Is there a way to prevent the production team from messing up my paper?

Production teams don't want to mess up papers; the ones that do are performing poorly. Unfortunately, poor performance seemingly occurs amongst all publishers, regardless of prestige. So, you cannot prevent the production team messing up your paper.

Requesting that the production team, do not edit the text, makes the team's job impossible. Attempting to pre-empt mistakes, e.g., by instructing that they do not remove the separating lines from the tables, as they convey important information, won't help much, since you cannot pre-empt all mistakes. Moreover, such contact with the production team will suggest that you have a low opinion of them, which isn't in your favour.

Following the publisher's prescribed style may reduce errors, since the production team won't need to make as many edits.

All is not lost, since mistakes can be fixed before publication, albeit this is expensive (in terms of time). In addition, preprints or technical reports (which aren't edited by the production team), can be made public.


Is it ethical to include additional material in lecture notes if students buy them

It is very thoughtful of you to be concerned with the increased costs to your students; indeed, professors should be aware of and sensitive to such issues. At the same time, it is important not to go overboard with such concerns. As an educator, your primary concern should be to provide the students with the materials that you feel they need. That can legitimately include material that you are not planning to cover in the course but feel would be beneficial to at least a reasonable number of students. When weighing the benefit of this extra material against the increased cost of 1-2 euros to purchase the lecture notes, personally I feel that the educational benefit wins out against the fairly negligible amount of money involved. So yes, I would say it is ethical.

As for distributing the extra material online for free, sure, that would work as well, but would probably send a signal to most of the students that this material is not important and should be ignored, and would dilute the pedagogical value of making the material available to the students.

Finally, note that my answer may be different if you personally were making a profit from the inclusion of the extra material. In that case there would be a clear conflict of interest that would warrant, at the very least, a good deal of extra caution and perhaps rethinking your entire approach to distributing course material.


How are mathematics PhDs from the USA viewed in mainland European universities?

Do American-educated mathematics PhDs generally have an advantage over natively educated PhDs (in, say, France or Italy) in applying for research positions?

Generally speaking, no: why should they? And for what concerns specifically Italy, take into account that some things that can make an application strong(er) in the US (e.g. stellar recommendation letters or awards), might go totally ignored by a selection committee in Italy. This means that you should tailor your application to the country you're applying to. Let's see why.

A selection process in Italy, both for permanent and non-permanent positions, is usually composed of one to three steps, where each step counts for a fraction of the final mark (details vary across fields and position levels):

CV and publications (this step can count from roughly 30% to 100% of the final mark). The selection committee, before knowing the candidates, decides how to evaluate each section of the CV. If, e.g., the call doesn't explicitly mention recommendation letters, these are typically discarded; if the committee decides that awards count at most 2 points out of, say, 30, even if you have a Nobel prize, they (probably) won't add more than two points (should they do, in case of appeal from some of the candidates, the call can be invalidated).
One or two technical essays (optional; when present can count from roughly 30% to 50% of the final mark). Here, the applicants are typically required to write a technical essay on a specific topic in the field of the call. I don't know about mathematics, but in my field one might be required to describe how a certain instrument works (e.g. a spectrum analyzer) or how to perform a certain experiment (e.g. how to measure the fine structure constant). The difficulty of the question depends on the level of the position.
Interview (optional, depending on the position). Here the applicants are typically asked to discuss technical topics in their field or, for instance, some of their publications. For an associate- or full-professor position, this step can be substituted by a (public) lecture on a specific topic in front of the selection committee.


How to write an effective but gentle reminder email to a journal editor?

Make it a question, not a reminder.

I see no particular reason to worry that your paper has been forgotten. It seems more likely just that yours is scheduled for the May issue (or later in the year) because there were enough earlier-submitted articles to fill up the January issue.

On the other hand, asking politely “Roughly when should I expect my paper to appear?” is a completely reasonable question — there are many reasons you might want to know it — and contains no implied criticism that an editor might take offence at.

And in case the editor has forgotten your paper, this will have the desired effect of a reminder anyway.


Is it normal to have no publications after 2.5 years in a PhD program?

I was in the exact same situation (also CS) and I would say that it is both normal and cause for concern. So there's no reason to take it personally, or to start worrying about your abilities, this happens to many people, but it is a situation that needs to be resolved. From now on, your number one priority should be to get a paper, put everything else on hold. Don't worry about getting enough papers, worry about getting one.

You have something under submission, so the odds are you'll get it accepted somewhere pretty soon. However, if you don't, I would recommend trying to find someone with experience who can coach you hands-on. Find someone who can read your draft in detail and tell you what needs to be done. 2.5 years with no publications is usually a sign that the supervisor is not paying very close attention, and it may be good to find someone who can pay close attention to you, at least for a bit. Getting a paper past reviewers is a strange, dark art, and it really helps to get some intense supervision for your first attempt.

edit after comment: Two further tips to help your situation:

Idea generation is a skill and you can work on getting better at it.
[1 2 3]. If you're not generating ideas, tackle that problem head-on. Don't think of yourself as a non-creative person, and don't blame your subject: there are always exciting directions if you look hard enough.
Try to write a collaborative paper, ask a postdoc or a fellow PhD in your group to do some brainstorming, and to find an idea that you can work on together. That way, the work becomes less lonely, and you have at least one other person who cares about it. It might be a little scary to initiate something like this, but if the alternative is working by yourself for the next 2.5 years, you may consider stepping out of your comfort zone a little bit.


websites in which I can look for professors in specific field

The instruction of findmyprof.org states:

  the structor is "keyword +country website code"
  example: Climate change +ac.uk --> search only websites located in england

I searched for

  atmospheric science +.ch

and received results only for Switzerland.


Is it possible to submit a PhD thesis with two authors?

It is definitely possible in the sense of "It has been done." However, the only example I know of is this thesis from linguistics: http://dare.uva.nl/search?arno.record.id=123669 (Groenendijk & Stokhof 1984)

Whether it is possible in the sense of "You could do it." will depend on your university's regulations concerning these matters, as well as your advisors and committee's preferences. They are the people you should talk to about this.


How to interview undergraduate candidates for research assistants?

My advisor, bless his heart, entrusted in me the responsibility of interviewing and selecting undergraduate students to work in our research lab while still being a graduate student myself.  Sometimes it's difficult to determine what a person is really like just from a few minutes speaking with them.  I found a few particular questions to be particularly helpful:

Ask them what their goals are for the future.  Most undergraduates give very general answers because they are not sure what they want.  A highly motivated student knows what they want, and are likely to link their goals as part of the reason why they want this particular research job opportunity.
Ask them to describe in detail a difficult problem that they had to overcome, and explain how they overcame it.  This is a question they typically anticipate, but it's the manner in which they answer that matters...  Observe how well they put together their answer, how long it takes them, and how well they articulate it and its relevance to the research job that they're applying for.
Ask them about their greatest strengths, and greatest weaknesses.  In particular, examine how they explain how their weaknesses may affect their job and how they intend to overcome these weaknesses.  A strong candidate will not only be self aware and honest, but will seek ways to overcome these deficiencies.


Within minutes they replied that they have already published, requesting me to pay x money for the publication fee.

This sounds like Journal A was a predatory publication (i.e., a scam without real peer review), and not actually a reputed journal.  If this is indeed the case, then having a publication withdrawn from them may actually be better for your reputation than actually having published with them.

That said, you shouldn't submit to a second journal until you've already withdrawn from the first.  In the future, follow that procedure and also make sure that you're actually dealing with a reputed journal before you submit!


Is it acceptable to email the author of a paper that you cannot follow?

It's okay, and more than okay, to ask for clarifications on specific bits that you were unable to follow. Academics love talking about their work, and they love spreading knowledge.

It's less okay to email someone out of the blue and say "explain yourself better". As SolarMike said, this paper has already been peer-reviewed; people in the field have looked over it and said "yep, that looks good". It may indeed be true that the paper was not written clearly enough to be understandable to someone without extensive knowledge of the subfield, and it may also be true that a better written version of the paper would have been more widely understandable without compromising its concision or its organization, but that's not a sin the author is required to atone for.

Try reading a few of the papers that paper cites, particularly ones sharing one or more authors; authors will often introduce and explain formalisms in one paper, and then take them "as read" in later papers (either accidentally or because they see the later paper as incorporating the earlier one by reference). If you still can't follow it, definitely contact the author... but make sure your request comes off as a request, not a criticism.


Why some papers are free while the other are not, even in the same journal/publication?

Why some papers are free, while others aren't, in the same publication

You can see that one of the papers was published under an open access Creative Commons license (hence freely available to everyone), and the other wasn't. So-called hybrid open-access journals have a system where some of the articles are published under open access conditions, usually in exchange for a publication fee. This appears to be the case for the journal in question. Probably the author paid to have it published as such, possibly mandated by their institution or funding agency, or possibly because they want to support open access.

How to tell if your university has access to a given subscription journal

Usually this is stated quite clearly on the university library website, when looking up specific journals. If the specific journal isn't listed, the university doesn't have access. Even when listed as having online access, there may be restrictions, e.g. online access may only be available for a certain time period, say 1983-2001. This is usually listed quite clearly.

One thing that usually isn't stated clearly, is that you might not have working automatic access, and may need to access the journal through the university website. If that website doesn't clarify things, or you still have problems, I would recommend asking a university librarian. Even if your university doesn't have access to the journal in question, they are often able to source a copy of the article through e.g. an inter-library loan.


I think it's going to depend vastly on what kind of position you want to be headed into, and how deep down the rabbit hole you wish to go.

The one thing I would say you ought to focus on is fundamentals: No matter what kind of work you end up doing, be it programming business processes or pursuing a PhD, getting your fundamentals straight will pay dividends over and over again. Courses in algorithms, software engineering, computer architecture, each will give you a different view into the work you do, no matter where you're doing it. A CS undergraduate degree would be a good choice, especially if grad studies is where you want to go after. I understand they vary in quality though, so that's something to bear in mind.


Research is about answering unanswered questions. Primarily those that are important in a field.
So, to get started, ask a lot of questions and keep a notebook. Find out if they are already answered by reading and asking others. Figure out if they are significant in some way or could lead to things that are.
Let the questions lead to hypotheses - what the answers to the questions might be.
In applied math (not my field) the questions might involve things that are particularly difficult in some domain. Ask why? Ask whether they can be simplified. Make a hypothesis about how they might be simplified. Then validate/invalidate the hypothesis. Along the way, other questions will occur to you. Write them down (notebook).
Then...
Ask more questions.


Falsely accused of providing project code to others in a class

There are a couple of things to realize. Many departments run assignments through plagiarism detection software. The software typically reports a "similarity index" which needs to be interpreted by a human. The exact process varies from department to department (and sometimes even between professors/TAs). It could very well be that any assignment with a similarity greater than X is automatically forwarded on to the academic misconduct committee. It could be the professor looks at the assignment and decides the similarity is great enough for further investigation.

The key is that investigations are not accusations of misconducted. The accusation happens after the investigation and at that point you can appeal. Every department I know of has an appeals process and none allow an appeal prior to the investigation.

Back to your case, the investigation will have two parts, that will likely be carried out together. The first is to determine if the current student cheated. The second will be to determine if you violated any polices in terms of helping the student.

  apart from saying that we did not provide the code, we do not have any ways to show that we are innocent (in fact now I think the procedure is very unfair to people like us)

While technically correct, there is the question of if the student obtained a copy of your code, how did they do it. My academic misconduct polices I am aware of require you to knowingly share past assignments with the intent of allowing the other student to cheat. Generally showing someone your past assignment, or looking at someone elses past assignment, is not cheating. Saying "here are my past assignments you can copy them if you want" is cheating. Saying "here are my past assignments make sure you only use them to learn and that you do not copy them" is not cheating.

If the student had access to your computer, or GIT hub account, or email, or notes, or ... but you didn't tell them they could look at your notes, you are probably in the clear. Knowing this would help the investigation. Maybe the current student is friends with the past TA. The key is to tell the investigation everything you know. You will also want to make sure the student tells the investigation how they got your past assignment.


How to find a math conference accepting papers?

In mathematics, you're very unlikely to find such a conference.  There are a few (the only one that springs to mind is FPSAC).  There are sometimes proceedings based on conferences, but typically those articles are solicited after the conference from the invited speakers.  The idea of taking submissions of papers before conferences and then judging whether they are appropriate for presentation at the conference is pretty foreign to mathematicians, and publishing in conference proceedings is much lower in prestige than in journals.

Thus, I recommend you submit to a journal instead.


When exactly are you “promoviert” in Germany?

The Promotionsordnung of my alma mater says this:

  §17(1): "Als Promotionsdatum gilt der Tag der bestandenen mündlichen
  Prüfung."

(The date of Promotion is the day of the successful oral exam.)

  §25(1): "Als vorläufigen Nachweis der Verleihung des Doktorgrades
  erhält der Bewerber vom Prüfungsamt der TUM eine Urkunde nach Anlage
  2, sofern die erforderlichen Exemplare nach § 20 fristgerecht
  eingereicht worden sind."

(You receive a preliminary certificate when you have submitted the required copies of your dissertation.)

  §25(2): "Vor Aushändigung der Urkunde nach Abs. 1 ist der Bewerber
  nicht befugt, den Doktorgrad zu führen."

(You are not allowed to call yourself a Doktor before you have received this preliminary certficate.)

  §25(3): "Der Bewerber erhält ferner eine Urkunde in deutscher und
  englischer Sprache nach Anlage 3 a oder 3 b, die mit dem Siegel der
  TUM versehen ist und das Promotionsdatum gemäß § 17 Abs. 1 trägt. ..."

(The date of Promotion is written on the final certificate.)

So, you could say you are promoviert when you have passed the oral exam. But since I'm not a lawyer I'm not qualified to give legal advice. Personally, I would avoid anything that could be seen as you saying you are a doctor before you are allowed to do so. Until then I would say "I've defended my dissertation successfully and am waiting to receive the certificate." When you have your certificate, the date of Promotion is the day of the oral exam.

In practice, you get the preliminary certificate rather quickly. I believe it was something like two weeks after the exam for me, but it depends on how quickly the head of examination and the administration works. The biggest problem was getting a Führungszeugnis in time since I hadn't considered that prior to the exam.


In most fields and for most journals, there is no time-table because it takes as long as it takes.

This means that after they receive your paper, they will send it out to a few referees, which have to be found first. How long finding referees takes is not under the control of the journal editors - they have to ask people until three of them said "yes".

Then, the referees have to write the review. Typically, they have about 3 months of time for that, and a request for extension is almost always granted. So think of it more like 6 months. Exceptions apply here (e.g., for the journal "Science", who manage to enforce shorter reviewing times).

Then your paper maybe accepted only conditional to changes. You do the changes within a month or so, and then reviewing starts again. So there goes another 3-6  months in addition to the time that the editor needs for organizing the process.

This means that for most reputable journals, there is a long pipeline of papers in-progress and whenever they make a new issue that is not a special issue, they take some papers that already went through the process and publish them. There can be a substatial "out-queue" of these papers, which is why some publishers came up with the concept of already publishing "done" papers before the paper has a journal issue assigned (e.g., for Springer, this is called "Online First").

As an example, in computer science, an overall time span of 1-3 years is common.

As a bottom line, the time to publish can only be influenced by the journal editors up to a certain, small, degree, e.g., how swiftly the editor performs actions whenever there is something that she can do at the respective point in time. So publishing a time line would make little sense.


Is it possible to do a PhD in one field along with a bachelor's degree in another field, all at the same time?

The usual disclaimer applies here: the answer depends on your country, your university, your program, etc etc etc. It also depends on you. There are many variables here and not enough of them have been defined, so no one can answer your question definitively.

Let's theoretically bound a few of those variables and do a thought experiment by answering this.

Let's say that for the sake of argument, you are a genius who can not only get done work at an incredible speed, but who can also comprehend and understand all the work in front of you without issue, and this applies just alike to everyone around you who you may have to do any form of teamwork with (thanks O.R.Mapper). Then yes, you can do both of these things at the same time (because the main limitations here are time, comprehension, and energy) - provided you aren't doing them both at a university which has a rule against this kind of thing. As long as you handle scheduling conflicts in a reasonable way, yes. This means: If you have a time where you NEED to be doing obligations for one degree or the other (physics degree = unmissable physics labs even in a theory degree, for example, or exams) and you can make it to all unmissable obligations for both degrees (say they're in the same university or the same area) then yes. However I can imagine quite easily that you will have to resolve scheduling conflicts often. You will probably have more schedule obligations with an undergrad degree than with a postgrad one and it's tough to be excused from those, even if you have a good reason. I'm thinking about things like practicals, scheduled exams, and other things you really can't miss. I'm also mostly thinking about how it was for me in the UK system, and perhaps in other systems scheduling is more flexible, so YMMV.

Unbounding that variable a little: I will state the obvious; a physics degree is difficult. A PhD in biotech is also likely to be extremely difficult. You are a human being. Folks struggle with bachelors degrees, folks struggle with PhDs. I think that any person who is likely to be imperfect (in a totally normal way) is liable to struggle with one of these, not to mention both of them at the same time.

Personally if it was me trying to do both these things at once, I'd be so overloaded and stressed and unable to learn after only a short while that I wouldn't be able to do it. You would have to have impeccable time management, extremely prudent stress management techniques, and you'd never really have a proper 'break' from working or studying because both of these things are full-time+++ jobs. You'd be taking on two of them at once. You'd be subject to the same chances for failure as anyone working two 40-70 hour work weeks. Whether you succeed or fail is a function of how well you handle all of these stresses, and how you allocate the time. And how little you value sleep. I think, but I don't know for sure, that how 'clever' you actually are has less of an effect on your success than the above stuff. You have proven your intellectual capacity already with your qualifications, but a PhD and a BSc at the same time is serious business and even the most clever humans in the world would struggle with it from even a logistical perspective alone. I know that if I tried to even have a part time job during my physics degree, I'd have probably failed. My friends with jobs did fail. I was told by the people coordinating our program that it's this way by design; it's designed to push us to our limits to show us what the research world is like, and to differentiate between good, better, and best.

And this isn't even stating the most obvious part: When you're writing your thesis, you will have time for nothing else.

Since my answer has really been a non-answer I will leave you with this:

I didn't do a theoretical physics degree, just a 'normal' physics degree. I had friends in the theoretical program. They still had to do one academic year of unmissable physics labs for 4 hours every week (to demonstrate the principles of basic physics). They still had to sit exams which were unable to be scheduled to a different day/time. They still had to study with us during 60 hour work weeks to understand the material in the months leading up to exams because there were so many of them and because the material was so vast (this applied even to the insanely clever ones). The only real difference between a theoretical degree and a normal one was that you're able to do theoretical physics from anywhere where you can concentrate (so you can do the 'research' part of your PhD mostly from home if your supervisor doesn't ask you to be in the workgroup's office and if you don't need their help to get things done). This is where my 'depends on program' disclaimer comes in; it might be different where you are. In fact, it almost surely is different.

A lot of it will come down to your motivation level and your ability to multitask without fail. Why do you want to do this (it seems like a strange choice)? I don't ask because I'm being snarky; I'm asking because if you really do do this, this is a question you'll be asking yourself in what I can only suspect will be a very short period of time.

If you want it enough and you're really really really good, sure, go for it. The long and short version: There is no reason why you can't, but there are many reasons why a person would not succeed at this.

Would I recommend it? No way. In the end, you are a human (even if you are really good) and something will have to give way eventually.


Sending non-fully translated academic transcripts for US PhD admissions

Many university departments have officers for the internationalization of the department. Talk to this person. If she/he is willing to sign a letter stating what these course names translate to and she/he puts an official stamp on it, this should be a good solution. You would add this official letter as an addition to your application.

Suggest to this person that you will prepare the letter. If your offer is accepted, this saves a lot of work for this person, and she/he is more likely to accept. If the internationalization officer wants to rather perform the translation herself/himself, then....well, less work for you!


Forgot to finish final paper submission in a conference

You're probably out of luck here. You can try to email one of the conference chairs or whoever might be higher up the chain than the publishing office, but that's a bit of a long shot, especially a week after.

I'm so sorry this happened to you. I've come close to missing a deadline once or twice and I now set days worth of reminders just to be sure I don't mess anything up.


Is there a theoretical-physics masters program that accepts mathematics graduates?

People are accepted into a physics program because they prove that they can do well in physics graduate school through their past performance in courses, their personal statement, their letters of recommendation, test scores, undergraduate research experience, etc. If you have a strong mathematics background, you might be able to convince an admissions committee to accept you if you demonstrate an understanding of undergraduate physics outside of course work (like performing well on the physics GRE). If you have not, at least self studied undergraduate physics material (at the very least at a Sophomore/Junior  level), then it is not likely that you would accepted into a physics graduate program (even a masters program). Now if you were exceptional at math (e.g. have published research in a peer reviewed math journal), perhaps its possible that a physics program would accept you, with a very good personal statement explaining why you want to study physics at the graduate level.

But why get a degree in physics? At least part of the answer should be that you enjoy doing physics and are (at least somewhat) good at doing physics. If you aren't 100% certain that you love physics, you shouldn't go to graduate school in physics. Instead, self study physics by reading a book, doing problems and watching online lectures. Once you can determine whether you enjoy doing physics, only then should you go to graduate school in the subject.

In addition you haven't explained why "knowing about physics could improve a philosopher's thinking about a number of questions". At least at the vaguest level, this could be said about nearly any discipline; it doesn't mean you should get a degree in those fields. You can take physics courses while studying philosophy at many universities. If you think you will derive deep satisfaction from this, you should seek out philosophy programs that allow flexibility in your course work so you can pursue an interest in physics.


I gave up on a PhD because of time management, shall I try a second time?

I understand that a PhD is a training exercise, where one learns to do research.

In a way, your misunderstanding is that you think that doing a PhD is strictly training you how to do research. I think it is more accurate to say that a PhD trains you to be an academic - and dealing with this kind of "instability" is part of that, the same as learning to do university teaching, dealing with the administration, networking, presenting at conferences, and all the other things professors do.

As for whether you are likely to see the same issues again in your new PhD, I think they break down into two categories:

  I needed to change office three times during that period,
  switched (university) email systems two times,
  all courses for the PhDs were announced with only two days of antecedence,
  courses were canceled with hours of antecedence if there were not enough people attending.

I am sure that many, if not most, universities are better run than that, and I feel you have a good chance of not experiencing that in another university. Even better, since you know somebody in your new PhD programme, you can ask her or him whether any or all of the above examples also happen there.

More problematic are the latter items on the list:

  reports were not scheduled, my supervisor literally popped in my office and asked for a report within a week (not once, a couple of times),
  some (internal) talks were to be prepared on an short (a day or two) notice.

This is exactly how, in my experience, the vast majority of research groups are organized, and if something like an ad hoc report to your supervisor, which is in the grand scheme of things rather trivial, stresses you emotionally, I fear that you will indeed not be very happy in academia.
Let me give you some examples from my own PhD:

Close to all my thesis meetings were ad hoc. The usual pattern was that I was getting coffee (the machine was next to my advisor's office), and my advisor would "incidentally" come out of his office and ask me how my thesis is coming along. I think I had 3 scheduled meetings with my advisor during my entire PhD.
On multiple occasions during my PhD I was at conferences, and my advisor figured out that he could not be in a side meeting that he promised his input for and sent me instead, often with less than half a day of advance notice and no preparation except for a pat on the back. In one or two cases, he even forgot to tell the other meeting participants that he would not be coming, meaning my first order of business was telling them who the heck I am and what I was doing there.
My PhD advisor once went to a project review meeting, for which I prepared (parts of) the material for him. Despite asking for it I never heard feedback, so I assumed it would be ok. The night before the meeting, 17:00, when he looked at the material the first time, he discovered that it was not at all what he expected, and I ended up redoing large parts in an all-nighter.

Unfortunately this will also not really change once you rise to higher levels of seniority - I am now a senior postdoc with my own research group to lead, and my work life still consists of plenty of surprises that need to happen right now. Some examples:

On the ~ third day of my current job, I was asked to fill in the next day for a lecture unit in a topic I had 0 expertise in because the head of the department had to leave to an urgent meeting.
I am currently working on a very important personal grant application that is due in a month. I loudly proclaimed to everybody that cared to listen that I really wanted to focus on this in the next month. Despite, I have been asked to lead an audit for a multi-million dollar software project, been taken to multiple surprise meetings for a transfer project that my department is running, and have been asked to give a one-hour talk next week in a high-profile event that my department is organizing.

(of course, all of the above are exceptions rather than the rule - most days I get to work and do exactly what I planned to do this day; however, I got the gist from you that these kind of unexpected workloads could ruin your concentration for more time than what they actually take)

So, to answer your titular question:

  shall I try a second time?

If you have found an industry job that does not lead to this kind of emotional stress, I would suggest you think long and hard before leaving it. I will be personally very surprised if you find academia to your liking, based on what you described.


Which year do I use for an in-text APA citation?

It needs to be the year of publication in the in-text citation (same for the reference at the end of the paper). This is backed up by the Purdue OWL:

  When using APA format, follow the author-date method of in-text citation. This means that the author's last name and the year of publication for the source should appear in the text, for example, (Jones, 1998), and a complete reference should appear in the reference list at the end of the paper.

https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/in_text_citations_the_basics.html

If the date the survey was conducted is important then you should definitely mention it in the surrounding text like you’re doing.

Due to the fact that writing a paper then going through peer review takes time, it’s not unusual to see some delay between the date the experiment was done and the date the paper was published. Even though this does seem like a bigger gap than usual, I probably wouldn’t even question it if I was reading it.


Is it OK to use "Group A, B, C ..." in a manuscript?,

In general, on the biomedical field Latin letters (A/B/C or a/b/c) are reserved for the figure panels (e.g. "Figure 1 A and B clearly show..."). Typically, biomed articles tend to have a lot of panels per figure, so it is suboptimal to use these letters for anything else. It is much more handy for the reader, if experimental groups have human-readable names that are clearly defined in the method section. A little fantasy may be helpful. For example,

Group 1 - placebo control - "Placebo"
Group 2 - 10 mg Blabla drug - "B10"
Group 3 - 25 mg Lalala drug - "L25"
Group 4 - Blabla drug + Lalala drug, once per day - "BLI"
Group 5 - 20 mg Blabla + 30 mg Lalala - "B20L30 and etc.


How to get rid of annoying graduate student "supervisor"

I am an undergraduate student who has developed a novel new model which according to my PI (principal investigator) will have a high impact.

Great!

  My PI assigned a grad student to supervise me. Supervision consisted of meeting once a week to update him on my progress so far. Sometimes he would provide certain helpful suggestions(none that are actual innovations just slight fixes/alterations that would improve the model). (...) Knowing his intentions I wish to distance myself from him(including not having him review the paper), as to lower his chance of becoming a co-author.

Less great. Much less great. Let me make something clear here: this is not your project alone, this is the project of you, your advisor, and the PhD student. The guy has invested a serious amount of time into this project (not as much as you, clearly, but still a significant amount), and now you have unilaterally decided that he is to be cut out when the time comes to publish your results? Likely, this is not to be going over well either with him or the advisor, and for good reasons.

Deteriorating professional relationships are never fun, but it is simply not feasible to decide midway through a project that you now would rather not have another researcher on board. If he has already made contributions to the project, and it certainly sounds like he has, it would be unethical to publish without him now.

EDIT: to make it clear, I am not saying that he should get equal credit to you. But it certainly sounds like he should get some credit.

The very least you need to do is follow user11192's recommendation:

  it is best to meet with your advisor (and possibly the grad student) to discuss an authorship plan.

Finding a "sneaky" way to get rid of the grad student before publication time is not particularly ethical, and has a pretty high possibility of backfiring on you.


Asking a celebrity Prof to sign a paper they wrote?

Just ask! In the past, before electronic publishing, one had to ask for physical reprints from authors. They usually signed them with a nice greeting, sometimes a signature, and occasionally nothing. I have sent reprints to other upon request and always with a signed greeting because I appreciate the request. I have a hard time seeing anyone being offended by it although an eyebrow may be raised by the request since it is now quite unusual. But it is a good way to strike up a conversation and contact the person. Personally I would try to approach the person away from an "audience" in order to not interrupt and have a real chance to state why you admire the work (person). I am sure some might say no but I would not be offended if someone asked me, not that I see it happening to me any-time soon.


Why does a professor cite his own works with unbelievable proportion?

While there can be good reasons to self-cite, and sometimes self-cite significantly, if many of the self-citations are not relevant, then it's pretty clear the citations are there in order to inflate citation metrics.

The appropriate response is to pay less attention to citation metrics. After all, by those sorts of metrics King Abdulaziz University is ranked above MIT in mathematics.


Whether or not to include declined fellowship in CV

List it -- your CV should list all honors that would help convince others that you really are as good as you claim to be. Having gotten a fellowship is such an honor -- whether or not you actually take it or not is irrelevant for your purpose.


Should I agree to submit a paper with my name as coauthor although I did not read and understand the whole paper?

Although doing a "service" by providing measurement data does not usually warrant co-authorship, some groups still decide to do so to show appreciation.

Many people in academia would accept this as it boosts their CV, and if anything wrong was found in the research after publication, the corresponding author has the highest authority.

I would give it a read and accept it if you are happy with the paper. If you are really worried, you can ask the authors to remove your name and explain you feel you did not provide a significant contribution.


if a school is accepting applications for faculty through September 15, when does the job start?

Only the hiring institution knows for sure, so you would have to ask them.

However, the start date is almost always listed in the job posting, so to avoid looking silly, be sure to read the posting carefully, as well as any  accompanying information that is included or linked.  If you don't find it, then contact the hiring institution (the posting probably contains contact info for a responsible person).


When developing a course, how to determine number of credits?

Your institution almost certainly has guidelines for what constitutes a "credit" - you will have to rely on those guidelines.

For example: http://archive.catalog.arizona.edu/2015-16/policies/credit_definitions.htm

At US universities that I am familiar with, the common definition is that 1 credit = 1 weekly 'hour' of class time, and ~2 weekly hours of effort outside of class, giving a total of 36-45 hours a week for a full-time load of 12-15 credits. Of course for some types of classes, these numbers get shifted around, and they are totally different in courses not over a full semester (though the effort is the same, the time is much less).


My general answer would be: No. Summaries should summarize the work/report and anyone reading the summary will not need to go to references to check on sources since those are given in the report itself. I can see exceptions from this if one or two references are key to the report by for example, being ground-breaking or by being in conflict. Then it may be important to show from where the key aspects originate and to perhaps list the single r couple of references after the text. But, the persons reading the summary may not be familiar with referencing so make sure you know your intended audience and the style they are familiar with. It may still not be necessary to provide references but to reference the material by stating the author name(s) and the place of publication without reference details. Again, the report summarized in your Exec. Summary will have the details.


Printing a collection of articles in a 'proceedings' for a maths conference

This article may assit you. However I believe that as long as you have permissions from the authors/journals there should not be a problem. Also I take it you have sourced these papers legally etc?


Is there a reference managing software that shows/extracts content of highlights?

Citavi has the mentioned functionality.

There are (at least?) four types of highlighting: Direct quotation (what you are describing - in blue), indirect quotation (pink), summary (green) and comment (not shown, same as in standard PDF viewers). All of them can navigate to their original location when clicking on the link-icon:

I downloaded one of the apparently most popular papers of 2017 and marked three random parts. The titles copy (part of) your marked text per default, but you can change it if you want.

I think it's free for up to 100 references. But if your school has some sort of partnership program, you might be able to get a full license.

I switched from Mendeley to Citavi a few years ago. It was a little confusing at the beginning as I was expecting it to be "like Mendeley, but better", so I even used both parallel for some time. There are still a lot of functions I have no idea about, but documentation seems very thorough. At my school, there are even courses on how to use it.


If the publisher now holds the copyright, they would have to provide the permission to reproduce it. The "law [that] protects such right" that you referred to in your comment is copyright law.

The publisher can explicitly allow everybody to replicate the work, e.g. through a Creative Commons license (although this often includes the clause to also reproduce the license information), or by a general waiver on their site. So you'd have to look for something like that at your publisher's website, and otherwise you might want to notify them of the reproduction - assuming you don't agree with it.

(Do consider that more publicity for your work might not be a bad thing.)


May I write a letter to support my girlfriend's application?

Just say no.  No, it's not appropriate.  This is not even close.  She might as well ask her mother to write the LOR.  "She was such a good girl growing up."

It's possible it might not get discovered but if it is, I expect it would (should!) quickly tank her application before most admissions committees.  She needs to find references who can speak to her qualifications without this obvious conflict of interest.


Can supplementary materials be used in different manuscripts?

From the point of view of originality, I would say that supplementary materials can be used in different manuscripts.

Indeed, supplementary materials is usually brought along the article/chapter to present a data set, as in your example, so it's like archival material, rather than its analysis/interpretation that is carried out in the article itself.

As a result, the same set of supplementary materials might be reproduced and used in different articles, but analysed in different and bringing to different conclusions.


Festschrift articles: is the peer-review as strict as for other papers?

In my experience in mathematics, papers submitted to a Festschrift are held to the same standard as any other papers as far as correctness and novelty go, but there is definitely some flexibility regarding importance.  The Festschrift is often considered a good place for articles that would be of particular interest to the person being honored, because they build on this person's work or involve topics close to their heart, even if the papers are not particularly important in absolute terms.  Referees know the paper is submitted to the Festschrift, and I think this vision of which papers are appropriate is broadly shared among authors, editors, and referees.  An embarrassing or inappropriate paper would be rejected, but for example a minor observation related to the honoree's work could be accepted.

It's hard to say how this compares with typical journals, since there's a range from low-end journals that will publish anything arguably new and correct to high-end journals that regularly reject excellent papers because they aren't quite wonderful enough.  A Festschrift will never match the very most prestigious journals (there simply aren't enough thematically-appropriate papers at that level to fill it up), but it can be comparable to a middle-of-the-road journal or occasionally better.

As in Stephan Kolassa's comment, a large majority of the Festschrifts I've seen are monographs, rather than journal issues.  When they are special issues of a journal, it's generally not a particularly prestigious journal.  (However, it can happen: the Duke Mathematical Journal published a Festschrift for Nash.)  My interpretation is that prestigious journals generally don't want to publish Festschrifts because they know the papers won't all meet the highest standards of importance.


Can a master's thesis still be good if it lacks demonstrable results?

My Masters project (synthetic chemistry) didn't actually generate results other than failure and black goop (so nothing novel!) until the last two weeks of time I had in the lab, and even then, there was insufficient purity and quantity of my compound to do a complete 'standard' panel of analysis. It was the 4th year of an integrated BSc/Msci course, was graded including a viva and I achieved a mid 2.1.

The main purpose of a research Masters, at least in chemistry, is to accustom you to 'proper' research methods, while allowing you to pursue something novel and to demonstrate your ability to conduct research to a sufficient standard. In my cohort there was typically a tradeoff between novelty of project and quality of results, where one forgave the lack of the other.

As long as your thesis is written with an awareness of its deficits (aims far loftier/broader than the time/resources available sounds like a good start!) and you write good further work and conclusion sections where you tie this awareness in, making sensible conclusions and observations on the few cases you have achieved, I think it is definitely possible to write a good one! As Paul indicated above, you should discuss these concerns with your supervisor and possibly head of class (or equivalent). I am sure they will have dealt with someone with your concerns and circumstances before.


Should I add references to conference presentations?

If the slides you're using are going to have "independent life,"—in other words, if you're going to make them available separately from the conference paper (on your website, for instance), then the citations should be included as part of the presentation. I would follow posdef's example and place the citations on the same slide as where it's needed; this will save the reader from having to flip back and forth between different parts of the presentation or between the presentation and the paper.

Not including the citations is a bad idea, because it means you are potentially failing to give people the credit they deserve for ideas that were originally theirs. Even though it's "just" a conference presentation doesn't mean that the rules of crediting people for their work should be ignored. (Citing the work of others is also the right thing to do from the perspective of "playing nice with others." Taking credit for other people's work can make them leerier of working with you.)


It means are the fees going to be paid fully or partially.

They want to know they are going to get the money.

It may also be partially-funded is covering tuition only for example.


How to find online discussion groups on research topics which are relatively less popular

If you are in a small niche area of a field then such groups aren't likely to be very visible. It might even be that none exist.
But, if there are productive people in that field who are still working  actively, you can contact a few of them and ask what might be available. Recent papers can be your guide. It might even be that retired folks know of active researchers, perhaps among their own students, who can help.
And, consider starting such a group yourself if you can get a few interested people to agree. It might pay dividends in the future.


Is this journal a scam: Requires payment, invited to submit via email, no comments from reviewers, journal not listed on scimagojr rankings

Definitely a scam. I get these invitations every couple of months, from an organisation whose acronym quite appropriately rhymes with "diarrhea".

  After having presented a paper of mine at a conference last summer,

I will guess that this conference published a list of presenters online, and that this list included your email address and your topic...

  I received an email from someone claiming to be part of an editorial team of a journal, to whom my paper was recommended.

If it's legit, I would expect them to mention who recommended your work. But unless you've produced something world-shattering, it's very unlikely that a legitimate journal would be cold-calling you to invite you to submit.

  I sent my work to them, and received an unconditional acceptance after four weeks... I received no comments from reviewers

Yeah, the quick turn-around plus lack of comments is a pretty good sign that their "peer review" is non-existent. I've never known a peer reviewer who couldn't find something to say, even if it was just "you should cite these eight papers by the very eminent Prof. P.R. Revua".

  The contact I have with them, exclusively with the editor's assistant, has been interesting. I receive emails at times when people in the US (it is an American journal) are unlikely to work. The person has an Indian-sounding name, and the hours of activity are more likely to be Indian working hours than American.

An Indian-sounding name doesn't mean anything on its own; there are plenty of eminent academics of Indian origin all over the world. But the rest of this is definitely suspicious.

The ones who spam me also have a poor grasp of English grammar; while that's not unusual for academics (even the native English speakers, cough cough), it's very suspicious for a publisher. The fact that you can't find information about other articles they've published is also a strong sign of a scam.

It's very unlikely that these people are trying to steal your results. More likely, they're just trying to get a $320 fee out of you for significantly less than $320 worth of work on their part. They may publish your work but it's not going to be worth anything to you, and may even count against you if you list this journal on your CV. It's also quite possible that if you do pay the $320, they'll hit you up for more.

Your advisor should be able to give you some advice on more reputable journals in your field. In the meantime, keep your money, and be on the lookout for more scam attempts - once a scammer gets a response from somebody, they're very likely to target that person for future scams, or sell them on to another scammer.

Edited 8/6 in response to further information with examples of the reviews:

I don't think informal tone or minor spelling/grammar issues from a reviewer are suspicious in themselves. Reviews don't have to be as formal as a published article, and many reviewers aren't perfect English speakers.

What I do notice is that the writing style is quite similar between these two reviews. I can't be sure from the few paragraphs provided, but I wouldn't be terribly surprised if they were both written by the same person.

One error that did raise my eyebrow was Reviewer 1's repeated "et. Al" which should be "et al., short for Latin "et alia". This is such a common part of academic English that I'm surprised any serious academic wouldn't know it.

More suspicious IMHO is the point that @NajibIdrissi noted: these reviews are very generic. Without any previous experience in your field, I daresay I could write something like this after five minutes of skimming your paper and five more of googling for references that match your keywords, and I could recycle 90% of it for the next review I needed to produce.

There are always more papers that could be included in the lit review, there's always more room to discuss further applications, and every author wants to be told that their model is valid and their methods are sound.


Is there a deadline for journal submission?

Generally speaking journals have multiple issues on some schedule from weekly to annually. A paper can be submitted at any time. The review process will then proceed and the paper may be revised on recommendation of reviewers. When the paper it ready for publication, an editor (managing editor) will schedule it for some future issue.

So, there is no real deadline for normal journal submission. However, there is no guarantee that a paper submitted right now will be published soon. The review process takes time and there can be delays. But earlier submission (of a well written paper) is preferred. Submitting a sloppy paper early and hoping for early publication is probably a bad idea. The review will take longer and rejection is possible.

However, some journals publish special issues, perhaps on a topic or to honor some person. For those, there is a deadline, but it is made clear when the "call" for papers goes out.

For the question which is better - journals or conferences -, it depends on the field. In CS, for example, conferences are the preferred venue for new work. In other fields conferences are much less important. Your advisor will know which is best for you and also whether you should have any concerns about your progress.


Follow-up email after faculty position interview

The email does not imply anything.

The hiring committee/chair really can't say much to applicants during the process other than "we are still working on it." I emailed a few while I was going through the process and they all sent back generic responses.

However, if you email them to let them know you have other offers, that is when you would expect a different response. Every school that I emailed in this situation was very forward with information (e.g., "We are making a decision on March 15th and will call you that day." or even "Here is an unofficial offer. The paperwork is processing for the real thing, give it a week."). Good luck!


Does failing in a different program affect graduate admission application?

It might.

First off: there is no record of you failing the program so it’s unlikely that anyone will know unless they actively try to find out. So, I wouldn’t highlight it. If they do find out, I strongly recommend telling the truth, it’s easy to find out whether you we’re enrolled. From now I’m assuming that the committee somehow finds out, or you tell them.

You have tried to get through one grad program and did not succeed. Taken on its own, this sends a negative message to the admissions committee, especially if your prospective topic is relevant to your past CS experience.

But grad applicants are humans, and humans make mistakes. You need to tell the grad committee what you learned from that experience and why do you think it won’t happen again. Don’t make it the focus of your application (again, they probably won’t know). You need to tell them what your strengths are and how you’d fit the grad program. As with every case, it’s hard to say how they’d react, because we don’t know what your portfolio is like.


How to handle conflicts with inventorship on a patent with my supervisors from the university and the company?

I suggest discussing the matter with the technology transfer office and asking them how to proceed.

They have expertise in patent applications, and should be able to advise you. If you can say "The technology transfer office says..." it may reduce pressure on you when talking to the supervisors.

At the best, the advisors know better than to expect to be on a patent without an intellectual contribution to the invention, and would have assumed you had only listed them to get their input on the application.


Should research service labs accommodate client requests for reformatting their data for publication?

Payment:

Don't do it for free.  Tell him what it will cost and make sure he gives you a valid charge code or prepay (if external) ahead of time.

To be diplomatic, I would say something like "We can't do this service unless paid and will charge [double whatever you are first thinking].  However as you have the raw data, please feel free to make these edits yourself."

Ethics/responsibility:

If you think the data modification and presentation moves you too much to making an analytical inference (and taking responsibility for it)...or for sure if it is in any way "overegging the pudding", then just decline and tell him to do his own presentations. With some diplomatic comment about your center only providing data files and presentation work being responsibility of researchers.  I would also lean this way if you are worried about becoming his "secretary" (having the images sent back and forth for inevitable revisions and further touchups).

People:

He's probably hoping to get you to do extra work for him.  There will always be people who push a bit and who try to get away with what they can.  Just be calm and firm.


Cheating university in the name of university campus in Malaysia.

DISCLAIMER: I used to work at the University of Nottingham UK campus in a school that was located on both the UK and MY campuses.

As is clear from the law suit described in the linked THE article, it is non-trivial for a university to set up a franchise. The parent university can get sued and therefore needs to take care in setting up the franchise. Presumable, any university with enough legal resources can set up a franchise

There are at least three different types of issues with running a international campus. The first, of which I have little understanding, is related to income, assets, taxes, liabilities, etc. The second is related to staffing (both faculty and support staff). The third is related to students. Setting up the university as a franchise affects the financial issues and the staffing, but really does not directly affect the students.

By setting up a franchise, UoN may be cheating the UK government out of taxes, but it is not cheating its staff, faculty, or students.

By being a franchise, this means that faculty are employed in MY and not the UK. This means they are governed by MY labor laws and not UK/EU laws. From the university perspective, this means that if a school in MY performs poorly that they can close the school and do not need to bring the faculty back to the UK. To an extent UoN is cheating the faculty in MY in that they do not get the same pay and benefits as UK faculty, but the UoN makes this clear during the hiring process. This is what the law suit reported in the THE is about.

There is no effect of being a franchise on students. In my former school, all MY faculty needed to be "appointable" in the UK campus. This mean that if they applied for a UK position and were the best candidate, that they would be offered a job. At least one UK faculty member is on all MY search committees. While there are slight differences in the teaching materials, the modules, coursework, and exams, and marking guidelines are identical for the two campuses. The two campuses shared a common exam board. The school on the MY campus was accredited by the same UK accrediting body that accredits the UK campus. In fact the MY school was the first international school to be accredited. The two campuses even share the same Quality Manual:

  The provisions of the Quality Manual and any other University regulations regarding the quality management of learning and teaching apply equally to the University’s campuses in the UK and Asia.


Professor told me up front that she normally doesn't write letters for students who haven't done as much work with her

Suggesting that you write the letter and she will just sign it could be the professor's way to drive home the message that she does not want to write this letter of recommendation. I feel she is really unwilling to write the letter and probably hesitatingly agreed either because you were insistent or because she felt an outright refusal might seem rude. It would be better not to push her to do something that she does not want to. In your place, I would definitely look for another professor.


Is calling a staff member "selfish" harassment?

It's brusque and ill-advised, but it's not harassment per se.

Harassment is the creation of a hostile work environment through pressure or intimidation. A one-off heated email and the use of a single adjective to describe someone in a negative light is certainly not sufficient of proving anything more than the person who wrote the email probably should have waited a while before hitting the "send" button. A sustained campaign of emails and a larger pattern of behavior would be needed to make a believable harassment argument.

There's no reason for this to be escalated into a larger situation that will ultimately accomplish very little except inflaming tensions further.


Which capitalization style to use for article titles in CV?

Sentence casing would be my personal choice, but actually it is just a matter of preference.

Academic CVs exist in either title casing or sentence casing in publications. Both are prevalent in practice. Whatever be your choice, make sure it is consistent throughout the CV.


Drifting away from the "boring" slide in the conference

In your talk, every slide tells a story.  That story can be as short or as long as you want.  Just like the overview slide tells the story of the whole talk in a single slide, each section of the talk and even each individual slide can be presented at multiple levels of resolution.
Familiarize yourself with the story you want to tell at these multiple different levels of resolution, and you can change the pacing to match the interest level of the audience.

For example, let's say you've got a slide explaining the details of how you performed a simulation.  You might present this same slide at three radically different levels of detail:

High detail: explain each of the parameters and why you chose it
Low detail: "To study this in simulation, we selected these parameters.  The important choices here are ..." [explain the critical choices]
Minimalist: "We studied this in simulation using these parameters, and ..." [move on to following results slide]

If you are concerned that you are boring your audience, you can shift to a lower detail presentation without actually disrupting your narrative.
This is also a good technique for managing your time, to ensure that you don't go over-time or badly under-time, and can help you customize your material for different audiences.


What to do if I have a good proposal for experiment but don't have an ability to fully conduct it?

If I were you, I'd look for a friend who is a postdoc/professor and he, or someone in his research team is good at coding. If they are interested in the problem, I could start with them.

Alternatively, I would ask my friends to put me into contact with someone in machine learning who can also code and might be interested in the idea.

Once you start working, you could contact the original author for questions, and in the likely event he's interested in what you do, you could ask him to help you with the work in exchange for co-authorship.


Put an AMS offprint (of my paper) on my academic page

The Sherpa/Romeo database is a great resource to find out what kind of re-use the journals allow. In your case, it seems that you can put online the final version of the paper that you submitted to them post-refereeing (with a statement like "published in..."), but not your offprint or the version which is on the publisher website. This is slightly inconvenient because the page numbers will differ, but it is the most common arrangement in mathematics.

The database is only indicative, though: the only legally binding terms are the ones in the copyright transfer agreement that you signed prior to publication, after your paper was accepted (they had you sign one, right?). Read the small print.

This is the theory --- in practice, I have never heard of publishers going after authors for putting the wrong pdf online, at least in mathematics. In general the AMS as a publisher is considered a Good Guy, so I would advise you to respect their requests anyway.


What is the optimal number of times one should meet one's PhD. advisor?

To expand on Peter's great answer, I'd also like to throw out the idea that the "ideal" frequency varies not only case-by-case, but also may change during the course of one's graduate education.

A beginning graduate student will very likely need much more supervision than a student in the middle of her program. Similarly, the student who is finishing up may need more frequent contact, but only because changes are probably happening at a very rapid pace, and it's important to make sure deadlines are completed on time.

From my own experience, I started out meeting weekly with my advisors; after about a year or so, the meetings became every two weeks, but then toward the end became weekly again (for the last two or so months before the defense).

Within my current group, I use a similar scheme: new students have weekly meetings, while older students (and the postdocs) meet every other week, or as needed. (Some of my students get along quite fine meeting with me only once every three to four weeks, and I'm fine with that, because they are independent enough not to need more "face-to-face" time.)

The important thing, I think, is that the PhD student should know that the time is available, if she needs it. However, it's also been my belief that it's when the student doesn't want to meet that it's actually most important to do so. This usually means that something's not quite right—and that's when intervention can make the most difference!


Application of standard techniques to new data: is it publishable?

You might consider sitting down with the people arguing for publication to try and understand why they consider it to be (potentially) publishable.  It's possible, for example, that this new protocol addresses some issues not addressed by existing protocols; or addresses them more efficiently, or robustly, or is otherwise better in some way.  In other words, it's possible that the protocol by itself (without your security analysis) is not publishable, and your security analysis by itself (without the novelties of the new protocol) is not publishable, but the two taken together may possibly be publishable.


Can I host my published software at Dropbox?

May I keep the files for online availability at Dropbox as public link.

Unless you agreed to some restrictive copyright agreement regarding that software or your employer imposes some restrictions (both of which I would consider odd, but then I do not know the customs of your field), it is your software and you can do with it whatever you want.

  If that's not a good idea what are the options.

If you did not already do so, you can see whether the journal allows you to publish software as a supplemental material or similar for your publication. Even if they do not state so on their site, they may still do it on request.
In addition, I would suggest that you publish your software on Github, Sourceforge or some other repository designed for publishing software. This way, you can easily update the software, others can contribute to your software and so on. If you do this, I recommend to add a link to the repository in your paper (or the source code attached to your paper), so people can obtain the latest version.

I am no expert on Dropbox, but it does not seem as long-lasting to me as most dedicated software repositories and probably has no special features for hosting software.


Dealing with mistake in scheduling an extra lecture

I don't really see how you could have done things that much differently: you made a mistake, tried to honor it so that nobody showed up and couldn't ask questions, and was open with everybody as much as possible.

The only thing you might have done is ask people to attend one hour or the other, but they would have in principle every right to attend the full two-hour session if they so choose.

(That is, of course, in the event that you announced the wrong time. The easy way to fix this is to check, double-check, and triple-check the announcement before you post the announcement.)


Can one publish papers which give an improved presentation of old results?

If the proofs are genuinely new, and genuinely simpler, then this is a contribution.  And if proper attribution is given and the relationship between the old and new work clearly explained, then this should be publishable, assuming that the results are still interesting for the wider community.


How many weeks of holidays does a Ph.D. student in Germany have the right to take?

The answer will be specified in your job contract, stipend agreement or whatever source you get money from. Most PhD students in Germany are employed under one of the collective labor agreements (TV-L, TV-H etc.), according to which a full-time employee has a right to 30 days of paid vacation per year.


How important is a rebuttal for a top conference (CS)?

First, it's worth noting that very few computer science conferences actually allow a rebuttal: mostly, the decision you get is the final decision.  In those rare cases that I have encountered that have a rebuttal period, it mainly serves to help disambiguate papers that are near the borderline.  Thus, it can certainly shift the status of a paper between accept and reject (e.g., by showing that reviewer #3 really was nuts and should be discounted or by eliminating the doubt that the authors were benefiting from), but is unlikely to do so unless the paper was already quite close to the boundary.


Ethics of "Double Dipping": Helping 2 professors with research during the summer

This shouldn't be a problem. The professors aren't your employers who demand 100% of your time - they might not even be paying you - so they are not likely to expect you to commit to their lab and their lab only (it'd also be unreasonable if they expect this). Meanwhile by working in two labs you're maximizing your exposure, which can only be a good thing for you.

The only serious consequence I can see from this arrangement would be that you might not be able to commit enough time to actually achieve something substantial. If you aren't going to get any real research done in both labs, you might as well commit to one lab only.


TA-ship requirement for funded international applicants

Not all TAs teach. Many are just graders. Some folks serve as research assistants instead.

That being said,  there have been many professors who have been stutterers. It's no reason to avoid graduate school and certainly you should try to get as much teaching experience as you can in graduate school. Your school is required by law to give you the accommodations and support you need to be a successful scholar.


Simple: a graduate degree (esp. PhD) is about research. GPA doesn't measure research ability to any extent.


Is it unethical to accept extra time on exams when I still do well?

Absolutely not. If you meet the full requirements set up by your University, it is perfectly ethical to use all of the resources made available to you. ADHD is a real medical condition and medical experts and policy makers have decided that special test accommodations are the fairest solution. Accommodations like this are based on medical decisions, not whether you are doing well in the course. Take the extra time if you want it. There is no need to feel guilty about doing so.


Waiting time/silence after a postdoc interview

I think this might depend on whether you have other options that you need to pursue soon, or just want to quiet your fears. In the first case, you should probably ask so that your options become clearer. But in the second, I'd wait, perhaps even after the 3 week window ends.

I think that if things were bad you'd hear sooner, so it seems that you are still in contention, but there is no way to judge your relative position among finalists.

I would recommend, at the moment, that you wait, but don't neglect other options. But the only information I have is what you wrote. You may have more.

Not to mess with your mind, but it is possible that they have made an offer to another person and are waiting for acceptance/rejection before contacting you again. That would push the time frame out a bit. If that is the case then you aren't going to get much useful feedback from an inquiry now.


Would having some flaws in a perfect English SOP be bad?

From the survey Kisses of Death in the Graduate School Application Process by Drew Appleby and Karen Appleby:

  According to several respondents, spelling and grammatical errors found anywhere in the application are an immediate Kiss of Death.

My job should finish here, but I want to summarize the paper after a quick skim. 5 major Kisses of Death are:

Damaging personal statements: personal mental health, excessive altruism, excessive self-disclosure, and professional inappropriateness.
Harmful letters of recommendation: undesirable applicant characteristics, letters from inappropriate sources
Lack of program information: not researching the general focus of the program, not exploring how the applicant’s research interests fit the focus of the program.
Poor writing skills: spelling and grammatical errors, poorly written applications
Misfired attempts to impress

Thanks Roger Fan for linking this survey.


Whatever spelling or grammar checkers you use, you may rely only on their ability to detect a problem, not on their suggested solutions. Alas, if your paper is not completely trivial, this applies to most human professional editors as well no matter how much they charge or how many years of experience they claim. So, in the end, it'll all come back to you no matter what. I have been writing and speaking in broken English for 20 years and the only people who complained were the undergraduate students who, as far as I can judge, would hate me even if I had spoken with perfect Cambridge pronunciation and Oxford grammar. Just write in short simple sentences and you'll be fine. It will not be an exaggeration to say that, no matter what field you are in and what subject you are writing upon, the probability that an attempt of expressing your thought in an overly flamboyant manner, including all nuances and sideline remarks into a single sentence, and alluding to the arguments described in several previous passages at once (especially when the the latter are structured similarly to the phrase under consideration and the references to them can hardly be called unambiguous), will not throw the reader off for good somewhere in the middle of an elaborate construction you have built with utmost patience and verified against all spelling and grammar tools at your disposal is nearing that of the event that a layman be able to recite a sophisticated ten page legal contract with all details including each and every involved party and covenant therein in a single outpour flowing as effortlessly and graciously as a wide river in a deep valley after a quick look at it, i.e., zero. Just make sure that your thought is clear. Then yor massage wll cam thru evn if wrds r misspld and wrng grmmar.


How important are review articles to secure a tenure-track position?

I will say, in Physics, I have never heard this advice. I will also say that I have never, ever, heard anything resembling "1 review article is more important than 5 research articles in a job application." I've been impressed by seeing a review when it is Nature, Science, or Rev. Mod. Phys. - though of course it often indicates the advisor's reputation, rather than the candidate's. However, I can also think of a few times when it makes sense to dedicate some efforts to review articles rather than original research, and I did end up writing one as I was applying for jobs.

1) You have been invited to write a review by a journal with a decent reputation in your field. Doing so demonstrates you are taken seriously by the field, and scientists care about your opinion.

2) You are a few months from a job/grant application, and you think you can write/publish the review within this time, but probably won't be able to publish a significant original research article before the application goes in. A review is better than nothing.

3) Your research plans for the future are focused on an emerging field, and your review gives you a chance to both plant your flag and emphasize how important that field is to a broader audience.

If all three points are mostly there, and there aren't other major holes in your CV/application (teaching, details of your research plan, grant-writing), consider it! Beware, though - I found out writing a good review takes more time than you expect, so Point #2 might not be a slam dunk.


How much can you share unpublished forum articles?

If you are unclear on the matter, I would ask the person who sent you the article. Asking the editor or authors may get the person who sent it to you in trouble. In most cases, the first answer is probably no. However, it may be true in some cases where there are no provisions on the confidentiality of the article. When sent out to be peer reviewed, they usually stamp the title page of the article with the confidentiality clauses. I don't think you should contact the authors until the peer-reviewing process is over, but that doesn't mean you can't. They might just refuse to comment. The last two questions you have posted... You most definitely cannot do that. You could get in major trouble for early distribution of research, especially if the project is not finished. You may face academic dis-accreditation which would make it very difficult for you to ever be involved in the academic community. This would be especially true if you wanted to peer review articles for that journal in the future or if you wish to publish articles with them. You would likely also face difficulties publishing in related journals, which may be problematic if you choose to work in an academic setting. If the author has a link to the article on their webpage, I would suggest you contact them and ask for their permission to post it on your blog. Doing so without their permission is an infringement on their property.


Where to draw the line when giving feedback?

A first point is to ask what is the purpose of the activity to be graded? Is it to test student's knowledge, or is it to provide a learning activity? If it is the former, then feedback before grading seems counter-productive. If it is the latter then the feedback is necessary to provide the sought effect.

I am experiencing this problem with student theses. In the system where I work, the thesis is considered an individual work and grading it should take into consideration qualities such as originality and independence and yet the student has a supervisor who should provide input. The task is caught in the middle between examination of a task and a learning experience; and each supervisor has their own take on where the limits are. So why is this such a mess?

The key lies in failing to define what is a learning experience and what is a test of knowledge or understanding. Hence it is necessary to try to define these points so that the division becomes clear to all concerned. The key lies in deciding the balance between the two. Feedback provided after grading is, in my opinion a lost cause since students have moved on to other activities and very few probably run through the comments. Better is then to, for example, build in the feedback into the grading. This can be done by setting a preliminary grade and stating that successfully working through (not just any work-through) comments to improve the task will provide additional points or step up to a higher grade. This may be incentive enough for most to do the extra work and for those who do not want to, well that will be their decision.

So a key ingredient will be to build in the feedback--improvement into the grading of the task. exactly how to do this will of course vary depending on the task at hand.


Publishing (and being cited) in youtube, twitter, or facebook

We prefer sources of different sorts for different reasons. Journals and conference proceedings that are printed on high-quality paper and bound professionally are considered archival. They have lasted for hundreds of years at least and may be found (even with difficulty) for generations. Online publishing of traditional-style articles provides easy and quick access, and properly converted to text, annotated, or indexed is highly searchable. Both of these modes are typically bound up with peer review in order to also provide some measures of quality, correctness, and authority, though no system of peer review is perfect.

Blogs, online videos, and social media appear to lack basically all of these features, but that doesn't make them unciteable. Given the choice between citing a video lecture of a professor demonstrating the proof of a theorem or a journal article where the same theorem is proved, cite the journal. But given only the video, the culture of academic publishing and writing is that you must cite it. If Terry Tao proves something new on his blog that relates to a paper you are working on, you should cite to it if your article is to be published before he can turn it into a traditional publication.

There's a hierarchy of sources with some disagreement to the ordering. But if there's something that you can point to which backs your point, proves your theorem, or demonstrates your idea, you have an obligation to consider it for citation. Different fields will have different standards for how compelling this obligation is. Pointing to a random blog to bolster your theory of the American Civil War probably won't pass muster in most History circles, but primary sources testifying to the fact you want to demonstrate usually will. In math or CS, the standards are probably a bit different.


Do PIs ever get outside help when writing grant applications?

The research company where I work is organized much like a soft-money university, in that we are largely organized around PIs who fund themselves and the others working on their research by writing proposals to external funding agencies.

One of the ways in which things are different, however, is that the PIs have a lot of help to draw on in writing proposals.  It's not "freelancers," because we're generally drawing on others at the company, but it's still help from outside the research group and can be extremely valuable.  In particular:

Our library staff can prepare templates and proposal checklists to make it easy to comply with formatting requirements and to ensure that the proposal writers address all of the points needed for the proposal.
We run proposals through two stages of review by people not involved in the proposal: the first is early at the "story-board" stage to make sure the narrative is coherent, the second is a week or two before submission to make sure the final proposal is really good.
Some of the company publicity folks can also be drawn upon to make nice proposal art
We used to have a professional copyeditor on staff, though I don't believe that we do any more.

These sorts of things can help a lot in producing a nice proposal, and I wish my university collaborators did this sort of thing more often themselves.  When collaborating, we often offer to organize the review stages, for example, because they really help; many university PIs, however, do "last minute" scheduling that makes it difficult to use these processes.

There is nothing to prevent a university researcher from using these sorts of resources, whether internal or external---at many universities, for example, there is a Writing Center that would likely be quite happy to help with copy-editing and the non-technical aspects of review.  Likewise, I have known professors who would review one another's proposals before they sent them out, in a less formal version of our review process.

It just takes some organization and pre-planning to do these sorts of things... and for many of us, that is lacking without an external framework that helps to chivvy us towards remembering.


How did Academia create and/or solve the chicken-and-egg problem of having a PhD?

The title PhD as the name of an advanced degree was first awarded in Germany at the Humboldt University of Berlin in the 19th century. From there it spread to the US, Japan and elsewhere in Europe.

The chicken and egg problem was simple: you don't have to have a PhD to certify someone as an expert in some field of knowledge if you are already a world-leading authority in that field of knowledge. The faculty at the Humboldt University at that time were all already widely known experts, and so they were able to credential other as experts.


A good definition from Wikipedia is

  Empirical research is a way of gaining knowledge by means of direct and indirect observation or experience. Empirical evidence (the record of one's direct observations or experiences) can be analyzed quantitatively or qualitatively.

Another good resource is EricDigests.com is a further resource that goes through in detail the steps to empirical research, the 7 that are defined from that link are:

Randomisation
Control
Reliability
Validity
Implementation of Treatment Variable
Analysis Issues
Implementation issues

(The full details are on the 2nd link - too much to fit here)

Hope this helps answer your question.


I got rejected from MSc program, should I tell my supervisor about the decision?

Yes, email him and explain and ask if there's anything he can do. The answer might be 'unfortunately not', but what if it isn't?

A very similar thing happened to a friend of mine (paraphrasing from an old email here). She was in touch with a supervisor she really wanted for a master's degree, and applied to the program. One of her reference-letter writers messed up the online submission form by uploading a letter but not clicking 'submit'. The application was incomplete, and Friend of Mine received a letter of rejection. She wrote to Prospective Supervisor and asked what could be done. Prospective Supervisor wrote back unaware that Friend of Mine had received a rejection letter and said she'd go talk to the committee about the incomplete application. She argued for putting Friend of Mine on the waitlist, and the committee agreed. A sufficient number of people turned down the program in question that Friend of Mine got in...and ended up doing both the master's and a Ph.D. program with Prospective Supervisor.

It's not going to happen like that everywhere. Each department, school, country is a bit different, and admissions committees vary widely in terms of how much input a separate faculty member can have. But you never know.


In departments I've been involved with, you need a masters in order to apply for a PhD. You'd need to complete your masters first, or find an equivalent. Thus, you cannot really transfer from Masters to PhD, as they are not on the same level.

On the other hand, in countries like the UK and Australia,  an  undergraduate honours degree that is enough to gain entry into a PhD program, at least, in those countries.


How likely is for the head of some University/Institution to ask other professors for further details related to the candidate?

Letters of recommendation often end with

  "...If you need further details do not hesitate to contact me on...",

and this is not a useless formality. If committee members have some questions about the candidate, they are very likely to email or telephone the person who wrote the recommendation and ask them. The content of the letter matters greatly, but it is even more important that the person who signs under the letter actually knows you well.

This is the main reason why a general and vague letter does not make you much good. Sadly, some professors are too busy to write the letter themselves, and they sometimes ask their students to prepare a letter which they are happy to sign. Be vary of this line, as the busy professor is likely to forget your name the next minute you step out his door, and therefore will not be able to provide details on you if asked. This also diminishes the effect of the recommendation, if not negates it.


Required items for undergraduate's CV who is applying to grad school

From what I've heard, CVs/resumes do not get a lot of weight in application decisions. The vital information is available elsewhere (particularly in the recommendation letters and statement of purpose), and the rest is almost always fluff and/or unverifiable.

There's a few things that you should definitely do. Focus heavily on research experience and any tangible evidence of research potential. Provide citations/links to publications or working papers. Include academic honors, especially national ones, mostly because they are unlikely to show up anywhere else. Depending on the field, there might be other relevant information (e.g. patents in engineering).

  Should I include my research interests? I understand that many senior undergraduates may not have specific research interests, but there are many others who have, and I think this can be a positive point in their application to research based programs.

No. That's what your statement of purpose is for. There's no need to duplicate it here.

  Should I list courses I've taken in addition to my main courses, that are important for the program?

You can, but I wouldn't. That's what your transcript is for. Some programs will also ask for lists/descriptions of classes. If a specific class is particularly important, you should consider mentioning it in your SOP or getting the professor to write you a recommendation letter; putting it in your CV is unlikely to draw attention to it.

  Should an activities section be included, in which my favorite, relevant activities are listed? As an example, I have written many bots in Python for daily repetitive Wikipedia tasks, and this shows my proficiency in Python (a positive point). Can I list under activities that I have written many scripts for Wikipedia?

Will almost certainly be viewed as fluff. If you an activity is important enough to mention, then include it in your SOP.

  Should an Objective section be added at the beginning? (I will write and submit a statement of purpose separately)

No. Again, this is what your SOP is for.

  Is a References section required at the end of the CV? (I've already made all of the mentioned names in the CV a link pointing to their homepages)

No. Generally there will be a separate section for entering your recommenders and their contact information, so it is unnecessary.

An exception might be when applying to fellowships. I suspect that some fellowships will consider leadership experiences, community service, and other factors that graduate schools generally ignore. Including these activities (e.g. varsity sports, student government, eagle scout, volunteering) might be helpful depending on the evaluation criteria.


What counts as a "prior version" in Springer's self-archiving policy?

I would interpret "prior version" here to mean any version prior to acceptance, which would include ones submitted for revisions.  Thus, I believe that you are correct in your conjecture: you can submit to arXiv and keep updating that at any time, as long as your first submission is before acceptance.

So, why does such a policy make sense? My take is this: if the manuscript is already out there on arXiv, then it's in the journal's interest to make sure it's the most accurate version.  From a business perspective, for-profit journals probably do not like having things appear on arXiv, but in those communities where preprint circulation and self-archiving are the rule, they don't really have the power to prevent it.


What should I do if I'm on the waitlist for a PhD program?

@Davidmh's advice is spot on, but I will definitely add that now is time to review your backup plan. (Of COURSE you have a backup plan, right?) There's always the possibility that you won't get into any of the schools you applied to; it sucks, but it happens. You should have a solid plan in place to make sure that your resume doesn't go stale in the interim. This could involve working as a lab tech/research assistant for a lab in your field, applying for internships in industry, taking on academic teaching positions, or even just finding any job to ensure you have income.

Whatever your plan is, now is a good time to start making sure it's feasible, and if it involves applying to jobs or the like, you should probably start doing that as well. You can always state that you cannot start working until after whatever the last date you can expect to hear from the university happens to be. The worst thing that can happen is that you have too many options. That is far better than the alternative.


How to handle swear words in quote / transcription?

If you're quoting someone, quote them as they said it. We're all adults. In the literature world, we quote swear words and other potentially offensive things all the time and no one bats an eye. I've no doubt other fields are the same.

Personally, if I saw an asterisk or similar, I would presume you interviewed them via chat or email, and they actually self-censored. If it were a printed text, I'd think it a part of the edition you used.


How are mathematicians paid to do research?

In the US, 99% of long-term positions that involve being paid to do research in pure math are tenure track faculty positions, colloquially known as professorships (in the US, they follow the progression Assistant Professor -> Associate Professor -> Professor). A professor is paid to teach, do research, and to a lesser extent, to do a variety of other vaguely related things that are discussed in many places on this website and elsewhere.

Professors teach and do research. It is not true that (quoting from one of the comments) “mathematicians are not paid to do research, but instead do research on the side and teach to make a living”. It is also not true that (quoting from another comment) “at some universities, research is the main job and teaching is a necessary byproduct”. Perhaps some professors have the mindset that their job is “mainly” about one or the other thing, but that’s simply a matter of personal perception rather than an objective truth. The objective truth is that professors teach and do research, and are paid to do those two things. Nothing is “on the side” or is “the main job”.

It is also not the case that (as seems to be implied by another answer) all math professors have, or need, grant funding to do their work. Grant funding is good to have, and getting it is both a catalyst for and a side-effect of career success. It can also give your salary a modest boost. But most of the funding doesn’t go directly into your pocket, and there are plenty of math professors who have steady employment and do quite well in their research without having it.

Finally, there is a very small number of mathematicians who have permanent, full time positions doing only research. Examples of places where such positions exist are the Institute of Advanced Study, and Microsoft Research. Those positions are very prestigious and rare, so hoping to land one of them is not a viable career plan.


Font size of text within image/graph for MS Thesis

Your institution's thesis template may specify this - some do and some don't.
If not then it's really up to you.  Typically, you want it to be smaller than your main text so that it doesn't stand out inappropriately much.  Beyond that, it's a  balance for efficacy of communication: larger sizes are more legible, but smaller sizes can help avoid visual clutter.  Remember also that many of your readers may be older or have imperfect vision and have a hard time with smaller fonts.