use all your images, so be careful.

Fully agree, very good points. Just an opinion: the publishers themselves generally insist written permission from the original publisher for any republished figures, so most probably they would ask for a written permission in this case, too.

Are you saying that there is no difference between a screen shot of a GPL and closed source software? How do pictures of hardware come into play. Is hardware even copyrighted or just patented?

@StrongBad: Hardware itself can't be copyright protected. Firmware inside a piece of computer equipment can be. Your photograph of such equipment cannot violate the patent on the hardware nor the copyright on any software it contains. There could be some trademark issues with the logos on such equipment, but there's a pretty strong defense to trademark infringement for uses which are solely for identification of the protected work. I think you're pretty safe to take a picture of a piece of hardware and use it in your article. You will own the copyright in that photo. ...

In fact, it's better than trying to reuse the manufacturer's sales or marketing pictures, since they hold a copyright in said images! As to screenshots of GPLed software interfaces, I think this is an unsettled area of the law. To my knowledge, the GPL only covers the source code to the software and any graphics elements designed to support it. The Lotus v. Borland case says that the interface functionality itself is not copyright protectable, so a clone of said interface is non-infringing, but if you take a photograph of someone's painting, that's a derivative work requiring a license. ...

I don't think the GPL applies to an image that you take of the interface thereby infecting your paper with the GPL. It's hard enough to apply the GPL to documents, so I don't think that's an intend effect. That being said, why not just get permission?

If there's no explicit prohibition against it in a EULA and it is publicly-available software, just mention the source of the screenshot, either in small print on the cover or in a colophon.  Remember the law belongs to you at least as much as them and academics have been too passive in helping courts settle these issues.  And the proof of it is shown in other`s answers suggesting you should contact a lawyer.  But in the United States, the Law is explicitly reserved for the People, not lawyers.  These aren't difficult cases to think about.  Academia has been dealing with the issue of fair-use for centuries.  Just look at the issue as if it were your own special software, and you'll be able to figure out reasonable and "fair use".

This is terrible advice from a person with legal training! While the sentiment is right, your advice opens its follower to lawsuit which they may not be able to defend. Just because use without permission in this case is in your opinion morally OK and likely a fair use, it's awful, awful, awful advice.

@I amended the answer.  Sheesh, I mean at some point we have to live with each other.  If we live as if we might get sued at anytime, what kind of world would we be creating?  The Courts can't defend against the People being stupid.

What does "the Law is explicitly reserved for the People, not lawyers" mean? You also appear to be conflating of publication ethics with "fair use," which is a specifically defined term of art.

It means that the law doesn't favor (and mustn't favor) corporations and their legal teams.

@TheDoctor I have no idea how you have come to that conclusion.

@jakebeal Sorry, I shouldn't have assumed that you were American.

@TheDoctor I am American, and my education and experiences lead me to very different conclusions.  I agree that law should generally serve the needs of the populace, but you are making much stronger statements that seem to be based on rather unusual and difficult to support assumptions.

@jakebeal:  The "unusual" assumption here is that people not companies are protected under the law, and that every person is equal under the law.   Case law establishing corporations as people are distortion of the American Revolution.  The "difficulty" that you speak of is standing up to corporate america and for something that YOU know is fair.  Are you scared to take control of your own government and law?

@TheDoctor - I'll let you take control of the government, thanks. Since you're not scared and all. I'll be right over here....

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Are academics more tolerant of biological and philosophical differences?
My internal model of academia is that (1) as a group we are one of the most tolerant of biological and philosophical differences (e.g., gender, sexual orientation, and religion) and (2) that we are likely to take extreme views on issues related to our research. I have no evidence for either of these and they seem potentially at odds in that it seems strange that people would be so passionate about their research and be blase about their religion (or any other philosophy). Is there any work that characterizes the level of tolerance of academics on various issues?

Are you asking about relative tolerance (everything bar your last sentence), or absolute (which is what your last sentence could be taken to mean, and seems to be what fkraiem takes it to mean)?

@EnergyNumbers I am not sure. I cannot conceptualize what an absolute measure of tolerance is and would expect most meaningful characterizations of tolerance to be relative (although I am not sure relative to what). That said I am happy with anything that is informative.

fkraiem's study only looked at tolerance within academics, not tolerance relative to non-academics. And it's that issue of whether you're asking about tolerance relative to non-academics, or not. I had originally commented on fkraiem's answer, which might be the reason why they've deleted it, but once I re-read your question, I realised that your question is ambiguous.

There is a recent study which generated quite a bit of noise and seems to indicate that racial and gender biases do indeed exist in academia (at least in the U.S.). The researchers sent e-mails to professors pretending to be a prospective graduate student, and response rates varied widely depending on the ethnic- and gender- markers in the purported student's name.

True, although similar studies concerning job applicants in the "real world" have shown a similar gap in response rates.  While these gaps obviously need to be combatted, I'm not sure whether this study shows that academics are any more or less tolerant than the general population.

Important and relevant, however employment (strictly speaking, a very thin cut even from the employment issue) is just one out of several faces of tolerance / intolerance / racism in academia.

As a matter of fact, academics tend to be quite left-leaning, especially in fields like sociology. (Here's an article about this, with links to multiple studies.) Sadly, they're not abnormally likely to be tolerant of conservative viewpoints.

i have only found one study behind the link.

My understanding is that the question was general both in terms of geography (not only US), and fields (not only sociology) and not necessarily politics related. The generalization you just made is rather dumb. Also, even if that generalization would make any sense, there can be hundred and one reason why one doesn't vote for republicans (esp republicans like Palin), yet it doesn't tel much about what she/he thinks about gender or race issues.

@Greg, what you said was snarky, uncharitable, and, yes, intolerant. If you have something serious to say, please rephrase it in more professional terms. :)

@MissMonicaE Pointing out an error, a serious oversimplification and/or logical fallacy is not intolerance.

You also read way more into my answer than was in it. I never mentioned Republicans, for instance. (Yes, I mentioned "conservative viewpoints," but that's hardly synonymous with Palin, even in the USA.) Moreover, your tone was way out of line.

The straw-man misrepresentation of this answer, and the heavy down-voting, go a long way to providing evidence of exactly the intolerance that was at issue.  Sadly this is also not unusual on academia.SE.

@MorganRodgers: The linked post references two general theoretical treatments that discuss the phenomenon, plus one specific empirical study.  (I assume that the answerer is referring to all three of these as "studies", which is not unreasonable.)  This adds information and references that are relevant to the question.  I don't think for one second that the down-voting is due to inadequate references.

@MorganRodgers: Well, you just referred to it as an "opinion piece".  It is a law review article by one of the leading economic theorists of the twentieth century (first published in 1948, but reprinted as a stand-alone work in 1949).  The kind of loose language of referring to an academic article as a "study" or an "opinion piece" is not terribly uncommon.  This post did not get five down-votes for loose language in referring to the nature of its references.

David French is the president of the Foundation for Individual Rights in Education, a nonpartisan group that monitors free speech on campus. In a 2005 interview with ABC News, French argued that "the universities have been so captured by the left point of view, that you're going to get more political and intellectual diversity at your average suburban mega-church than you are at an elite university." The cause, he believed, was the systematic suppression and censorship of conservatives.
That same year, Rothman, Nevitte and Lichter published a paper using data based on a telephone survey in 1999 of approximately 4000 faculty, administrators, and students. The purpose of this study was to test if professional advancement is influenced by ideological orientation. What they found out, was that conservatives and Republicans taught at lower quality schools, compared with liberals and Democrats. This suggested, they argued, "that conservative complaints of the presence and effects
of liberal homogeneity in academia deserve to be taken seriously".
A 2014 study by Iyengar and Westwood underscored how powerful political bias can be. In an experiment, Democrats and Republicans were asked to choose a scholarship winner from among fictitious finalists, with the experiment tweaked so that applicants sometimes included the president of the Democratic or Republican club. Four-fifths of Democrats and Republicans alike chose a student of their own party to win a scholarship, and discrimination against people of the other party was much greater than discrimination based on race.
For a 2016 study, Shields and Dunn surveyed 153 conservative professors. “As two conservative professors,” they wrote in The Washington Post, “we agree that right-wing faculty members and ideas are not always treated fairly on college campuses. But we also know that right-wing hand-wringing about higher education is overblown.” Nevertheless, about one-third of the professors professors admit to using "coping strategies that gays and lesbians have used in the military and other inhospitable work environments", ie they "closeted" themselves by passing as liberals. Some also said they were badly mistreated on account of their politics.
In a 2017 speech before the Stanford Board of Trustees, former Provost John Etchemendy argued that he "watched a growing intolerance", "a political one-sidedness, that is the antithesis of what universities should stand for". "It manifests itself", he argued "in the intellectual monocultures that have taken over certain disciplines; in the demands to disinvite speakers and outlaw groups whose views we find offensive; in constant calls for the university itself to take political stands".
In 2009, world–renowned political scientist Norman Finkelstein was denied tenure at DePaul University for his criticisms of Israel's human rights violations against the Palestinian people. In 2014, co-discoverer or DNA James Watson was forced to sell his Nobel prize after losing most of his income for stating that people of African descent are less intelligent than white people. In 2017, graduate student Lindsay Shepherd was hauled before a three-person panel at Wilfrid Laurier University, which interrogated her for more than 40 minutes for showing a first-year communications class a video snippet from TV Ontario of Jordan Peterson debating another professor on the use of gender pronouns. In 2018, University of Pennsylvania Law School professor Amy Wax was removed from teaching mandatory first-year courses for saying in an interview that she didn't think she'd ever seen a black student graduate in the top quarter of the class.
These are some of many examples where academics / scholars have been reprimanded for making statements deemed too "politically incorrect" by their employers. While such cases are obviously but annectodal evidence at best, they do suggest Etchemendy may have had a point when he said he watched a growing intolerance "that is the antithesis of what universities should stand for". They do suggest it may indeed be safer for conservative professors to pass as liberals. They do suggest that French may have had a point when he argued there was systematic suppression and censorship of conservatives. And they do suggest that Rothman, Nevitte and Lichter may have been right to conclude that that conservative complaints of the presence and effects of liberal homogeneity in academia deserve to be taken seriously.

Your answer seems to focus exclusively on political views while I intentionally wanted to focus on biological and philosophical differences.

@StrongBad : How are differences in political views not a direct consequence of philosophical differences? For example, consider a typical Christian Conservative and an Atheist Liberal? Do you really not see how a different philosophical perspective is at the core of both their religious and political differences?

"While such cases are obviously but annectodal evidence at best[.]" Right.  In your collection of examples, some of them are obviously not instances of problematic treatment of academics -- e.g. in the case of Watson, getting partially dismissed from your position for making unequivocally racist remarks is not an instance of academic censorship.  Some of your other examples are much more convincing -- e.g. inappropriate censorship seems to be precisely what happened to Lindsay Shepherd, as evidenced by the university's apology to her.  Your list would be more convincing if it were shorter.

Your Watson link is actually about Shephard; I think you got some URLs mixed up.

@PeteL.Clark: It's tough if the "unequivocally racist remarks" are the result of (possibly shaky, possibly misunderstood, but still) statistical measurements. Is it worth diluting the term "racist" until it simply means "uncomfortable"? We don't normally throw moral judgment at research we don't believe in, even in much more harmful situations like medicine -- and for good reason. (I agree, though, that there is ground for controversy here, unlike the Lindsay Shepherd case.)

Please stop posting the same answer all over the place.

@darij: I looked at the details of the case, and the remarks were not exclusively based on quantitative analysis.  Rather he said "people who have to deal with black employees find this not true."  That is not a scientific statement but it is certainly a racist one -- no dilution there.

To call the Foundation for Individual Rights in Education a non-partisan organization is a bit disingenuous. It is explicitly Libertarian and at the very Right Wing end of libertarianism. To see that they have an agenda, you need only look at their funders. See, for example: https://www.sourcewatch.org/index.php/Foundation_for_Individual_Rights_in_Education

Obviously, you'll find more right wing & libertarian people supporting and funding an organisation dedicated to "defending and sustaining individual rights at America's colleges and universities", because it is mostly right wing & libertarian ideas that are under attack in 21st century America. With the establishment having adopted a hybrid of neo-Liberal economics & cultural-Marxism as their program for the future, the counter-culture of today consists mostly of the identitarian right and others who refuse to accept pervasive cultural-Marxist indoctrination & censorship.

I think it might depend on the field. For example, if you are in a Biology department, you're likely to be labeled as "ignorant", "dumb", or "coward" if you are Christian (or Jewish, or Muslim or any religion that believes in a God who creates), regardless of whether you believe in evolution or not, and regardless of what your actual religious beliefs are. Generally, in natural sciences that's a pretty common trend I think. One could argue that this is more related to the second point you mentioned, rather than the first one, but given that this intolerance, as I said, is regardless of the opinion of the religious person about the origin of life and rules of physics, one could also argue that having this opinion that "any religious person is incapable of appreciating science" as an assumption, is a form of intolerance.
(There is a documentary about Christian professors in science (or biology) departments who were not tolerated by their colleagues and were discriminated against, but I couldn't find it now)
When it comes to ethnic and racial tolerance, in my experience, a level of racism and orientalism that would face condemnation in the US (but not necessarily in Europe) is not uncommon in academic communities in Europe. That being said, my impression is that they're still considerably more tolerant than an average person (or at least an average conservative) in that society.
But overall, I perceive academics to be more tolerant than the median member of the society.

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Can the terms Alpha/Beta release be applied to an online course?
Alpha and Beta releases are stages in software release life cycle. Could these terms be used to denote the stages of ripeness of an online course?
The background for this question is that I have created a website to sell and teach online courses of my own making. The courses are about preparation for a technical interview for software engineering positions, so that most potential students should be aware of the mentioned terms in their original context.
I would say that a freshly developed course is in Alpha release (and charge less for it) to account for the fact that some errors and glitches are to be anticipated. I would then improve the course based on student feedback and advance it to the Beta release. In other words, I would rather say straight that the course might need improvement based on the students' feedback and offer a significant discount to people who are willing to struggle a little bit to save money, than to lose my reputation for producing top-notch courses.

It might sound cool but I wonder if it is necessary. I would call that material / course something like Name of the course - Academical year / semester - Name of the teacher / instructor

The question of what to write on a commercial website selling courses developed by a single individual sounds like it’s in the realm of marketing and business strategy. So I’m not sure the question is about academia, and deleted my earlier answer posted before the current edit to the question.

I wouldn't do this. You can of course anticipate errors in the material, but that is obvious and also happens in real-life courses. Those aren't alpha-courses either.
If I'd see a course that was labeled 'alpha-course', I wouldn't know directly what it means for a course to be 'alpha'. If I then read it is an alpha-release, I wouldn't want to be a test-student for some course. To you it says 'beware: there may be some small errors', but to me it says 'this course isn't useful yet'.

I would read the "alpha version" as "not ready for prime time". Alpha versions of software are only released for wide testing, not for actual use. Subjecting real students to something like this is probably unethical.

The problem with this denomination is that in other contexts, 'alpha' has a completely different meaning as e.g. in 'alpha-male', where 'alpha', 'beta' and so on indicate a type of hierarchy with 'alpha' being on top.
Students unfamiliar with this type of labelling might mistake an 'alpha' course as being superior compared to a 'beta' course for that reason, while the opposite is true.
Also, to underline Jeroen's answer, no-one really likes to be an educational guinea-pig (at least not knowingly), especially in places where you have to pay for college courses. So advertising this kind of "unripeness" of the course might not be beneficial in general.

I have modified the question to make it clear who the potential audience is.

I have written several textbooks that started with drafts I wrote while teaching a course (in person, not online). I always informed the class that I was developing the material, sometimes learning it myself on the fly, and that their feedback was part of the process. I think the stronger students liked the idea. Some of the weaker ones thought they should have an instructor who "knew the subject matter".
I never explicitly labeled work as an alpha or beta release, and could not (nor would I have) charged less tuition. I distributed the notes for free when the department had funds, at copy cost (much less than a text) when necessary. I credited students as a group and sometimes by name in the acknowledgements when the book was published.

Would you have done the same for your private school, where the students pay money directly to you, not to the university?

Whether school were public or private is irrelevant. My financial support is my salary; I wouldn't collect directly from students. If I were developing an on line course independently I might well want to offer it free for a while to get feedback. Then I might charge for the finished product. I would probably not offer a reduced prince "beta".

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Categorizing relationships between research articles
When a research article X cites another article Y, it could be because of any of the following:

X develops the ideas of Y
the ideas presented in X bear a degree of resemblance to those of Y
X compares its results to those of Y
etc.

When I study the literature in my research area, I would like to categorize the relationships between papers in a way similar to the above example. However, I would prefer to use an existing categorization that people have thought through instead of inventing a wheel. I performed a few searches, but have not discovered any such categorization. Do such categorizations exist? I would appreciate some pointers.

You may want to look for "bibliographic relationships", "citation function", or "citation types". There are many different annotation schemes, for example see here.

@101010111100 I looked at quite a few papers, but have not found any categorization that is simple and straightforward. Most modern studies seem to be interested in automated categorization and fit their categories to that need in artificial ways. The studies on manual categorization are old and not freely available. So, what schemes for annotating citations do people actually use?

I do not know. But I also do not see the problem in using the classes described in papers about automated classification (e.g. this one). If you want something simple, just look through a few papers and compile yourself a list of classes you like. Then use these classes to manually classify your data.

WHY do you want to categorize the citing literature in this way? I ask because without understanding your purpose, it is difficult to offer you a helpful answer. Personally, I think that automatic bibliographic citation mapping has very limited usefulness for most purposes, but without knowing your own purpose, it's hard to guess what you might consider useful. Also, what is your domain of research? The purpose of literature reviews varies somewhat depending on the domain, so knowing that would be helpful.

@Tripartio Right. I want to do it manually (i.e. to specify the type of citation next to each citation in my notes). The area is heuristic search (a sub-area of artificial intelligence).

@AlwaysLearning, my question is WHY do you want to classify the type of citation? What purpose is this supposed to serve you or your readers?

@Tripartio  Well, I maintain my notes in the org-mode of Emacs (see also org-ref), which is fully configurable. This means that I will be able to define commands that use my annotations to perform tasks such as listing or citing or whatever all the papers whose ideas a given paper develops etc. The possibilities are endless.


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PhD Program with a bad GPA
I am a student from Poland. I am bachelor in Economics and Logistics and now I am doing my Masters from Econometrics. I have quite good achievements (1-year scholarship in Japan, ambassador program for a big NGO, few wins or good places in the contests etc). I am also waiting for publishing my first research paper and plan to do 2 more untill I will graduate.
There is one problem though. My GPA is not very good. It's a combination of 3 varriables. First, on the beggining of my studies I planned to go to bussiness rather then academic work. Second I have a mild/average form of brittle bone disease which result of having to take 3 years of medical leave (not at once). And sometimes in cases when the injury was not to bad (for example 2-3 months) i tried to make up the classes and I left deciding that i rather not lose another year and pass on B- or C then to go the other way. Third factor is the fact that going from economics to very math-based field as statistics and econometrics is not easy. I am managing this but with having to make up the material from bachelor's in this field it's rather B on average then straight A.
I love to do the research, and to analise data. My papers and articles are usually recieved as really good. And I would love to be able to get to one of top 100 Universities for a PhD program. Is there a chance if I would have a good Master's thesis, nice GRE/TOELF score and 3 academic papers?
I would be gratefull for all the answers :)

Although there are top 100 universities outside the US your mention of GRE/TOELF make me think US making https://academia.stackexchange.com/questions/38237/how-does-the-admissions-process-work-for-ph-d-programs-in-the-us-particularly relevant

I suppose you are talking about the top 100 econ phd programs?

I have voted to close as possible duplicate even though you don't specify US because most of the advice in that post applies here as well.

I am not in your field, though I have been a faculty member in several PhD programs in the social and health sciences. So, I'm not sure how much of this would be relatable. However, PhD programs typically have a minimal GPA requirement. You do not mention what your GPA is exactly, but typically programs don't require an A (4.0) average. If the application requires a cover letter or personal statement, you can explain challenges you have had in the past, though you should make sure that you describe how these challenges would not impede on your future success. Also, you mention a good TOEFL score, though I would suggest working on your writing in English or have a native English speaker proofread your materials, if you are applying to US programs.


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Review process for comments on an article
Recently I have submitted comments on a article to Elsevier journal. These comments include rectification and proper implementation of certain technique. The editor of journal told me that, they will first send my comments to author of article for response and after that my comments will be sent for review.

Now my query is, why and for what purpose they are seeking response from author of paper ? Although I have no problem with that but I am curious to know,  how that author would responds to my comments on his/her paper ?

PS. I have checked similar question here but I find this question not so useful.

The procedure is quite common, and frequently comments and response to comments, if significant, are then published together.

Now my query is, why and for what purpose they are seeking response from author of paper ?

Why shouldn't they? You are actually criticizing their work, highlighting some flaws. You might be right, you might have misinterpreted their paper, or you might be plainly wrong: whatever the case, it's fair to allow the authors to reply to your criticisms and explain their point of view, if different.

Although I have no problem with that but I am curious to know, how that author would responds to my comments on his/her paper ?

Well, there's no general answer for this: it depends on the kind of comments. Sometimes they might simply acknowledge the issues, whereas sometimes the authors write another commentary explaining why they think the comments are wrong. And sometimes the two parties reach a common point of view.

What if the author do not respond to editor?

Also for APS is is the same procedure. Since you have criticized their work, it is natural to give the comments to someone who has spend high amount of time only on that paper, so the authors and the previous referees seems to be the best option.

@IgotiT I think it's an unlikely event that one, but the journal will probably have a procedure to handle the case. Which procedure depends on the journal.


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Advisor threatening to pull his name from accepted paper that I submitted without his knowledge
Recently, I submitted a research article in the journal "Applied Mathematics and Computations" and fortunately my work got accepted with a very good response from reviewers.
However, I made the mistake of submitting this paper without the knowledge of my coauthor (who is my advisor). When I told him that our paper had been accepted, he became really upset with me and warned me that he would withdraw his name from the article.
Nothing is wrong with the article except that I did not ask him before submitting it. The reason I did not ask him was because he took an unnecessarily long time (2-3 months) to edit the draft of the manuscript.
How should I convince him now?
PS. Please also see this "Query".

Unfortunately? You chose that path for some reason. That reason needs to be dealt with by you as soon as possible. Your relationship with your adviser is hanging in the balance.

RetractionWatch is full of stories of papers that were retracted for having been submitted and published without a co-author's knowledge. You really can't do things like that.

Yes, you are really wrong for not asking your coauthor in advance whether he agrees that the paper is ready to submit.

Usually when you submit an article it explicitly mentions that you must have checked with all authors.

I'm not sure I agree with the edit to change "Advisor" into "Coauthor".  This frames the question in a rather different circumstance.  In principle the same rules apply, regardless of who the coauthor is, but the perspective in the situation is rather different.

I'll just add that you really do need your advisor because without him you can't graduate.  Now, whether or not you need him after that is up to you.  It may be you want to stay in academia, in that case having a strong relationship with your advisor is essential.  My advisor and I did not get along, and I think as a result of that it pretty much killed any interest in science I may have had (both my advisors were pretty looney, looking back with 20 years of clarity).  So, kiss up to your advisor now, then figure what your next steps are.

When you say "I did not ask him because he took an unnecessarily long time (2-3 months) to edit the draft of the manuscript." do you mean that you received his edits, then chose to submit without telling him, or that you submitted because he was taking too long, and you submitted it before he finished reviewing and editing?

@AdamDavis .... Exactly, time he take for editing is just waste as he just keep manuscript with him for 2-3 months and then suddenly edit in few days, I feel he internationally delay the process.

Linking the specific journal is completely needless.

I don't actually know much about academia, but I had the impression that authorship was more about credit than endorsement, and that it would have been just as or more unethical for him to submit without the advisor's name on it. Is there a right way to publish a paper that someone who contributed enough to the work to earn coauthorship doesn't want their name on?

@Random832 If said contributor wishes not to be listed as an author, but gives consent for the paper to be published without his name on it, that of course is perfectly fine. (But you should best get that in writing.) If he doesn't want it to be published even without their name, then there's nothing you can (ethically) do but shelve it.

Time will heal bad spirits.

@ChristianClason But you can't legitimately claim sole authorship if you are not the sole author. It isn't clear that your coauthor can give you permission to use their work without giving them credit.

@Random832 authorship is both credit and endorsement. If it had turned out that the OP fabricated the data, for example, the advisor would be in deep trouble until proven that he didn't know anything about it. (I am not implying the OP did anything like that, just a hypothetical).

@ChristianClason Maybe it is discipline sensitive? In mine, it would certainly not be acceptable if most of the ideas for a thesis came from the advisor.

@ChristianClason....what if all ideas are of student only and advisor is serving as administrative tools only ?

@ChristianClason someone can write up a manuscript and give it to the first person they meet in the street to do at they see fit, but even with this explicit permission if that person would publish it as their own, they would be committing academic fraud and plagiarism. Permission only means that the author waives their right to object and e.g. copyright issues, but a journal can and will request an affirmation that this is your original work, and you would have to either defraud them or disclose the original author(s). It's the same as with hiring someone to write your thesis for you.

@Peteris Fair enough, the man on the street was a bad straw man. Nevertheless, if the coauthor explicitly relinquishes authorship but agrees with the publication without his name, this should be his right. How to do so is an interesting but different question. (I would think that at the least, this situation should be clearly explained to the editor-in-chief when submitting, together with a written permission. They would then to decide whether they would consider publishing the paper under these circumstances. This is similar to how one would treat anonymous publications.)

@ChristianClason coauthor's permission would be completely sufficient to publish the paper without the coauthor's name in almost all non-academic places - you can print a book ('ghost writers' are common enough), put it on your website, etc. However, almost all respected academic venues for publication will have policies that they won't allow that - they'll state that the author list must include all appropriate researchers, period; instead of something conditional on their wishes or permissions. For example, http://www.nature.com/authors/policies/authorship.html

@Peteris As I said, it depends on the journal. An alternative to leaving the coauthor completely off the paper is to make them anonymous. There's precedent to this (and a few questions about it on this site, if I recall correctly). (Although in this specific situation, I agree that few editors would touch that manuscript with a ten-foot pole.) But we're getting off-topic here. (Moderators: Feel free to clean up my comments here.)

@ChristianClason I also said 'most' and not 'all'.

@ChristianClason As I say, I think that must be discipline specific. It would not be acceptable in mine.

@ChristianClason So what are we arguing about?

So, after the adviser edited the manuscript, did you further edit it before having it published, or was it published exactly as the adviser edited it? Assuming the latter, it seems to me that if mutually, your intent was to have the paper published when it was ready, the paper as they had edited it, and your agreement with the adviser's editing, would indicate it was in fact ready. But, to be clear, you should have discussed this with them ahead of time... but that ship has sailed. Now, you must apologize and try to repair your relationship with them.

@IgotiT If this (advisor is only "administrative tool") is indeed the case, he should not be listed as an author at all -- but this is often not an easy call; see the many questions about this on this site.

Ethically, it isn't great form if the coauthor does not want to be listed and you publish without their name even with their permission if they had significant contribution. It is essentially inferring the work is your own. I would not be comfortable making that claim. Best solution in this scenario imho is for finding common ground to publish with permission and have the coauthor on the paper.

@Peteris There is now a separate question on this aspect: http://academia.stackexchange.com/q/19454

You are wrong for putting the name of someone on a paper and submitting it without asking them for permission. Having them as an author communicates to the world that they approved the content and agree with the conclusions. Implicit in that is that they signed off on the manuscript. Some people get angry when this happens even if the paper is fine and they agree with the conclusions. Some don't. This happened to me recently, and even though I didn't agree with the recommendations of the paper, they weren't wrong, scientifically, so I decided to let it go.
You need to figure out a way to smooth this over with your advisor and to work with them to get edits turned around more quickly. That being said, don't lead the discussion by bringing up the turnaround time issue. That's combative.

Someone could certainly be upset about an article being submitted, even if they are happy with the content, because they do not agree with the choice of journal. Especially when it's an Elsevier journal.

@JessicaB: What's wrong with Elsevier? (Yeah I really have no idea.)

@Mehrdad Their business model, in short. Quite a lot of mathematicians have chosen to boycott them.

All good, except note that OP did ask the professor to review it; they just didn't get the thumbs up before submitting.  Doesn't make it right, but consider editing your first sentence.

@user1717828, "I did not ask him because he took an unnecessarily long time (2-3 months) to edit the draft of the manuscript." It's literally the last major sentence of the post besides the final question.

@BillBarth, I must be interpreting that sentence different than you are: OP asked the professor to review the paper (i.e., edit the draft of the manuscript).  OP did not ask about the final submission when he got tired of waiting for it to come back.

If you're worried about time sensitivity (though in this case the OP screwed up badly, so this is a "future lesson"), you can always say, "If I don't hear back from you by the Umpteeth of Decemberween, I'll assume that you've reviewed the paper and are OK with me submitting it." That's a great way to deal with procrastinators/busy people. If they really care, they'll respond to you immediately, but chances are they don't, and you've given them a fair chance. Though for something like a research paper, I'd probably also send them a second reminder.

@user1717828, I can see your interpretation, too. Either way, it's no real excuse.

@WayneWerner I don't agree that giving a deadline allows you to presume consent if you don't get a response. I think you need to be able to assert that the coauthor has given consent positively.

@cfr that may be the case for papers, but still, how hard is it to reply and say, "Let me review the paper and get back to you"? If you wanted positive consent, then the text of your "final warning" email could be something to the effect of, "I haven't heard anything from you, so I assume you've reviewed the paper or you trust that it's correct. I'll be submitting it to X in a week, but I'd like to have confirmation. Simply respond to this email with 'Yes, submit it!', 'No, I do not want to be an author on this paper', or 'Let's meet and go over it first'."

If you give the meet option, also make sure to provide three possible meeting times (or just meet during their office hours).

+1 for avoiding the turn-around issue. That's pretty much a fact of life in academia, where many of us are moving from one deadline to the next. @WayneWerner gives good advice on this point, though the really awkward point is when you get a continued lack of response. At that point I think the only thing you can do is remove them as an author, perhaps acknowledging them as mentioned in http://academia.stackexchange.com/a/69018/22582 but remembering to inform them ahead of doing so.

To complement Bill Barth's answer, here's some concrete tips on how to move ahead in this case:

First, you need to come to terms with the fact that a very likely outcome is that you do in fact have to retract the paper -- your primary objective here should be to get back on good terms with your advisor, not to publish the paper, because the former is much, much more important for your career in the long run. (If he relents in the end, that's a bonus.)
Second, what you need to convince him of is that you fully understand how utterly and inexcusably wrong your action was -- no ifs and buts. He needs to be certain that in your (hopefully) long career to come, you will never, ever, do such a thing again.
Offer to do anything he feels necessary, up to and including writing a very apologetic letter to the editor-in-chief explaining your mistake and requesting to withdraw the paper. No arguing.
Then, you can try to (carefully) find out if there is any additional reason why he reacted so strongly in this particular case (beyond justly being upset over your scientific misconduct). Does he disapprove of the choice of journal? Does he think the paper is not good enough to be submitted (yet)? All of the above? This way, you might get some constructive feedback out of this mess.
(If your advisor is not the only coauthor, repeat the above steps for the remaining coauthors -- the earlier, the better.)

"Ask him if there is any particular reason why he reacted so strongly"... uh, this seems like awful advice. He reacted strongly because he was portrayed as endorsing something he was unaware of. Is that not sufficient reason? Either reword this or remove it, because the way it's worded right now, it might even be more infuriating than the original thing, considering it's stated after the OP supposedly understood what he did wrong.

@Mehrdad I think what was meant is that, after dealing with the immediate problem, the OP might try to establish what might be the future of the paper.

@Mehrdad Of course it is sufficient reason; but there might be additional reasons in this specific case which could be helpful to know explicitly. (Also, as Bill Barth points out, not everyone gets angry for not being asked, so it is conceivable that there is in fact something specific to this paper.)

+1 The immediate and unqualified apology, no ifs and buts, is central here. Don't even try to justify what you did. Ask what you can do to fix it.

Just curious (as a longtime lurker) as to why an advisor is that important? Is an advisor like a longerm "boss"? Say this individual gets his paper published with no retraction -- is his advisor still a more important "resume item" than his published / proven work?

@HC_ More like a longterm "friend" (ideally, without the quotes). To put it briefly, one lost paper is easy to remedy by writing another paper; your advisor's bad opinion of you as a potential member of the scientific community (which will get around) is much harder to make up for. One way of looking at it is that essentially you have two resumes: The objective one on paper, and the subjective one made up of your peers' collective opinion of you -- and the latter can be just as important for your career (if not moreso), in particular later on when the first one becomes too long to evaluate

(cont'd): Even in the short term: The first thing I (and probably most of my colleagues) do when considering an application is to call up the advisor and ask for his personal opinion on the candidate with respect to what topics I had in mind. If said advisor then mentioned any scientific misconduct, that would be a huge red flag unless the lesson was clearly and permanently learned.

@HC_ You are asking a new question.  It does not belong in the comments to this answer.

This basically is the counterpart of the question:
Is it ethical for advisors to automatically coauthor papers?
In fact, the same ethical standards apply here. Authorship is only justified by a significant contribution to the actual work. The supervisor role by no means automatically qualifies for that – in neither direction.
The following is – again – from the "DFG Proposals for Safeguarding Good Scientific Practice" (pp.82f, emphasis added):

Authors of an original scientific publication shall be all those, and only those, who have made significant contributions to the conception of studies or experiments, to the generation, analysis and interpretation of the data, and to preparing the manuscript, and who have consented to its publication, thereby assuming responsibility for it. [...]

So putting his name on a paper he did not consented to is actually a case of scientific misconduct.
However, if we assume that your supvervisor has high ethical standards, the situation is even worse: The unfortunate, but way more common system of misconduct is that professors insist on "automatic coauthorship" on their students papers (which, in some cases, they do not even read). By automatically putting his name on the paper, you leave the impression that he is a supporter of this unethical practice!
If you want to thank somebody or underline their great support, you can safely do so in the Acknowledgements section of the paper.

Why do you assume that the co-author did not contribute to the paper? Nowhere does it say that he is a co-author only because he is the advisor. (And of course readers of the paper have no reason to assume he is an "automatic" co-author and did not contribute, so I don't see how By automatically putting his name on the paper, you leave the impression that he is a supporter of this unethical practice! makes sense at all.)

+1 for referencing some actual guidelines. No idea why this answer is getting hammered.

@ff524: Apparently I misunderstood this, sorry about that. However, my general message still holds, so I wonder if that is the (only) reason for  the surprisingly high number of downvotes? I am a bit puzzled...


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Is there a way to filter publications by their grant information (say NSF grant ID)?
We're working on building a tool to evaluate the efficacy of NSF proposals, broken down by topic. We extracted the topics per grant using this dataset.
One of the criteria for evaluating the impact of a grant could be the aggregating and analyzing publication-level citation-metrics, perhaps using this list of databases.
However, there doesn't seem to be a way to filter papers that were wholly or partly funded by a particular grant. Do you have any suggestions about how this data could be retrieved, or how grant-giving bodies typically analyze this themselves?

Typically, if I know the contract number and I want to know which publications resulted from the grant, I'll include the contract number in a Google Scholar search; most/all of the papers that I read list the grant contract numbers in the first-page footnote. I assume that you are looking for a more robust approach than this, though.

@MadJack Exactly, this is what I'm doing right now, which is not ideal. I wrote a parser leveraging scholar.py that searches for each grant award in my dataset. However, the generated data needs a lot of (expensive) cleaning.

Grant giving bodies typically rely on self-reporting: the progress reports submitted to them will typically include information about publications generated during the funding period.
That said, one option is to check the OpenAIRE database. The OpenAIRE initiative aims to create a database of publications and research data, and as part of their design, asks the individuals who deposit the material for funding information. This certain does not encompass all funded projects (as it also depends on the researchers doing self-reporting), but does create a searchable database. (See, e.g. this link for a list of NSF funded proposals.) (Note, the OpenAIRE project was started by the EU and they currently have about twice as many items funded by the European Commission in their database as there are by the NSF.)


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Reliable Asian university rankings datasets suitable for evaluating applications to a graduate program
Our (American) university has a lot of applications coming in from Asia- especially China, India, Japan and Korea.
Each of these seems to follow a different grading scheme and it is hard to do  apples-to-apples comparisons of students scores across universities. We don't request WES transcripts.
What is a good way to normalize students across Asian universities? Which ranking schemes (global and local) are reliable? Do these ranking schemes provide fine-grained, easy-to-parse data that we can use for CS and ECE admissions (not just relative ranking)?
ADDENDUM: There seems to be an XY problem with the original question, as @FedericoPoloni points out. What we're interested in is indeed-- "What is a good way to compare transcripts for graduate admission, especially from Asian universities? Admittedly, this is a broad problem and solutions may be reductive or simplistic, but it seems unfair to not consider the quality of teaching, research and the cohorts worked with, when evaluating student transcripts.
The current answer and comments, while helpful, will leave admissions restricted to IIT, Tshingua, KAIST-- since we do not trust transcripts from other universities, and though exceptions can be one-off, this approach does not scale. I'd be grateful if you could share references to meaningful datasets and ideas to use the data without unfair bias.

The educational system in India is sooooo different from, say, China; I don't think any general "Asian" ranking will be useful to you. (Also see: Is it ethical to apply different criteria for graduate admissions based on country of undergraduate study?)

@ff524, more local rankings would be great too, if they are reliable. At some point, we do have to normalize expectations for students from different countries. Even something simple like "acceptance rate" for particular programs-- say .0005% for Tshingua v/s 0.001% for IIT-B...

"Reliable" and "university ranking" are concepts that usually do not go along well. Maybe you should demote that aspect and ask directly "What is a good way to compare transcripts and student scores for graduate admission, especially regarding Asian universities?"

@FedericoPoloni I'm fine if this question is read in that way. Alternatively, if anyone is involved in CS/Engg admissions for international students, "What approach and data do you use to admit fairly across nations?"

@Jedi: "Even something simple like 'acceptance rate' for particular programs" - do you mean an acceptance rate on "your side" (i.e. what percentage of applications from university X are accepted by your university), or an acceptance rate at the source university as a way to rank the source university (which, I think, would be utterly random)?

@O.R.Mapper The latter. Admittedly there will be lot of noise using only this single vector as a signal. We're just looking for any objective data to compare universities.

@Jedi: The particular issue I'd see with that vector is that it is not clear a low acceptance rate is universally considered as desirable by universities. As such, at universities that do not strive for a low acceptance rate, knowing about the (certainly objectively measurable) acceptance rate will be as meaningful as knowing about the average floor tile size on campus.

The approach we use for MS admissions in my ECE department is, "Looking at data from our enrolled students, identify characteristics of students from X that seem to predict success/failure in our program. Then for students from X, admit those with "success" characteristics and reject those with "failure" characteristics." Where X may be a university, a group of universities, or something else (depending on the data we have). For students whose background is unlike anything we've seen before, we make an educated guess as to whether they'll do well in our program.

@ff524 that has historically been our approach as well. We hope to widen the net in the hopes of finding "diamonds in the rough" (not my words)

@ff524 What we normally do, when we don't know anything about the university or system and when possible, is consult with one of our faculty who is familiar with the universities in that country.

@Kimball, that's what we do too. The goal is to have an automated system; it should be more scalable without a human in the loop.

I believe that using university ranking as a criteria for admission is fundamentally unethical.
Extremely good students end up going to middling or poor undergraduate institutions for any number of reasons. To downgrade somebody's application just because they went to a mediocre institution is actively going against the academic ideal that merit should be able to rise, and even poor institutions generally have at least a few students of excellent potential.  Complementarily, pedigree is no guarantee of quality: rubbish students graduate from elite institutions all the time.
Now, there is, of course, a strong correlation between the quality of an institution and the quality of the students that it produces, and there are, of course, basic matters of accreditation: nobody should respect a degree from Trinity Southern University.  In general, however, you should judge the students and not the institutions.
So, how do you judge a student from Asia? The same way that you judge a student from an unfamiliar university in Europe or North America, by the accomplishments for which they can give evidence.  To judge classwork, one of the methods is to ask which textbooks were used (this is what some MIT departments do).  To judge other work, look for the concrete products, such as research papers, code or web pages online, etc.
Students from universities you do not know will still be at a disadvantage, and doubly so for students from a very different environment and who may lack English communication skills, such as will often be the case for many Asian universities.  But you can at least take steps to not prejudice yourself unduly by sorting their universities by their ability to game semi-arbitrary ranking systems.

The goal is indeed to judge the student not the institution. You err in assuming that we are not evaluating research, their Github repositories, open source contributions etc. . However, a narrow subset of our student ranking also requires evaluating sheer academic performance in their field of study. All else being equal, would you prefer someone from the top of the CS class in Bombay University, or a top 20% student from KAIST?

@Jedi In your example, I would consider both students to have satisfied the basic requirement for academic performance. You can't really know much more than "appears qualified on paper" from pure academic ranking in any case.  If their outside-the-classroom record is also qualifying, then the final differentiation and decision of one over the other would come from interviews or the like.

Based on our experience we would not consider that both students will cope with the rigors of our university. Our experience shows that a 80th-percentile student from KAIST is significantly better prepared for grad school here compared to a 99th percentile student from Bombay University. However this has led to us restricting admissions to a few dozen "safe" universities across Asia.


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Generic name for "manager" in social science theorizing
Please bear with me as I try to explain what I'm looking for; my question concerns getting help to find the right words to describe it. Also, if there's a more appropriate Stack Exchange site for a question like this, please feel free to redirect me in a comment.
I am looking for a generic and appropriate term in social science theory for a particular meaning of "manager" in business management theory. The particular meaning I use here is this: a "manager" is someone with the ability to willfully change one or more variables in a theoretical model. Here are a few examples:

Theory S: sales are affected by store location, advertising and weather. A manager in this case can freely change the amount of advertising. They might or might not be able to change the store location. Although they have no influence over the weather, they can make decisions (such as to advertise outdoors or not) in response to the weather.
Theory ES: employee satisfaction depends on stress levels of the job, salary, and daily commute time. A manager (of the employee) might be able to freely change the salary, has some control on the stress levels, but has limited control over commute times (if telecommuting would be infeasible).

The key point in these examples is that a "manager" has some control over some of the independent variables of the theoretical models, and so can influence the outcome dependent variable in a desirable direction.
Let's go deeper. In my desired meaning of "manager", in Theory ES, the employee is also a "manager" concerning that theory: they have some control over their own job stress levels (by changing their work habits) and their own commute times (by changing their mode of transportation, or by moving their home). So, they, too, have some control over the outcomes.
I am looking for an appropriate technical term that captures the role of such a person who can willfully change the values of one or more of the independent variables so to influence the dependent variable outcomes in their favour. While "manager" works as a term in the case of Theory S, it obviously doesn't work well in the case of Theory ES since the employee is also a "manager" in that sense. Thus, I am seeking a more general term that captures this meaning.
But my application of this term goes far beyond business management. I want a term that is ideally meaningful in any theoretical context, especially in the social sciences, but hopefully even in any empirical science. Here are other examples of "manager" in other disciplines (sorry for the poor examples; I'm not an expert in any of these fields, so I will have to resort to stereotypes to make my point):

Psychology: a parent could be a "manager" in effecting their children's self esteem (DV) by changing their parenting approach
Sociology: a group member could be a "manager" in affecting group performance outcomes by choosing whether to willingly cooperate with or willingly frustrate other members of the group.

I think perhaps the term for "manager" in this context might be "social actor".

Physics: when an experiment is carried out, the scientist conducting the experiment is the "manager" since they purposely alter parameters in order to change outcomes.
Geology: in studying, for example, the shape of cliffs from interaction of sea waves with wind patterns over a ten-year period, there is no "manager" in this case, since the outcomes and variables of interest have no human will involved. (Even if human-caused climate change were implicated, there is no "manager" since there is no human consciously taking directed willful action with a specific intention in this case.)
Medicine: if a patient influences their cancer outcomes by their choice of frequency and type of tobacco that they consume, the patient is a "manager" in influencing their cancer outcome.

So, I am looking for a more suitable term that someone captures my broad meaning of "manager" here. "Social actor" from sociology seems close, but I'm not sure if that quite captures it.
EDIT:
One answer suggested "agent". I like the generic idea of "agent". However, although I already thought of that as a possibility, I hesitate on it because in business management (my field), "agent" and "agency" have a very particular widespread meaning--an agent is someone who is not an owner (the principal) but who acts on behalf of the principal. In that context, the term "agent" is usually employed when exploring conflicts of interest when the agent's best interest does not align with that of the principal. So, I would prefer a term more generic than "agent" if one exists.

What's wrong with "actor"?

Could some of those who voted this question as off-topic please suggest a more appropriate SE site to post a question like this?

@henning, I'm not in sociology, so I'm not quite sure all that is implied by the term "actor". Could you please point me to any introductory references to better understand how they use the term?

This might be more appropriate on a language oriented site, but I'll speculate.
You are describing a person who has agency in an organization or a situation. That is a bit different from, for example, a typical manager of a low level employee. So, agent or a synonym might be appropriate for that. Executives in organizations normally have agency. Mid level employees have little, if any, depending on the organization. They pass through the agency of others.
Having agency is the ability to affect the course of things and, perhaps, the outcome. Most, at least, of your examples seem to fit that idea.

Thanks for the good idea, but I've added an edit (which should have been part of the original question) that explains why I hesitate on "agent".

I think in any such situation, you need to pick a term and define it in the paper according to your intent. And in business an executive with such agency works as an agent on behalf of the organization. I don't see a conflict. But you have agency here. :-)  Also see: https://www.thesaurus.com/browse/agent

But my question is a prelude to defining my own term: I'm trying to find out if a suitable term already exists. I would much prefer to use an existing term than to invent or redefine my own, with whatever loaded meanings that might entail. Besides, if someone can suggest something very close, I could hopefully learn a lot by reading some literature that explains it.

Maybe, but language is seldom so precise as to preclude misunderstanding. Better you give the definition you intend, even for a common/generic term. As you note "manager" only captures part of it.

@Buffy Is totally right here. The best term from sociology for this is "agent". It may not work for you, but it is what we sociologists would use, it's the "existing term". If the existing sociological term is unusable for you for the reasons you state, sociology isn't where you can draw upon.


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Which methodology of a research paper around a proposed software system
Part of a systematic literature review, I'm looking to the methodologies of the papers I review, and many papers doesn't explain the methodology used. My questions is : Can I assume that a paper which talks about creating a system or a software is a Case Study? Please note that some researches do some exploratory steps to gain insights like from StackExchange for example, in this case I also assume that mixed methods used. Please help if you have ways to identify methodologies if they are not explicitly given or shown.

Even a case study needs to define its methodology, that is, how it collected the relevant data. I find it hard to understand how a paper could be published that did not explain the methods it used to find its results. To be honest, I'd simply throw away any paper that only presented its results without explaining how it found them, because I'd have no way of understanding whether the method was valid.

I agree, that's why in systematic literature review, you also must define a quality for each paper you consider or appraise their approach

The value that is placed on explicitly discussing the research methodology varies from field to field. Many more systems-oriented papers have a methodology that basically goes "problem -> proposed solution -> evaluation [rinse and repeat until results are ok]", but that is usually more implied than explicitly discussed. I guess you could call it a "case study", but the authors probably wouldn't consider it like that.

What you've described is called design science or design science research; it is most certainly not a case study. In a comment on your original post, @XLeitix nailed it as the pattern:

problem -> proposed solution -> evaluation [rinse and repeat until results are ok]

In conducting a broad-based literature review of research on Wikipedia, my colleagues and I had to come up with a list of different research designs. Design science is in a category of its own, because it is quite different from the methods in social sciences. Design science is the default approach to research in computer science and software engineering, and so no one is going to explain the "research method" when they follow this pattern. It arises from the engineering paradigm where the goal of research is not to discover what exists or how or why things work, but rather to create something that is useful to people and prove that it is useful (usually by comparing its usefulness to some specified benchmark).
Ironically, the name "design science" does not come from computer science or software engineering, but rather from information systems (IS) research. IS research is primarily social science research, and so IS researchers had to come up with a name or a way to describe this type of research that is so different from social science, and yet scientifically rigorous. There are at least two major articles that describe its scientific characteristics in depth:

von Alan, R. Hevner, et al. "Design science in information systems research." MIS quarterly 28.1 (2004): 75-105.
Gregor, Shirley, and David Jones. "The anatomy of a design theory." Journal of the Association for Information Systems 8.5 (2007): 312.

As of Jan 2024, the link is dead :-(


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Is there a contradiction between open access/science positions adopted at many universities and their reliance on Google services?
I work at a faculty which is completely dedicated to open access and open science. They do everything in accordance with best practices. Very cool.
But at the same time they are totally embedded in the Google infrastructure, using Gmail, Calendar, Drive and so on. Even I, a Google skeptic, find myself using it because it’s so gosh dang easy.
I’ve been recently invited to join the Open Access Committee, which is obviously terrific. I think of taking up this issue, but I can’t really get a grip on the extent to which this may be a totally different issue, or a related one. Therefore I’d like to hear your advice on the matter!

What exactly is your concern about Google's infrastructure here? The main issue people have with Google usually is privacy, but that's not a concern if your data has to be 'open' anyway.

Open science and open source may share some principles, but they are very different things with very different goals. You should add to your question why you feel the two things are in contrast with each other.

I suppose the university could just stop using those services and leave it up to everyone to find their own. Or spend more money to set up something remotely similar. Not all services are free (and universities pay Google for them).

Could you possibly point at a statement of what is meant by "open access" and "open science"? I have heard several different definitions of each.

@Andrea The OP never mentioned "open source"?

VtC as needing detail as to what you think is in conflict. Remember, the vast majority of scientists are not hacker nerds that are excited to host their own email servers and pass things around with scp.

I’m not a “hacker nerd” either and I’m def not suggesting that anyone host their own email servers. Not sure what gave you that impression.

@Teusz Sorry - sometimes people on this site offer extremely techie solutions to things, forgetting that not everyone in academia is in CS/math and excited about LaTeX/hosting their own Discord clone/having students upload files to somewhere outside the LMS/etc... That said, since you didn't really explain your objections, there wasn't a lot to go on.

Its a totally seperate issue.
Other than closed  science = bad, large monopolistic tech company = bad, I not sure I see any connection.
Open Science/Open Access is about publishing all your data and methods in fora that allow free access to everyone as soon as possible. Is there anything specifically about google that prevents or makes this harder?
I can't think of anything.

Indeed. It isn't like Outlook would be any better/different.

@JonCuster, hmmm, Outlook could be and is worse. Much worse. Much much ..... worse.

@Buffy - as a user experience, sure. Perhaps even from a university IT perspective, but in terms of supplying email and collaborative spaces Microsoft does OK. My institution does just fine with them, but has no option to use Google.

@Buffy At least for Outlook an institution can set it up to not read the contents of all your emails. For Gmail, that's not possible, so it's impossible to use any Google services when you deal with HIPAA-protected anything, for example (not that it's great to transmit any PII via email anyways, but even tiny bites of information can be HIPAA protected, like emailing a research participant about a scheduled appointment).

@BryanKrause Can't an institution make the (paid?) Google Workspace version HIPAA-compliant? https://support.google.com/a/answer/3407054

Outlook not only reads and filters all my email, any link I click in an email is filtered through MS servers before it is sent. This is advertised as a "security" feature. My outgoing email is also filtered. (We know who you are. We know who you talk to. We even know what you read.) Yes, I know that my institution is one of the sinners here.

@Anyon Ah, maybe they can now! Guess I'm wrong.

You can't think of anything? Ask your librarians, always!
https://docs.google.com/presentation/d/1_ny6hxY46M1i2eML3-uzePfmeY7vi3lio9vOp755Fig/edit#slide=id.gce900bb84f_0_41
There is a reason why Google is so successful commercially ... they do things you can't think of!

@earlgrey So Google provides a service that isn't perfect for sharing OA manuscripts. I'm not sure u see this as being actively harmful to OA. It doesn't prevent a GApps  shop from using other services. At worst it provides a substandard service where those without a Google drive have no service. The original post seems to concentrate on Gmail, goal etc  which seems unconnected.

This is such an incredibly naive question, I'm glad it was asked. I find many in academia don't trust their IT support/software dev support and come on here and end up asking questions like this one. The Google services listed aren't going anywhere because so many organizations and businesses rely on them. Sure Google has retired services, but that's because they weren't making money or were not actively used. The argument that Google could suddenly retire said services could be said of any vendor/third-party service.

@IanSudbery again, *The original post seems to concentrate on Gmail, goal etc which seems unconnected.", that's the reason google is so succesful. I am not arguing they are connected. At the very minimum, if you access google drive while logged in your gmail (personal or corporate) account, it is still data mining from google. Are you interested in people accessing a paper on the Uighur community discrimination? the day that Alphabet will be bought by chinese government you will regret that.
I am arguing that the open access movement should care also about "fringe" themes.

@EarlGrey I'm not arguing that there aren't big problems with Google. I'm saying those problems are unconnected to OA/OpenScience. . Apart from anything else the problems remain even if you are not into open science.

@EarlGrey. That said,  i dont see any of the alternatives being any better. At least in Europe,  legal limitations mean that data is stored in European servers,  subject to European data protection law,  and isn't data mined, and if it were that would be both a breach of contract and law. Obviously the law wouldn't allow institutions to continue to contract Google if alphabet were bought by someone that couldn't be trusted to up hold the law.

@IanSudbery obviously, it is non-sense to put your service in such an expensive locked in risk. And still we do that, without arguing because no alternatives are any better (of course there are none, if alternatives are not discussed, possible future issues are not foreseen and things are seen in tight compartments instead of in a general framework... it is even easier than actively suppress any alternative development)

@IanSudbery who said european institutions are so smart? see the numerous instances where google has been fined, one of the most visible is this one
https://edition.cnn.com/2019/07/22/tech/google-street-view-privacy-lawsuit-settlement/index.html

@EarlGrey Completely different - Google being fined because it turns out one of its standard services breaking GDPR is comlpetely different Google delibrately breaking a specifically drawn up service agreement with a large customer to store data on a EU server, and not harvest data from it. Apart from anything else, being found breaking those would be bad for business, but those you quote above don't really harm their bottom line.
Yes, google are evil, supporting them is generally bad, but what has this got to do with Open Science?

@EarlGrey With lock in, its not just that google isn't any better than any others, but I see no possiblity for a system that isn't locked in. Migrating away from any email, calander or storage service is always going to be difficult, irrepsective of the service or its provider. The only problem I can see is if google becomes the defacto server of academic literature. But I see no sign of that happening. No one I know uses google scholar for searching or google's service for author manuscript (which I'd never even heard of).

While the main concern against Google (privacy) does not apply here, there are some avenues in which the big G can cause damage. Having a good, almost-free-but-not-really service discourages the development and use of free (as in freedom) alternatives; but then this lack of openness can later become problematic because of lock-in, or because a previously-free service becomes expensive to use or is discontinued.
Examples: data is hosted on Google sites, or on Google Docs in a proprietary format; suppose Google pulls a Geocities and closes that service; then the data disappears or becomes difficult to migrate. Large datasets are hosted on Google drive, but then the user runs out of space in their free tier and decides to delete them.
[EDIT: very relevant real-life example: we just got word that the free Google Drive tier that Google offers to our university will be reduced from "unlimited storage" to "100 TB for the whole institution", so the university has until January to free up 372 TB of extra used space, or upgrade to a paid plan.]
The real problem, though, is that open alternatives are difficult to set up and expensive to maintain, while Google's stuff is free (at first) and easy to use. Becoming Google-free requires investment, and not all universities are prepared to make it. A positive example is Germany, which in the past years has pushed for free self-hosted services in all universities at the nation level. But this is not a simple road to take.

Absolutely yes.
Nowadays, Google is just the offspring of a big advertising conglomerate (let's call it Alpha, because it is the alpha character in the room and not anymore a bet).
As such, Google will try to integrate and inglobate everything. See google Scholar, which is being the reference tool to find paper and citations. A part from the data collection-harvesting, its algorithms are absolutely obscure and unclear, so there is no way to evaluate why the results of certain search appears the way it appears.
So you are well in time for setting the boundary, and raise awareness of the potential pitfalls in integrating too much of the university software ecosystem in the big colossus.
For example: they are even trying to make you upload open access papers to their platform, which then will be accessible then only via google drive (see slide 8), bypassing whatever publisher and allwing them to collect even more data without a clear consent from your side (well, you gave it long time ago, not that you had an alternative ...) !

There are certainly gripes to be had with Google, but which of those you listed are actually in tension with an institution engaging in open access and open science?

@Anyon ask your librarians!


text:
Discussing gift authorship with advisor in diplomatic way
I am a phd student in an engineering discipline at a US school and am graduating this year. I recently finished a paper and want to submit it. I sent the manuscript, which only has me listed as an author, to my advisor, letting him know I will submit it soon. His reply:
"Thanks Anon, that's great. I will proofread it and let you know my comments so we can submit it asap. Please use [X] as my author affiliation"
clearly indicates that he was expecting to be a coauthor on the paper.
I have gifted him authorship in the past, more than once, on papers which were 100% my contribution (idea, work, code, writing, proofreading, everything). He has never had any comments on my work, and I already know he will not have any suggestions for the paper.
I should add that during my phd, I have worked completely independently. I have tried multiple times to work with other professors, but no one has ever wanted to supervise me in any meaningful sense. The reasons given have been that they either don't believe they could supervise me, or are too busy to supervise me. It's also relevant to note that in my program you are assigned an advisor upon admission and you are expected to stay with them (or possibly add a co-advisor later). My advisor has provided funding to me (roughly 25% of my funding comes directly from him) and he has paid for some conference/travel fees. There is no need for labs, experiments, etc. in my discipline. Although he has no intellectual contribution to my research he has helped me with other things like explaining how to find a good journal to submit to, how to respond to reviewers, etc. and is also helping me with my application package.
Now for the question. I want my current paper to be a solo publication. How can I approach this in as diplomatic a way as possible?
I thought the best way to deal with this question is over email. My basic idea for my response is as follows (I have a draft response but don't want to post the quote of it).
"If you want to be an author, I will add you to the paper. One question I've been thinking about is whether it would help my future career to have a solo publication. I'm worried that other students may appear more productive because they work in large groups. I thought if I have a solo paper people will get the idea that I'm very independent and have a lot of unique ideas."
Obviously I need a good letter from my advisor, especially seeing as I don't have anyone who can write me good letters. Giving another gift authorship, when I have already done it several times, is not the hill I want to die on. At the same time, I do believe a solo paper would help me quite a bit. This paper in particular I am quite proud of and it will probably be the highest impact paper I have written yet. The cross-disciplinary flavor the paper has also appears especially impressive given the solo authorship. This paper is also totally outside of my advisor's area, whereas previous papers I gifted authorship on have been in the same general area.
I should lastly add that I do not know how he will react if he is not an author on the paper. The question has never come up before, and as far as I know all of his past students have always included him as a coauthor. I think it's possible that he will actually be supportive of the idea. Still, it's a sensitive issue and not one I want to blunder.

I comment because this is opinion based and I lack the feeling of the situations and individuals. It seems that what you wrote here could be done in reality. It remains open if you should do that by email or in person. In the latter case it can be evident that is a genuine desire of you, and the supervisor can even smile - "well true, I did nothing at the end and it will be good for you..."

@Alchimista, I would add that usually, e-mails are not the best way trying to resolve a conflict. It leaves too much room for misinterpretation that cannot be corrected immediately, which you could do in a face to face meeting easily. I understand why it often feels the easier way to write an e-mail, though.

I thought that email is better here because it's a sensitive issue. I don't want to force an immediate reply or leave either us in a situation where we don't have much time to think about how to respond.

Not an answer but ideally whenever gift authorships is a common practice you'd settle this before writing took place, not after. Citing wanting a solo paper is still valid even now but harder to navigate. Off-topic: oh how beautifully concise is the disagreement between "in-person is better" vs "email is better" in this comment section. Truly, there are only two kinds of people and they are always at odds...

Your situation is difficult now that you have already sent the paper to him, although this may have been completely unavoidable in your work environment. By asking for his comments (even indirectly), from a third person perspective, he read and corrected a paper which crosses into the grey zone of a contribution.
He has handled the situation very diplomatically, using an indirect pointer to be included as the author. He will "proofread" it is also a "contribution" for co-authorship.
He also probably did not see your other papers as all your work. Remember careful proofreading is also a contribution.
To enter into a diplomatic channel with him, you need to broaden your approach. Approach the situation indirectly, as follows. Ask him for a meeting to seek his opinion as advise on your future career prospects. If you are interested in continuing with him as a PostDoc, tell him that. Propose something you could do together where he can gain something, even if you are not 100% sure you want to do it. By giving him something he may want (maybe write a proposal for him?), you enter the diplomacy with a strong foot forward. Then tell him about your plans and why a single author contribution is a must for your career. Mention that in the latest draft you have included him as the author. Then mention that the standards in your career require single authorship and you would be happy to contribute in other things if you can take single authorship for this one.
The other approach is not about dividing the apple. Ask yourself your final goals. Do you want a job in industry? Maybe he has some contacts. Do you want a PostDoc? Maybe he knows someone who has a position. Often there are other ways to achieve what you want and still have him as a co-author.

I would disagree with that proofreading is a contribution to the writing of the article. Proofreading an article and suggesting the correction of typos, re-wordings, and the like are no original contributions. According to the CORE guidelines (https://publicationethics.org/resources/discussion-documents/authorship), all authors should have been involved in the writing of the manuscript at draft- and revision stages.


text:
Tense in summary chapter of a thesis
I am currently writing a cumulative dissertation which is based on several published papers. I am supposed to shortly (one page) summarize each of the papers. These summaries come before the actual papers in the thesis.
Now for me the question about the correct tense in these summaries comes up. For example I have the following sentences

The results reveals that in all weeks the methods led to reduced costs of 10 %.
On average, method B needed 14:06 minutes.

Would you rather use the past tense or the present tense in these examples. Here it is said that I should only use the past to refer to something that has been mentioned before. Basically the results and simulations have not been mentioned before. But at the same time the linked page says that I should use the past tense for summaries and to refer to specific simulation runs (which is obviously the case in my examples).
I tend to use present because I have used the present tense for the whole thesis.
What would you advise me to do?

This is probably better suited to the English Language and Usage stack exchange.

@astronat I dunno, I followed for some time ELU SE, but honestly it didn't impress me when it comes to academic writing. See also this meta answer of mine.

@astronat: I concur with Massimo Ortolano. The use of tenses as described in the question is primarily an academic convention and thus it is certainly on-topic here. It will likely even get better answers.

It's not really about if you have mentioned the work before (don't get confused by the instructions), but that the work itself was done before.  So stick with the past tense for the situation here.
In general*, the past tense is safer than present or future.  Probably 95%+ of the time you should be in past tense when writing a technical report.  And if debating, past or present (either might work), you are usually better off going with the past.  Only do the present or future if you know what you are doing as a writer and have a strong reason to change the tense.
*Caveat.

Thanks for your comment guest. To be totally honest, I was told many many times that the basic tense fro scientific papers is the present tense. Most of my writings are in the present tense. I just do not know what to do in this special case. Normally in a summary chapter I also use the past tense as I have already explained everything. But in my special case it is differnt. The summary is about content in papers that have not yet been metioned. So I am really totally confused at the moment.

Actually using present tense could be dangerous, depending on the situation. Your data was probably gathered in the past. Your conclusions are based on that data. If the study is statistical, based on samples, then there is the measurable possibility that it reached the wrong conclusion.
If the way you write seems to imply, even indirectly, a prediction for the future you could be on dangerous ground. It isn't a question of writing style, but of honest presentation of what you did and what was (past) concluded.
The examples you give certainly seem to imply that past tense is preferable here. You are describing a study that was carried out in the (perhaps recent) past.

Thanks for the answers. No I have two answers with different opinions. I guess I have to make a decision and there is no wrong or right here.

Actually, the question isn't an opinion poll. Evaluate the reasoning behind the answers.

You should consider all of:

Present tense: "The results reveal that XYZ", "This method reduces costs by 10%". Use this one when being more abstract, dispassionate, theoretical. You're "committing" less on concrete facts with this tense (but not much less).
Present perfect tense: "The results have revealed that XYZ", "This method has reduced costs by 10%". The period or duration you're alluding to with this one can be the course of your own research, the period of time in which your research was conducted (as experienced by others, e.g. in the field rather than in academia), or even to recent years up to the present, independently of the time you've done research.
Past tense: "The results revealed that XYZ", "This method reduced costs by 10%". With this tense, you're alluding to specific events and processes which have concluded already in the past and are known - or will be known by reading the thesis. This is more of a commitment to things having actually happened, and having had impact.
Future tense or sorta-future infinitive with qualification: "We expect the results to reveal how that XYZ", "This method will, in all likelihood, reduce costs by 10%". With this tense, you're discussing ongoing processes which have not concluded, but of whose conclusion you are certain or almost certain.
Present Progressive: "The results are now revealing how that XYZ", "This method is reducing costs, by an expected 10%". With this tense, you're strong alluding to very meaningful ongoing processes in the field which are the application of your research. Actually, it's rather similar in rhetorical effect to the future-tense option, except that you're committing that progress is occurring at the very moment you're writing your text.

Don't expect all of the text to use the same tense. Try to choose an overall narrative tense (Present or Present Perfect would be my preference), and choose other tenses in specific sentences or paragraphs in which they're relevant (not too many IMHO).
Also, as others suggest, your university or department may have guidelines on this matter.