CS PhD application with low GPA but extensive research experience I have recently graduated from a non EEA university—though arguably one of the better/best schools in its field in my country—with a CGPA of 2.90, majoring in Computer science. I used to study Bioengineering/Bioinformatics—from which I hold a publication—before switching to CS. I suffered from an extensive period of burnout and some personal problems starting my second year in college—after getting a 3.30 in my freshman year, not exactly an upward trend in my grades in following years either—resulting in my current CGPA. I did a summer research at my school after my 2nd year which resulted with that conference publication I mentioned above, did two internships of Computer science (first one at a company, second one at one of the top 3 CS universities in the USA), I have two posters from my graduation project (one presented at an international conference the other one not-so international), and an upcoming journal or conference paper depending on deadline circumstances.

So, my cliche question is: should I take my chances with good/top Computer science master's programs throughout Europe (e.g., TU Eindhoven, EPFL, RWTH Aachen or TU Munchen) before applying for a PhD, or should I stay at my school for my MSc and then apply for the PhD? I'm not even hoping for a scholarship at this point, just an acceptance. I haven't taken the TOEFL and the GRE yet since now I'm in my gap year, I will be taking them soon in order to start my application procedure.

You need to check the requirements of the individual schools to see if a transfer is even possible. For the German schools, at the very least, the computer science degree is often subject to "continuity" requirements, which make it very difficult to enroll in a master's program unless you already have the bachelor's in the same subject from a German university (or can demonstrate "equivalence" of your degree if it's coming from abroad).

In addition, admission often depends fairly strictly on GPA, at least at the master's level. Recommendations hardly matter, if they even count at all. At the PhD level, the process changes, and becomes more like getting hired for a job. So it may be better to wait until you're applying for PhD positions.


Is it possible to claim my Elsevier submitted papers on my ORCID publication list? Elsevier submission portals (normally) have a link to your Orcid number. Regarding this, is it possible to add your submitted papers to Orcid, directly by a link?

No! Unless you uploaded a copy of your submitted paper to public preprint server like PeerJ Preprints, ArXiv or BioRxiv. If you uploaded a public preprint you can add that to your ORCID profile.

Extra note: About your published works, as you know, you can add your publications from any publisher to your ORCID profile (after you sign-in to your ORCID account) by clicking on "Add Works".

More information is given here: http://orcid.org/blog/2013/12/05/i-claimed-my-orcid-id-now-what

I'd recommend the CrossRef Metadata Search as often the easiest method of importing one's publications, provided those publications have a registered DOI.


What are some reasons to get your work rejected? I have submitted one of my work in a good journal (impact factor 6) and I got rejection after a few weeks. Though I was pretty sure that I covered all the experiments or stuff they can ask for. The reply mail did not show any cause. They just regretted that they cant publish my work. What can be some reasons behind this?

It would depend on the field obviously but I'll have a go at the most common I see in my area.

Outside the scope of the journal
Has been done before
Incremental - minor value
Value of the work was not clear
Not appropriately supported with experimental results
Badly presented in the context of the discipline
Badly written


Question on etiquette while trying to secure a postdoctoral position Let us suppose that a certain senior Ph. D. student is interested in "securing" a postdoctoral position under a professor whom he does look up to. Would it be right for the student to write the researcher and ask him if he stands a chance of eventually being hired as a postdoctoral fellow in the institution wherein the researcher works? The Ph. D. student is certainly interested in some topics on which the researcher has written in the past; furthermore, there is a certain problem at which the student plans to try his hand once he manages to graduate and this problem is also somewhat near the area of expertise of the researcher in question.

Thanks in advance for any suggestion you may want to leave for me below.

How close are you to graduating? If you're still a few years away, then perhaps get an introduction from your advisor to that professor and see if there are natural ways to seek feedback or advice from that professor.

If you are thinking about the next year and a half, then your questions should be more concrete. In particular, you might tie your question to funding, as that determines a lot of the possibilities. Even if a professor loves your work, they can't hire you if they don't have the money for it.

If you see from the professor's CV that there is an active grant, you could ask about whether there is space on that grant.
If there are regularly postdoctoral openings in the person's department, you can ask about whether the professor is looking for another postdoc soon. (You may learn that people in the department tend to take turns hiring postdocs, and the professor is (un)likely to be up this year. Apply anyway, but know your odds.)
You could say that you're preparing to apply for an external grant for a postdoc (e.g. NSF in the U.S.) and wondering whether the professor would be open to having you work with them on that. (Often a faculty sponsor is already required to apply.)


Should I quit or leave my current PhD and find another one? I am currently a year-one history PhD student at a UK University. I didn't get any fund from the school or outside. I just supported my study by myself relying on my personal savings and some helps from my parents.But the tuitions fees for international students in the UK are very high. The school cannot provide enough financial support for my outside research in China, the US and some other places. I feel difficult to continue my PhD now and I want to find a new institution which can provide me with a fund. But I have no ideas about how to talk with my current supervisor who is so kind as to help me to improve my research proposal for year one. Also, I am not sure the supervisor's attitude to the student like me in the new school. Can you give some advice for this? Thanks.

You seem to be in a box that is difficult to escape. You need funding and it sounds like you can't continue without it. So, think about that first, not about changing places.

I think the way to approach it in the short term is to sit down with your advisor (i.e. face to face) and say just that: I need funding or can't continue here.

After the conversation starts let it flow. Give the options you think you have, but ask if there are other options. The advisor probably has more experience with this.

Perhaps the advisor can either find you that funding, or suggest a way, or suggest a better place to continue your education. They can be a resource in figuring out what to do. Perhaps there are TA/RA positions open. Perhaps there are grants that apply.

If that fails, then look for another place, but make sure you have adequate funding before you jump.


How bad is making mistakes in the lecture slides? I am giving a lecture in IT (for the first time) to more than 100 students. I refused to use the slides of the previous lecturer and I wanted to make my owns. They take me a lot of effort and I believe that are better than most lecture slides on the same topic.

The lecture includes so many mathematical equations (almost every slide). Because I am making them from scratch, I made already 3 mistakes in the equation (e.g. multiplication instead of addition). I discovered two of them during the lecture I said that it is a mistake. I corrected the mistakes before I uploaded the slides.

the third mistake I did not notice but when I gave an example I used the correct one. In the exercise, the students were claiming that the equation does not give the same result as expected in the exercise (which is graded). I decided to give all the students the full note for that exercise.

My question is how bad to have these mistakes? Should I use the slides of the previous lecturer?

Everyone makes mistakes. Teachers, students, everyone. It isn't terrible that you make them, but it is good, and can be extremely instructive when you correct them.

Your description suggests that you do the right thing here. Proof your slides and make corrections. But also, when mistakes are pointed out in class, not only admit them readily, but work through the correction as needed. If it is just a typing error then it is easy, but logic errors might require more effort.

However, seeing a professor work in real time to solve a problem, rather than just showing prepared stuff is extremely enlightening. Students can get the idea when presentations are perfect that this stuff is supposed to be easy. In fact, it may not be easy and so seeing a solution develop, even seeing false starts and corrections, will give them more confidence in their own work. Especially if they struggle with some of the ideas.

Your students will be evaluating you overall, not just your slides. If you act in a human and humane manner, especially by responding to their needs, you should do fine. But occasionally a student will be unreasonable. Don't worry too much about this.

But perfection in a lecture isn't necessarily the most effect way to teach. That doesn't excuse sloppiness, of course, but consider the overall picture, not just the minute details.

I've had students complement me more often on "lectures" that forced me to work "live" than on those that were very polished. In fact, I once tried to develop a "perfect" description of a hard problem and it left the student baffled. "Where did that come from?"

Be good. Very good. But recognize that you are human, which means being adaptable.

As to using the previous slides, I have no opinion. They might be good, but they might be too perfect. They might also force you into stilted delivery, which you should avoid.

But as a newcomer to this stuff, you might have conversations with colleagues about your teaching materials and get their feedback. People learn a lot by interacting with students, but it isn't obvious to a new teacher how that all fits together effectively. Some places have more senior instructors visit the classes of new faculty and then give feedback, either formally or informally. There is no real reason why you can't ask a trusted colleague to do that, even if not required. While it might feel risky, it also shows you are trying to improve your craft.


Data publication basics - where, why, how, and when should I publish my unpublished data? Many researchers have unpublished data. Some of this data may never be published as a manuscript. But I would like to make scholarly contributions of data that I have no intent on publishing, e.g. by publishing a "data paper"

The term "data paper" may be too new to be familiar, so here is a description from the Ecological Archives website:

  Data Papers are compilations and syntheses of data sets and associated
  metadata deemed to be of significant interest to the ESA membership
  and the scholarly community. Data papers are peer reviewed and are
  announced in abstract form in the appropriate print journal as a Data
  Paper. Data papers differ from review or synthesis papers published in
  other ESA journals in that data papers normally will not test or
  refine ecological theory. Data Papers can facilitate the rapid
  advancement of ecological knowledge and theory at the same time that
  they disseminate information. In addition, Ecological Archives
  provides a reward mechanism (in the form of peer-reviewed, citable
  objects) for the substantial effort required to compile and adequately
  document large data sets of ecological interest

This brings up the following questions:

What makes a good data repository?

Which data repositories provide a doi: for raw data?

Should published data be separate from articles on a CV?

There are a few things that I would consider when choosing a data repository:

Does it let you release your data under a license you're happy with?

Applying too restrictive a license can prevent anyone from doing anything useful with the data, so think about what you're prepared to allow. In particular, remember that most of the research done in academia could be considered "commercial" from a legal perspective. On the other hand, you may wish to choose a license that ensures you get credit for your work. You may or may not agree with them, but reading the Panton Principles will give you some idea of the issues here. Also take a look at this list of licenses written with data in mind

How easy will your data be to find?

People will only use your data if they can find it. I recommend Googling (other search engines are available) for some datasets you know of in your field and see if they come up — those repositories which are indexed by the major search engines will put you at a big advantage when it comes to attracting citations.

What repositories are well known in your field?

Your institution may have a repository which you can easily deposit in, but it won't be the first place colleagues in your field will think of to look. If there are well-established repositories I would prefer those, or make sure your data is indexed by a well-established aggregator (I know ANDS runs a national aggregator in Australia).

What does your institution allow?

In many cases, your institution will own (or otherwise have a claim to) the data you generate as part of your research, so check what your local policies are and if need be ask your supervisor, head of department, legal team, etc. This will particularly affect your choice of license.

The other parts of your question can probably be answered better by others here (or maybe it should be split into several?)


How is a PhD applicant's potential as a researcher evaluated? I have been approaching PhD applications under these assumptions:

The focus is mostly on the letters of recommendation.
Every admitted applicant has several letters that make a convincing argument that the he would be an extremely successful researcher in the given field.
These letters are only credible if they are from reputable professional researchers who know the applicant well.

But how much evidence is necessary to show that the applicant would be a successful researcher? First, what does the recommendation letter author need to see in the student to make that argument sincerely, and how much interaction is necessary before the author knows the student well enough to make that judgment? Second, what evidence does the admissions committee need to read in order to believe that argument?

(I am studying computer science in the US, if it makes a difference.)

The author is supposed to be able to discern and determine some strengths from
the applicant's personality and his academic procedure, could which
considered as valuable points in her view point, to be known and
succeeded as a graduate student. As an instance, the author might
praise his teaching capabilities, based on his benevolence to help
the other students to understand the academic subjects, in a better
form. As an another example, she might assess him as an assiduous
person, as he had summarized many articles to conflate his essay's
introduction, systematically. More interaction she had with the applicant, more
robust explanation she would present about the person... As a matter
of fact, the author can focus on every positive aspect of the
applicant and try to elaborate the details, reasonably...
Readers do not often expect any official evidence for the asserted
points within the LoR. They would be convinced by the letter's
credibility, if the author has shown the relevance between the level
of the support for the person and the depth of the relationship with
him. Obviously, knowing the author's identity would act as an indispensable factor to authorize the LoR and its content.

Good luck


Ask the author of a paper for suggestions of where to publish replication results I based my thesis on a published paper and ask its original author if he was interested in seeing the results. After approaching him (with your help provided: How to address an author showing replicated results from his paper? ) he replied

  Your application of the XXX method looks very good.  Congratulations,
  and thank you for sharing your work.

and made some recommendations about the bibliography.

Now, should I end this conversation with a thank you or can I insist a little bit more and ask him if he thinks it can be published somewhere or even if he can suggest where could I publish.
(It's a bachelor thesis so it's not something groundbreaking, it's more of a replication paper).

Scientific method is based on the idea of reproducibility. So being able to replicate experimental findings, or not replicate them, is an important contribution to your community. Of course it would be more groundbreaking if you were NOT able to replicate results, as that would be a sign that there is more to learn. But even a mere replication using independent data would be make a solid paper. And of course, it matters all the most if the original paper found something really exciting.

It is a bit different for "theoretical" papers as putting forward ideas when somebody else did it already, does not add much to the community understanding. Unless you derived the same conclusions starting from very different assumptions, or following a very different path, replicating theoretical ideas typically does not warrant a publication.

As for what journal, again it depends on whether you are using independent data/though process, and how relevant was your original result. You could aim for the same journal of the original paper, and if that fails, aim for something just slightly lower in ranking, and more field-specific. Good luck!


How do you decide how to categorize a new idea? Patent? Present at a Conference? or Publish in a Journal? I came across a patent that proposes an idea for a device, and in the background section of the patent, other similar devices that were published in conferences (not even journals) were cited. Seriously nothing unique about the proposed design - not a jaw-dropping.

So consider the following scenario. You are sitting on a front porch, and you come up with an idea.

How do you know if it is worth to be filed as a patent, submitted to a journal, or presented at a conference?

Also, I came across a number of patents, and they were merely theoretical, without proving if the concept works flawlessly. So, how does this concept convince the people in the patent office? I’d like to know what elements make a patent too.

How do you know if it is worth to be filed as a patent, submitted to a journal, or presented at a conference?

To commercialise, file a patent. To disseminate, publish a journal article or a conference paper.*

* Distinctions between journal/conference publication is dealt with elsewhere and, given the context, is seemingly out of scope.

  [Many patent ideas] were merely theoretical, without proving if the concept works flawlessly. So, how does this concept convince the people in the patent office?

US patent law demands usefulness

...an invention is "useful" if it...is capable of use...the doctrine prevents the
patenting of fantastic or hypothetical devices...

and European patent law demands industrial application

...a patent can only be granted...for an invention which can be made...

These requirements should prevent granting patents for theoretical ideas.


Why do people in academia tend to write their email address with "(dot)", "(at)", instead of ".", "@"? This may be a silly question, but why do people in academia tend to write their emails as jhon(dot)doe(at)gmail(dot)com?

To avoid email harvesting spam-bots. (As if someone can't write a Perl script to make the appropriate substitutions.)


Changing some part of the paper after getting accepted for a conference My paper got accepted in an A* CS conference, however, the reviewers criticized several points and suggested many others. They suggested improving the method by adopting and involving other approaches which need implementation and other further evaluations.

I agree with the reviewers on some points and I believe this would make the paper better. Consequently, the paper will be really different from the original submission. Since it is a conference and there are no further review rounds, I am wondering whether I should modify the paper (part of the method, result and maybe conclusion) based on the comments of the reviewers.

I am wondering whether I should modify the paper...based on the comments of the reviewers.

Yes you should. Acceptance was (most likely) coupled with an expectation that you'd address some or all of the comments. The reviewers (presumably) consider their comments relatively minor, since they'd have rejected otherwise, and are trusting you to make sufficient changes (that they won't check).


duplicate published data figure I read two papers just published online (paper no.1 accepted about 1 month before paper no.2) in the same journal by the same authors.
Two papers have the same topic, using the same numerical method, same at least one simulation object. I found in paper no.2 some figures that very similar to paper no.1. The example of the figure in these papers shows in the picture below. Fig C is exactly the same in the two journals (just change the view angle a bit) while Fig A, B, C, and D are different. However, there is no statement that the data in Fig C has been published in paper no.1 and no citation. Additionally, there are also some similar figure data in the two papers but just change the axis scale.
So can it consider as duplicate data?

Duplicate data is mostly a problem when the data are experimental/real-world data and where repeating an analysis with the same data makes the overall literature seem to support a conclusion more strongly than it would if it were presented only once.
Let's say you have an experiment showing that green jelly beans cause acne. You publish it once, but people keep some healthy skepticism. Now suddenly 2 more papers appear that say green jelly beans cause acne... oh my! This is becoming quite the interesting field of study! Well, if these are 3 independent data sets, it appears to be a fairly strong conclusion supported by replication. If they're actually the same data set analyzed 3 times, now the authors of the second two papers have committed academic misconduct if they haven't made it clear that this is the same data. If you were conducting a meta analysis you would want to be careful not to include more than one of the studies.
The second issue is with copyright of figures. Typically the journal publishing a paper has copyright of figures published in that journal. Copying a figure from one paper and presenting it in another may violate that copyright. However, you can't copyright data itself, and there are only so many ways to plot some types of data, so the extent to which this sort of copyright is valid is quite narrow.

In the situation you describe, you have simulated data. The jelly bean issue isn't really relevant for simulated data. The papers are also in the same journal, so it's not going to argue with itself that the figures are too similar to a copyrighted figure that they own the rights to (to cover all the bases they could ask themselves for permission, but why?).
If the simulated data are created by some complex methodology, it is important to cite a previous paper using the same methodology to properly credit those authors, but sometimes this isn't really necessary. For example, if I generate simulated data by adding noise to a sine wave, it's probably sufficient to describe this. Sure, if another paper in a very similar area used exactly the same parameters, it's good to cite it to be thorough, but a sine wave plus noise isn't really much of an intellectual contribution and if it's skipped I don't think any major crime is committed. Maybe less so if it's the same authors not self-citing.
The only issue I can possibly see here is that the authors have perhaps padded their publications a bit by splitting one paper into two and publishing them separately. Reviewers can certainly comment on this, and can argue that the similarity of the second paper to the first makes it less suitable for publication, but this has very little to do with one set of simulated data that are the same/similar in the two, it has more to do with the rest of the publication.
I'm not sure why you're worried about this case except for some perceived unfairness in how you were treated versus them, but I don't see any benefit to you in pursuing this any further.


Faculty position decision timeline I can't seem to find a answer regarding this point, I would like to know what the usual timeline from the point of application (for tenure track faculty position) submission to  contact for interviews looks like. I have applied to numerous positions, some in February of this year. More than half have neither rejected or contacted me and May is just around the corner. What can I expect?

It's hard to answer your question without knowing the country and field. I'll answer from my perspective, which probably extends to your situation, but take it with a grain of salt.

Here's a helpful resource describing in detail a typical (successful) job search timeline for computer science tenure-track faculty positions in the US: http://www.pgbovine.net/faculty-job-search-timeline.htm

Most interview invitations are sent out by the end of February. If you haven't heard by mid April (now), then unfortunately I think it's almost certain that you won't be invited.

Another source of information: Most departments list seminar speakers on their website. When their seminar starts filling up with interviewees, then you know they have been sending out invitations.

Most places never send a formal rejection or, if they do, it comes so late that the outcome was already obvious. So don't expect to hear anything.

Commiserations. The academic job search is tough! I wish you the best of luck in your other endeavours.


Co-supervisor comes to the office to help her students, which distracts me My co-supervisor (2nd supervisor) comes to the office where I work to help her (main) Ph.D. students. The noise distracts my work. I find it unprecedented. Why not help her students in her own private office, instead of coming to the shared office space!?

I am not sure how to resolve this issue. Shall I message her, mention the issue to her students or to a superior academic, or change office?

Like it or not, there is a lot of hierarchy in academia and she has helped me in the past. I don't want to break relationships. In addition, I know I am not the only in the office who has noise issues.

What would be the diplomatic way to have a quiet office space?

Edit & Update:

1) Noise canceling earbudsor headphones are good and I have tried they do help, but to be honest if you want to concetrate to carry a task it's hard to maintain focus with loud volume.

2) I believe I have a common understanding with most of you guys. If there is a small chat in the office is fine but if it's a meeting more than 30 mins they should find a room. In my case, the co-supervisor helped her student for almost the whole day... And as I mentioned in the comment section from what I am aware she has an available office and there are plenty of meeting rooms in the Uni. If it's the computer thing they have laptops...

3) Thank you everyone for your support and suggestions, hope you are getting well with your offices. As mentioned from you, there cannot be a perfect office but at least have some common understanding I guess.

I'm not sure if I would use the word "unprecedented" here - I have definitely had my supervisor come into my office to explain stuff (or just chat), and I have also done the same with my own students. I can't imagine that we are total outliers here.

That said, unless you have a particularly bad relationship to your fellow students and your co-supervisor, is there anything wrong with asking them to discuss in a meeting room (or their office) if these discussion are lengthy and/or happen very frequently? I certainly would not mind taking our discussion elsewhere if other people are bothered.

To directly address your proposals:

  shall I message her

Why not just ask her friendly when they are discussing next time if they would mind moving to a meeting room?

  mention her students

You can, but talking to both involved parties at the same time feels a little less passive-aggressive to me.

  mention the issue to a superior academic or change office.

That sounds like a massive overreaction, especially if you haven't even mentioned anything to her directly so far. Reporting your (co-)supervisor to some higher authority is a nuclear action of sorts, which you should definitely not do without exploring other options first. And even if you report this, I have a seriously hard time seeing anything coming out of it (aside from a pissed co-supervisor, that is).

The more fundamental issue here may be that your expectation of a "productive" workplace may be different from other students in the room. If you go over to Workplace.SE, there are plenty of questions of workers trying to convince their co-workers to hush up - but the fact of the matter remains that a dead-silent, only-strictly-required-talking workspace is simply not the preferred option for many people (I actually find it extremely uncomfortable if I sit in a shared office where nobody ever chats).

The only real practical solution to this problem is either to change office, or get / order noise cancellation headphones.


Does publishing research in physics during bachelor degree help in applying for master’s in mathematics? Before I applied for my bachelor degree, I was unsure whether to take physics or mathematics because I liked both of them equally. Then I decided to go for a mathematics degree. Currently I am in the last year of that degree. During my time at university I published several research papers in theoretical physics in top journals in the field and I got several awards from my university. Also, in my mathematics degree, I have so far achieved the highest marks in my mathematics department. I have three months to graduate and I am looking to start a master’s degree.

I am an international student (outside Europe and America), and I am looking to continue my study in Europe, but there are several things that I am unsure about and I would appreciate some help on:

Does publishing research papers in physics help me get a scholarship for a master’s in mathematics in Europe or is it irrelevant?
Does publishing research papers in physics help me get a scholarship for a master’s in physics in Europe even though I have bachelor in Mathematics?

The answer to both of your questions is "yes".  Indeed, publishing original research in any STEM field has at least some (and usually quite a substantial) positive impact on graduate school applications for programs in other STEM fields.


How long it takes for a Mendeley Data repository review? I've just "published" some Datasets as the Mendeley Data repositories. After pressing the "Publish" button I was surprised with message that my dataset(s) are "in the moderation" process that I wasn't well aware of in advance (my bad).

Now, I'm puzzled how long it takes usually for Mendeley Data staff to approve a dataset/repository for being published on-line? Does someone has any experience with the service?

I planned to submit an article (linking to these dataset) today, but it seems I'll have to wait for the dataset moderation first.

Mendeley Data moderated and accepted all 6 datasets, in between 2 and 3* days since submission.

I can't say when exactly it was as I received no email confirmation and I've checked last time the status of datasets 2 days after submission. Also, looking on the Mendeley Data UI, I can't find any clue about when it was approved.

However, 3 days is very good in my opinion :)

Hope this info will help someone else :).
Live long and prosper!


Is it ethical to "arm-twist" a faculty-member into passing more students or improving the class average? I recently got "arm-twisted" [2] (by the department chair and the dean of faculty) into passing the whole (undergrad Math) class who appeared for the final (minus that one student who we all knew was not going to make it anyway) by the most lenient grading-on-a-curve I have ever done. Isn't it immoral to pass students ahead who aren't ready or those who are gaming the system? Or am I overthinking this? The final exam was set easy and "OK-ed" by a senior colleague (I am a new faculty member). I had to pass 6 students who were way below average...

Some additional remarks based on posed questions:

This is not a rant, it's a serious concern if I should go to higher authorities.
Arm-twisting ==> pressurised a lot over 4 days of meetings.
I don't think the dean of faculty is unethical at all but it looks like she is strongly influenced by the department chair, who, in my opinion, could be borderline-toxic (but I am not sure).
Grading wasn't tough - it was nominal, of course, to the best of my knowledge.
How does passing students who are way below average make them a good educator? After having spent a semester with them and/or just looking at how they scored on exams and quizzes, they definitely could benefit from repeating it.

I think the ethics depends on a few things. First and most importantly, what was the intention of the department chair and dean of faculty when they “arm-twisted you” into passing those students? One can imagine two different scenarios:  in the first one, the chair and dean are greedy, amoral people who are driven by selfish, short-term considerations such as maximizing their institution’s profits and winning themselves a promotion, and are pursuing a strategy that they know for a fact is bad for the students. That would be pretty unethical. In the second scenario, the chair and dean are passionate educators who are looking out for the students’ best interests, and simply disagree with you about what is best for the students, and believe that the students you wanted to fail deserved to pass. In that case, you could argue that they’re wrong, but it would be quite unreasonable to accuse them of unethical behavior.

Of course, there are also situations between those two extremes that fall in a gray area where it would be hard to say much about the ethics of the actions. You simply haven’t given us enough information to say anything meaningful.

Another factor that I think matters is what you mean by “arm-twisting”. How exactly did they twist your arms? Did they literally command you to change your grading decisions and refuse to listen to any opposing arguments? Or did they leave you some room to argue the case? It’s clear that you think they behaved unreasonably, but it’s not clear to me if they also would agree to your description of your actions as “arm-twisting”. Could it be that their perception was that they had convinced you of the merit of their request and that you went along with it willingly? In that case, the responsibility for the actions might lie (at least partially) with you. It all depends on the details of what took place, so again I don’t think anyone can give a general answer based on the information you’ve provided.

Edit following clarifications by OP: I understand that you perceive that you were pressured to change students' grades, and that the department chair specifically is an unpleasant person to deal with. All of those things may well be true. However, ultimately I think that it is a mistake, both logically and from a strategic/practical point of view, to use the words "unethical" or “immoral” to describe the behavior of any of the actors in this story. These are very strong terms (stronger than you may realize, I suspect) that suggest the worst possible intentions behind the actions you have observed. It would only be reasonable to use these words if you had very concrete evidence that something truly nefarious is going on (e.g., the department chair taking a bribe from one of the students, or telling you to pass all the students because his own nephew was one of the below-average students who were about to fail).

A much more likely interpretation is that the department chair simply has a broader set of concerns than you and a broader perspective on the situation. Perhaps he feels that it is important to have consistency across all instructors, to avoid students feeling that they were treated unfairly just because they had the misfortune of taking a class from an especialy harsh instructor. Or there could be any number of other legitimate concerns or causes for disagreement between you and the chair. None of this involves anything remotely unethical - it is simply a professional disagreement between colleagues.

Finally, I will add that the mere fact that the department chair "put pressure" on you is also not evidence of anything unethical, or even bad. I was a department chair for several years and had occasions where I had to go to an instructor and have a frank discussion about their grading methods, and even suggest that they retroactively change a few grades. I never had to resort to any sort of direct pressure (I suspect because of a combination of my being fairly good at articulating my side of the argument on its merits, and dealing with people who were ultimately pretty reasonable), but it was very clear to me that by my mere presence as a party to the discussion I was exercising a kind of "soft authority" that may well have been perceived as pressure by the other party. This is unavoidable and sometimes necessary, and in fact I dare say that a department chair who hesitates to exercise his/her authority in this way is unlikely to be doing a very good job.

That being said, if the chair's behavior is indeed "borderline-toxic" as you say, then that's a problem, but it sounds in any case like a very different issue than them being "unethical".


Is it normal for a supervisor to never talk to you or give you any direction? My master’s supervisor talks to me once every six months and is uninterested in my research unless I have a half-written paper with a working model already.
There are also no post-docs or assistants managing the students or providing alternative guidance. It is only a professor. And he has about five master’s students and PhD students each under his supervision.

Is this standard operating procedure? I thought I would have more guidance.

No, this is not standard.
One of the main purposes of a thesis is that you learn how to perform research.
While there is some learning by doing, without supervision you are very likely to at least do one of the following:

misunderstand the task or the topic,
miss some important existing work when getting familiar with the field,
make mistakes that could easily be spotted by somebody experienced but may cost you a lot of time or make a lot of your work worthless,
focus on rather uninteresting aspects and miss interesting discoveries,
produce bad writing (and thus having to rewrite it entirely before submitting).

This is probably the first time you work on a larger subject. Nobody can expect you to do all these things right on yourself. And even if you do everything right naturally, proper guidance could make you better utilise your talent.

I thus recommend that you do (if you haven’t done it already):

Talk to other students or the student union to get an idea what exactly is common at your institution.
Talk to other students in your advisor’s group about their experience. Perhaps the others have the same problem and you can address it together.
Actively seek feedback from your advisor.
Consult with your examination rules and the responsible people at your department for ways to switch your advisor, get your advisor to do more advising (ideally anonymously), etc.


Going into a PhD in Europe or US I am an International Student perusing a Masters in Actuarial Science in the US. I did my Bachelors here in the US (Actuarial Science), worked for 2 years as an Actuarial Analyst in the US. I am doing my Masters now with emphasis on AI (I could not get into an AI program for Masters due to my circumstances, so this is the closest I could get).
I want to continue with AI and I am looking into a PhD in the N.America or Europe. I am excited about Europe (never been there), but feel N.America will be a safer bet. Which location would be better to do my PhD in, if I am looking at eventually migrating and getting into tech entrepreneurship?

I am afraid your question reveals a rather superficial attitude to the matter. You are talking about the whole continents as places for "better PhD" and mention "AI" as a field you are interested in. A fairly standard textbook on AI sitting on my shelf is nearly 1200 pages long, so how can one judge a continent for being a better place for studying every single topic listed in this book?
You are going to spend several years doing your PhD. So, first go spend at least several days (or, better, weeks) thinking harder what exactly are you interested in. One good starting point would be to think first what you are good at right now. Then, figure out good publications in this area (Google Scholar is your friend) and find out which labs they come from. These labs are the places of your interest, and they might pop up in quite unlikely places (though, granted, in most cases they don't come as a surprise).
Then, of course, there is a question of a job market, but I believe people coming from reputable labs are able to find a job. In any case, this isn't a question of your immediate future.


Download automatically all articles from references in a pdf file or on a journal website I'm wondering if it is possible to download all articles from references  in a pdf file or on a journal website. For example I'd like to download all articles in the following references (I'm using the internet connection of my university, thus I can download all articles if they were purchased; I suppose my university did it):

https://www.hindawi.com/journals/isrn/2012/170594/ref/

Thank you for your help.

Ps: I have also the pdf file of the article.

As far as I know, there is no automated service to do this. One of the reasons is that mass download of research papers is frowned upon by the publishers (look up the sad story of Aaron Swartz, for instance).

If you want to build an automated (or semi-automated) solution yourself, one of the trickiest steps is identifying correctly the cited papers from the citation strings. For this you can use a research paper database, such as Scopus, Web of Science, or Pubmed. For instance, Scopus displays the references of a given paper in its page, and for each paper you get a "view at publisher" link that redirects you to the article page on the publisher website. This web page usually has a "download pdf" link inside it (usually paywalled, too), and since most papers come from the same major publishers it is should be possible to scrape this link automatically at least for these publishers.

Unfortunately the paper that you link to does not seem to be indexed neither in Scopus nor in Web of Science --- maybe because Hindawi is not one of these most "mainstream" publishers. It is in Pubmed, though. I am less familiar with it, but if you click on the references you also get a page with a "full text" link in it.

Note that Google Scholar does not display "forward" citation information, instead; only the reverse (papers citing a certain paper).

As mentioned in the other answers, you may be violating some terms of service if you do so. Terms of service are not the law, though, and I think you can only get into a very limited amount of trouble for that.

A Google search returns a few tools to do similar things:

https://github.com/ppwwyyxx/SoPaper
https://github.com/zaytoun/scihub.py
https://github.com/olivettigroup/article-downloader
https://pypi.python.org/pypi/metapub

I do not have experience with any of them, though, and I don't know if they are mature/stable enough for casual use.


How to present publication output on CV when you publish in fields where author ordering conventions vary? I'm doing research in two different subfields, one of which usually orders names alphabetically and one of which usually orders by contribution. My last name starts with Z, so I'll always be last author in the former field. Both fields are close enough to the divide that it's not clear to an outsider which convention they would use.

How can I point this out in my CV? I can see three options:

Don't do anything, and just be last author on half of the papers.
Write "the author listings in items 2, 4, and 7 are alphabetical", which feels tacky.
Write "the author listings in papers in this subfield are alphabetical", which also feels tacky.

Is there anything else I could do? Should I be worrying about this at all?

I would suggest adding a remark like the following to your list of publications in your CV.

  I publish in multiple fields, with different standards for ordering authors, some ordering by contribution and others ordering alphabetically.  In the list below, first authors are indicated in bold when authors are ordered by contribution; the symbol = indicates a paper with alphabetically-ordered authors.

  [1] Bozo T. Clown and K. N. Zhao.  This is a chemistry paper. Science, 2014.

  =[2] Bozo T. Clown and K. N. Zhao.  This is a mathematics paper. Annals of Mathematics, 2016.

  [3] K. N. Zhao and 4278 others. Higgs bosons are made of cheese. Nature 2020.


How can co-authors check the status of a submitted manuscript in Elsevier Editorial System? I know that after submitting a paper through Elsevier Editorial System, the corresponding author can check the status of the submitted paper online. But how about co-authors? Can the corresponding author give a permission to the co-authors to enable them to check the status of the paper as well? If yes, how that can be done?

The answer is No, he/she cannot cannot give any permission to the co-authors after submission to EES and before acceptance, as mentioned here:

  I am a co-author on the paper, I would like to be able to see the
  status of the manuscript. I have the manuscript number and I am
  registered on the journal website.

  After submission, you can only see the status of a submitted paper via
  the corresponding author's EES homepage. You will not be able to
  search for this submission via your own author's EES homepage.

So just the corresponding author can check the status before acceptance. But after acceptance, co-author can track the status as well:

  After acceptance, the article is recorded in our tracking system, you
  can use the production reference number along with the Corresponding
  Author's name to track your paper status and add your paper to your
  personal homepage on http://www.elsevier.com/trackarticle.


Marking a journal paper as “Minor revisions needed” for minor typos? I’m doing my first review of a journal paper.

The paper looks good other than a few spelling/grammar typos and one formatting issue where a line has a single letter extend into the center margin between the two columns. These issues are not ones that confuse the content of the work in anyway.

My decision options include accept, minor revisions needed, major revisions needed, and reject. Should I be choosing accept or minor revisions needed? Do these small types warrant a revision for journal papers? Or is it ok to accept these issues?

Unless you are reviewing for a truly lazy editor, it shouldn't matter.  No matter which selection you make, the editor will see from your report that you are asking for extremely minor revisions and act accordingly.

Generally, I recommend minor revisions in such a case, because authors might not be given the chance to correct typos in a straight acceptance, and they might appreciate a second chance to do what they should have before submitting (but almost no one does), which is to find more typos and correct them.  For every one that you found, they will probably find another one.


Filing a patent which my research advisor will found a company on it I'd appreciate your advice on my current situation a lot!
So I'm an international phD student getting close to graduate.
My research advisor got so interested in my recent project and he's working on filing a patent out of it with the institution's office for the related work.
Seems like he'll start the company as well based on the project.
Followings are the questions I have. As I do not have the experience or knowledge on such a situation, I'd appreciate your help so much in advance.

To guarantee any potential rights that I can possibly claim as a co-inventor, is there anything I need to make sure with my PI during the patent filing process? For instance, although I am not gonna accept his offer to work in his company, would it be still possible to secure my equity as a co-inventor or so?

In case my PI wants to exclude me out of the patent filing or any financial benefit created out of it, is there any way I can claim my portion?

Thank you so much for your time checking this, and any advice would be appreciated.

Disclaimer: I'm not a layer so the answer is not an advice but a collection of thoughts based on my experience. And each particular situation can have many facets which one with limited knowledge may not foresee. Also intellectual property law varies from country to country, so additional details would help answering.
I start from last question:

No, your supervisor can not exclude you from the patent as you are a coinventor. If she or he files the patent without you, you can claim against it in front of the patent office. Make sure you have some proofs of your authorship. If you had exchanged emails with your supervisor on this topic, it can be also useful. Note that in patent right public disclosure of invention leads to loss of patentability. In simple words if you tell someone (non-inventors) about invention and they can prove it, the patent application can be rejected.

The first one is the more difficult question. Here it strongly depend on your relations with your employer and country laws on intellectual property. In some countries having a contract with your employer would mean that intellectual property (IP) generated within this contract belongs to the employer. Depending on country you may keep parts IP of it or get only a bonus from employer. In situation you describe, it is difficult to give you an answer without knowing details of your contract and IP laws of the country. In any case typically the patent can be licensed to whoever wants to use (the startup company in your case) it by IP owner (inventors or/and your employer).

Hope it helps to proceed with more detailed search.


Submitting a paper without having a review from the supervisor I am doing a PhD with the aim of publishing about 3 papers. One is already submitted, with my supervisor being listed as a co-author. My second paper will be submitted soon. However, the subject I am treating now is beyond its scope, so he cannot help, except on improving the writing to make the paper more understandable. Recently, I spent an hour to present and explain him the entire concept of my research plus some details on calculations. He hasn't really said anything, nor provided advises.

Now, I'm worried. I would like to submit the paper without his name on it. However, I have perhaps 2 problems:

the last time me and my supervisor talked about publications, he told me something like "... I don't do research anymore, I rely on my PhDs for that...and publishing...", plus adding that he really wanted his name on my manuscripts. However, this is in conflict with a course I got about ethical principles in research at my university, which stipulated that one should not publish with someone that has not provided any input (reviewing being set apart).
my research aims at making assessment of natural resources (at the Earth scale), that will potentially be reviewed by worldwide experts in my discipline. I have faith in what I'm doing, and am pretty confident, but would a journal accept this type of work from a "simple" PhD candidate?

It is usually (I'd guess it depends on the institution, but I haven't encountered any that doesn't adhere) the case that advising a student is sufficient ground for co-authorship. Depending on different fields and individuals, there are cases when the adviser encourages or even insists on students publishing at least something by themselves (I observed it usually in theoretical fields).
If the work passes the peer review, the journal will accept it. It doesn't matter whether you are a "simple PhD candidate" or a part of a team of researchers. There are even double-blind peer reviews, where the reviewers don't know your identity.

All that being said, it is often the case that you, as a student, are more familiar with the narrow thematic of your PhD research than your adviser (perhaps more than anyone in the world) and that is part of the PhD. However, your adviser guided you and it is partly due to his experience that you are able to publish something let alone to work on original research by yourself.

You said that he "hasn't really said anything, nor provided advises", could that be an indicator that you are on a good track and that he only intends to intervene if he feels you are sidetracked?

Further, I don't know any details about your research, but I can assume that you used your adviser's lab. Perhaps you were funded by his grants or worked on his projects?

Advising PhD students is a hard job and your whole PhD experience largely depended on your adviser. If you don't want to include your adviser, I would think very hard if that is merited. You could even discuss it with him. The ethical thing for your adviser is to insist on you publishing by yourself, if he feels that this is your independent work. If he does not, however, due to the lack of experience and perspective, you might not agree. At that point, it is really up to you and (the preservation of) your relationship, but I would definitely err on the side of caution and trust in my adviser's judgment (after all, he got me so far, didn't he).


Is it better to have a single-author paper or a joint-authored paper? I am a new graduate student and I am about to start writing my first paper. Some of my adviser's other students have been working on similar topic to what I have been working on and he has been pushing us to combine our results into one paper. However, I feel my results could be a paper on their own. I want to start beefing up my CV so that I can get extra funding and, hopefully down the road, a research position but I am afraid that if I am only a coauthor on a paper it won't look as good as if I am the sole author (especially since I worked completely on my own for my section).

So my question is: would it be better to try and publish a paper in which I am the sole author or would it be better to try and publish a slightly better paper in which I have 2 or 3 additional coauthors? Do funding selection committees and the like give precedence to people with papers that they are sole authors over ones who have coauthors?

Edit: My field is math, in case this matters.

You should really listen to what your advisor says. "...he has been pushing us to combine our results into one paper." That about says it. Your advisor knows what works and what doesn't work as a paper in your field. He also knows (presumably) about the scope of your work and how it fits into what you and the other students have been doing.

There is little downside to this. The importance of the paper to your career has far more to do with how well received the paper is than with how many authors there are. Having more authors means the paper is stronger, means you have a network of people to help rewrite and deal with any negative reviews you may get, and (as suggested in Peter's answers) it shows you can collaborate with others.

It would not hurt to bring this up with your advisor, make your point (ask your question), and see how the advisor reacts.


Ethics of/rules regarding submitting multiple presubmission inquiries It is well-established (and typically spelled-out in journals' instructions to authors) that is unacceptable to submit a single manuscript to multiple journals for peer review simultaneously. However, the rules for presubmission inquiries (which are essentially cover letters asking whether the journal would be interested in reviewing a given paper) are not clear to me; a presubmission inquiry does not constitute a formal submission.

Is it permissible to submit a presubmission inquiry regarding a single manuscript to more than one scientific journal?

Is it unethical to do so?

Further details on what presubmission inquiries are:

Presubmission inquiries are relatively common in genetics and biology. From the Nature website:

  Presubmission enquiries are provided purely as a service to authors
  (for example, to see if a manuscript is likely to be of interest to
  the journal) and are not compulsory... Presubmission enquiries are not
  required for Articles or Letters, and can be difficult to assess
  reliably; Nature editors cannot make an absolute commitment to have a
  contribution refereed before seeing the entire paper. Entire papers
  should not be sent as presubmission enquiries, but should be formally
  submitted through our online submission system.

As an author I have done two presubmissions in the past. I do not know how they are handled by editors, but as an associate editor myself I gather they are informally skimmed by 1-2 editors within hours after submission. This means it is unlikely some "multiple presubmission" would be detected and I have never seen specific rules about priorities in presubmissions.

Thus I think one is safe from editorial action if "caught" in multiple presubmission enquiries. However I believe it will not be seen with good eyes by a handling editor, and might leave a bad impression.

Thus I would not recommend doing it. Particularly as an editorial answer usually comes in less than 48h.


How and why did the top journals become top journals? Journals like Nature and Science have impressive impact factors. How and why did these top journals become top journals? Why are they able to sustain their statuses?

All journals that have a high standing have the standing because of the support of the community. If the community loses interest, the journal will drop in the ranking. The top journals have therefore attracted authors for one reason or another. The editorial staff of journals try to maintain this status by making sure the work published there is of good quality and will be cited. It is thus not impossible for new journals to attain high status as long as authors provide the necessary papers. To this mix, we now also add the impact factor and other bibliometric factors. They matter now but have not been the driving factor for making the older journal what they are today.

I work with a more modest journal and I can definitely state that improving your impact factor is far more difficult than to drop in ranking. But, if your ranking becomes high enough (no specific number will be relevant since it varies between fields) a journal will be self-fuelling since many want to publish their material there and competition stiffens leading to a strong selection.

So the standing of Science and Nature, is part their long history, in part the hard work by the journal itself and in part the, now, need for authors to publish in as high ranking journals as possible since that is what forms the basis for most evaluations in academia.


The French school of mathematics "has entered a demographical dip" In an interview made for the 25th anniversary of the Institut de Mathématiques de Jussieu-Paris Rive Gauche, its head Professor Loïc Merel says at 1:25:

Les doctorants que nous formons aurons une lourde tâche: celle de reprendre le flambeau de l'école mathématique française, qui est rentrée dans un creux démographique.
[Personnal translation: The graduate students that we educate will have a daunting task: that of taking up the mantle of the French school of mathematics, which has entered a demographical dip.]

What are references backing this claim, and how pronounced is the effect ? For instance, will there be an actual shortage of talent and even some areas taking a toll, or just slightlty less competition for a while ?

Here is some additional info compared to the other answer (which does not have a lot of detail).

Loïc's comment is mainly about fundamental (AKA pure) mathematics. The IMJ-PRG is a pure math research institute. There is a trend in French academia that funding is going more and more towards research that has immediate applications, with some level of disregard for fundamental research. This is the case in pretty much all fields of science (maybe with the exception of computer science). It goes without saying that the situation is dire in social science and the arts, apart from economics, management, and law. (I did not choose these at random, they are legally treated separately from the rest.)

The French ministry periodically releases some demographic information. Here is the latest one for faculty in Section 25, i.e. pure math. Even if you can't read French, the graphics speak for themselves. On the first page, the first graphic is about professors, the second about lecturers (maîtres de conférences), the third about the total. The brown line is pure math, the light blue line is "Group 5" (pure math + applied math + CS), the dark blue line is Science, the black line is the whole of French academia. The graphics are normalized at 100 in 1998. You can get graphics for other years and fields on this page.

To summarize: the number of faculty in pure math has decreased by 15% in France between 1998 and 2018. This is enormous. The number of students increases every year. Administrative tasks are always increasing. This puts an enormous amount of stress on the remaining faculty. (As a comparison, the number of faculty in applied math increased by 11.4%.)

The situation is also dire for new doctors: finding a permanent position is an ordeal, even more so than in similar countries. In the PDF I linked, Figure 3.2 on page 4 is especially telling: in 2018, there were 420 candidates for 22 lecturer positions, and 136 candidates for 14 professor positions. This does not include candidates who were rejected from the "qualification" (94.7% of candidates for professorships and 88.7% of candidates for lectureships are "qualified").

Note that this graphic also shows that there is not much shortage of talent. The number of candidates per position (column "Ratio B/A") decreased between 2014 and 2015, but it's increasing since 2015. The decrease in 2014–2015 was due to the fact that there was an exceptionally low number of available positions in 2014.

A remark, for intellectual honesty: not all French math researchers are faculty. Some are full-time researchers employed by the CNRS. Update: According to the CNRS's official statistics, the total number of researchers in Section 41 (pure maths + applied math, no, it's not the same section as the CNU) is 373: 210 junior and 163 senior. To compare, in 2018 there were 1321 faculty in pure math and 1776 in applied math. That's 3097 total, so CNRS researchers represent about 12%. I cannot say what the distribution between pure and applied is. "Common knowledge" tells me that it's around 10% for pure math.

PS: The ministry's website has a wealth of information. There are statistics about pretty much everything, as well as explanatory notes about the conjonctures. I highly recommend it to anyone who wants to learn about the evolution of French academia. However, be careful about aggregates: data about a "Group" (e.g. pure+applied math + CS) may not tell you everything about a "Section" (e.g. pure math).


Is it acceptable to ask a university professor to add his/her name to a paper? Is it acceptable/normal to ask a professor to add his/her name to a paper to increase the opportunity to publish the article in high-impact journals?

No, it's not okay to do that, it is academic misconduct to have authors on a paper who have not made a contribution rising to the level of authorship.
There is no single central set of authorship guidelines, but you'll find them from various discipline-specific societies, universities, publishers, etc. Some examples:
http://www.icmje.org/recommendations/browse/roles-and-responsibilities/defining-the-role-of-authors-and-contributors.html

The ICMJE recommends that authorship be based on the following 4 criteria:

Substantial contributions to the conception or design of the work; or the acquisition, analysis, or interpretation of data for the work; AND
Drafting the work or revising it critically for important intellectual content; AND
Final approval of the version to be published; AND
Agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.

https://provost.yale.edu/policies/academic-integrity/guidance-authorship-scholarly-or-scientific-publications

Under no circumstance should individuals be added as co-authors based on the individual’s stature as an attempt to increase the likelihood of publication or credibility of the work.

https://www.elsevier.com/__data/assets/pdf_file/0006/653883/Authorship-factsheet-March-2019.pdf
Under the category "should not be an author":

Guest’ authors, who make no
discernible contributions, but are
listed to help increase the chances of
publication;

All of these would ban the practice you are suggesting.


Prospective PhD-How to keep in touch with potential PhD supervisor I'm applying for several Ph.D. Programs in Human-computer Interaction. I contacted a potential supervisor and asked him a bunch of questions about the program. The professor wrote a very detailed answer and recommended some books for me to read.

I would like to keep in close contact with him until result of the application is available.
How should I thank him for the information?

I fear that "close contact" is probably too much to hope for. Academics are very busy and it is rarely possible to devote a lot of time to prospective students. Close contact (hopefully) comes once you are their student, but usually not before. The best thing to do would be to see if conversation grows organically. Thank them for their email and recommendations now and let them know you are applying. Meanwhile, get in contact with them if you have something kind to say, interesting to report or important to ask: that you are coming for a visit and would like to meet, that you have finished all the suggested readings and wonder if they might have more recommendations on another subject, to congratulate them on a new publication, etc.

Don't be offended, however, if you do not get much response to these. Like I said, we don't have much spare time for such correspondence before you are a student.


What are some good ways to structure material before writing a theoretical paper/thesis/book? Let's say that you are going to write a theoretical paper/thesis/book (that is, you're not conducting empirical work). More often than not, I find it troublesome to just start writing right away, especially when I don't know what the results of my investigation is going to be.

What are some good ways to structure and organize your material, as well as your workflow, before starting to write?

Of course, it's disastrous to be so disorganized that things get lost, work has to be duplicated (even if it's just typing), etc.

On the other hand, I observe that many novice writers over-allocate their time+energy to "planning". I say "over-allocate" exactly because (as in the question) when one doesn't have too many details about the sequel, it is hard to plan. Further, especially in thesis situations, and, even for more experienced people, in book writing, the very process significantly changes one's viewpoint, so that an initial plan/outline/table-of-contents/statement-of-intent easily becomes grossly inaccurate over time+experience.

For example, although it is interesting, and an interesting exercise, to try to write an introduction or preface at the beginning, it will most likely prove wildly irrelevant, and have to be scrapped nearly entirely.

A second crucial mechanism is (as suggested in the questioner's self-answer) feedback, and, equally, iteration of the writing/editing cycle.

The two concepts combine to suggest that one should not waste time doing nothing, but pretending to be trying to fathom what one will think, and what one will discover, some months in the future. Hesitation delays the very experience that will bring to life one's future viewpoint! :)


Is it legal (USA) and ethical to use international edition textbooks? When I pay for a textbook, where does the money go? Background:
I am a student.  I didn't have anything in life for four years, and I worked myself silly at times for it. So now I ask - when I pay hundreds of dollars over the production cost (new textbooks are over a week's pay each) what and whom am I giving my money to?

It's probably not those working in  the publishing factory,  I don't think it's the professor who wrote the book;  I imagine a rich entrepreneur , who, by positioning himself well in life, makes an immense amount of money while directly producing nothing of value, aka, the brass of a publishing company (correct me if I'm wrong).  In fact, when our college tried to use an "open source" textbook, publishing companies promised to stop selling us books - all over that one class!

Now, I can buy an international version for some 20 or so hours of my life (aka, payrate) for each and every class. However, there are plenty of people in this process who deserve to be paid (yes, even the brass.)  That said, books are so (over)priced I think it is more unethical not to pirate the book or buy a used or international edition - by feeding the predators, I become part of the problem.

However, there are many people on this site who are vastly more informed and experienced in academia than me and so I ask the following questions.

Questions:

Is it ethical for me to buy international textbooks?
Incidentally, is it legal in the United States to buy international textbooks?

The US Supreme Court ruled that it is legal to buy and sell international editions of textbooks. As for the ethics, it clearly goes against the wishes of the publisher, so one might conclude that despite being legal that it is unethical. As for where the money is going, I believe most big publishers are publicly held, so the profits in general go to the share holders. Of course the costs include the salaries of the executives, royalties to authors, and the salaries of the individuals running the printing press.


Is it common for a thesis-based master hasn't got the thesis topic? The supervisor just tells students to learn knowledge and practice skills that will be required in their research in the first year but doesn't have their topic decided. Is such case common?

This can happen. The formal thesis topic is quite an open field.

Perhaps, the supervisor doesn't want to spoon-feed and force a topic on to you, but rather would want to have you come up with one. By exposing you to various tools and techniques, and (presumably) side-by-side pointing to some useful literature, and asking you to dig for more works yourself, he/she is essentially doing a good job. Basically, what he's saying is - this is what happens usually in the field, tell me if you come up with any ideas regarding what you want to do. He/she is basically throwing the field open to you.

Since your master's is thesis based, I won't find it very surprising though if he/she has already planned something as a backup option, in case you don't come up with anything reasonable. But he/she will likely not reveal that unless he/she is absolutely convinced that you are struggling to come up with anything doable.

In my experience, this approach is not very common, but not very rare either. And of course, it is a good approach, the goal of course is to train you to think.

Hope that helps. :)


Getting notified when an article I cited in one of my papers gets retracted Is there any way to get notified (e.g., by email) when an article I cited in one of my papers gets retracted?

Perhaps you could set up a Google Alert or set up a similar event handler at http://www.changedetection.com/.

I have tried both of these services.  Once in a while they both catch the same thing, but for the most part they complement each other.


Is it appropriate to apply for assistant professor positions a few months before obtaining my PhD? I am finishing my PhD at a famous research institution located in Europe. I am quite delayed due to COVID-related disruptions, which forced us to devote most lab equipment to vaccine development and trial assessment instead of doing some experiments I needed to validate my hypotheses.
Nonetheless, I will obtain my degree within the next few months. My thesis has already gone through a mandatory internal assessment process, which is similar to peer review. And my advisor has already appointed examiners.
I have some interesting publications in good journals (Nature Comms and equivalent ones), but a big part of my thesis is only published as a preprint in medRxiv. My findings are very novel and, in the words of my supervisor (who is a big name in the field), it's a major breakthrough. We've contacted other big names in the field, who are also really interested in this new approach, and they are helping to validate things. We already have enough for submitting to a top journal, which is good.
My advisor and his peers are writing grant applications and preparing clinical trials based on my findings. I am interested in continuing with this line of research, but I will need to find a different host institution once I graduate. I would like to continue as soon as possible in order not to loose a head start on my own ideas.
I am a bit confused with research-oriented Assistant Professor openings. Is it appropriate to apply at this stage? I have contacted one US professor behind an open position, and he encouraged me to apply. However, is this the norm for most American and European positions?

In most biology/biological sciences departments in the US and Canada it would be unusual for someone to be hired into a tenure-track assistant professorship immediately following their PhD; most candidates would have at least a year or two of postdoctoral experience. (This may be different in biomedical and/or clinically oriented programs). If you have a spectacular research record that could make you an exception.
Postdoctoral experience is less expected in math (although 1-2 years is probably still the median), and even less in statistics; this is probably also the case in other fields such as engineering where people with a fresh PhD can get well-paying jobs in industry.
It doesn't hurt to apply for such positions, but I would say if would be safer to at least consider a few post-doctoral positions as a backup plan.
Finally, as with most questions like this, you will get the most relevant advice from your supervisor and colleagues in your lab/program; they know the most about the norms of your particular sub-field and geographic region. Unless you have some particular reason not to, you should probably ask them.

Here is some data from a reasonably recent survey of (mostly North American) ecologists (note, this paper was contentious because of the way it handled gender and informed consent of respondents):

Recently hired TT assistant professors of ecology typically were about 4 years post-Ph.D. at the time of hiring (mean 4.2 years, median 4). 69% had anywhere from 2 to 6 years of post-Ph.D. experience, with a range from 0 to 11 years of post-Ph.D. experience. The majority of ecology faculty job seekers also are 2–6 years post-Ph.D.

These data are consistent with a job market in which most hiring institutions prefer applicants with at least a year or two of post-Ph.D. experience. But once you have a few years of post-Ph.D. experience, the marginal value of additional post-Ph.D. experience appears to be low at best, though it's hard to say precisely based on the available data.

Fox, Jeremy. “A Data-Based Guide to the North American Ecology Faculty Job Market.” The Bulletin of the Ecological Society of America 101, no. 2 (2020): e01624. https://doi.org/10.1002/bes2.1624.


Is there a good site for holding online discussions of scientific papers? Many of my computational scientist colleagues used to use Google Reader to share and discuss new journal articles.  The loss of Reader's social features killed that, and we have subsequently tried Google+ and Reddit, but neither seems to work nearly as well as Reader did for holding this kind of discussion.  Does anyone have experience using a site they like for this purpose?

I'm aware of a few options, like http://annotatr.appspot.com/, that seem promising but appear not to be actually used much.

Might I suggest http://scicomp.stackexchange.com ?

While the StackExchange system isn't the best - and indeed isn't designed - for "discussion", I've found that many "What did you think of this paper" type questions can be phrased in SE-compatible formats. CrossValidated has a semi-periodic "Journal Club" bit, and questions and musings about scientific papers come up a fair amount there.

I think if framed correctly, they might find a useful home here.

Generally though, I think the online discussion of scientific papers suffers from a few problems. Generally, the two I find the most problematic:

Lack of a clear community to talk about papers in. Essentially, the problem your question is looking for an answer to. I haven't found a really good general purpose one, though I would love to if I did find it. There's blogs and the like, but even the ones talking about peer-reviewed papers are somewhat one sided in terms of their communication, and not great for anything but transient chatter.
A hesitation to talk about that online. Among colleagues, it seems somewhat easier to summarize things like "Bad paper is bad", or slice apart someone's methodology. I'd be somewhat more hesitant to do that anywhere where my identity is both traceable and the conversation is saved for eternity (the internet).


Is it bad etiquette to contact a named reviewer? A named reviewer has made some suggestions, which I'm exploring, and I'd like to ask for input on a particular point. I have exchanged emails with this person before asking for input on the same work. Would it be appropriate to email directly to ask?

If the reviewer has given you their name, then that is their choice. In my experience journals give the reviewers the option of anonymity. If they've chosen to reveal their name then I think there is no issue with you contacting them directly. Especially if you've discussed the work with them previously.

When you resubmit the paper, with the changes, perhaps you could then include this persons name in the list of people not suitable for reviewing the paper (Assuming that this journal asks you to submit names of suitable, and not suitable, reviewers).


If a paper is rejected by many journals before finally being published, will that cause conflict with the reviewers who rejected the manuscript? I had a manuscript written 3 years before. The results of the manuscript was obtained accidentally while doing some easy trial methods. Although the results were very interesting, but the method was very very simple. So I thought to publish it in a low impact journal to increase my number of publications. But things went very opposite and got rejected in 5 journals. Everyone were commenting that the method is very simple and may introduce the unknown errors to the estimations or computations.

As no one was commenting other than the methods, so I had no way to modify anything. Very bad thing is that none of the journal took less than 4-6 months to take the first decision and my manuscript remained unaccepted for two years and half.

Finally I thought to submit it to a high impact journal. Very surprisingly, the reviewers appreciated the simple method used and accepted the manuscript with a major revision to highlight few other things.

My accepted manuscript highlights the same methodology which was rejected by 5 other journals.

Will there be any conflict or issues when those reviewers (who rejected my manuscript) see my accepted paper after final publication?

Your referees at specialist journals said, basically, "These methods aren't good enough to answer these questions, because X." But the generalist high-impact journal may have looked more at the results than the methods.

If X is "we just don't think this is very sophisticated, and the tools are out of fashion," I suspect nothing will happen.

If X is "there are uncontrolled errors larger than your effect," and you haven't explained in your paper why that isn't true, someone might write a comment on your paper. This comment will look a lot like your earlier referee reports. The field will then decide who is right. (See, e.g. the "arsenic life" experiment for a recent high-profile example.)

Beyond this, if I saw the second case from a paper I refereed, and there was no attempt from the authors to address the points I raised, I would not be happy with the authors, and might be less likely to extend them the benefit of the doubt in future referee reports.


Is it possible to find an unpaid and "half-time" postdoc? I've defended my thesis, and I would like to do my postdoc abroad. But the problem is that I am married, and I have two little children. So, I can't just leave my family for a couple of years, and neither I can bring them with me (too expensive, too difficult etc.).

I have a couple of colleagues in the same situation, and they seem to find a solution: a kind of unpaid postdoc (they receive only small sums of money covering travel expenses) which supposes visiting the inviting university regularly but without staying there for a long time. In this format they prepare a monograph and give some seminars, it is counted as a postdoc by ANECA (homologation institution) here in Spain but doesn't require full-time occupation if you can maintain certain level and volume of academic publications. In both cases they were invited unofficially by their postdoc coordinators, it was not an announced grant or scholarship.

For me it could be the best option. It will give me an opportunity to get some foreign postdoc experience, stay on academic track (in Spain it is really difficult in the umanities) and at the same time I don't have to leave or move my family...

But I really don't know how to start. Is there any opportunity to get an information which universities offer this way of collaboration and how to apply? In the case of one of my colleagues, it is one of the Swiss universities and in another case it's Finland, but the information offered by these universities on their webpages is related only to the "normal," fellowship-based, full-time postdocs. And maybe there are some other opportunities of this kind in other countries and universities?

I know that some institutions can offer the "associated member" status to a researcher who is not on their payroll. The researcher needs to be recommended by a senior professor from the institution, who typically presents a project with this researcher to justify the request. However I've seen it used only with somebody after they had been a postdoc in the institution.

Obviously one needs at least to prepare a research project with a member of the institution, so I think the best way would be to contact the academics in your network who could be interested in a project with you. I'd suggest to propose to work with them for free on a grant proposal, since this would be interesting for both the PI and for the institution. If you find a suitable EU call, you could even try to involve a partner in Spain which would hire you if the grant is successful.


What does it mean when a manuscript submission systems lists the status of a paper as "Archived"? I submitted a paper in journal. After one day status is Archived. What is meaning of it? I did't get any communication information. Thanks.

This will depend on what system the journal is using, what processes the editors are following, what that editor in question was thinking that day, and maybe other factors.

Point being that there is no way for you -- or in fact, anyone -- to know for sure. You have two choices:

Ask the editor.
Have patience.

I would suggest the second. You will get a notification in due time when someone has made a decision. You can also look up what turn-around time the journal strives for (say, 3 months) and then round about that time email the editor if you haven't heard back until then. But after just a single day, the only reasonable answer is: Have patience!


Is it ethical to use proprietary (closed-source) software for scientific computation? I have data from an ordinary scientific experiment. Now, in order to analyse the data, the most convenient way for me is to use some proprietary, closed-source software.

Is it ethical to use such kind of software in research?

If do use it then this part will be a big black-box in my research. So if someone cannot reproduce my data analysis with the same or with some other software, then it depends on the mercy of the software company if we can find out what went wrong. If the software company does not want to cooperate, then what went wrong might never be found out. I have the feeling that this opposes the principles of science.

I do not think that this is an ethical question in the first place. Reproducibility is not harmed by the requirement that money needs to be spent on buying software or setting up an experiment (or are there open-source particle accelerators?).

While open source solutions are preferable for many reasons, there are clearly cases where using some proprietary software P is appropriate:

When it is known (and has been verified) that P's implementation of method M is correct while the known open-source implementations of M have not (yet) been established as reliable. Conversely, when open-source implementation O is known to give correct results whereas for P this has not been established, then clearly O should be used when there is a choice.
When one can reasonably expect that P is widely available in research institutions (and thus to researchers), like for example certain mathematical / computational packages.
When P allows for a much more (time-/resource-)efficient execution of experiments.
When P is a software package needed anyway to extract / process data from a big-ticket instrument.

Note that I am assuming that P can actually be bought by anyone. If P is not commercially available but rather a closed-source in-house solution then an open-source package is preferable.


How to improve technical writing Whenever I write an article, I feel the result is not good enough. Although every theorem is solid and correctly proven, something is always "squeaky".

The main evidence for my feeling shows itself when my co-authors revise theorem I've written. Suddenly everything becomes compact, precise and clear. Properties that were used several times get a name; modular parts of the proof become lemmas; etc. The math remains the same, but the presentation is way more efficient and easy to follow.

How can I improve my technical writing skills?
Any tips and resources would be appreciated.
Comment: I'm not a native English speaker, which is an additional factor.

The only way to improve writing (technical or non-technical) is by writing and submitting your work to the criticism of peers. Thankfully, in mathematics there is a culture of blogs. When you learn something new, write it up on your blog and share it with your friends. This will help you better understand what you wrote AND let you practice writing. At first, you won't get much feedback, but as your audience grows you will naturally learn from the feedback they provide.

Another great tool is math.SE and mathoverflow; on these sites you are guaranteed feedback. Ask and answer technical questions, this will let you practice your writing. As your writing and clarity improves you will also notice an average increase in number of up-votes, etc. This will give you useful positive reinforcement.


A conjecture proved in drafts I am preparing my math research monograph for publication.

In the current draft there is certain conjecture.

This conjecture was proved in my drafts (available on the Web) of the second volume for this monograph.

Should I:

just remove the conjecture from the book because it is proved?
leave the statement in the book titled as a conjecture because it's proof is not yet officially published (and also may be not enough checked for errors)?
write in the book that I am going to publish the proof (either in a separate article or the second volume of the book)?

One of the most important principles of academic writing is that you shouldn't write anything misleading.  If you present the result as a conjecture with no indication that you have already proved it, then you are giving readers a misleading impression (namely that you don't know how to prove it), so you shouldn't do that.

  Should I just remove the conjecture from the book because it is proved?

That's an acceptable option.

  Should I leave the statement in the book titled as a conjecture because it's proof is not yet officially published (and also may be not enough checked for errors)?

Don't just leave it there without comment.  If you are worried that the proof might be wrong, you can address this by stating things a little more tentatively.  As for whether it is officially published, most of your work seems not to be officially published, so why is that an issue for this conjecture?

  Should I write in the book that I am going to publish the proof (either in a separate article or the second volume of the book)?

Sure, why not?  It's probably preferable to deleting the conjecture: if it was worth mentioning as a conjecture, then presumably it's still worth mentioning as a theorem.


Is it inappropriate to email a senior academic with whom I have no pre-existing relationship, asking to check/inform my work? Is it inappropriate to mail a senior academic (e.g. professor), whom I don’t know, asking –

to check  Lemma, Theorem ( less than 3 to 4, short/ little)
how a graph can be constructed (with given conditions), this might require his ‘intellectual time’ as the class of graph is unlikely to be familiar.
reference related 1,2 .

In general, if I need 1,2,3 as described above how I communicate with an academic over e-mail?

Inappropriate or not, you aren't likely to get a response. Professors tend to receive a lot of email. If they don't have a compelling reason to respond, they might not.

You're asking them to put time and thought into a response to a stranger. The best course would be to talk in person to a professor whose class you've taken. Ask if they would mind looking over your work, and get feedback in person.


How to alleviate tension when interacting with researchers at a conference from enemy countries? In academic conferences, I often meet students and professors from enemy countries, whom I could never have met in normal situations. We both know that we are here for research, and we do talk about research, but there is still tension in the air. Maybe even mutual fear. What can I do to alleviate the tension, so that we can focus on the research?

There has long been a link between scientific collaboration and diplomacy between countries.  During some of the deepest parts of the cold war, for example, the United States and the Soviet Union worked together to stamp out polio, and the echoes of "vaccine diplomacy" continue today, uniting people against their common non-human enemies.  Even when there is not an explicit cooperative goal of that sort, contacts in a neutral situation can be valuable for helping to promote peace and understanding between different cultures and countries.

I would thus suggest beginning to approach the question not from a perspective of "Who is my enemy?" but from a question of "What are the areas that we can cooperate, even if we are enemies?" and perhaps to read up on ideas in "science diplomacy."


Is it okay if research problem is vague in the initial phase of research? In short, I am a Ph.D. student computer science ( theory ) currently in the mid-stage. I have one serious doubt about the research process. I have worked on just two problems in the past and from that experience, I have felt that the research problem in the initial phase of research will be vague ( means research problem will be broader and somewhat less clear ) and as we start working on the problem, it will become clear and many times we will change the even original research problem. In the end, we will think about what results, we have and on the basis of those results, we will again change the research problem ( if needed ). There are a few problems with the above research process

Takes More time
More frustrations etc

Is the research process will be the same even after my PhD, I mean or I will become more careful with time which may lead to giving me a better way to do research.

Question : Is it okay if research problem is vague in the initial phase of research?

In my opinion this is the definition of "research" everything else is "development". Of course, from "devlopment", serious research questions may be derived.

In my personal opinion, a PhD work whose proposed result is known from the beginning is worthless.

It's a different story if the problem is too large for one person or maybe not solvable at all - then it needs to be re-adjusted based on the experience made so far. But this process can / shall be part of the PhD!


How does a professor know when a research project will get expected results? I read that "One difficulty with research problems is that it is hard/impossible to know if the problem is easy or not" or when it can be solved. So how a graduate-research student (i.e., PhD or MRe) knows what to pick as his/her work, and/or how can his/her professor 'predict' it? Because if one knows if it is possible or easy to solve then he/she likely knows also how to solve the problem, hence it is no longer an open question.

If professors can't decide the period of time a project to be finished, how they risk tuition paid by students or scholarships granted?

EDIT - My intention is mostly on Pure Mathematics.

The interaction between student and professor should not be a one-shot set-a-problem. Instead, they should be talking frequently, often once a week, and adjusting the nature and direction of the project based on what is being learned during it.

The project starts with some idea, from either the professor or the student, that the professor thinks likely to lead to an appropriate outcome within the available time.

As time goes on, the student should come to learn more about the project than the professor, and be reporting progress or lack of progress. The professor should be continuously evaluating whether the current line will lead to a good result, and encouraging redirection if not.

I am sure my doctoral dissertation was not at all what my advisor would have expected when I started on the project - it was a result of things I learned during it.


How to cite my own report that hasn't been published? I wrote a research paper in high school in the field of lasers and optics but did not get published. It is on the internet open for anyone to read. How should I go on citing this? I want to refer to it in an application where it asks me to cite all works I have been a part of.

If you create a profile on researchgate you can upload your work and it gives you a citation. It also gives you your own personal dio code so that you can cross reference your work with other sites. This is what I have used. Here is the web site: www.researchgate.net

Additionally you can also create a google scholar profile sync your work from researchgate and it automatically gives you a citation.


Is it good style to create http links in a B.Sc. project? We are two students in computer science doing our term project for B.Sc. in computer science.

Now I wonder if it is alright or advisable to make inline hyperlinks in the report e.g.

  We look at the specification, it should report the memory mapped
  registers (which are input/output and can affect the state of the
  UART).

Or should there be a footnote instead? Or both? If somebody prints the report on physical paper then obviously an inline http link won't work.

I would say that at least a footnote, preferably a reference. The rules how it must be vary between universities, but the rules are old, and generally there may be a rule that some physical copies must exist and such, so I would play safe and do it always as if it would be printed.