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Found plagiarism in published paper - what to do?
I was recently reading a paper in some journal which described part of their method in the following way:

Our goal is to perform [something] on our data, which is drawn from [distribution]. This poses a problem because [reason]. We therefore took inspiration from Author et al. (1970) and propose to augment our method by [description of the modifications, including equations]. There are two challenges in this case: [first challenge, including a citation] and [second challenge]. We solve these by [mathematical description, including equations].

I wanted to learn more and looked up the cited paper (from different authors). Unfortunately, there wasn't more to learn as it turns out that the description (about 2 paragraphs, including the brackets) was copied near verbatim. In the quote above, the italic part was obviously added, and the wording was slightly changed a few times (e.g. from "there exist many ways to ..." to "there are many ways to ..."), but most of it is completely identical.
IMHO, this is way above the threshold of plagiarism. But it is a good idea to do something about it (e.g., contact the journal, or politely tell the authors to get their scholarly act together if I happen to meet them at a poster session) or is it better to let it go?

I suggest you edit the question to clarify if you are personally involved.

So article A copies from article B while prominently citing article B. This is technically plagiarism since the text copied from B is not clearly presented as a quote.
However, this type of plagiarism is harmless if not beneficial to science. After all, the authors of A have rescued the old article B from obscurity and made it more easily accessible.
You might ask the authors of A to add explicit quotation marks, but this looks like a waste of time.

"the authors of A have rescued the old article B from obscurity and made it more easily accessible" Not really. The original paper has 4-5x more citations and isn't really obscure in any way.

Thank you for these additional details. Still, old papers are not always easy to access. It is often convenient to have some material reproduced, paraphrased or otherwise reviewed in more recent texts.

Plagiarism is not about computer programs (or humans) counting the number of identical words and comparing them to an arbitrary threshold. "Plagiarism is the representation of another author's language, thoughts, ideas, or expressions as one's own original work."
In other words: if they solve the same problem as the original authors in a different way, and explicitly cite the paper used for inspiration, this is not plagiarism. If the problem is the same as in paper A, it makes sense to take the problem description from paper A. If it is cited correctly (which it is - very explicitly even), this is not plagiarism. It could possibly be a copyright issue if the wording is copied literally, but copyright and plagiarism are different issues.
Of course this changes if the solution presented in paper B is the same as in paper A, and the authors of paper B pretend that they came up with the solution themselves and only cite paper B for the problem statement, that would be plagiarism.

You misread the question. The parts in the brackets have been copied almost verbatim, as well as the rest. I just didn't want to make the paper findable via search.

Clearly, other people's expressions have been presented here as own work?

No, it is not about the expressions (that is what the citation is also for), it is about the originality of the research. Also, I did not misread the question - you edited it.

I edited to clarify. The information was already there before the edit. Also, "expressions" comes directly from your quote. I don't know why you use this quote as an argument if you don't agree with it.

So to summarize your argument: copying text is not plagiarism (but may constitute a copyright violation), only presenting other's ideas as one's one. I don't think I agree, and the Wikipedia article you cite certainly doesn't as it mentions writing multiple times. Before you say "they copied the writing but added a citation, so it is ok", it is not, as they did not indicate to which extent text was copied.

This is not "my argument", this is the definition of plagiarism and copyright, see for example: https://academia.stackexchange.com/questions/31315/what-is-the-difference-between-plagiarism-and-copyright-infringement

Post about your suspicion on PubPeer, a platform for post-publication review.


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Web scraping/email harvesting to contact survey respondents
I'm working on a research project that includes a survey of academics in a specific field. One method we've discussed for building a sample frame and obtaining contact information for potential respondents involves using web scraping to automatically obtain email addresses from various University websites. Names would be obtained by downloading citations for papers related to our topic, then we would use a script to search the web for email addresses that match those names. I'm not sure that this is an appropriate method for obtaining contact information, and have found some sources online that suggest my hunch is correct. However, most discussion of these methods relates to marketing research, rather than an academic context.
What do you think? Are there rules or guidance about this that I haven't found (I've read the CASRO and ESOMAR guidelines for research market which suggest that web scraping/email harvesting is not appropriate).

There is nothing wrong with collecting publicly available (non-copyrighted) data. The question is what you do with these data next.

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Sharing past exam papers with friends
I am a PhD student and we have a whatsapp group with all previous students from over the years.
I was trying to earn some good karma and offered to provide past exams.
I was always frustrated when other students didn't have them so I decided to provide them for free.
I, unfortunately, sent them from my university email account and I now have a potential misconduct charge.
Any advice?

Did you break a rule? Or are you just guessing that you might have done?

If the policy for the course is that exams are not available, then the lecturer can have good readons for that. Why do you think you know better?

How did you get the exams? Did you write them down by yourself? Then I would see no issues. Did you copy them from some servers? Then - most likely - you are into deep trouble.

So exams are available via the library, however, some students rip them out of the exam books so they gain an advantage. The lecturer sometimes post these exams online via an intranet. I simply sent the ones from the intranet. Deep deep trouble :(

@Buffy I am guessing I did

I must add, I got the exam papers as I was a previous student, I haven't used any PhD powers to get them or anything like that. They were available to all other students at the time of my previous course.

If anyone notices then you may be in trouble. You will have to deal with that if it occurs. Since you are "guessing" then it may not be clear that any actual rule, as opposed to an implicit expectation, was violated.
However, it would be helpful to your university for the future to clarify policies in writing. My suggestion would be that the policy make clear that all old exams are explicitly open for use and study. The opposite policy/assumption seems unrealistic in the extreme. Professors will need to deal with the fact that giving an exam is like "publishing" it and adapt future exams accordingly.
I note that a number of universities do, in fact, treat old exams as if their contents is available and well known. It makes the professor's job just a bit harder, but, again, the opposite assumption assumes they are a bit lazy in coming up with ways to determine the knowledge of their students.
There are also universities that would treat such things as a serious violation. Some of those, and I would hope all, ask the students to formally sign an Honor Code, listing what is allowed and what is not. Violations are serious, but there is clear notice at the beginning of the course of study.
If you want to short circuit any sanction, though what I suggest is a bit risky, I realize, you could bring up your actions to the faculty on your own and suggest that the policy be clarified if necessary. If the policy wasn't clear to you ("I'm guessing...") then it isn't clear to others. This disadvantages some students in a way that can easily be avoided.
But it also sounds like your university has a permissive policy about exams, from your statements about the library. If there were "violations" it would seem to me to be those of students who would remove materials so that they aren't available to others.
But you will need to asses the risk of coming forward unbidden.

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Is it common to be asked to take days off to go to a conference/workshop? (US)
My colleague and I started as postdocs this year in a US lab.
Recently, we respectively decided to go to a conference and a workshop. The conference was planned since a long time for my colleague, so before the beginning of their postdoc. As for me, I registered for a 3-days workshop at my host institution (not in the US) after the beginning of my postdoc. I asked my PI before registering and I registered because the workshop will bring me additional technical knowledge that I want to use in the future. However, I probably won't need it for the first article of my postdoc.
When I talked with my PI recently they mentioned days off and I realized they expected me to take some to attend the workshop. I asked my colleague, and they had to take days off too to go to their conference.
To give more information, I am a modeler, so I spend my time programming. I work alone on the project, so I don't have short deadlines with fellow coders. My colleague and I do not have a teaching or supervising load. I am currently hosted by the university that is organizing the workshop, so I have no travel, accommodation or registration fees.
I have studied in European countries (Master and PhD) where conferences and workshops are considered work and as such you don't need to take days off. But is it normal in the US?

I'm surprised. Are you paid by the hour or the week? I'd expect an annual salary instead. What does your contract say? Talk to HR.

What do you normally do? While you are gone for 3 days, will these things not get done? For example, do you normally do some teaching? Will the university have to provide a substitute while you are gone?

@Buffy It's an annual salary indeed. I don't think my contract mentions anything about days off and conferences/workshops, but I'll check as soon as I can.

I added more info on my responsibilities in the main post.

I happily pay for my postdocs to go to conferences they applied for before coming to my group. Professional courtesy and all that…

If the event is related to and useful for your job, you should not need to take time off, but you likely need your boss's permission.
If the event is not related to your job but rather your general professional development (for example, it'll help your next job but not your current one) you may need to take time off. You may also need to take time off if your travel is not officially approved but you'd like to go anyways.
It would be extremely unusual to be asked to take time off to travel if the travel is paid for through your job.
I think most typically, since post docs are training positions, mentors will consider "job related" to be very broad, since part of your job is to gain breadth of experience.
There may be complications when your official job/source of revenue does not encompass your entire position, for example if you are paid for teaching or for statistical consulting, but your position also involves research, it may be that you don't really have financial support for the research side of your job. This sort of arrangement is more common for graduate students, though I suppose it's possible some post docs are in a similar situation. It doesn't sound like you fit this, though.
Generally from the details you give, I think this is unusual but probably not against any policy (but for that you'll have to check your institution-specific rules). It seems these are not events where you are representing your current lab, so they fall more in the discretionary area rather than "definitely part of your job" area. I think your boss is foolish to be so protective of the work hours of salaried employees, but that is likely their perogative.

If OP works in a different country where they need a visa, they may be obliged to inform the international office, or even seek permission, for personal international travel.

If the travel is related to the grant that’s paying your salary to work on the project you will give a talk or a poster about at the conference, then the grant should pay your expenses, within reason, i.e. getting there, feeding you, etc (whatever’s reasonable and legal, check with your department’s administrative staff). If your prof wants to pay for you to go out of their department funds some other money they have access to them. I’d say getting travel paid on grant funds is more likely, though the agencies keep coming out with longer lists of what you can and cannot pay for with grant funds (in the US), your university will have its own rules, too.  E.g., in most states you can’t pay state taxes (hotel) using grant money, it’s self-serving.
To answer the question: abnormal in the US. I’ve never been a postdoc, but I’ve seen them  budgeted for and paid, and I think I’d know if they were paying accommodations out of their own pockets. We all pay out of our own pockets initially, but we turn in receipts when we get back for verification and reimbursement.

This is pretty similar to what I've experienced in Europe so far. I didn't mark your reply as answer, because I wanted to know more about needing to take days off for workshops and conferences.

@Argent going to a workshop or conference and giving a talk, paper, or poster is work: so, you get paid. My job as a researcher expects research due to these kinds of events, and so does my funder. Spread the knowledge gained and meet new people and see their new stuff. My funder will pay for some of this, too. Gives us a chance to try to use the latest research in our own projects. I’ve seen whole new computational problems solved during talks.

It certainly wouldn't be normal or usual for an academic to be docked from a "salary" for attending a conference in the field. But the work needs to get done whether you are on site or elsewhere. Perhaps the prof just used poor wording to remind you of that and to note that you may need to take some responsibility to see that there are no disruptions caused by your absence.
Your salary is for your work, not your physical presence unless that presence is essential to the work.
It is possible, I suppose, that if the prof is paying you out of a grant that they have a different conception of things, or even a misconception. It probably requires a conversation with them to clear it up. And be prepared to assure them that you will take steps to see that the work is carried on without disruption.
It is also possible that your contract specifics a certain number of "vacation" days. Perhaps it is a request (demand?) to count the conference days against that. I would disagree with the appropriateness of that, but others might not have the same view.

Is this normal in the US?

It varies by institution and even by department.  I'm guessing this "days off" policy for postdocs is the same as the policy for faculty and administrators at your university.

Your first paragraphed seemed to be requesting clarifications on the post, so I went ahead and converted those to comments (the answers should eventually be edited into the main post). I'll leave the second paragraph, which does appear to be an answer.

The conference was planned since a long time for my colleague, so before the beginning of their postdoc.

This is a bit ambiguous, but my impression here is that you are going to a conference to present research you did for a previous employer.  It that is what is happening, it is reasonable that you be asked to take time off.
In my experience, one does not go to a conference if one is not presenting.

Perhaps you need to get out more. In my experience one goes to a lot of conferences whether presenting or not. But this differs by fields of course. In CS, conferences are how we keep in contact and learn about new trends.

@Buffy In physics, unlike CS, conferences accept essentially all submissions.  Going to a physics or chemistry conference without presenting would be bizarre.  It just suggests you forgot to submit an abstract.

And to me, a conference attended by only presenters would be bizarre. And worthless.

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What if the lead author disagrees with the coauthors on manuscript content and target journals?
The lead author has conceived the initial idea, developed the methods, the experiments, the analysis, and has written the draft. Coauthors have contributed to that draft mainly by rephrasing and restructuring it, in a way that lead author disagrees.
Additionally, coauthors insist on submitting to a journal which lead author disagrees with, but also the coauthors do not agree for submission on journals which the lead author prefers.
Lead author wants to stop collaborating with the coauthors, but doesn't want to leave this work unpublished (coauthors say they will ask for retraction if work is submitted, since they believe they contributed considerably). Would it be possible for the lead author to omit the coauthors' contributions by rewriting the manuscript, and submit it as the only author?
Given that the solution of negotiating and finding a middle way is excluded, do you have any other solutions to propose?

Would it be possible for the lead author to omit the coauthors' contributions — No.  You have to work it out like adults.

@JeffE, thanks for dropping by, but a single 'No' without any reasons doesn't help. Besides, the solution of negotiating and finding a middle way is excluded.

Generally, if there is a disagreement you compromise or you're stuck. Would it be possible to find a neutral party that helps mediate negotiations?

This is clearly a messy situation, and the authors must come to an agreement in order to get the paper published. Mediation could help.
Another possible way out would be to split the contributions into two papers.

@Anyon, thanks! It feels like stuck at the moment! Both sides have tried to negotiate; I said this solution is excluded after trying a lot. I guess it doesn't work because of the different demands on time for publishing, and journal 'prestige'. Lead author just needs this published soon, and ideologically doesn't care about Impact Factors, whereas coauthors don't have pressure of time, and want to go down the Impact Factor ranking. Of course, journal affects content, and there's the disagreement.

@user3697176, thanks too! Splitting sounds a good idea, but only if coauthors had actually contributed substantially. As I said, the coauthors' contributions are just rephrasing, not even ideas. I don't think they can even follow or reproduce the technical parts of the work. Yes, it's a messy interdisciplinary situation!

It seems to me that choosing where to submit is within the responsabilities of the first author. Even though the acceptance of the co-authors is encouraged and desired in order to maintain a healthy relation, I think the last word is his.
I also think that there's a lack of empathy in this matter. Co-authors should be asking themselves how would they feel in the author's position. How would they feel if they had an idea, developed methods, analysis and drafts and kept being undermined by the rest of the team?
For closure, keep in mind that a work is best if published, regardless of place. Spending all the effort taken because of such disagreement seems petty and dull to me. It is better to let it go and focus on the next project.

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How do I determine whether "Global Scientific Journal" is reputable or not?
I have published my paper in Global Scientific Journal. But some scholars are telling me that the journal is not reputable. How do I determine if Global  Scientific Journal is reputable or predatory?

Using capitals like that is very poor form and not reputable at all.

The general answer to this question is here: https://academia.stackexchange.com/questions/2158/how-to-identify-predatory-publishers-journals

This post also has some good answers (and the selected answer has some great references) https://academia.stackexchange.com/questions/83764/with-bealls-list-gone-how-can-i-tell-if-a-journal-is-spam

Although the question may be flagged as "off topic", I think that it is essential to expose predatory journals nonetheless. Hence my answer is:
Yes, most probably Global Scientific Journal - GSJ Publication is predatory (which is worse than non-reputable).
My assessment is based simply on the reputable Beall's list  here (updated two weeks ago, 18 Aug 2019):

Here we include journals that were not originally on the Beall's list, but may be predatory.
Global Journal of Advance Research on Classical and Modern Geometries
Global Journal of Research on Medicinal Plants & Indigenous Medicine
Global Scientific Journal - GSJ Publication

I wonder if Beall minds others naming things after him, given that he no longer contributes to the list?


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Revocation of Master Degree
I didn't give the dimensions of the machine that I designed in my master thesis. My supervisor said that you don't need to give dimensions and said that they are useless for a thesis: you don't make a design as an engineer, you are doing research. So I didn't share the dimensions. And I have dimension-related findings/figures in my thesis. I mean, if you change dimensions, half of the graphs/results need to be revised. But now, I learned that some people say that it makes your thesis misrepresent. Is it the case for my thesis?
On the other hand, I spent three long years for this thesis and I never plagiarised. I asked every question to my supervisor. But today because of this situation I'm very stressed. I didn't want to a mistake but because of my supervisor's reckless situation I don't know if it will cause my thesis to be revoked :(
You can imagine that; in 80% of my study I have 2 data sets: one of them subject data the other one is my design. So, you can't change the subject data I mean they are constant numbers and also I give reference to that data. But my design's dimensions can be changed and if you change them all my figures are changed because the structure is changed. Can you make a comment on this situation please?

Welcome to AC.SE. Please take a look at our [help]. We are aware of your edits and your desire for the question to attract more attention. Unfortunately, the community doesn't think your question is a great fit. it is hard for me to find the question within the long narrative. I suggest you distill the text down to the core question.

"Can you make a comment on this situation please?" is not a good question for this site.

Your thesis should not be revoked for not including the dimensions of the machine. You haven't attempted to deliberately misrepresent or misstate things—you and your advisor made a decision something wasn't relevant to the thesis.
But I honestly don't see why your thesis shouldn't include the dimensions of the machine. If it's relevant for establishing a comparison between the existing data and yours, then it really is essential to the thesis and should be included, at least as an appendix. Your own comments suggest that the information is necessary for the reader to process and understand your figures.
If your thesis has already been submitted and approved, don't worry about it. If it's in the revision stages, talk to your advisor about why you feel it should be included.

It should be obvious to someone in your field that if you change the relative physical dimensions, the results will likely change. Given that, you shouldn't worry about revocation of the thesis. But like I said, it wouldn't hurt to stick a table with the dimensions you used somewhere (in a future paper, in a revision of the thesis, etc.).

I don't think you have any issues as long as your advisor is happy. The thesis should be accepted and the degree awarded. After that it is up to you whether you want to publish based on the thesis and what you say.
You can certainly revise and extend anything in the thesis. Just cite it appropriately. But for now, just make your advisor happy.

You should be fine. Time to relax and have a beverage suitable to your culture. Your English works fine, by the way, if not perfect.


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Wrong information in my thesis
At the beginning im so sorry about what i did. But in literature review of the introduction part of my thesis i realized that i made a mistake :(
It is about giving state-of-the-art part of my study area. When i describe a study i saw that, in paper it says that;
"this paper describes the design for bla bla (paper)... we will evaluate the design(at conclusion)" but also in paper it says that for example;
"knee design take advantage of the fact that knee generate needed power bla bla.
But when i describe the paper i wrote that; "In[5], they emphasized that the design produced correct power" here the faily part :( they didn't evaluate but i mention that the design PRODUCED correct power. and 2 similar sentences:(
For example i say: "ankle didn't produce unneeded power for bla bla".
but in paper it says; "ankle design take advantage of the fact that ankle doesn't produce large power for bla bla"
The case is here; they introduce the design or lets say, ,idea, proposes but i described as it produced that power etc but actually it wasn't made, those of them were ideas or claims of authors.
is it reason of revoking of my thesis later :( please help me.

If you aren't allowed to make a correction then you can't and it is what it is. But since it was accepted, there should be no issue for the thesis or for your degree.
However, in the future, if you do a publication that needs to cite the thesis, you can make a correction there. I assume, of course, that the error doesn't call your main result in to question. In that case you would need to either ignore the past or give a rather extensive update to your thesis in a new paper.
People make mistakes. People correct mistakes. Science moves on and advances.
Your thesis probably won't be the last piece of work that you do.

Does the error affect your main result, or is it just embarrassing?

Then there is no reason that you need to mention it, and no need to not mention it. It was an error, but not critical to the thesis. However, if you do, just say that you made an error of interpretation of past work. It wasn't intentional, nor an attempt to mislead. It has no effect on the outcome. The authors of the other study might want to complain to you and you can apologize to them if so, and correct yourself in any future work.

I don't think mis-quoting a particular reference will cause the revoking of your thesis.
Edit based on edited question:
If you are mis-representing the results ie changing the results to be for the ankle instead of the knee and then basing your results on that, then that could well be a concern.
Can you submit a correction to that section? You should check this with your advisor - they will know whether you should edit it or leave it...


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Two researchers want to work on the same extension to my paper. Who to help?
I recently presented a paper in a top-tier conference in a computer engineering field. I did that work as a research assistant under a Professor but now I am working in the industry. Two different researchers, let's call them John and Sam, wish to work on an extension to this work. But both need help from me since they feel I will be able to solve their problem quickly based on my experience. John is a PhD student with whom I had worked with and was the second author of the paper. Sam is a PhD student, in another university, who I met at the conference. Since both have a request for help and both are working on the identical extension of the work, who should I help out?
Background:
I originally planned to work on my paper alone along with my advisor. After I was done with about 80% of the work, I met John (who is a Phd student under my advisor) and decided to collaborate with him because he too was working on a similar problem (he at that time was working on the extension itself). John didn't contribute directly with the work (I was sole author of all code and did all analysis with help my the advisor) but he helped me with conference selection and writing of the paper. As John was sponsored by a company, having his name as an author meant that now all the ownership of the work laid with the company, at least that was what I was told by John and the advisor. This meant they had all the rights to the code (though I never signed away my rights explicitly). My advisor is particular about legal issues and hence don't want me to make the code open-source. But since the company was not interested in using the code and I didn't want my work to go to waste, I have made the code open-source, unknown to my advisor or John.
Question: I wish to maximize the use of my work (since it is my first research work). So should I continue to help both John and Sam who are both working on the same topic? My concern is that one of them will have wasted their time if the other is successful in publishing a paper first.
I am more confident about Sam's skills (based on his past papers and John doesn't have much experience in this field) but John has indicated to me from the start that he was more interested in the extension than the work that I did in the paper.
My other option is to reveal to both of them about each other so that they can possibly collaborate. But since I have told Sam that my code is open source, Sam can possibly tell John this information which might irritate my former advisor. I would like to avoid this because I might require future favors such as a letter of recommendation should I choose to pursue PhD.
Edit: I have open-sourced the code via GitHub (changed the repository from private to public). I still haven't added any license (so legally by default it is not open-source as in free to use but anyone can browse through it) so I still retain all rights. Basically, I used the wrong terminology, the code is public (instead of open-source).
I haven't talked with any representative from the company, only my advisor and John have been in contact with them. From what John tells me, the company is no longer interested in the project and I think John's funding is also stopping because of this.
Based on the answers, I am going to ask Sam and John to work together (at least tell both of them about each other) and ask Sam not to reveal about the public code. I am still not convinced about making the code private again because this being a computer engineering field (applied field), just based on paper, it will be hard for anyone to replicate the work (the evidence is that both John and Sam need my help).

"I have made the code open-source, unknown to my advisor" - this was an extremely unwise decision, which is already starting to come back and bite you. Never do this again. What will you tell your supervisor if he finds out and asks whether you plan on open-sourcing code you write for your employer, too?

You are allowed to publish your own code.
The code itself does count as literature, to which you as the author own the copyright. John or the company from whom he was sponsored need licensing rights to publish your code.
Nevertheless the company can own the publishing rights to the paper or the fundamental method of your code in form of a patent.
But considering the fact that you, the main author and creator of the intercultural property, never signed any working contract or licensing agreement the company does not have any rights or only have the rights to Johns contributions.

Both comments above are rubbish. At least in the United States, the ownership of software written as part of work (including being a graduate student, whether paid or not) resides with the employer (the university) or with any other entity with which the university may have made an agreement in return for money (e.g., the company that sponsors the research). So you can put your code on a website and put an open source license on it, but that's legally not your decision to make and has no legal validity if you don't have the approval of the university.

@WolfgangBangerth: Yet in many cases, the university has a general policy that the copyright in such work is automatically assigned back to the student or employee who created it.  (The University of California has such a policy, for example.)  So in at least some cases, it is the student's decision to make, after all.  I really don't think it's possible to make a blanket statement one way or the other.

@NateEldredge: The university may choose the assign the copyright back, but it has the first right of use. Without formal approval from the university, the university would never be able to commercialize anything.

@WolfgangBangerth: Well, my reading of http://policy.ucop.edu/doc/2100003 doesn't seem to allow for such: "ownership of copyrights [of scholarly and aesthetic works]... shall reside with the originator" unless certain specific exceptions apply.  I don't see how the university could change its mind unless they modified the policy in advance.  Now, there is a separate policy for patents, which the university does get a share of if they want.

"I still haven't added any license (so legally by default it is not open-source as in free to use". Um. What? If the code is there without a license, then what makes you think there are any restrictions on it whatsoever? IANAL, but I'm pretty sure having it there with no license means anyone can do anything.

@terdon: Just because a car is sitting in a parking lot with a key in the ignition does not imply that it's there for you to take. The same is true for software: Just because you find it on a website does not imply that you can whatever you want with it. In fact, in most jurisdictions just downloading it would be illegal. The point is that the legal rights you do or do not have are a property of the software; they are strictly speaking independent of whether someone has or has not attached a license statement to it.

@terdon: To be precise, a license statement on a piece of software only has legal meanings if the person who attached it was legally allowed to do so. A disgruntled employee putting the company's software on a website and attaching an open source license to it is not legally entitled to do so in the name of the company, and as a consequence the existence of the license shown with the software has no legal implications: The software is not open source. That's no different than an employee taking the company truck to the parking lot and attaching a sign that says "free to take".

@WolfgangBangerth I don't claim to know, but what you describe is certainly surprising to me. After all, that's the whole point of licensing. If code is available, then it's open source kind of by definition. And if it's available with no license, I would expect it to be very had to make a legal case against others using it. But, again, I don't claim to know. This is just my (probably naive) understanding.

@NateEldredge: I read III.A.1 and find "Ownership of copyrights to scholarly/aesthetic works shall reside with the
designated academic appointee originator, unless they are also sponsored works
or contracted facilities works, or unless the designated academic appointee
agrees to participate in a project which has special provisions on copyright
ownership pursuant to Section V.C. of this Policy.". Then III.A.4: "Ownership of copyrights to sponsored works shall be with the University unless
the sponsored agreement states otherwise." III.C governs release of copyright to the employee.

@WolfgangBangerth: please refrain from describing comments as "rubbish". My comment is not about this being illegal, it's about this being unwise. OP may be completely in his rights about publishing the code, but nevertheless I maintain it's a very bad move to do so behind his supervisor's back and against his express wishes. Lots of things are legal but nevertheless unwise. Does this explanation change your appraisal of my comment?

@stephan OP here. Yes, I too agree it was unwise and I was aware it was unwise when I made the decision to make the code public but somehow I couldn't bear the fact the culmination of all my 8-month effort was just a paper which probably is not going to help anyone out more than the code is. I hate to admit but based on the comments here, I am thinking to make the code private again, at least as a temporary measure.

@WolfgangBangerth If source code is published on a website then in what jurisdiction is it illegal to download? There must be an implied license to view content published on a website, no?

@Matt AFAIK, without a license, you can view the source code but it can't be used commercially hence it is not open-source in that sense.

@Saksham Absolutely correct. But Wolfgang claimed you cant even view source code published on a website in some jurisdictions. Which doesnt make any sense. I guess the word he used was 'download', but since all website content is downloaded as a part of viewing it, viewing implies downloading.

@terdon: "I'm pretty sure having it there with no license means anyone can do anything." - please have a look at some related questions such as this, this, or this over at [opensource.se], whose answers all make it pretty clear that by default "no license" means "no rights granted".

@Matt: There are two facets to that. For one, copyright legislation sometimes includes special exceptions concerning temporary copies created for technical reasons, such as the copy of a website in your browser cache while you are viewing it (for instance §44a in the German copyright code, some other jurisdictions probably have similar provisions). At the same time, if you as a user of online materials can be assumed to know you have no rights to access the provided material, you may indeed not be allowed to view it, as evidenced e.g. by a ...

... verdict of the European Court of Justice that clarified that users who stream movies that were made available illegally are infringing upon copyright themselves and not covered by exceptions.

@terdon: The point you're missing is that to legally license anything, you need to own the copyright of the thing you're licensing, or legally speak on behalf of the entity owning the copyright. If you don't, then that's no different from me hacking into Microsoft's servers, downloading their codes, uploading it to a website, and putting an open source license on it. Because I didn't own the copyright, I could not legally make this code open source. In other words, just because someone says so, doesn't make it so. That decision is still Microsoft's to make.

Work with both John and Sam on the same paper. You all have something to offer, so pool your efforts and work together.

... and to increase the impact of your joint work.

This is the right suggestion IMHO, because if they both work independently on the exact same thing, not only will there be some/a lot of wasted effort, but they are also likely to get into some conflict over who gets the credit, or - one of them will publish and the other one will be stuck with nothing to show for his work.

@usr1234567: A larger group of authors is not a guarantee of a higher-impact paper IMHO.

+1 Also OP's name should be on both works. How do you explain to an editor that your name is on two manuscripts on the same subject, but with different coauthors? Split personality? ;-)

This is so obviously the right answer it's almost embarrassing that it needs to be said...

This open-source issue is really knotty. My first concern is your legal footing -- make sure you do not have any legal liability for making that code open source. You may need to consult with a lawyer.
Second, John is an author of your paper. So, this is joint work, regardless of who did what. Now that it's published, anyone can do anything with the published work -- but anything unpublished (e.g., code) could be considered IP (see previous paragraph). Even beyond the legal issues, this is joint work, so leaving John to work on his paper while you help Sam scoop him is rather ethically questionable. Even if John and Sam were both total strangers, it would be reasonable to either put them in contact with each other, or tell one that you've decided to work with the other on the same problem.

@GeorgeM Unless (a) the OP signed a contract giving the university rights to her code, or (b) the OP was paid to write the code (would make it a "work for hire"), the OP owns the copyright on the code and can legally do with it as she pleases. [Doesn't mean some people won't be angry about it...]

Well, I think OP should be careful -- telling the university's legal department that they illegally published university-owned code on the internet could end poorly (though I can't say definitively that this was illegal, of course). I think that's the real issue here, sort of a shame that the top-rated answer ignored the most important point.

The "open source" issue would probably have been easily solved, except you have now made the situation worse by going behind people's backs.
I'm coming from the "industry" side of this sort of situation, and from long experience it's unlikely the company actually wants the code. They want the ideas expressed in it, to implement their own way.
John has apparently got the message the "IP is important" but he isn't the person in the company making the decisions, or signing off the sponsorship money! It would have been much better to deal with whoever is managing the sponsorship, and get a proper agreement in writing if necessary.
It's very unlikely the company would want to prevent the university doing further research, especially since it appears they are getting this code "for free" and weren't aware of it when they set up John's original sponsorship. In fact they might even sponsor more research.
But from the industry side of the table, the one thing that really p*sses me off is when people start trying to play silly games with IP - and "putting something in the public domain" behind my back seems like exactly that, a silly game. If the IP "belongs" to the sponsoring company or to the university, that's fine either way. both sides can do business starting from that point if they are both willing partners. But when one partner suddenly takes unilateral action, that sends a message that they are no longer a willing partner.
In the short term - well, from an industry point of view you don't expect every research project to pay for itself, so if this one doesn't produce any useable end product (and code with an open source license might not be useable by the company!) that's not going to surprise anyone.
But in the longer term, if there are several universities who are possible places to sponsor research, and one of them has a track record of playing IP games, guess which one I'm less likely to recommend, next time around...

You should all do a collaborative study. John and Sam should have shared first authorship or Sam first and John second, with you providing guidance and consultation on the entire project.
If you are specific about the open-source nature of the code, discuss this issue with both John and Sam. Do this, before going to your legal advisors.

As John was sponsored by a company, having his name as an author meant
  that now all the ownership of the work laid with the company, at least
  that was what I was told by John and the advisor.

I'm sorry but this seems very shady to me and I think John is playing you for a fool or John himself is a fool. If you are the author of the code, it is your code. If the code is present on a private repository (is it?) in the cloud, it establishes that you are the creator and contributor to the codebase. The contribution by author part in the paper establishes the contribution by both You and John.
Unless you sign some sort of agreement relinquishing your rights to the code, it does not become IP belonging to a third-party. Furthermore, you may have already signed away whatever rights you had to the code when you became a student at your university. Go back and check all the papers they made you sign back then. In such a case, the code belongs to the university.
Also, it is worthwhile to check the licenses of the dependencies you may have imported and also the licenses of the language that you used to write the code. In many cases, the licenses will stipulate (check Apache) that usage of this software means that you will have to preserve and maintain the license in your codebase.
Do all this before you speak with a legal advisor.

Why do it before talking with a legal advisor? Do you expect a legal advisor to advise halting further research?

No, I do not. But in my experience, speaking to the institutional legal advisor almost always means that the project will get mired by a lot of red tape, which means progress will be slowed down.


text:
How common is it for grad school admissions to use a whitelist of undergrad institutions?
I was talking to a professor recently and he mentioned something that I found surprising. Namely, for graduate admissions in his department (top-30, US public) they had a whitelist of universities and they only consider applicants whose undergraduate studies were at one of those universities. He went on to complain that initially the list was too US-centric and it had to be expanded because they missed good international candidates.
I was very surprised by this. I did not know that this whitelist approach is used, but evidently it is. My question: How common is this? Have others heard of this practice?
I'm pretty sure my undergraduate institution would not make it onto any such list. So I'm sad to hear about such practices. Fortunately, I did get admitted to several very good US grad schools, so evidently the practice is not universal.

The implementation you describe sounds more explicit and rigid than most, though, yeah, I'd guess that a lot of places end up doing something like that in effect.  Dunno how easy it might be to get a survey of recruitment practices, though; that sorta thing tends to be private info.

An explicit whitelist? Sounds like a PR and possibly legal nightmare if it ever got leaked.

@SolveIt: Not sure about that; schools being "selective" (e.g., GPA of entrants) is usually considered a positive thing.

@DanielR.Collins Selective is good. A public institution outright refusing to consider some students (and I'm sure there are many other public institutions not on the list) is questionable.

I think your use of "white-list" is not accurate. Namely, usually it does not mean the exclusion of all others, but only the inclusion of those on the list.
As far as graduate admissions, yes, prior experience with letter writers from a given undergrad institution, especially via the people admitted to our program from that institution, establish a track record for those letter-writers, and for those programs. That's not to say that every individual from a good program is equally good... but that we have data points about the meaning of the letters of recommendation, and about prior preparation.
In fact, our graduate program pays considerable attention to individuals who most likely fall outside the doctrinaire "best undergrad institutions", exactly because we know that many grad programs will under-value them, so that (if we can see a good hint of potential) we have a better chance of recruiting them. So, no, there is absolutely no a-priori exclusion of people from ... odd... places.
But, again, sure, prior experience (for better or for worse) with institutions, their faculty, and their programs, obviously gives us information. Yes, it seems to be true that some institutions are a bit delusional/arrogant, but we don't hold that against their students. :)

The way he described it sounded very strict.

I do think the OPs use of "whitelist" is reasonable. As a security concept, it usually means the negation of a blacklist (that is, for blacklist B, deny x if x ∈ B; for whitelist W, deny x if x ∉ W; possibly confused in usage of email programs under exclusive/non-exclusive criteria to override a pre-existing blacklist action). That does sound like an accurate description of the situation.

Multiple usages of the word "whitelist" exist in different contexts, but in this case I think it was fairly obvious the "deny if not on list" definition is meant, not the "automatically accept anyone from these institutions, even if their application is in crayola on a soiled napkin" definition. (That would be an interesting practice indeed!)


text:
Advice for getting professor to submit letter of recommendation
I'm applying to four master's programs. My former professor submitted his letter to the first two schools last month. But he has not submitted to the other two schools. One of them is rolling admissions so sooner the better, and the other had a "priority deadline" that passed last week so is now also rolling admissions. I've emailed him three times over the past 10 days but have not heard back.
One of the schools is clear that they won't look at your application until the letters are received.
I have the professor's cell number, should I text or call him about it? Should I give him more time before bothering him again?

Call or better visit in person if you can.  We all get a lot of email these days, maybe too much and it is too easy to overlook an email.  If you phone and the person recognizes the number he/she might ignore the call.

Your sentence about ignoring the call seems to advocate for going in person?

Yes.  Personally, I feel that we live in the information overload age and there are too many things (e.g., emails) that distract us from other work.  Sometimes the only way to get the help you need is to be there in person.

Thanks, I texted him as first step (I'm an hour away from campus) and he submitted them later that day.


text:
How should I withdraw a paper from a predatory journal?
My Co-author made the mistake of sending a research article to a predatory publisher(OMICS), which got accepted after 2 months of review. On the same day of their acceptance email, we sent a withdrawal request mentioning that there were serious concerns with the results of the paper(We lied). No contracts were signed, no fee was paid and there was no transfer of rights etc. They requested a fee of 300 USD for the withdrawal process. I ignored their email thinking that they won't publish the paper as no contracts/money was involved. Fast forward, a few weeks ago they have published the paper on their website on our name with the complete DOI and all, whereas the paper is already in a review process for another journal.
What should be my next step now?
Unlike the previous question cases, my paper has been published on their website without any fee


text:
Someone "reinvented" our algorithm, is there anything to do about that?
A couple of years ago, we have published a paper in a reputable IEEE conference in field A. Recently (two years later), a paper in field B solved the same problem with the exact same algorithm without mentioning our work (the problem is of value to both fields).
We have tried contacting the authors but they do not respond.
While I cannot know if they have seen our work or not, other works are already citing the new paper as the one that solved the problem (without mentioning us).
Is there anything we can do about this?

Remind me of this question https://academia.stackexchange.com/questions/9602/rediscovery-of-calculus-in-1994-what-should-have-happened-to-that-paper

The place to start, if the authors don't respond, is to contact the editors of the journals that published both papers - or at least the editor of the other - pointing out the issue and giving references.
Perhaps nothing improper has happened, but you can at least ask for a note/erratum posted with the other paper so that you get more visibility.
I doubt that you can get more than that, but if you start there, at least, you can get proper recognition.
Parallel work is pretty common. Not recognizing something similar if it appears in another field seems pretty natural. Maybe something worse, but hard to know. Contacting their editor may get them to contact you, one hopes.
BTW, the reason for contacting your own editor is that they might also get involved in a solution.

Both papers were published in conferences. Not sure who to contact in this case.

@BenA A conference will have Program Committee (PC) chairs instead of editors.

Or both Conference chairs and Program chairs. The Conference chair has overall responsibility. Also, if the proceedings were publishes (common in CS) then there is likely an editor. Conference websites typically have everybody listed and typically stay available long after the conference ends (years).

Unfortunately, conferences typically don't publish errata (in contrast to journals).


text:
What to do when distantly related project is draining research time
I'm a PhD student in mechanical engineering, although my research is more interdisciplinary. My supervisor's background is in electrical/mechatronics engineering.
There is a mechanical design project I volunteered to help with early on during my studies, thinking it wasn't too much work. It turned out to be a lot more complicated than I thought, involving designing and putting together a custom battery pack, which I didn't have any experience with before. This project is not related to my main research and I don't want to make it the main project since I am no longer interested in mechanical design.
My supervisor thinks it is as straightforward as welding some conductors to the batteries and running it once without a balancing circuit to get a heat distribution. My supervisor has been pushing me to complete this, but both me and our project manager (with experience in mechanical design/fabrication) are not very confident about it. Some issues I can think of are batteries getting shorted during the welding process (because of our custom holding structure), the risk of running the pack without monitoring/balancing, or if we want to use a commercial battery management system, the time it will take to set that up, both software wise and wiring wise since we don't have provisions for the wires.
On the one hand I know this project needs to be done as soon as possible so my supervisor can deliver it to his funding agency, on the other hand I don't know how much more time I need to drain into this before getting it to work and I can't make my supervisor believe this is more complicated than he thinks.
In terms of the funding situation, I'm not entirely sure where my funding is from and which source this project is for since my supervisor has multiple sources. Although it was made clear that my supervisor doesn't intend for this to be my main project.
Would appreciate it if I could get some perspectives on the situation.

Are you being funded to work on this project?

Probably yes, although my supervisor has multiple funding sources and I'm not entirely sure which project/person belongs to which.

If you are an RA, then your PI can tell you what to work on 20 hours a week. You should figure that out first.


text:
Copyright on a research photography
I was part of a research group in a research institute I called 'X'. In this research we used a very interesting, colorful technique so I take some pictures for myself that are very artistic. Now I want to present them in a Scientific Photography contest organized by the same institute 'X'. I signed a confidentiality agreement with the institution and my research advisor. The thing is I need an author's written authorization for reproduction of the images in order to participate in this contest. At first I thought I was the author since I was the one who took the photo, but seems that in the agreement I signed says that all products of this investigation are property of the institute 'X' and I don't know if this has something to do but the camera was also property of the lab. So, who should I ask for the authors written authorization? Or I don't have to ask for it at all?

Ask the head of the research group that you were part of.


text:
Will submitting to mediocre journals (MDPI) hurt me in the long term?
I have some preliminary experimental results that won't fit into the next round of experiments. The first only shows there is problem but can't make any conclusions about why. The second will hopefully both point out the problem and explain why. The experimental methods are independent of each other but data analysis overlap.
I was originally thinking about submitting it to a conference (electrical engineering, conferences publications are not really looked upon), but was offerred the opportunity to publish in a MDPI journal (Batteries, IF 4.0, our top journal has IF around 10). My personal experience with MDPI (Energies & Batteries) say that they are mediocre at best, and I have stopped reading/citing their articles just to save some time.
My PI suggests I publish the MDPI & submit future results to a good journal. He did previously comment on how MDPI journals are having decent impact factors and I think is basing his judgement on the IF.
My friends are suggesting a conference + journal makes more sense than bad journal + good journal, and publishing in MDPI may harm the reputation of my good journal because when people look into it, they will find the preliminary results are published in a borderline predatory journal.
This would be my first ever journal publication, so I thought it won't harm my personal reputation too too much since I have lots of time to prove myself later, but I also don't want to waste energy publishing something I'm not even proud of.
How will this look when I later apply for post-doc and tenure track? Am I overthinking this and should just get one publication out of the way since my lab requires 3 to graduate? Would love to hear some thoughts on this.
Want to add some clarifications since this question still seem to be attracting attention:

This is not intended as a debate over the quality of MDPI journals. I'm asking that given the not-so-good reputation, which I think people can agree on, could it hurt my personal reputation or the reputation of my future potentially interesting paper. Specifically, if you see an interesting paper, does it make you suspecious if the prior related research is published in an MDPI journal? My speculation is yes which is why I decided to submit to the conference instead.
There are comments on if I don't read/cite them, why publish. I don't prioritize reading or citing their articles simply because there is too many to read already. I still think they are good as a documentation kind of journal to document some not-so-interesting-but- nonetheless-done kind of research from and occasionally compare my results to MDPI papers for additional validation. Additional, I have the motivation of having 1/3 of my graduation requirements out of the way, which gives me more freedom to try things in the future. Finally, I think my results right now is exactly the "we found something here it is" kind of paper I still occasionally read from MDPI, so it could potentially benefit someone.

I don't know your field well, but it may well be that there are not so high IF journals that would accept this kind of thing and are not predatory (and in particular don't make you pay).

MDPI deserves a lot of hate, but by golly, most of the reasons people give for hating MDPI read like disinformation at best.

To answer both questions, I was considering MDPI cause of the fast publication process makes it as easy as a conference. I don't think the manuscript right now deserves more effort than this since there is another paper coming. I was more weighing that with the same effort whether a conference or a MDPI would be better, but I ended up just going with the conference after reading more on MDPI.

How do you get from "fast publication process" to "easy"? I'm curious how you draw a causal relation. Like, how does a fast publication process make it easy? Unless you mean the production process is easy for authors (which it is, relatively) - but presumably that's not what you mean.

@Allure They are not related, but from our past experience MDPI has a nearly non existent peer review that made it really easy for the author, this what I was implying. I'm not saying it's good but just thought it suits the situation.

Considering the amount of complaints MDPI gets about too many review invitations, "nearly non existent peer review" should be inconsistent ...

@Allure how so? Not saying that's what happens, but there is no a priori inconsistency: many, many papers submitted mean many, many reviewing invitations sent. That doesn't mean enough reviewing invitations accepted.

@ClementC. usually you send reviews until X number of reviews are received. If everyone declines, you send more invitations. In no situation can I see "nearly non existent peer review". Besides, a lot of MDPI articles have public peer review (example: https://www.mdpi.com/2076-393X/9/7/804/review_report).

Again, MDPI deserve a lot of hate, but most of the reasons people give for hating MDPI are really bad - easily deflected, demonstrate a lack of understanding of academic publishing, or are based on wild speculation. I wouldn't put it beyond some people to speculate that the reports that MDPI makes public (like the one linked above) are written by MDPI staff. Sme other people might even believe it. /shrug

@allure I was just saying that two things can be true: a feeling of being spammed by review requests, AND a scant peer review process for some journals.

Now, for MDPI, I have to say I am biased by anecdotal evidence, but there also are systematic studies (again, looking at average over journals), such as https://news.exeter.ac.uk/faculty-of-environment-science-and-economy/avalanche-of-papers-could-erode-trust-in-science/ : "The study found that MDPI had an average turnaround time of about 37 day"

@ClementC. same question as above - How do you get from "fast publication process" to "easy"? I'm curious how you draw a causal relation.

I did not draw that relation anywhere? (I don't think I wrote "easy" in any message here. I wrote "scant". Maybe you're lumping what I wrote with someone else's comment? :) ) @Allure

Let us continue this discussion in chat.

And yes, I would argue that an average of a month to review, revise, and accept a journal submission is "barely sufficient or adequate" (i.e., scant). Now, that's probably enough for comments here... That is a full topic for a week long discussion.

@ClementC. not sure if you're aware, but the average time taken to review an article is 9 hours (https://www.stm-assoc.org/2012_12_11_STM_Report_2012.pdf, page 36). Accordingly, I do not see how taking a month to go from submission to publication is "scant".

Warning: that journal is going to see a decline in quality. They published 5x the number of papers in 2022 than were published cumulatively in the six years prior. Giant, giant red flag unless this field has had a sudden renaissance. Impact factors don't tell the whole story.

I've encountered two schools of thought. One, you start where you want to end - i.e., early in your career you aim to publish as high as possible to set the standard. Obviously this isn't always realistic. Most people cannot conjure up a Nature paper out of thin air. Two, you work your way up, understanding that as a student or early career researcher you might not be producing work right off the bat that will make it into top journals (this is more about "impact" than scientific quality) and it's more important to establish a track record.
I don't think there is a right or wrong approach. Your situation will dictate what you do. The caveat is that no matter what, avoid predatory journals. A high quality journal does not necessarily need to be high impact though. And while MDPI comes up in many discussions about predatory journals, it is field dependant.
MDPI doesn't have a stellar record. It would not be my first choice in general. But it's really journal dependant and it may be that Batteries (I am not familiar with the field) is a perfectly fine journal that no-one will look twice at. If your PI is encouraging it, I might at least look into it a bit more. Do the papers you read cite articles published there? Are the recently published articles decent quality? Do you cite them? If the answer to these questions is yes, then you could send it there. Otherwise I would either look for a different journal, or submit to a conference.
This advice is assuming your work is actually publishable in its current state.

Thank you for the thoughts! I should have probably mentioned in the post, but I first ran into MDPI when I started noticing their papers were constantly subpar, not necessarily bad but just uninteresting and don't draw convincing conclusions, which is exactly the manuscript I have right now. There are occationally terrible or good ones of course, but I eventually stopped reading & citing them. Given that with your advice, I think publishing at a conference may be a better choice.

And there are always kind-of interesting results that you aren't going to spend more time on, and it would be fairly quick to get an OK paper out on, but not one that would go to the top journal. Just don't submit to a predatory journal.

Short answers: Yes. Publishing in journals that are well recognized as low-ranking, or even predatory, hurts severely your CV in any decent research university.
Longer answer: I don't think that MDPI is "mediocre". It is perfectly fine to publish in mediocre journals. MDPI on the other hand is considered by some as predatory, which means it is much below "mediocre". Its credibility is put in doubt.

@leonos, fixed. thanks.

I agree with this. The #1 most valuable thing you need to safeguard in academia is your integrity. If I suspect you may have "bought" a publication, why would I hire you? You can argue whether MDPI is predatory or not, but the fact that people do argue indicates that as an early career individual, you need to avoid them.

I have several publications in MDPI and also peer review for them. I also have many publications in society journals, and these society journals are considered high quality in my field (Nutrition science). In the cases that I had published in Nutrients or IJMS (MDPI journals), the reviews were pretty critical and helpful in enhancing the paper. Whereas the two most recent publications in society journals, the reviews were extremely minor. As a peer reviewer for MDPI, I'm also extremely critical and I'm often rejecting a lot. My rejections are taken seriously by the editor, even in cases where the other two reviewers say accept. I think there's overall a bad reputation but I don't think it's universal. Depends on the reviewers and depends on the editors.

The OP specifically mentions which MDPI journal they are considering, adding "My personal experience with [this journal] say that they are mediocre at best, and I have stopped reading/citing their articles just to save some time." So while the question seems to be at first quite general, and maybe about MDPI overall, it's actually about a specific journal the OP already has a very bad opinion of.

I analyzed some data with my advisor for a collaboration, and it ended up in the highest impact factor MDPI journal. If I could take it back, I would. Not only I feel like I don't really need the article and that it doesn't speak for what I do in science, but also they harass you with an endless barrage of unwanted emails about sketchy conferences and journals. And this kinda shows the full picture, it's not about science and a peer review service, it is about publishing and charging APCs as much as possible. Even you said it, you don't bother reading those journals, then why publish there in the first place. I know it is tempting because of the metrics, but no one will read your article, even less so cite you. It won't impact your h-index. And those metrics are SO skewed due to the self-citation rate in those journals.

I have to disagree with the sentiment because I still occasionally run into MDPI papers that can be somewhat valuable. I find them mostly boring rather than false science and can occasionally be good to compare my results to. And for spam, I get enough even with only two IEEE conference publications so it may not be a MDPI specific thing although I get it it's more annoying when it's coming from the publisher itself rather than some unknown emails. I agree I don't absolutely need this article and it may not affect things in the long run so not worth dealing with it though.

They have drastically increased the impact factor of several of their journals by adopting the "guest editor" model where someone you respect asks you to submit, often offering you discounts etc to do so.
I published with mdpi under this model and I thoroughly regret it. Having canvassed my mentors and peers since then, I'm confident in saying the journals are not at all well regarded despite the impact factor, and I won't be publishing with them again. I've also been harassed with emails and spammy invitations ever since and I can't get them to stop despite asking several times to be taken off their lists.

Do you have any source for how the guest editor model increases IF?

@leonos Can you be more specific? I've seen that paper and as far as I can tell it only shows MDPI has abnormally high "impact inflation", which is not impact factor, and it is evidently not caused by the guest editor model since Hindawi, Frontiers, etc all use the same model.

@leonos IF is measured by number of citations divided by number of citable articles published, so "increasing number of papers published" does not a priori inflate the IF. Also, are you suggesting that SI reviewers (who are technically drawn from the same pool of reviewers that review non-SI papers) are more lenient on self-citations? I would certainly like to see evidence of that, since I don't see a link.

@leonos the "move discussion to chat" button didn't work for me for some reason, but see https://chat.stackexchange.com/rooms/150230/discussion-between-leonos-and-allure

Research isn't done until it's published.  My first publication was a herp review note as a masters student.  I wrote it and submitted it on my own. Then, brought it to Edward O. Moll, full professor at eastern Illinois University.  He looked at me very seriously when I downplayed it, and said, "This is important.  Good job!"
When I graduated with PhD I had a pile of small pubs, and one in j of wl diseases and in zootaxa.  I was recruited to a very good postdoc position.  When interviewed, I downplayed the number of pubs (over 20).  The prof, full prof at veterinary school at top 100 University said, "you know what these small pubs tell me?". I shrugged.  "You finish what you start.  That's valuable."
I suggest that it also means you value publication.  Then, I was offered a tenure track job I took.  After my dissertation defense, a new faculty member told me, "those small pubs are going to help a lot when you get a few big ones.".  My doctoral advisor said, "publications are the currency of academia." Low ranked pubs are pubs.
Now, in advice for a young scientist, the author, a nobelaureate, stated that people who publish a lot of important papers also publish a lot of duds.  (Not his exact words ).
So, if you want to be considered someone who finishes what they start, cares that trivial data may be important to someone else and thus further science, and has a nice portfolio of assorted papers, then, what should you do?
Published in mdpi, is in legitimate journa.  I know a lot of r1s faculty published there, and even hindawi ).  A publication in mdpi trumps someone with none.
If it's the best you are capable of, who cares. I publish everything.  The reader can decide if it's important to them.  I have one note that has been cited more than most peoples' 40 page diatribes.
I encourage you to publish it.  It matters.
Even if in a non-impact rating journal.

Hindawi is now owned by Wiley.  Wiley has continued the same practices by hindawi.  Mdpi is just a low quality publishing house.  So, now thast Wiley has continued hindawis practices, do we abandon Wiley?  Wiley is even removing hindawi from journals to make it more difficult to assess.  Best to look at the individual journal.  I have a marketing friend who actually published a paper in a scam journal because his discipline didn't want it published.  Now, it's widely Accepted that what he said was accurate!

Others have provided some very valuable comments you should reflect on.
My view is that you've already answered your own question. If you consider journals from this publisher to be 'mediocre' and you don't read or cite from them then why on earth would you consider publishing with them?

Exactly. If someone doesn't think papers in journal XYZ are worth reading (let alone citing), why publish in it?

The reason you publish is to get your name out there and improve your CV. The reason we publish is to get knowledge distributed. If the data you are talking about publishing isn't exciting but shows a problem, that's absolutely something people shouldn't need to redo from scratch if you decided to join the circus.
Also, having published it, when you do figure out whatever it is and want to publish a major paper, you can just cite this paper to show the details of the problem and don't need to rehash it.
Don't just answer one of those spam emails asking for contributions, but do feel fine publishing in a "lesser" journal that is still known in your field.

It appears to me that you actually don't have enough data and interpretation of it to publish anywhere, MDPI journal or not.
I agree with some of your friends who suggested to present your preliminary results at a conference. Depending on the conference and the field, it might even go into the proceedings of the conference. Depending on where you are and the scientific practice in your country/department, you could also use these preliminary results to submit a grant proposal too.
I personally don't understand the hate for MDPI. In my field, MDPI IF is on par, if not above, most traditional pay-wall based journals.
Why would I complain for getting access to scientific publications for free when my university is not able to pay the huge subscription fees of more traditionally established journals?
As for the alleged better "quality" of non-MDPI journals compared to MDPI, I think this is completely misguided. What happens is that many journals have decided to ramp-up their editorial policy by introducing a rejection quota based on editorial decision alone and have made the marketing move of making researchers believe that rarity equates quality. An editor in PRL, Nature or Science can reject a paper on the sole basis that they believe that the results and take-home-message are not 'impactful enough' to sell well; and this is going to be ideology based at times. A good example I am aware of is that in 2013 I believe, PRL changed its editorial policy and decided to reject 50% of submitted papers on editorial ground only.
As for review quality, it's not like MDPI sends review requests to people in unrelated fields or that you just need to pay to get published. I have actually seen papers getting rejected many times. I actually have suggested rejection in few occasions myself to MDPI (which I seldom do because often I like to think that papers can often be improved to the highest standards). In fact I think that reviewers have a better incentive to do their job right with MDPI than more traditional journals because a) they are getting 'paid' in vouchers to publish in MDPI (granted, it's only a fraction of the fee but still) and b) MDPI is adopting an open review policy which can get your review published alongside the article if it gets published; which compels reviewers to try getting it right and remain polite throughout their review.
In my opinion, the reason why MDPI journals are becoming more popular with authors is because, as long as the scope of the paper fits with the scope of the journal, editors will try to find reviewers for it, period.
Their 'guest editor' strategy also allows researchers to explore research avenues that would likely be 'unwanted' in other journals too.
They have not fallen into some weird  ideology like ArXiv that is now asking for 'endorsements' and whatnot just to submit a preprint there. I am aware of stories where ArXiv even deleted a submitted preprint which had already been peer-reviewed and published in an established journal in the field just because they apparently did not like the take-home message. I find that much more worrying than MDPI personally.
Finally, I think that MDPI journals' IF is increasing because most universities in the world simply cannot afford the pay-wall from traditional journals, and therefore researchers working there access whatever they can get for free. That does not mean that MDPI journals are rubbish, that means that IF is impacted by the local scientific culture.
From a regular researcher with reviewing experience for PRE, EPL, J Chem Phys, Nature Communication, PRL, PRX, Physica A, J. Stat. Phys., Entropy (MDPI), Systems (MDPI) and Applied Sciences (MDPI).

I agree that the manuscript is not good to get published anywhere and realized I was thinking MDPI just as an “easy publication quota”. However, my supervisors and myself all think we have a decent chance of getting accepted, partly because the quality of papers we’ve read from it, partly because of previous experience with them. Based on this I decided to just go with the conference.
This is of course not a post focusing on the quality of MDPI journals, but I think it’s unfair to regard them as a normal reputable publisher given the controversies and proven questionable peer review practices

You are overthinking the situation. You have never published before so why are so concerned with IF? If you can publish something then publish because your work doesn't exist until you do. Get your feet wet with this publication and build toward higher IF journals. Publishing in high IF journals is more than a notion. As a grad student your focus should be your thesis. A publication (regardless of IF) is a big step toward your thesis.

you can go for Scientific Reports! A little bit more expensive and as long the resulst you present are scientifically sound and technically correct you do not hav3 any impressive innovation or novelty!
best luck for you first publication

As it’s currently written, your answer is unclear. Please [edit] to add additional details that will help others understand how this addresses the question asked. You can find more information on how to write good answers in the help center.

While I wouldn't overestimate the influence of a first, small MDPI publication, I suggest to look for alternatives first. There are often smaller journals in the field, having a lower IF, but a better reputation, discuss with your PI if there's something around. If there is not really an alternative, then just put it out. Just don't do it too often, early career researchers with 5 MDPI publications and one "bigger" would still have a difficult time proceeding in some high reputation labs. Also make sure that this Publication counts for your PhD record, I know some universities don't count them.

I would go for the MDPI journal in this circumstance, it does at least get peer reviewed so they're not a true predatory journal. Certainly in my field, conferences are not peer reviewed and ultimately disappear from the record.
MDPI are worse than a good journal but certainly better than nothing especially at the start of your career. By the time you're looking at tenure track jobs your first paper will just be a statistic anyway.


text:
What are the benefits of organizing a science conference for a company?
I'd like to propose the organization of a conference about mostly research related topics in the IT area (and probably a handful of business related topics as well). As an example, I like the assortment of topics presented during CppCon - I am thinking of a different scale, but something in that vein is my basic idea. I know that there are a lot of different conferences, but to be honest, I couldn't find one that covers the topics I'd like to propose.
I have to convince my upper management that organizing such a conference would be a good idea. As part of my pitch, I'm thinking of discussing pros (and possibly cons) of organizing a conference. Now here is my question - What should I mention as potential benefits a company might have from organizing such a conference?

Companies that are serious tend to build “real” research and study opportunities with universities : both to get focused research completed and to get their staff further training...

There are a couple of reasons that companies sponsor major conferences (rather than directly organizing them). First is that they get name recognition among the attendees and also, to a lesser extend, among the public. More important, however, is that they also have an opportunity to meet and interact with leaders in research in which they have an interest.
A company doesn't have to organize the conference to do this, and organizing a new conference may not be the best way as it takes some time for it to be well known enough that those researchers want to attend (or submit papers).
Some companies just do this as fulfillment of what they see as an obligation to the research community on which they depend for both ideas and employees.
Companies, of course, have other ways to reach these researchers, but providing an environment in which some collaboration can be initiated is valuable to some of them.


text:
How do I phrase (in my thesis) that results in an important study are wrong?
The title probably comes off wrong, I tried to keep it short. I do not necessarily want to make an absolute statement like "that is wrong". But I do need to address the problems I am facing with a study that is important for my thesis.
There is a relatively influential paper which I have used again and again in my studies, and it shows many very interesting experimental results. I could successfully recreate most of those results, and my research is based on them. However, there is one result where I have to conclude that it is basically nonsense. I have repeated the exact measurement again and again and could never recreate their result. With my new theoretical knowledge I can also safely say that the result shown in the paper makes no sense and has to be wrong, while the one I get from my own measurements makes perfect sense.
So my research means that a result that was described as useful and interesting in this paper is wrong, and therefore not useful. My plan was previously to do multiple studies based on it, and now I want to make clear why that is not possible. So I need to show that their results are wrong, and mine are correct, and I need to explain why that is so.
I have the facts on my side, but I just cannot think of a way to do this in a professional manner. I do not want to sound like I'm reveling in a "gotcha" moment, and I do not want to step on anyone's toes. I just want to make clear that this particular topic is a dead end.
I want to address this in my "Discussion" section of this chapter. I would be grateful for ideas how to approach this. Should I give them the benefit of doubt? I worry that this will water down my own results, which are directly opposed to theirs. Should I think of other potential explanations, like "maybe what they show is a measurement artifact", or will that come off as condescending?

"maybe what they show is a measurement artifact" - always be aware of this number

Not quite an answer, but: if at all possible, get feedback on your results + writeup from someone more experienced in your field — ideally your advisor, or someone else who you trust, and who doesn’t have a personal stake in the original paper.  This is important to (a) get an outside opinion checking your new results are correct; (b) find out how the original authors are likely to react (badly?); (c) find out whether others in the fields already suspected this — sometimes “insiders”/“experts” know that certain results are dubious, but this never makes it to print.

(perhaps you already did get such feedback, but since you don’t mention it, I thought it’s important to check)

I think you can be pretty straightforward, especially in a thesis.  Describe the experimental disagreement first (amount of it and number of measurements in your study versus the earlier work).  Next para, state that theoretical considerations also support your measurements versus the earlier study (~amount of difference and explication of the theory rationale).


text:
Using sentences verbatim from a referee report without attribution
Two part question
Part I
For a revised paper following a review by referees, to what extent is each of the following acceptable or unacceptable:

Use the exact sentence from a report without quotations or acknowledgement of the source?
Use a series of sentences (almost) verbatim from a report without quotations or acknowledgment of the source?
Repeatedly engage in 1. or 2., possibly to the point where sum total of a page in the revised draft are unattributed quotations from a report?

Part II
What the reviewer should do in case #3 above, when reviewing the revision in a subsequent round.  Should this be brought up in the report for the authors?  In private communication with the editor?  Both?  Neither?

Is there a note at the end along the lines of "We would like to thank the referee for suggesting improvements to Section 3"?

@NateEldredge Only a generic  "thanks to the editor and anonymous referees" along with the thanks to other people.

Is it an intellectual contribution (as assumed in the answer by @Ben) or do you mean that the reviewers have suggested some text that makes a point more clearly? If it's phrasing, then the usual referee thanking is sufficient.

In these cases it is usual to paraphrase the words of the referee into your own words, but also give attribution to the source.  An example of a paper that makes extensive (attributed) use of referee work is Kuenon (2000).  In that paper the author paraphrases the work of an unnamed referee and attributes that work as follows (emphasis added):

"But as pointed out by a referee, (1) is an immediate consequence of Bonferroni's inequalities (Feller 1970, pp. 110-111) and therefore enjoys the property that the error incurred by truncating the sum after any number of terms has the sign of the first omitted term and is smaller in absolute value."
"Moreover, a referee pointed out that taking s as the saddlepoint for S, the sum of independent and identically distributed left- truncated Poisson variables, implies very accurate approximations."
"Levin's Edgeworth approximation at the saddlepoint of S allowed a referee to reproduce all of the exact values shown in Table 3, except of the value in the lower right hand corner, which was 1,481,168."
"A referee has kindly calculated the median number to be 451,617."

Here you can see that some parts of the paper (e.g., the exact values in Table 3) were done by the referee, and are reproduced by the author with attribution.  This seems to me to be an appropriate way to proceed.  Still, if for some reason you would like to quote the referee verbatim, then I would expect that this would be treated just as any other quotation from another source ---i.e., it should be in quotes, with a citation to the source (Referee report, unnamed referee).

If you are the reviewer, just let the editor know the plagiarism problem.  Hopefully this is prior to the paper getting out.
A reasonable outcome would be for the text to be paraphrased AND a more specific acknowledgment made "one reviewer for specific content in section 3".  I would gently suggest such to the editor.  "Please go ahead and take whatever action you feel best as editor, but I suggest modify the text and make a more specific acknowledgment".
An alternate outcome is to leave the text as is and become a co-author,  (If the contribution meets the threshold.  Perhaps it might on a review or theory paper.)  But I would not be seen as pushing for such an outcome and it comes with issues of its own (now you are tied to the rest of the paper).
If the paper was already published, I would still let the editor know, but I would copy the editor in charge (since the subeditor let the plagiarism of the reviewer text get by).  It's not the end of the world for the subeditor but he needs to be mildly held to account also.
All this assumes it is not some junky journal.  If it is and they don't take action, you should obviously stop reviewing for them (and shouldn't review for junky journals regardless).  If it is a conference proceedings the issue is a little trickier since they don't really have all the same systems and editorial strengths, but I would still notify both subeditor and editor of the problem.

Perhaps you (or the author, if not you) are misunderstanding the purpose of the reviewer's reports. It shouldn't be to give the author words that s/he must/should include. It is to help improve the ideas and expressions in the paper.
In most cases the author don't actually know the reviewer and the words haven't been published. But, rather than use their words, the author(s) needs to think about what they want to say and the best way to say it, taking the reviewers suggestions into account when appropriate.
However, in some fields, such as mathematics, it is known that there is, in essence, only one way to say something (equations and the like). But even there, the referee is expecting that the author will just say the right thing based on, perhaps, a new understanding that they now have after reading the referee's report.
So, in essence, it is the author's words should be to used, perhaps influenced by those of the reviewer.
But yes, the author needs to include a note thanking the reviewers for valuable suggestions.
In the case of a reviewer who objects to his/her words being used verbatim without attribution or acknowledgement, yes, the reviewer should raise the issue. The editor may need to make a judgement about propriety and that may depend on how much was taken from the report.

I agree with you about the purpose of the reports.  However, your answer does not address my question about the degree of acceptability or unacceptability of engaging in the behavior described in points 1), 2), or 3).  Also, I ask not as an author in this scenario, but as a reviewer in this scenario.  I'll edit the question to make this more clear.

updated as per your comment


text:
How should I approach my studies in the Humanities area if I'm a contrarian?
Before I start, I should mention that the closest thing I found here was this post, but the comments say something I really want to avoid, which is to sound like a [political ideology here]-nut.

I am enrolled in a undergrad degree in Brazil called "Comunicação e Marketing, which I believe translates to Communications and Marketing. In any case, this degree focus mostly on the marketing side, but we still have to learn some theory first. I love it, but I feel like I'm having some issues at the moment.

I have been told both by my professors but also by people in Humanities that we're basically being critical all the time about what happens in society. Right now we're talking about the impact of mass media on society in class, with positive and negative examples.

Whenever I try to study something within this field but not mentioned in class, usually more "recent" things, I'm bombarded with terms like "decolonize this and that", "Global South", and something related to Chomsky's work.

My question is how to approach certain topics from a certain POV that denies what the professor is saying?
Whenever I want to give a counter-point to what is shown in class, I have a hard time finding academic sources that aren't totally wack or associated with the far-right. I rely mostly on what I have experienced or seen people talk, rather than quoting a theorist in this field (or adjacent fields like sociology). I'm not sure if this 100% frowned upon, not recommended, or I should be more careful when doing it.
Are there better ways to search for content in the Humanities? I pretty much just use Google or use some of the references on Wikipedia to see if I find anything useful.

"I rely mostly on what I have experienced or seen people talk, rather than quoting a theorist in this field" why?

@EarlGrey I think N.I has addressed this. May be my fault

What's the point of just disagreeing with someone regardless of the merits of their claim? Does it make you feel smart or assertive? Are you somehow angry toward anybody? I don't get it.

@henning Not necessarily feeling smart or assertive, but I know that I often come across as a smartass. Maybe I should have worded it better. We just had a class yesterday where our professor mentioning being cautious of not being extremist when societal standards change, mentioned a book I don't recall the name (sorry), and I wanted to contribute somehow. I wasn't really disagreeing with him in this point.
But when it comes to terms like "Global South", which I know is not a exclusive to academia, the first thing I feel is something negative. It's definitely some kind of confirmation bias.

Studying a new field will always feel like being bombarded by new terms. What is it about these specifically, do you think your instructor is using them without defining them properly?

@AzorAhai-him- Not really! I knew those terms before starting uni, and I think my professor is pretty good when I ask about these things and terms. Maybe this is another proof of confirmation bias, but I've heard of these terms first on social media, and whatever I read left a bitter taste. I imagine this is a bit out of scope to ask here, but that's part of the reason I feel a bit strongly against it for now.

Whenever I want to give a counter-point to what is shown in class, I have a hard time finding academic sources that aren't totally wack or associated with the far-right.

That's because you are committing a basic and fundamental error. You have a preconceived opinion, and you are looking for sources to corroborate it. This isn't being "contrarian." This is a textbook example of confirmation bias.
Your method should be the reverse. You should first read the literature, analyze and compare texts, and only then form your opinion based on what you have read. You will then naturally have a body of texts to support your opinion, because your opinion will have been formed based on these texts, not the reverse. Who knows, you might even learn a thing or two, instead of assuming you know better than all your teachers from the outset and trying to prove them wrong.

A tad direct, I think you are very right , but still you can remove the (abused) mention of confirmation bias, since OP is realizing that what they are finding is unsound, there is no confirmation yet, only the bias.

@EarlGrey "Confirmation bias is the tendency to search for, interpret, favor, and recall information in a way that confirms or supports one's prior beliefs or values." Please tell me how that doesn't apply?

+1. Note that this doesn't mean accepting the literature -- you can still read the literature critically, identifying problems, gaps, and omissions in the published work. But engaging directly with the mainstream theory is better than just saying "I disagree" and justifying that position by looking for other scholars who also disagree.

@N.I. (I still like your answer, this is just to better understand your point) Assuming I have read all the recommended books and articles mentioned by my professors in the next months, and I will probably have a better opinion, how exactly this address the confirmation bias I know I have?

I want to give a counter-point to what is shown in class, I have a
hard time finding academic sources that aren't totally wack or
associated with the far-right.

You are probably trying to confute some theory, simply by looking hard into "errors" of the theory.
It is not the way science works. New idea replaces old ideas because new ideas explain some phenomena better (or correctly) than the old ones, but no one is going to fight ideas. Galileo didn't start to burn Ptolemaic books.
Let's take your "topic": surely Chomsky or whomever is going against some Adam Smith theory. Well, either you look for the original citation of Smith, follow the citation chain until you get to some recent academic work expanding on Smith work, or you look hard into contradicting Chomsky and you end up with far-right crap (similarly, if you try hard to contradict Smith and following works, you end up finding a lot of far-left crap misquoting Chomsky).

https://en.wikipedia.org/wiki/Adam_Smith

@AzorAhai-him- Stieglitz on Smith: "one of the reasons that the invisible hand may be invisible is that it is simply not there." or a longer review of the excessively simple assumptions behind Smith work https://en.wikipedia.org/wiki/Debt:_The_First_5000_Years