How to judge quality of manuscript to decide whether to submit to high-ranked journal?

As a couple of others have noted, generally speaking you will get a feel for this as you read the literature in your field. However, your target journal may have published criteria for publication. For example, PLoS Pathogens states:

To be considered for publication in PLOS Pathogens, any given
manuscript must satisfy the following criteria:

Originality
High importance to researchers in the field
High importance and broad interest to the community of researchers    studying pathogens and pathogen-host interactions
Rigorous methodology
Substantial evidence for its conclusions

For most journals now, the reviewer is asked to score your paper against areas like this as well as provide general comments.
For comparison PLoS ONE states simply:

The study presents the results of primary scientific research.
Results reported have not been published elsewhere.
Experiments, statistics, and other analyses are performed to a high technical standard and are described in sufficient detail.
Conclusions are presented in an appropriate fashion and are supported by the data.
The article is presented in an intelligible fashion and is written in standard English.
The research meets all applicable standards for the ethics of experimentation and research integrity.
The article adheres to appropriate reporting guidelines and community standards for data availability.

Basically, as long as it isn't fundamentally flawed it stands a good chance with PLoS ONE.
The biggest differences between journals are typically how important your findings are, and to how many people. From personal experience the 'broad interest' criterion (where you are asked as a reviewer to comment on it) is the one I most often find myself scoring papers badly on; most people don't think about this enough.
Without wishing to sound negative: as the others have said, if you genuinely can't tell whether your own paper is 'good' then it probably isn't going to set the world on fire. Then again, nothing ventured, nothing gained; you won't generally get 'blacklisted' for submitting a low-quality manuscript to a journal, and it doesn't cost anything. So if you're being modest but are secretly quite proud of it, you might as well give it a chance with a high-impact journal first. You can always resubmit somewhere else if it gets rejected.
One final word of advice, since it sounds like you're fairly new to this: don't get upset, embarrassed or disheartened if your submission is rejected or torn to shreds by a reviewer. Rejection is common (especially if you're ambitious about the journals you submit to), harsh and apparently unfair reviewer comments even more so, and the editor will normally take the reviewers' side unless they're clearly in the wrong. (And if you stick with academia, you'll find this last bit this goes double for grant applications!)


Is it appropriate or acceptable to thank a professor for their dissenting public opinion?

Yes.  Telling someone you appreciate their taking a public stand you agree with, thanking them for it, is always appropriate and appreciated, especially when you suspect they've taken some heat for doing so.


What to do when you want to research something your advisor does not want you to?

This sounds like you are mad at your supervisor, however, keep in mind that researchers are often very specialized in a particular field, and would have difficulties supervising a project in a different field, or using a method they are not familiar with. THerefore, if you want to do a particular project/work in a particular field/with a particular method, it's up to YOU to find a supervisor that has the matching expertise. Otherwise, you may indeed do what your supervisor suggests you.

Where I work, students have the opportunity to choose their own supervisor that matches their interests. If they don't, they will get assigned to someone. In that case, the students are warned that they may have to do a project that is suggested by the supervisor.

Sounds like it is the same at your place. And in that case, it is normal to do something that you don't really like.

Let me tell you, it's better to work at something you do like. Therefore, get out and find a supervisor that works in your field/method. And don't blame the supervisor for having his own interests.


Is it acceptable to propose the same PhD research plan to two universities?

Chances are that your supervisor at the first university is sensitive to the challenges in acquiring funding. If you have been clear to him/her that you cannot pursue the studies without support and are solely dependent on external funding, then he/she should certainly understand if you pursue them elsewhere where funding is available. Furthermore, if you are up front about it, the supervisor may scramble more to find funding for you. The situation is not unlike courting two potential employers during a job search.

I would not recommend suggesting to the second supervisor that he/she is a backup option, but only that you have also applied with a warm reception to the first university. This way, you do not risk stepping on egos, but still make it clear that you are entertaining other options.


Is significant repetition across multiple journal papers (intro and model) an issue?

It will depend on a bunch of things.

Basically these papers are not "stand alone." They are elements of a series. The way to answer such questions is to put yourself in the place of your readers. Imagine you were a researcher from a related discipline, and you were encountering these papers for the first time. What level of duplication would make your life easy?

For example, if these are 5 page papers, and you have three pages of repeated intro material, that's a problem. If these are 50 page papers, three pages of repeated intro is probably not a problem.

For example, if the papers are in the same journal every time, you should be more inclined to simply cite a previous article for material you are considering repeating. If it's a different journal, you may want to avoid forcing your reader to hunt up that other journal to figure out what is going o n.

Maybe there's a way you can get some kind of consideration from a journal. If you are going to have several papers on the same topic in rapid succession, maybe you can get them published back-to-back. Or at least in the same volume so a reader will get them all at once. That way you could simply say "see the first paper" or something like that. It is certainly not unknown, though it is also not all the common either.

Another possible strategy is to publish a "state of the union" paper in a review journal, then reference that. When I was in grad school I wore out several volumes of Physics Reports that had review articles about my research subject. So much so that I eventually had to buy my own copies. Is there a similar journal in your field of research? You could put all your intro material and notation and introductory calculations in there and just cite it. Publishing a review article on a subject you are "pioneering" in can also be a good boost for your CV. And it will tend to get cited by a lot of people who are just getting their toes wet in a subject.


How to encourage students to seek alternate citations for an assignment?

A good way to think about this is to de-charge the religious aspect of the question by considering a parallel situation involving an equally dubious published paper with no religious aspects, such as this one.  What would you do if a student wanted to cite such a piece of nonsense as support for their claims in a paper?

Rather than simply prohibiting the citation, you can treat this as a teaching opportunity to talk about how to determine the credibility of a scientific paper.  It is, of course, certain that the paper that the student wishes to cite will fail any reasonable test, given the notoriety of the journal involved and its complete disconnect from the rest of the scientific literature.  This is also an excellent opportunity to talk about how in science publication is not the end, but the start of the real conversation.

Perhaps rather than immediately talking to the individual student, you can take a few minutes in class to talk about how to evaluate a paper and its place within the scientific community.  Compare a nice strong peer-reviewed paper to a lunatic one like that linked above, both of which are completely secular in nature.  Then explain that part of what students will be graded on in their assignment is their ability to evaluate references.  This gives you good grounds to warn the student that their citation is a problem without even having to bring religion into the picture, as well as teaching the whole class some valuable information.

Let the creationist citation fail on its scientific (lack of) merits, rather than making this an argument about authority and belief. The beauty of science is that, in the long run, authority and belief are simply irrelevant.  Eppur si muove.


Do automatic tools to check thesis exist?

I use a Academic Writing Check for most of my academic writing, including my thesis. It checks for:

passive voice: don't use the passive voice if you can help it.
duplicate words ("the the"): this has saved me many times.
wrong abbreviations: for example, i.e (no second period)
bad typography
and some others

To check missing or duplicate labels, I use pdflatex (with this very cool Makefile). It prints a warning message anytime some of the above occur.

I'm not sure how you would check for wrong citations, but pdflatex will tell you about undefined references. For certain words you don't ever want to occur, just use grep.

The last check I do is for overfull hboxes, you can visualize them in your document by setting this in your preamble:

\overfullrule=5pt

I found that on the LaTeX stack exchange, you will no doubt find the answers there a great resource as your write your document. Good luck!


Should I obtain permission for publishing a vector drawing based on a published photo?

What is your original motivation to create that drawing? Escape reproduction rights? Or else?

The usual practice with museums and objects that are not involved in copyright any more because they are too old, is that you don't pay for the picture of the image if you take the picture of the image yourself. You pay if you use the image that the institution provides.

My guess is that publishing your drawing is not like 'republishing the photograph itself' because your drawing makes an original contribution that goes far beyond reproducing like for like the original photograph.

Agreed with commentators about approaching the institution out of common courtesy, if nothing else.


I regret my choice of grad school, is it possible/common to accept an offer I turned down a year ago?

There's almost a 100% certainty that you'll have to apply again. Graduate programs get a fixed number of admission slots (or fellowships to support those admits) each year. Your position was likely given away to someone or returned to the graduate school when you told them you weren't going.

As Nate Eldridge notes, you were a good candidate last year and you'll be a good candidate this year. There's a slight stain on your record regarding whether or not it was a personality conflict or something else that is causing you to abandon the other school.

If you have a good relationship with your current advisor, then s/he can address that in their letter of recommendation. Or you can ask your undergraduate advisors to note the reason why you're leaving the university.  The faculty on the admissions committee will be curious why you're leaving a more highly ranked program and admissions committees are risk-adverse, so you do need to address this somehow.


How to justify motivations for a second master?

I don't find your justification wise enough for a second master degree in distributed systems and networks. Moreover, I don't find a real target behind the second master degree other than getting associated with professors and the country.

If your prime purpose is to learn new stuff, you don't need a second academic degree which is very similar to the one that you already have. You can learn on your own. Moreover, you could directly apply for a research degree (say Ph.D.) in Germany instead. This would definitely make more sense. Unless you have some serious career goals to pursue on the specified courses, you should not do it. In my university, my colleagues who have Ph.D. in software engineering are now doing serious research in IoT, Distributed Systems, and Network security.

Ask yourself this question: If you get interested in computational economics after 2 years, would you again apply for a masters degree in the same field?


Is the abreviation 'Doz' equivalent/interchangeable to 'Prof'?

A "Dozent" is just someone who teaches / gives lectures.

This means every Professor/Prof. is a "Dozent" (if he teaches).

But not every "Dozent" is a Professor (e.g. some people who are working in industry and give lectures as a side job or people who just haven´t made it to "Prof" yet.)


I don't see how it would be socially unacceptable. You might have to weigh the response you get from Professor A if you think he or she is keen to have you as his/her student -- but that often happens. The conflict often arises: the desire to do the best by the student in terms of suggesting other supervisors or institutions against the desire to have a good student working on a shared topic.

Regardless of whether you get Professor A's advice, seek out students -- current and past -- of Professor B and ask them for their opinions.


Why would I want to register with ORCID?

The advantages are:

Unique identifiability (as you noted, not everybody needs this).
Stability: There may be some other researcher with your name in ten year from now. Or you might change your name due to whatever reasons.
It's handy: Many editorial system allow you to log-in by just clicking "log in with ORCID". Some years ago I had zillions of log-in for different systems, often conflicting and I ended up requesting passwords frequently, delaying the submission of reviews. Now I use ORCID for everything and the problem is basically gone (sometimes I get invitations to review for journals I did not use before and they give a new log-in but I insist that they use my ORCID, and this works). For example several sites with the url editorialmanager.com allow you to sign in via ORCID. If you do so you do not a new log in and on top of that all your affiliation is already filled in after log in.
Your university library may be happy: When you use ORCID it is pretty easy for them to see how you publish with different journals/publishers and this may give them useful data for negotiations with publishers. You may have heard of the "Project Deal" where Germany is fighting with some publishers and it turned out that the data about the publications habits of German scholars is helpful in the negotiations (at least this is what our librarian told us).

Actually, I don't know of any competing standard and I do not see any downside in using ORCID. The organization behind ORCID is non-profit. I view ORCID as trustworthy and helpful as the arXiv (in case this means anything to somebody…).


How to contact author whose work I built off of?

It's appropriate to contact the authors, particularly if they are still active researchers. Before sending them the manuscript or telling the entire story, perhaps ask if they would be willing to keep your results confidential until publication.

As far as formal permission to reproduce their graph, it's very likely that the authors don't hold the copyright. Most authors sign over copyright to the publisher, so you may have to query them. Even so, it would be polite and advisable to notify the authors that you are planning to reproduce a piece of their work for comparison.


Is a second career in statistics and science realistic? Accountant inquires

Not too long ago I faced the same issues as you. I wanted to go from economics to software engineering, particularly machine learning. I'm in a department with a decent emphasis on statistics, I know several future PhD statisticians, I have a general idea what those groups look for.

1—You don't want a masters in applied statistics (MAS). You want an MS in statistics. Huge difference. A graduate student in my department got an MS in stats from a top-ranked stats school that also offers an MAS. He said what he teaches in undergrad math stats is above what the MAS students learn in their first semester. If you write a thesis for your MAS, it will probably be a data analysis paper, not a minor contribution to the field like you would for an MS. The MAS degrees aim for people who don't know much about stats, and they mostly emphasize how to do things like statistical programming over original contributions to the statistics field. You get an MAS to go work in industry for a PhD, not to go on for a PhD.

2-I hope and suspect that your age won't count much against you. My department regularly admits people in the their mid-to-late thirties, as well as 22-year-olds. But we focus on applied mathematics and like to industry work. Again, you should get an MS instead of an MAS.

3-It can't hurt, but may raise eyebrows. Don't count on getting in with a biostats researcher, however. There are some security issues, and grants sometimes restrict who can access data for a variety of reasons.

My unsolicited advice: start to bail on accounting now. Start a second bachelor's degree in mathematics or statistics. That gives you a better shot at graduate school and a foot in the door for a stats graduate program. When you get into an MS in stats, go. Don't do it part time, go full blast, finish and get into a PhD program. It's a good time to get into statistics. When you finish, hunt for consulting gigs or go a route like machine learning, and you'll more than make up the lost accounting salary. What you'll never make up is the time.


Can future works sections be similar in different papers?

Future work or goals may be broadly similar, there is absolutely no problem there. But if they are identical, the natural question is, what objective does your present work achieve?

You have extended the method (simple to more complicated), so you have already advanced something. Your future work and summary should reflect that - from a writing point of view more than an ethical point of view. If a reader were to only glance at your abstract, conclusions and future work, it should be clear that you have accomplished some goal that was previously unmet.


Speaking as an editor, two possibilities seem likely:

The journal website reports "additional reviewers" when more reviewers are assigned, even if the reviews are not returned yet.  Thus, it might be that 2 reviewers accepted invitations, 1 declined, and another invitation or two are outstanding, and this would still be reported as "assigning additional reviewers" because they system's not very subtle.
Some reviewers returned either very fast and contradictory or very fast and worthless reviews, and the editor is getting more to help resolve the decision.

Either way, don't fret about it: your paper is being handled, and there's nothing that you can or should do right now.


How do I register a paper URL into doai.io or oadoi.org?

doai.io relies on BASE (Bielefeld Academic Search Engine)'s data. So to  register a paper into doai.io, one has to put it in an open-access repository that is harvested by BASE. There are more than 5700+ indexed repositories, the complete list can be found here

oaDOI.org relies on its own harvesting of open-access repositories, that are listed at https://api.oadoi.org/data/sources.csv


Including Results in Dissertation Before Publication in a Journal

Good question! No, your thesis does not count as published (yay). Self-plagiarism is definitely not an issue here. Good on you for clarifying though!


I don't know the country of your residency; but in the UK and in the US, you can start a Ph.D. after a bachelor degree; without a master degree.

Now because you already did most of the bachelor degree, and want to the Ph.D. afterwards, I would recommend to do the followings:

Documents: First you need to gather two things. First, your transcript of the subjects that you passed. Second, a CV that shows your industrial experience, in details (e.g., what programming language you used exactly, etc.) on building software.

Meetings: Now there is some work to be done here. What you want is to meet someone in the software engineering/computer science department; that can listen to you and give you guidelines, on how to apply for the course. This is very important, because after he/she sees your CV, he/she might be able to help you what courses you need to take besides the final year project to get your bachelor degree. I would start, emailing head of the departments and see if they can help. If not, I would start emailing the senior lecturers. Don't expect a random staff in the department to help you with this. Simply you need someone senior with loads of experience in the department.

Further Notes: For your final year project, you need to do massive amount of work, because you need to get a Ph.D. position afterwards. Don't do a final year project with an unknown advisor in the field. His/her recommendation letter for the potential Ph.D. supervisor is essential. Also, you need to get a very good mark; so the potential Ph.D. supervisors accept you as a Ph.D. student.


Travel Budget for Faculty Members in USA

Although I am a mathematician and not a CS or engineering professor, I would overwhelmingly expect that at a place like the University of Washington tenure track faculty members would be expected to secure external grant funding (for example from the NSF) and use this to cover their travel expenses.

Universities often provide startup funds which you can use for this purpose during the first couple of years -- but these don't get renewed when you run out.

In the long run, if you don't succeed in obtaining external funding, it is unlikely that your department would rush in to fill the gap. My department (less prestigious than Washington) provides a little bit of money to faculty members without grant support, but it is only enough to attend to one or maybe two conferences a year.


Should I call professors on their office phone for inquiring about research internship opportunities?

What's an "office phone"?

We used to have these white (sometimes black) boxes with buttons on them many years ago, but the last round of budget cuts took them away. I don't think many people noticed their disappearance.

On a more serious note, you're sounding a bit like a stalker or an annoying salesperson. If the emails aren't being answered (you should send one follow up after the initial one, but no more than two total), take that as a strong NO**. Phoning the professor is only going to annoy them.

** You didn't ask, but reasons for the NO:

I have no internships.
I have internships but they've all been allocated.
I have internships but they're restricted to our undergraduates or to local high school students who are in the internship program.
A quick scan of whatever you sent me makes it clear you're inappropriate (you can't spell, you just graduated high school, you have no background in the field, our internships are restricted to particular categories of enrolled students, etc.).  However, HR told us to never say 'no' in terms of justifications that could open us up to lawsuits, so it's best to just ignore.
Internships are handled through a committee or other open process that if you did some googling you could easily find.  And I really have no use for an intern who can't find things by themselves.

As to why I don't send a 'no': I have five grant proposals, an external tenure review, two journal reviews, and my own research papers to write. Writing a polite no takes more time than a simple 'no' and again opens me / my university up to a lawsuit. Finally, answering what is essentially spam e-mail is my lowest priority.

If you are going to phone anyone, phone the department front office, university HR, or university student services or career services program (assuming you're an enrolled student). Be prepared for a 'no' answer and don't badger.


How to show patents in my google scholar profile?

Your patents published on 13 August and 3 September 2020, respectively. I suspect Google Scholar will automatically add them soon.


Is going straight from undergrad to a PhD program cheaper than doing a Master's degree first?

Edited according to new information OP gave. I'm not a CS major so someone else could provide a better answer.

In my knowledge on the field of CS, I believe that most universities will give you full tuition waiver and living stipend, and you will be expected to work as RA or TA along the way. I do know some of the last year PhDs who taught intro class in undergrad CS as instructors.

  I've been led to believe that it's much easier to get money (assistantships and fellowships) as a PhD student than as a master's student

PhD students are more likely to be under assistantships and fellowships, and most likely it may be required for them to be under assistantships or fellowships. Some excellent Master's student may also get such opportunities. However, if you are referring to opportunity cost, the answer becomes more of personal preference than an absolute answer. If you know that you ultimately want to do PhD, it is financially better to go straight into PhD without having to pay for your tuition for Masters. However, going through masters may provide a better chance for your admission acceptance. You will also be more sure about your research interest; jumping into PhD is a huge investment, so it's wise to explore before committing. There are many CS majors that I know personally who went on to MS before going into PhD.

  And are there other significant factors in determining whether or not it's cheaper to go straight to a PhD program?

I think ultimately you have to check with the graduate programs about their funding. There are many Master's programs in CS that provide partial tuition waiver, and if you become a TA, they may even waive all your tuition in some universities. Look into your universities to see if they have such programs available.

If finance is one of your concern, the advice that I've heard is to work after undergraduate in research institutions or industry. In that way, you can earn some money for yourself, while boosting your resume and giving time for yourself to discover if you like the research topic you were initially interested in. If you end up in an industry job with little research aspect, publishing papers along the way is excellent way to show admission committee that you are interested in academia.


Can you "refer" an offer to another applicant?

Graduate programs don’t operate based on charity or friendship - admittance is based on merit. If you turn down the offer from B, the only rational thing for the administrators of that program to do after you turn them down is move on to the next person on their ranked list of candidates, if they still have room to admit more students, or simply write off your decision as one of the expected number of declinations they were assuming they would receive for this admissions cycle, if they have done the quite normal thing of sending out admission offers for more students than they actually have the capacity to accept.

In other words, all kinds of weird things can happen in some places that are poorly run or where for accidental historical reasons things run differently than in most places. It’s hard to prove a negative. But as a general rule, your friend is wrong and no such referral option exists.


Which format should I use to submit a paper for review?

Submit in the format they ask for, otherwise paper is likely to be rejected without being read. You won't be reviewing the paper, so don't worry about how awful you think it is.

It's all here: tweb.acm.org/author.html including

  Articles must follow the "Small Standard Format" described in the ACM formatting guidelines.


Does an advisor owe his/her student anything? Will an advisor keep a PhD student only out of pity?

Having 4 papers published or submitted during a PhD period is actually quite substantial. Which journal they go to may be secondary, and there are many considerations. For example, at your stage of your career, getting anything accepted and published is more important than trying really hard to get that one paper into Science or Nature -- which entails a far greater risk of rejection and consequent delay, something one might be willing to accept as a well-known researcher in a field for whom one publication more or less makes no difference, but that you can ill afford.

But that's maybe not the question you're asking, so let me address that as well in the form of a story about myself: When I was a graduate student, I had always wanted to work at MIT or Stanford or a similar place, and to make breakthrough discoveries. Indeed, I know this to be true for many of my academic friends. But the longer I've been in academia (I've been a professor for 13 years now), the more I've come to realize two things:

By and large, science progresses not through discrete breakthroughs, but by continuously grinding problems down through the work of hundreds of people until the rare new ideas have been put into forms that can be used widely. Think about gravitational waves: yes, the follow from Einsteins equations and were theoretically well understood not long after, but then it took a hundred years until a whole community of hundreds or thousands of people had made the materials, detectors, and computational tools to actually use gravitational waves observable. All of these people made valuable contributions without which this would not have been possible, even though few of these contributions were published in the highest impact factor journals. What I'm trying to say here is that there is honor and value in doing good science, even if it never rises to the level of breakthroughs.
About breakthroughs to begin with: Of course, every grad student also wants to be the next Einstein. But few of us actually get to be. In fact, if you stay in a community, even if you're really really good, you will come to realize that there are people that are just so much better than you are. So not only do we not get to be the next Einstein, but almost all of us will actually never be at the top of our small sub-disciplines. But that doesn't mean that we're worthless -- there is honor in doing the everyday work moving science along and contributing to the scientific enterprise as a whole. Academia is composed of the high end of the ability scale, which is quite rarefied, and one has to learn to live with the fact that there are always people better than oneself. Take solace in the fact that the proportion of the general population who gets a PhD is already quite small, and you're in that fraction.


How to deal with advisor not allocating time to me?

First, do not assume bad faith and go talk to your advisor. There is an issue which you feel threatens the successful continuation of your PhD, the natural person to talk to about it is your advisor. In this case, it so happens that the problem involves him too, which means you have to be diplomatic about it, but he's still the right person to hash it out with.  Behave professionally, do not accuse him of anything, just state the problem factually (“I need more involvement from you in order to successfully overcome this problem”), and see what he and you can come up with.

Not assuming bad faith at first is good advice in most professional situations. In this particular case, the elements you mention are:

lack of time, which could be completely explained by other factors such as the advisor being swamped (don't get me wrong, it still needs to be fixed somehow, but it doesn't necessarily mean he's being an ass)
rumor (“complaining about me to other faculty”), which might be just that

Now, if after trying in good faith to solve the issue with him (give it a few tries), the situation doesn't improve and it is hurting you and you think he is of bad faith: I listed several possible recourses in this related answer (and another write-up here). But don't jump the gun, because a lot of the options on this list will mean burning a bridge.


Lab tech had research project that is now being developed by honours student: Who deserves to be first author?

There is no general rule on how you determine the order of authors. In some areas (like Mathematics, for example), the order of authors does not imply the relative size of their contributions --- it is typically alphabetical. This strategy has its benefits: for example, we are less likely to include "star" and "virtual" co-authors, because there is no way of distinguishing them from real ones. And of course it simply saves time and helps to maintain good relationships.

In some areas, the contributions of each author are explained at the end of the paper (e.g. "data collection: Dr A, Dr C; statistics: Dr B, Dr C; visualisation of results: Dr A; writing the manuscript: all authors").

If neither of the above helps, the best way to handle author ordering is to discuss it before you start working together. Definitely, by the stage you have your first draft everyone has to agree on this, and no last-minute changes can be done without full and active consensus.


Manuscripts are received, possibly revised (several times), maybe accepted, then online, and finally published (for non online-only venues), venues may show some or all of the dates of those events.


Feeling regret for sending my code to my classmate

You are entirely at your professor's mercy or lack thereof.

As a student, you are responsible for knowing the regulations of the course and the school. This includes plagiarism and academic misconduct charges. You were told to do all work individually. On multiple occasions you violated that principle and knowingly did so because you did not want to lose a friendship. You intentionally made a choice and now you must face the consequences for making that selection which fell afoul of regulations.

The fact that you did all the work individually does not clear you of misconduct because you intentionally aided someone else in violating the academic misconduct regulations. If your friend had stolen your work without your knowledge, that would be an entirely different issue. However, you willingly participated in the process, which makes you just as much of a "cheater" as your "friend."

So, you may try to argue about your lack of culpability but your instructor is within rights to pursue academic misconduct charges against you. Any offer of a "reduced" sanction or punishment is entirely at your instructor's discretion.


What's holidays entitlement for postdocs in the UK?

Maybe you are thinking you need to take a full 24 hours of vacation to get the day off?
Typically you take hours off for your working hours (I'm in the US but I can't really imagine this being different for the UK; also the math works out). So for a job as stated where you have a total of 36.5 hours of working time per week, 219 hours would then be exactly 6 weeks (aka 30 work days) of vacation, which you can take in whatever increments are suitable (say, 4 hours if you need just half the day, 7.5 hours for a full Tuesday, etc). There might be some limits on when this time can actually be taken to not conflict with certain job responsibilities, but given proper notice they should accommodate your requests.
It would be reasonable to clarify exactly how vacation hours are awarded and taken (I'd search on the university website for some regulations before asking someone about it) but the numbers stated seem like they fit with the "30 days" in the job description.


Should I include a recommendation letter in my MS applications if it is not required?

Generally speaking, any material that is not asked for will not be considered in an application for a postgraduate degree. Admissions procedures attempt to create a level playing field for applicants as well as minimise the amount of time it takes to evaluate an application, and extras that aren't asked for are tossed in the bin. Some places may treat that material differently, but you asked for general.

Now speaking specifically, I would be surprised if you were not asked for recommendations during the admissions process. The line you posted does not preclude recommendations, rather it might reveal what elements of a recommendation letter they will pay attention to. You need to either start the admission process online and see what documents you are asked for or call the admissions office for clarification.


Is it plagiarism if I don't mention where I found a quotation originally?

Yes, this might be very close to plagiarism, but without knowing the details this is hard to tell. The litmus test is this: consider you are author A and somebody else does that: what would you feel?

To be on the save side, just give credit to author A for introducing the quotation C in the context of topic B (but not more). There is no harm done in this way.


Business cards for a postdoc: what affiliation?

The cards should list the employee's current place of employment, just like business cards for any other job.  The only thing that should be different for a postdoc is that you should make sure the image file for the cards is easy to update when she gets a new job.


How to begin proper research at undergraduate level?

Although I am not versed in how undergraduate research is viewed in South Africa, I will answer from a U.S. perspective.

Your best bet as an undergraduate is to approach professors who are doing work that interests you. It is okay to not have specific research experience in a field: you have to start someplace, and professors will know this. There may be jobs posted for undergraduate students, or you could ask professors you have taken courses with if they have room in their lab or if they know another professor who is looking for undergraduate help. Tell them what you are able to offer: you want research experience, you are interested in topic X, you can commit Y hours per week, you took a lab course in Z. Be prepared for and not discouraged by rejection, not everyone will have time or space for new undergraduate.

If you are most interested in clinical research, your opportunities may be more limited but the basic approach is the same: approach physician-scientists who do work that interests you.

Sometimes (again, this is in the U.S.) there are credit-based positions available for undergraduates where you will do some work and get credit rather than pay for the time you put in.

In general, as an undergraduate, my opinion is that your experience in a lab should be a hybrid between the work you do for the lab and the knowledge you gain. The work you do might be menial at first: washing dishes, preparing solutions, caring for research animals or cell lines - these tasks take minimal training, so you can be useful immediately. However, you should also be involved in technical conversations, you should be reading new literature in your field (and discussing papers with your colleagues), and over time you should be learning more advanced or specialized techniques.

If you are able to spend more than a year or so in a lab, you should expect to be involved in a real project that could potentially lead to a publication, though it will probably not be your own project - that's okay, you will still be learning skills that apply to your future research endeavors (or, alternatively get you enough experience to learn that you don't enjoy a particular approach).


How can I accredit my Russian kandidat nauk in biology to PhD in USA?

The US does not have a centralized system in this regard.  Each organization decides for itself how to consider your degree.  Anyone with international awareness who hires PhDs regularly should know that your degree is equivalent, but everyone makes their own judgement; there is no centralized body.


For the following, I will assume that you were on a F1 visa from arriving in the US until after your 26th birthday. In that case, you should have been exempt from selective service. If you had any kind of change in immigration status from a non-immigrant visa (such as having the F1 visa expire) during this time, well, that could complicate things and you really should talk to your university about it.

The Selective Service System's page for Men - 26 and older suggests that you can get a status information letter to prove that you're exempt. You could ask your university's financial aid office if it's required in your case or not.

Reading more on the Status Information Letter page, I found the following (which suggests it isn't required):

  Financial aid officers:
  If the man falls within one of the following categories, a status information letter from Selective Service is NOT required if he can provide a copy of supporting documentation proving his case to your satisfaction. <...>

  Non-U.S. male on a valid non-immigrant visa

  For example, if the man entered the United States as an F-1 student visa and remained in that status until his 26th birthday, he would need to provide documentation indicating that he was admitted on an F-1 visa and attended school full-time as required.


How feasible is a remote postdoc in Mathematics?

I’ll only address the US in this answer. Some of this may not be applicable to other countries.
The large majority of US pure math postdocs are mixed teaching and research positions, typically with a three year term. Even though teaching is happening remotely at many schools nowadays, you are asking how departments view the idea of a remote postdoc; well, from a practical point of view, if one is making decisions three years into the future, one cannot assume that teaching is going to continue to be done remotely that far ahead. So, my guess is that you getting such a position as a remote-only postdoc is a non-starter.
That leaves the fairly small number of postdocs that don’t have a teaching component. These come in two flavors. The first is grant-funded and controlled by a specific researcher or research group. These seem to me to be vanishingly rare in pure math these days, but if you are lucky enough to be doing research precisely in an area someone with funding for a postdoc is interested in, you may have a chance. At the very least, it seems more plausible for an individual researcher to be receptive to your suggestion than for a department, committee, fellowship, or other institutional sort of entity.
The other type of positions without teaching are prestigious research postdocs funded by well-known fellowships such as the Miller and Clay. There are only a handful of such fellowships and they are ultra-competitive and extremely difficult to get for anyone, let alone someone who insists on doing a remote postdoc; so getting one of them cannot be thought of as a reliable career plan. But if you’re good enough to be considered seriously for one of those, I can imagine at least a theoretical chance that they might allow you to do the postdoc remotely. You’ll have to check.
The bottom line is that the job market for math postdocs in the US is unfortunately not very friendly towards people in a situation like yours who have geographical location constraints. In any case, good luck!


How to write a graduate study personal statement for a technical field without related bachelors degree?

I was recently accepted to a MS program that is different from my undergrad and graduate training.  In my personal statement I tried to relate my experience to the field I was pursuing.  I had field research experience in public health, but I was applying for a MS in biology.  I still used my research experience, but I focused on the general research skills that I developed, things that would be useful in the lab.  I mentioned things that are universal to all research.

I think if you convey passion and direction for the new field, you'll be alright.  It can be an advantage too.  Think of ways you can incorporate your previous field if possible.  If not, show them your maturity and passion.  It seems like admissions committees can tell who is going through the motions and who is genuine.  Make your voice heard.


Are there any known Universities that refuse to pay for paywall access to academic journals?

No University has enough funding to spend on subscription fees for all existing paywalled research articles (e.g., Harvard University says it can't afford journal publishers' prices). As a result, some of their faculty and student resort to free alternatives SciHub/LibGen/emailing colleagues/etc.

Many universities located in developing countries cannot afford paying for paywalls.

If you need a particular University name, here are some:

University of Sierra Leone:

  When he needs new books to teach one of his courses, Professor Ibrahim Abdullah orders at least two from abroad: one for himself, one to give to the university library. If he needs scholarly articles, he writes to his friends overseas and asks them to send copies, since the university cannot afford journal subscriptions.

All public universities, research institutes and state agencies in Peru (translated by Google):

  Bad news for research and technological innovation come from Peru. The
  National Council for Science, Technology and Technological Innovation
  (Concytec), a government agency, will no longer offer free access to
  the ScienceDirect and Scorpus databases by the end of the year. The
  lack of funding from the central government has been the cause of the
  closure of these platforms for Peruvians.

  Access had been enabled for public universities, research institutes
  and state agencies. ScienceDirect (Freedom Collection) gathers more
  than 1,800 titles in full text scientific journals in 24 thematic
  areas and Scopus meets "relevant sources for basic research, applied
  research and technological innovation and is a tool for bibliometric
  studies" according to the portal Concytec .

  Access was open since 2014 and during that time 3.7 million full-text
  documents were downloaded. The downloads, according to Concytec, would
  have cost US $ 131 million if they had been isolated. While
  subscribing to these services for three years cost the agency only US
  $ 10 million.

A few other places:

Dutch universities start their Elsevier boycott plan
Germany-wide consortium of research libraries announce boycott of Elsevier journals over open access
Taiwan Tech to Discontinue Subscription to Elsevier ScienceDirect Starting 2017

Some interesting maps showing the location of Sci-Hub users (at least the location of the machine that makes the final request):


Invited to interview for several postdoc positions - how to proceed?

No matter what you do, or how carefully you apply, a better job can always come up later.

The decision you have to make is not "is this my perfect job?", because unless there's a specific single position that you have your eye on, there's no such thing; it's "is this position good enough that I'd take it if offered?". If it is, then do the interview, and if it goes well (in both directions), choose between the offers that you have available to you at that time.


Reference-style in the cover letter for resubmission of a manuscript

In my opinion, what you really need to worry about here is clarity.  Cover letters do not generally have a prescribed style, so you can probably pick whatever style is most clear in place---that will not be a number pointing to a different section or document.

Personally, I'd probably not do any formal citation at all, but instead just reference the work in prose, e.g.,

  I developed and strengthened my criticism of XYZ's 2010 paper in the following way..."


Is it right to use 'X is a new research topic of interest to our lab' to indicate that the lab has not done research on 'X'?

I have angst about writing this answer. When you say our lab, it potentially sounds like you are speaking for the lab in an official context and taking an ownership stake in the lab. Depending on your role, I am not sure you can talk about the lab as being yours. I am also not sure you cannot, and hence the angst.

As a PI of a lab, I have research interests that the lab has never followed through on due to a variety of reasons including a lack of funding and expertise. I would be a little upset if a student/post doc implied the lab was not interested in a topic just because the lab didn't have the expertise or equipment to do any research on the topic. Similarly, I would be a little upset if a student post doc implied that their personal interest automatically becomes an interest of the lab.


Legality of downloading books from websites such as Library Genesis

The legality of possession of pirated content varies across countries. In many countries, it is perfectly legal to have copies of copyrighted content as long as you don't share it with others. In the US, downloading such content is illegal, but you are unlikely to get into trouble by having illegally copied content on your hard drive. I found a great answer on Quora by an attorney, parts of which I'm going to quote:

  Yes, it is illegal to download ("make copies") of material that is protected by copyright.  However, all that is illegal is not criminal.  Copyright for the most part is a civil statute, with civil remedies (i.e. the copyright holder sues you for money).

  Criminal copyright infringement is much more limited than civil copyright infringement.  The criminal portion of the Copyright Act (17 USC § 506) states that it is a criminal act to willfully infringe copyright 1) for the purposes of commercial advantage or private gain; 2) by reproducing or distributing within 180 days one or more copies of works with a retail value of more than $1,000; or 3) by distributing a work being prepared for commercial distribution (i.e. a work that has not yet been released for sale to the public by a copyright holder, but that will be made available or a movie that is currently playing in a theater).

It would be very difficult to classify what you describe as criminal. As long as you only download (and not share) publications for your private use, you are unlikely to have issues.

  For the average person, generally there won't be any criminal consequences under copyright law from having pirated items on your computer.  That isn't to say that a creative prosecutor couldn't make a case (particularly if you have file sharing software installed, in which case you could possibly be looking at a violation of the second prong of the statute).  But in the real world, this is not the type of crime that most police go snooping for when they decide to rummage through your laptop.

There are some cases where students are getting into trouble by using school equipment or connection to pirate content (mostly audio and video), so it is probably a good idea to keep this business on your private computer. You can further decrease the chances of any legal trouble by using TOR, VPN and keeping the pirated content in an encrypted container with a strong password.

tl;dr: It's illegal. As long as you don't get caught downloading the files, you are unlikely to get in trouble. It's more about your own views on the ethics of scientific publishing and copyright.


What factors determine application fees?

Application fees are primarily there to moderate the number of applications and in the case of universities receiving huge numbers of applications partially finance the application process. There is of course many services for which one can argue to cover costs. This includes personnel to handle applications, personnel to evaluate applications, costs for paper handling (at least earlier including postage if anything had to be handled through regular mail). When looking at the costs for taking in the money and possibly distributing it within a system that likely involve many persons it becomes clear that a well defined cost analysis is not likely done, it is not cost effective. Instead the pricing can be used to signal, for example, prestige and to ward off chance applications. The level of the  pricing will likely be determined by these factors but also include considerations to what levels will be reasonable for the uptake of students visavi ethical and social goals for the university. In short, the pricing is more of a tool "for" recruitment than a precise estimate for the costs involved in the application process.


High impact journals - Do they always guarantee high quality papers?

No they do not.

That is the short answer. But that is mostly due to the fact that nothing is guaranteed in this world. High impact factor journals are most likely to have a high percentage of high quality articles since rejection rates are high and the editors have the possibility to choose from a large pool of submissions what they deem worthy. In consequence, the editor's opinion about the quality of an article is of significance.

After the editor's decision, reviewers are still able to reject articles. In some journals rejection rates are still as high as 40% after the first review.

You should keep in mind that a high quality, Nobel prize level publication can be published in any journal in its field, but a low quality article might only be published in a low impact journal or be rejected altogether.

TL;DR: On average, high impact journals should have a high density of good publications.

A last note on your last bullet point: A large number of citations certainly shows that an article is significant in its field. A low number of citations could either mean that the article is insignificant or that nobody noticed its significance yet. In the end, that is why you publish in high impact factor journals: You want to get noticed.


Is it acceptable for a referee to suggest changing "theorem" into "proposition"?

I think we should begin by acknowledging that it is the author's choice whether to label results Theorem, Lemma, Proposition, Remark, etc., so a referee should not insist on changing this as they should insist on the correction of an actual error or gap.

  Suppose that one is refereeing a paper where the authors have decided to call almost all their results "theorems", making a paper with a large number of "theorems" that even emeritus professors don't usually reach by the end of their career.

Don't say that to the author, by the way.  It's snarky and not really helpful -- you seem to suggest that the author is somehow cheating their way to "too many theorems."  That's not a thing.

Referees can make stylistic suggestions, of course.  How much they should do this is quite a judgment call. I think a good referee should make stylistic suggestions when these suggestions impact the readability of the paper or affect its appraisal by readers.  Will it look a bit weird to many readers to have multiple theorems on every page?  Yes, I think so, and perhaps the author deserves to know.  However, if by having "too many theorems" the author makes it hard for the reader to see what are the important results of the paper -- and, as a statement about human cognition rather than mathematical achievement, a paper simply cannot have, say, 50 important results -- then that's a much bigger deal.

If I were you, I would lead with the latter: explain that you had trouble isolating the important results of the paper because so many results are being presented in the same way, then suggest that changing some theorems to propositions or lemmas might be helpful in alleviating this.  (Then, if you like, say that having fewer results called theorems might make a better impression on the reader.)  I think this is putting things in the right order and does the best possible job at getting your concerns addressed.

But it is possible to address the main concern -- that the important results not get drowned out -- while still calling every result a "Theorem."  If the author pulls that off...okay.  Up to them, really.


Should the website contain information which is discouraged to have in the CV?

In moderation, I don't see anything wrong with including content on your website that you would not include on a CV.  In principle it could hurt your career if you post something ridiculous or objectionable, but information about chess, ordinary volunteer activities, children, etc. doesn't seem problematic.  The main issue is making sure it doesn't overshadow the academic content: if you provide more details about your chess activities than about research, then it may give the impression that you are devoting more time and attention to chess than to research.  (Even if that's not the case.  For example, a grad student who is just starting with research but has a lengthy chess history might give the wrong impression, regardless of current priorities.)  If you want to cover non-academic activities in substantial detail, then it may be safer to set up a personal website that is clearly separated from your academic site.


Will I be regarded as academic dishonest if I submit one paper to a conference as well as a journal?

The issue of duplicate publication concerning conference and journal versions of similar papers is a difficult one. What is acceptable to do and what not depends highly on the field and maybe even individual venues. Of course it also depends on the degree of overlap between the two papers.

Whenever you plan to reuse some content in another publication, be sure to make the duplicate publication transparent by stating the other paper in the cover letter, and citing it from within the paper. In general, it will be required that the later paper goes beyond the results of the first paper, and it is important to point out how it does that both in the cover letter and the paper itself.

In your case, from the conference's side it's probably fine since you informed the reviewers about the duplicate publication and they obviously had no objections. However, since the journal paper was not yet accepted, you should have at least checked their guidelines on duplicate publication, or better verify with your handling editor that it is fine to submit a shortened conference version. Maybe you can still do that now, and offer the journal editor to withdraw your conference paper if the duplicate publication in that case is against their guidelines.


What to do when you are a finalist for a tenure-track position but you want to wait until you complete interviews at other schools?

After serving and chairing search committees, I agree with Brian that gamesmanship is often central to the faculty search process. The other candidates for School A may have finished interviewing (assuming that you are correct - how do you know the other candidates' schedules?) but now School A has to make the offer to the candidate they like best AND will say yes. So, they are putting pressure on you.

Personally, I feel like the response can be simple. Your question implies that the chair is telling you that you're probably going to get an offer, but do not have one in hand. So, you can tell the chair, "I would be willing to cancel other interviews for an offer IF it's the right offer. If you draft an offer, I will look at it and decide if I can accept it without pursuing other opportunities." This is VERY important, because you legally do not have an offer until they send you one in black and white. Once you have an offer, if you are satisfied with it and like the department, then it may be easy to make the decision.

In my first academic position, I was told that an offer would be sent to me and there was an administrative hold up...for two weeks or more (this was several years ago). I called the chair and told him that I was going to go to other interviews before I have their offer in hand. GOOD LUCK!


Before submitting a paper, should I remove acknowledgement for the sake of anonymity?

I would remove the acknowledgement. It's better to be on the safe side when you are submitting and do not disclose the data that could be used for author identification. You could always add that part back after review process is over.

If I recall correctly, I have once used a publisher-supplied Latex template that automatically generated pdf file with authors' names and acknowledgement section removed for the sake of anonymity, so the practice of not giving out that kind of information in review copies seems to exist. (EDIT: I remembered well. ACM's sigconf template can be configured for anonymity - in that case acknowledgement section is removed from output pdf file, while in non-anonymous mode this information is retained in the output).


Conference presentation as an advertisement for a paper

Actually, all three of those points apply and in fact what is recommended for a conference presentation.

Additional suggestions would be the following.

In case of an original research, focus on the overview of algorithms/procedures and its nuances with respect to the existing ones (if any) or the novelty involved without jumping right down to the algorithmic details.
For a survey paper, note only the highlights of the survey and studies that provide the most impact to the field in each sub-topic. Avoid jumping to rabbit holes and missing out the opportunity to cover the big picture.
Spend a bit more time on how your findings impact your area of research. Discuss the applications and scope and detail the conclusion. I see may participants miss this one out by just elaborating on the technical aspects of their implementation without conveying what is it applied for and how could it be applied.


Invitation for campus visit for post doc position - salary negotiatons?

It is certainly fine to ask for clarification of what you were told about the salary and other financial details.  Keep in mind that nothing is certain until you have an offer in writing.

See How to handle salary negotiations while negotiating a postdoc position? regarding negotiation of postdoc salaries.  My guess is that the salary would be negotiable only within a narrow band, if at all.  If you get offered the tenure-track job, you shouldn't expect the postdoc employer to try to match it.

The main reason to choose the postdoc over the tenure-track job is if you think that the additional years of full-time research will help you get a better job afterwards, or improve your research success over the long run, and if you think this will compensate you for a couple years of a lower salary.  It very well might.

Keep in mind that a position that "focuses on teaching" will likely have teaching loads that leave you very little time or energy for research, and may also not give you much funding for that research.  I think people who take teaching-oriented positions very often overestimate the amount of research they will actually be able to get done.


Why did you not explain your circumstances? I understand that you want to avoid the topic and do not want to justify your bad grades with something personal. But in your case, especially considering depression, I think that mentioning the reason for your low grades should rather help than damage your case. The key is to be honest, reflect on your past and give them a reason to let you in, e.g. you have overcome your depression and want to start over in your masters.

I don't think work experience matters much to be honest. Engineering in german universities is rather on the theoretical side as far as I can tell.


How can I find out if a student’s thesis is just the translation from his native language (Spanish) to English?

Your question suggests that you are not sure which of the following is true:

Your student worked hard and produced an excellent thesis
Your student plagiarised a thesis from another language

In either case, this warrants extra attention from you.

The first step would be to discuss the work with him further. If he was able to discuss said work intelligently, this would be an indication that he did write the thesis. However, you said that you spoke to him, and he seemed confused about what he was doing, which raises legitimate suspicions.

To find out whether he can (and has) produced good written work, but finds it hard to discuss said work in person, you can ask him to edit his written work. Unless the thesis is 100% perfect in every way, you can identify a potential area of improvement that should not place an undue burden on the student. For example, you can ask him/her to

add some extra detail to one section
compare to another related work in the literature review section
etc.

If the student did the work and independently produced a great thesis, this is positive attention that will help improve the work. If the student did not do the work, it will become evident when he tries to improve it following your suggestions.

Of course, if you know someone who speaks the student's language and who can be counted on to keep your request quiet, you can (without sharing the student's name) ask him/her to search the web in the student's language for publicly available theses on the subject, and see if a match turns up.


When to retract a submission due to excessive length of peer-review process

There can be multiple reasons for lengthy review process.
1) Your work is very novel and its hard to find a reviewer.
2) You submitted your article to a journal who's scope is not fully relevant to your research area. According to my experience this is one of the major reason.
3) The ignorance of handling editor.
 First make your own assessment if your work is very novel or if you have submitted to a journal who's scope is not fully relevant to your research area in both cases you may expect a much longer review process.
if its not the case 1) and 2), then Check the average time of first decision for recently published article, and contact handling editor after passage of average expected time. If Editor don't reply for another extra 25%~30%  of average time, then write a withdraw letter and mention the unexpected delay as a reason for withdrawal to EiC.


(Maths/Engineering Copy Editor speaking.) Well, first, I advocate against these two solutions (see below for some reasoning):

Number all displayed equations.
Number only referenced equations.

So, the solution lies somewhere in between. The basic idea is that you do number:

All referenced equations (obviously).
All important equations. To measure this, I would say that an equation is important if the reason why you made it a displayed equation is to emphasize it.
Unreferenced equations "parallel" to a referenced ones. Imagine you have two similar equations in similar contexts in your work; then you should either number both or none.
Equations you "feel" (whatever it means) someone else might want to reference.

What you in general do not number:

Equations put on display for that they are too large.
Intermediate steps of computations.
Equations in abstracts.
You number a multiline equation only with one number.

Hope this helps. Almost-final words: Use your common sense. Final words: Be self-consistent.

Why I don't like all displays numbered:

It clutters the page if there are many equations. You also might number things that are basically one equation (think LaTeX's \intertext).
The numbering ceases to function as an emphasis.
If the equations are long or the columns narrow, it can eat up precious space.

Why I don't like only referenced equations numbered:

You don't allow anything else referenced than what you yourself decided to reference.


Does a PhD student need to focus more on working in theory, in order to have a real chance of becoming a professor?

I agree with Buffy's answer, but also want to expand on what knzhou alludes to in a comment: STEM has many sub-fields, some of which are more theoretical or applied than others. As it turns out, the walls separating these different fields are far from impermeable. Perhaps your friend's PhD really is too applied for his current department, making a tenure case difficult in that field? Perhaps their research would be a more natural fit for another department, or a national laboratory? For example, there are plenty of people with physics PhDs that have ended up as tenured professors in various engineering departments.

Now, if the research best fits departments with the current name, then your friend might just have to go down the status ladder a little bit to have a realistic chance of tenure. For example, an expert in a field-specific numerical method can be seen as too much of a one-trick pony for the absolute top institutions.

The bottom line is this: if your friend enjoys their research there are a lot of possibilities to explore before giving up on it completely. They really should talk to their mentor(s) to get personal career advice.


How to approach my supervisor when I've finished the task he assigned early?

Just talk to your advisor when you feel you need his input.

All of the busy people I know (myself included) want the people they work with to let them know if things are ahead of schedule. When I supervise a student, someone has to be moving things along. If the student takes responsibility for that, and can be counted on to come to me when he/she needs my input, it's much less work for me than the students I have to monitor more actively.

Having said that, there are several things that can also help:

Ask your supervisor to discuss the "big picture" with you. This way you'll understand what these small tasks are getting at and can make a reasonable guess as to what the next task will be. This will help with your problem and will also help you develop your skills as an independent researcher (which is what you're training for, after all).
Develop your own research interests (either side projects, or related to the work you're doing with your advisor) and work on those when you're "blocked" waiting for your advisor. This, too, will also help you develop your skills as an independent researcher.


Who should recommend applicants for administrative positions?

The key when soliciting recommendation letters is to find persons who can provide insights into your credentials applicable for the job you are looking for. From this perspective the view you shared that letters "should be written by academics in the same field who knows the applicant's works" is only a special case.

When applying for a high level administrative job you need to find people at as high a level as possible. These should know your background, experience etc. but also be aware of the demands of the job for which you apply (this can be seen either in general or specific terms). There is thus no limit to whom you ask for letters but they will definitely not be as limited as for a regular academic position. Clearly anyone who has seen your capability to lead and administrate, for example, large projects, a department or research group will be appropriate. I can also add that you will most likely mostly look for letters from people in positions at similar or higher level than you (within academia, not necessarily so if you ask for letters from other professionals). But, the key is still to solicit support for the key aspects of the job to which you apply.


Publishing a paper that cites my previous work

If I take your question literally, then this would be my answer:

I citation serves two purposes:

You avoid that you take credit for work by others, and thus avoid plagiarism. This point also applies to your own work published somewhere else.
It can act like an "external appendix" (e.g. the interested reader can read the proof in...).

So, if you make a statement in your current article that relies on findings in your previous articles, then you should cite yourself. If your previous articles contain information you would otherwise have put in an (web)appendix, then you can cite yourself. Otherwise, you should not cite yourself.

However, I suspect you want to know how far back you should go when writing the section "previous research". Here the answer is it depends on what is considered normal in your (sub-)discipline. At the very least I would look at that section from the perspective of a reader: Can they understand how you want to place your article within the research that has been done in this area? Discussing the creation of the computer is typically not necessary to achieve that goal...


Is it necessary to publish a research paper while pursuing MS?

The first question depends on your university's requirements. I think that it is sometimes required, but not universal.

The second question might also depend on what sort of job you are interested in. Most jobs for MS graduates aren't especially research oriented, so, while it would be a plus, it might not be essential.

But if your future is in academia, it is good to get started on research as soon as you can.

I you have an advisor, consult him/her for advice on what you want to do in your future.


What is the best way of breaking a mathematical development into a sequence of articles?

Each journal article should "tell a story". Break the thesis up into coherent stories.

It looks like you're already doing that. The first article concentrates on generalizing the classical theorem, and the second gives the results that are relevant to current research.

I would suggest just putting the groundwork you need for the generalization of the classical theorem into the first article (unless you can save a lot of space by developing some of the groundwork for the second article at the same time as the groundwork for the first). And you should definitely mention the second article to provide more motivation for the groundwork. But putting groundwork that's not needed in this first article will detract from the "story".

In the second article, you should include a quick review of the groundwork developed in the first article, and refer the reader to the first article if they want more details. Then add the extra groundwork needed for the second article, and  proceed to the results of the second article.

One comment from experience: if you put a result that does not fit the "story" into a paper, when people read your paper, they are very likely not to even notice this result. So it's much better to put it in a separate paper.

On the other hand, as you can tell from the comments here, many people consider it bad form to spread one story over two papers. So you should split a long result into several papers only if you can formulate it as several related "stories".


What does it mean to write a "glowing" letter of recommendation?

A "glowing" letter is one that praises the candidate in the highest terms on several criteria: "One of the three best .... I've ever worked with...". The letter will detail both past performance and make positive predictions about the future.

However, it is possible for such a letter to overdo the praise and then be discounted by the reader as shallow.

What you want a letter on your behalf to say is that you are knowledgeable and that you work hard and that you have a lot of ideas and potential. A glowing letter will reinforce those ideas with examples and/or comparisons. In some fields, positive statements about teamwork can also be important. In others, being seen as self-directed is more important.

But it also needs to be realistic. "Candidate calms hurricanes and has the compassion of a saint" is probably too much to believe.


Should I name a system or software I described in a paper?

Should I also use a name for my system?
What are the advantage or disadvantage of it?

In the following, I will assume the author name "Mary Miller" and the system name "MSOAP" ("Miller's solution of all problems"), as well as the additional author name "Oswald Otherman" for the sake of explanation.
Advantages:

It will be easier for other authors to refer to your work. Rather than a convoluted expression such as "the system proposed by Miller", they can simply write "MSOAP".
Work by other authors that directly extends the original system can continue using the same name. Rather than "Otherman's extension of the system proposed by Miller", it is "Otherman's MSOAP variant", or (if the overall system structure remains the same) even still "MSOAP" (just with the reference to Otherman's work rather than Miller's, if it's the aspects introduced by Otherman that are actually talked about).
If the system was not created by one sole author (even if the scientific contribution focused in the first paper that mentions the system is by Miller), it is even much fairer to refer to the system with a name rather than linking it to a single author.
The system name is more specific for a certain work than the author's name. Even if the system might be expanded in several iterations, it is still probably centered around one core topic or approach. Hence, searching for "MSOAP" will always yield results related to the desired topic. At the same time, Mary Miller might create several different systems throughout her career that focus on wildly different things, so the same cannot be said about searching for "Mary Miller".

Disadvantages:

The name of the system's creator is not quite as apparent any more, as it does not directly pop up in each sentence referring to the system. However, the author name is by no means concealed; the system name "MSOAP" still provides a very good starting point for finding more information about the project (including attribution), and the reference to thus-related papers in the bibliography contains the author information, as well. Therefore, whoever wants to know who contributed to MSOAP will face no real obstacles finding out.

Neutral:

Finding unique system names is increasingly difficult. "MSOAP" might refer to a number of unrelated projects. On the other hand, the same can be said about an author's name, as "Miller" is not in any way less ambiguous.
Another issue with a self-chosen system name, as suggested by jakebeal, could be that you pick a name that you do not like any more at a later point in time. On the other hand, you might also dislike your personal name. If you do not pick a name for your system, there is even a slight chance that people citing your work end up associating it with a name that you do not like. Your mileage may vary on which one of these is least desirable or most likely.

Therefore, my conclusion is: By all means, do whoever wants to refer to your work a favour and provide a name for your system.

Are there any conventions or guidelines for it or for the names?

No, and there are various factors that influence why there is no general answer to this question:

First of all, this is very field-specific. Some communities might enjoy reading fancy names that contain some kind of slight jokes or at least convey something in a witty acronym (like this one: Schürr, A.: PROGRES, A Visual Language and Environment
for PROgramming with Graph REwriting Systems. Technical Report, RWTH Aachen, Germany, 1994.), whereas others might have a strong preference towards more descriptive names.
For systems developed as a part of a larger project, it can be a nice touch to pick a uniform naming scheme. (As a fictional example, there could be "MSOAP", "MSOAP-W" for weather-related solutions, "MSOAP-L" for literature-related solutions, and so on.)
Maybe you even want to develop a certain recognizeable style as an author and therefore try to establish a uniform method of naming your systems over the years.

As a clarification, system names need by no means always be acronyms. A system name such as "Ultimate Solution" is totally fine. Just provide something that can be used as a (composite) noun.


How do pass/fail classes look to PhD admissions committees?

In short, this looks bad.

When I see a "Pass" or "S" grade on a transcript that I'm evaluating, my default assumption is that the student did work equivalent to the lowest passing letter grade (e.g. a "D" in the US system.)

I tell the undergraduate students that I advise that if they want to go on to graduate school they should avoid taking courses on the S/U grading scale.


How long do I study on my own before applying to math grad school?

I disagree that this is the right approach. Many grad schools in the US would require you to have a Bachelor's degree in some subject and to make up the courses you missed by not having a Bachelor's degree in math. So your best option is to get started actually completing those courses. I think that unless you have some publications in math with someone who can vouch for your skills even though you don't have the coursework, you're not going to get into a good Master's degree program without the necessary coursework. The further your history is from the required classes, the more work you're going to need to do. Some programs might admit you with the requirement that you take a few semesters of undergrad classes to catch up, but if you need more than a few catch-up courses, you're really looking at a second Bachelor's degree or working on the side through a non-degree-seeking program at your local university.


What is the legal status of an open access academic publication?

Qualifying a paper as open-access only indicates that the paper can be legally accessed free of charge by anyone. It does not make any further implication regarding its license. E.g., some license will allow the use of images in a commercial context, some will not. More details: Gratis versus libre.


Do publications outside your primary field of study help or hinder your early career?

If you have 5 publications in 5 different areas, I would be concerned that you might become the eternal prodigy or that you are not willing to perform some long term research. However, if you have a clear focus and can document that you are working continuously on one project, then activities outside your core area indicate that you are able to work together with very different people. So you won't be hired because you have many publications, if there is no area where you are really convincing. But among applicants, which are similar in the area the position is aiming at, other activities become a significant advantage.


No. I think that procrastination is a lifetime problem. I'm doing it right now, and while not a professor, I'm a senior researcher at a university.
Yes. Everyone procrastinates.

I suppose that some people manage to never procrastinate, but my brain doesn't work that way. Don't worry, it's normal.


How to get a mentor or supervisor for PhD studies in Computer Science?

Apply to PhD programs in your area of interest.
Visit the schools that accept you into their programs.
During your visits, talk to professors about (a) whether they're taking students and (b) whether you share mutual interests.

You can also try emailing professors before you apply, to get a sense of whether their school/department/research group is a good fit.  But be warned that many will ignore your email unless you've already been admitted to their program.  (Expert tip: pay close attention to the warnings and admonitions posted on their personal home page!)

A much better way to make first contact is to attend conferences or workshops in your area of interest (and make a paper/poster presentation, if possible).  These events let you meet many potential advisors all in one place.  Plus, you get to hear about their work, and get a sense of their personality, hygiene, etc.

  I feel afraid of not having enough background.

You and me both, pal.  It's called impostor syndrome, and everyone* in academia has it.

Good luck!

*…except for the real jerk-Os.


How to contact professors for a Ph.D position in France, when I don't have a research question?

Professors (and possibly alumni) at your university in the Netherlands probably have contact information for collegues around the world. If not, they could help you find someone who does.

Otherwise, the GIFAS (the national association of aerospace industries)  has published a catalog of École Doctorales and a website which has a section about training.


Inline citation within my inline citation (MLA)

According to the MLA style detailed here you can use the following for inline citing as per the example you gave.

  Citing indirect sources

  Sometimes you may have to use an indirect source. An indirect source is a source cited in another source. For such indirect quotations, use "qtd. in" to indicate the source you actually consulted. For example:
  Ravitch argues that high schools are pressured to act as "social service centers, and they don't do that well" (qtd. in Weisman 259).

  Note that, in most cases, a responsible researcher will attempt to find the original source, rather than citing an indirect source.

So from the information you gave, your cite would be (qtd. in My Source Author pagenumber)

It may also be of benefit to enquire if your department have a style-sheet that would give guidance on referencing.


Elsevier Journal waiting time after review process

I have no idea about  PHYSICA A (I am from another field).
You may try to write to Elsvier Support: https://service.elsevier.com/app/contact/supporthub/publishing/
Maybe they can somehow push the things.


What resources do you use when developing a new course from scratch?

I'd go back and consult one of those "How to teach" books you've probably got lying around and focus on doing a good job of stating the course's Learning Objectives. Then, I'd make sure that the course material, the learning activities and assessment tasks are properly aligned with those objectives.

I would then make sure the students get to see those objectives and to understand how what they will be doing fits with those objectives.

I would design some sample assessment activities, such as sample exam questions (if that is one of your planned means of assessment). Then I would make sure that the content of your course is sufficient to enable students to do such assignments or answer such questions.

Mckeachie's Teaching Tips is an excellent resource for helping you do this. And it never hurts to refresh your didactic skills.


PhD in theoretical physics: good or bad for engineering jobs?

I would say that strongly depends on what you do in the HEP PhD.

If it is more like pen and paper theory I would say this is not very interesting for industry. Perhaps even in the contrary as you might seem too "academic". Pen and paper theory jobs do not really exist in industry.

It is more the big data processing and computer simulation related skills what is relevant. The tools (python and methods) you use in your MPhys research sounds exactly what some companies are also using internally.

Industry considers hiring people from adjacent fields, when demand is much higher than the supply for certain jobs. Currently I see that this is the case for "data scientists". So I would say now your chances are good to find a job there as many companies are now exploring big data applications. They are scared by the success of Google, Facebook, etc.. and do not want them to take over an important part of their business. So many are investing here. Industry also has these jobs so it is not just finance. It is very diverse. One gains some feeling for it when one looks at current job offers (which is what I did, so I have no deeper experience than that). However, you have to keep in mind that the situation may be different is in a few years when you might have to give up your academic career (hopefully not).

A PhD is liked for certain types of jobs even in industry. As the PhD is teaching more a generic mindset (-> how to work scientifically,/thoroughly, know how to tackle big, unsolved problems) this is considered useful in some industrial jobs. Appropriate job descriptions would perhaps have names with "scientist" in it, like "data scientist", "research scientist" and so, not so much the "engineer" type of jobs. Sometimes PhDs are also found in sales/marketing, when a product needs deep explanation, training (and the customers are themselves PhDs) or must be customized to the users needs (and this is not straightforward).

Note: Even though I have worked in the US, I a most familiar with the German system. Nevertheless I hope the answer helps somehow.


Does the admission committee for graduate studies look down on foundation courses

In general, if the GPA is high, this shouldn't be too much of a big deal. Normally I would look upon such a class as equivalent to an introductory-level course, and would not "look down" upon such a course. If the grade in such a course is poor, however, that could affect the decision.

If you are concerned about reviewers at another school evaluating this course appropriately, you could always include a note about it somewhere as part of your application (either master's or PhD).


Group-work course, part of the group failing

I assume you're asking about a situation where different members of a group are given different amounts of credit for a report that they all worked on. (For a different assumption, see the next paragraph.) The only way I can see this happening is if the professor has, in addition to the report itself, some information about the individual students' contributions to the report, information that forms the basis of the variation in the grades. In such a case , the students who pass are not doing so on the basis of the work done by the failing students but rather on the basis of what the professor knows about their individual work.

Another possible (though less likely) interpretation of the question is that all the students in the group got the same grade on this report but their other work (other assignments, exams, class participation) were different, so that some passed the course and others failed. In this case the ones who passed didn't benefit any more from the failing students' work than the failing students benefited from the passing students' work. The difference would be only that this work was, for some but not all students, enough to bring their overall grade for the course up to the passing level.

(Contrary to what you might infer from this answer, I'm not a fan of group work, except insofar as it makes grading easier. But my concern about its fairness is not the concern raised in this question.)


What is the advantage of the two-column journal format?

There's a widespread belief that shorter lines (fewer characters per line) are  easier to read, because the eye doesn't have to move as far horizontally from the end of one line back to the start of the next.  The left edge of the text (assuming left-to-right languages) may already be in your peripheral vision.  Thus it's easier to visually find the correct line to read next, and avoid accidentally rereading the same line or skipping lines.

This is the justification for the extremely wide margins that LaTeX uses by default in one-column styles, for instance.

I don't know offhand if there is research supporting this belief, but maybe someone can fill me in if they know.

Two columns makes it easier to have short lines, without resorting to small paper size, large font sizes, or huge margins.  Thus you still get a high density of text per page, and it keeps page counts down (and the associated costs).


On how/if I should ask my supervisor about lead authorship?

Yes, it is appropriate to ask, but it may not be best to demand. But personalities can get in the way of ethics, as many posts here show. "I worked pretty hard on this and having first authorship would give me a big career boost." That could work. Much better than simply demanding it as a right, even when it might be considered so.

But, having some publication, no matter where you appear, is better than none. And don't think of this as do or die. There will be other papers and your professor's good opinion of you is worth more than first authorship on an early paper.

But yes, it is appropriate to ask. It won't be rude unless you make it rude.

Ideally these things are worked out before the research begins, but it often isn't. And the  power imbalance between professor and student gets in the way as does ego.


Can you be working remotely on your PhD thesis of another country and then enroll and get a master/PhD in US at the same time?

To my knowledge, there aren't any laws prohibiting anyone from joining a graduate program for any reason. It might be a problem if there is a conflict in grant funding or with the confidentiality needs of a particular research program, but otherwise it should be fine. He should Just make sure he fulfill any obligations in the programs.

It would probably be best, just to avoid later questions, for your friend to be open with the new program about his relationship with the old one. But I don't think that is actually required.

I wonder, of course, why the OP thinks two degrees are necessary and whether there is time to be faithful to both, but that isn't a legal concern.


I would consider them important, but it would depend on the books in which they are contained and what your contribution is to the overall content. It could also indicate that you have a circle of collaborators already in place, which is a good thing for a new faculty member.

But, I'm not sure why you ask. Certainly they are something to include in your CV and they will be evaluated like everything else in your application materials.


Who owns the research data at US research institutions?

No one.

The short answer is that “data” as the term is understood by US law is not covered by copyright, thus in popular parlance it is not “owned” by anyone. If you google “can data be copyrighted” you will find various articles explaining this in more detail. Here is one.

The longer answer is that, as seems to often be the case in matters of law, the legal meaning of “data” seems to differ slightly from how people use this word in normal speech. What academics might refer to as “research data” may also include aspects of what is referred to in some sources as “presentation” or “compilation” of data, and to the extent that this is the case, copyright might apply to it after all. In that case, the copyright would be owned by some combination of the PI, graduate students, the institution that employs them, and any funding agencies who might have funded some of the research, depending on the policies of the institution and funding agencies. For example, at my own university, researchers own the copyright to the work products they create.

I also notice you are mixing up copyright and patent rights by mentioning them together as if they were the same thing. They are not. Data is not a form of invention so I don’t see how patent rights would apply to it. But more generally, if a graduate student and PI come up with any patentable inventions, those would be subject to quite different rules and policies than those covering copyright. For example, at my own university, patent rights for researchers’ inventions will generally belong to the university, though the inventors can receive a share of any royalties generated from their inventions. As far as I know this applies equally to graduate students and regular faculty. But you should check the policy at your own institution.

Disclaimer: I am not a lawyer.


Should I include a title page and abstract if the journal does not specify anything at all?

Papers aren't normally published in the exact form of their first submission. I suggest that you write the paper as you think it should be written and submit it. Let the editor and reviewers decide if you should make modifications.
The title page is unlikely to be necessary in a first submission as it can be added later if needed (unlikely here). But an abstract might be helpful to the editor in choosing reviewers and to the reviewers in getting a quick overview.
But they will likely, in this case, ask you to remove them for publication. It is a process. Flow with it.


Requesting the mentor regarding the PhD research topic selection

It is a mistake for most students (Ramanujan excepted) to go against his or her advisor. I'm sure that the advisors complete thoughts are more complex than you present here, but probably involve the risk of taking on a big project as a student and ending up with nothing - no results and no degree. Some problems are hard and take years-decades-centuries to resolve.

The advisor is giving good advice and following it will put him or her on the side of the student.

If "your friend" wants to take on the big project there is no problem, but will be working from a stronger position by finishing the doctorate first.

Take the advice. It is the faster path to success.


How common are romantic relationships between faculty and students?

I've found a rather old survey (1982) of David L. Rowland, Larry J. Crisler and Donna J. Cox that claimed

  Of the 184 respondents (59.8%  female and 41.2% male), over
  one-third  of  both sexes reported flirting with their instructors,
  while 46% of females  and 32% of males felt that instructors had
  flirted with them.

Flirting is, of course, is not the same as a romantic relationship. Patricia A. Rupert and Deborah L. Holmes (1997) survey earlier studies of the sexual relations between faculty and students:

  in a survey  of  807 male faculty,  Fitzgerald,  Weitzman,  Gold, and
  Ormerod (1988)  found that 26% of the 235 respondents  reported
  having sexual encounters with students;  in a similar  study  of
  483 male and female psychology  professors,  Tabachnick,
  Keith-Spiegel,  and Pope (1991) obtained  a rate  of 11%. Although
  there was a considerable  difference  in these rates  no doubt in part
  due to the inclusion  of female faculty  in the second survey -
  both indicate that sexual encounters  between faculty  and their
  students  are commonplace  on our campus

One notable example is the marriage of Professor Philip Bobbitt (Princeton (A.B.), Yale (J.D.), and Oxford (Ph.D.)) and Maya Ondalikoglu,Columbia Law School graduate.


Is it reasonable to take hobby classes during a doctorate?

Lots of people do this, especially if their funding allows them to take out-of-program courses. But you should

Check first that your advisor is OK with it. Tell them that music has always given you a safe, healthy outlet for stress and anxiety. Skip the well-rounded student part.
If you don't yet have an advisor, check with the graduate director. In fact, you might want to check with the graduate director anyway if you have any reason to doubt that your advisor's say-so will cover your bases.
Take the outside course pass-fail or undergrad level if possible. Tell your advisor/grad director that that's what you're doing.

Some programs might have the kind of issues you describe about "focusing on your studies," but most won't. A few might have issues about paying for an out-of-program course. But in any event they're going to find out about it anyway, so you should approach them about it first.